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Murphy, Susan Kay

Overview:

Ovarian and cervical cancer epigenetics, imprinted genes in ovarian and cervical cancers, identification of methylation biomarkers of disease, ovarian cancer stem cells, chemotherapeutic response in ovarian cancer, tumor dormancy, the influence of the in utero environment on DNA methylation and risk of disease

Positions:

Associate Professor in Obstetrics and Gynecology

Obstetrics and Gynecology, Gynecologic Oncology
School of Medicine

Associate Professor in Pathology

Pathology
School of Medicine

Member of the Duke Cancer Institute

Duke Cancer Institute
School of Medicine

Education:

B.A. 1992

B.A. — University of North Carolina at Charlotte

Ph.D. 1998

Ph.D. — Wake Forest University

News:

Grants:

Translational Research in Surgical Oncology

Administered By
Surgery, Surgical Sciences
AwardedBy
National Institutes of Health
Role
Mentor
Start Date
January 01, 2002
End Date
August 31, 2021

Duke University Medical Center (DUMC) Pelvic Floor Disorders Network (PFDN) Clinical Site

Administered By
Obstetrics and Gynecology, Urogynecology
AwardedBy
National Institutes of Health
Role
Collaborator
Start Date
April 01, 2007
End Date
June 30, 2021

Organization and Function of Cellular Structure

Administered By
Basic Science Departments
AwardedBy
National Institutes of Health
Role
Mentor
Start Date
July 01, 1975
End Date
June 30, 2020

Children Exposure to SVOC Mixtures Indoors and Associations with Obesity

Administered By
Environmental Sciences and Policy
AwardedBy
National Institutes of Health
Role
Co-Principal Investigator
Start Date
July 01, 2007
End Date
June 30, 2019

Duke KURe Program

Administered By
Obstetrics and Gynecology, Urogynecology
AwardedBy
National Institutes of Health
Role
Mentor
Start Date
August 01, 2013
End Date
July 31, 2018

Epigenetics and the Development of Nonalcoholic Fatty Liver Disease

Administered By
Medicine, Gastroenterology
AwardedBy
American College of Gastroenterology
Role
Mentor
Start Date
July 01, 2015
End Date
June 30, 2018

Duke University Program in Environmental Health

Administered By
Environmental Sciences and Policy
AwardedBy
National Institute of Environmental Health Sciences
Role
Mentor
Start Date
July 01, 2013
End Date
June 30, 2018

Neurodevelopment and Improving Children's Health Following EtS Exposure (NICHES)

Administered By
Obstetrics and Gynecology, Gynecologic Oncology
AwardedBy
National Institutes of Health
Role
Principal Investigator
Start Date
June 05, 2013
End Date
May 31, 2018

Neurodevelopment and Improving Children's Health following EtS exposure (NICHES)

Administered By
Obstetrics and Gynecology, Gynecologic Oncology
AwardedBy
Environmental Protection Agency
Role
Principal Investigator
Start Date
June 01, 2013
End Date
May 31, 2018

Validation and interrogation of differentially expressed and alternatively spliced genes in African American prostate ca

Administered By
Duke Cancer Institute
AwardedBy
Department of Defense
Role
Co Investigator
Start Date
September 30, 2014
End Date
September 29, 2017

Immune regulated amino acid pathways in Alzheimer's Disease

Administered By
Neurology, Behavioral Neurology
AwardedBy
National Institutes of Health
Role
Collaborating Investigator
Start Date
September 30, 2016
End Date
August 31, 2017

Pilot Project: Effects of Cannabis on the Epigenome of Humans and Rats

Administered By
Obstetrics and Gynecology, Gynecologic Oncology
AwardedBy
John Templeton Foundation
Role
Principal Investigator
Start Date
February 01, 2016
End Date
July 31, 2017

Building Interdisciplinary Research Careers in Women's Health

Administered By
Obstetrics and Gynecology
AwardedBy
National Institutes of Health
Role
Mentor
Start Date
September 26, 2002
End Date
July 31, 2017

Joint Environmental, Genetic and Epigenetic Regulation of Tyrosine Receptor Kinases and Childhood Respiratory Disease

Administered By
Obstetrics and Gynecology, Gynecologic Oncology
AwardedBy
University of Southern California
Role
Principal Investigator
Start Date
September 13, 2013
End Date
June 30, 2017

Functional Genomic Screens of Tumor Recurrence in Ovarian Cancer

Administered By
Molecular Genetics and Microbiology
AwardedBy
Department of Defense
Role
Co Investigator
Start Date
August 22, 2014
End Date
February 21, 2017

Cancer Biology Training Grant

Administered By
Pharmacology & Cancer Biology
AwardedBy
National Cancer Institute
Role
Mentor
Start Date
July 01, 1993
End Date
March 31, 2016

Obesity and deregulation of imprinted genes in early life

Administered By
Obstetrics and Gynecology
AwardedBy
National Institutes of Health
Role
Co-Principal Investigator
Start Date
July 27, 2010
End Date
April 30, 2015

Epigenetic influence on early childhood self-regulation capacities and obesity

Administered By
Community and Family Medicine
AwardedBy
National Institutes of Health
Role
Investigator
Start Date
September 30, 2011
End Date
August 31, 2014

Ovarian Cancer Initiating Cells: Metabolic Characterization

Administered By
Obstetrics and Gynecology, Gynecologic Oncology
AwardedBy
National Institutes of Health
Role
Principal Investigator
Start Date
July 08, 2012
End Date
June 30, 2014

Gene Regulation in Recurrent Ovarian Cancers

Administered By
Obstetrics and Gynecology, Gynecologic Oncology
AwardedBy
Gynecologic Cancer Foundation
Role
Principal Investigator
Start Date
December 01, 2011
End Date
June 30, 2014

Disparities in cervical cancer precursors and deregulation of imprinted genes

Administered By
Obstetrics and Gynecology, Gynecologic Oncology
AwardedBy
National Institutes of Health
Role
Co-Principal Investigator
Start Date
June 01, 2010
End Date
April 30, 2014

Nutrition, Deregulation of Imprinted Genes

Administered By
Obstetrics and Gynecology
AwardedBy
National Institutes of Health
Role
Co Investigator
Start Date
April 01, 2009
End Date
March 31, 2014

Characterizing Alcohol's Effects on Repair of Liver Injury

Administered By
Medicine, Gastroenterology
AwardedBy
National Institutes of Health
Role
Co Investigator
Start Date
September 30, 2009
End Date
August 31, 2012

Identification and Characterization of Epigenetically Labile Genes

Administered By
Radiation Oncology
AwardedBy
National Institutes of Health
Role
Investigator
Start Date
September 25, 2006
End Date
June 30, 2010

In-utero Exposure and Infant Loss of IGF2 Imprinting

Administered By
Duke Cancer Institute
AwardedBy
National Institutes of Health
Role
Co Investigator
Start Date
September 20, 2006
End Date
August 31, 2008

Imprinted PEG3 Domain at 19q13.4 and carcinogenesis

Administered By
Radiation Oncology
AwardedBy
National Institutes of Health
Role
PI-Fellow
Start Date
September 26, 2001
End Date
August 15, 2003
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Publications:

NAFLD is associated with methylation shifts with relevance for the expression of genes involved in lipoprotein particle composition.

Non-alcoholic fatty liver disease (NAFLD) is characterized by the accumulation of triglycerides, cholesterol and toxic free fatty acids and is related to low vitamin D levels. In an analysis of specific gene sets we elucidate to what extent NAFLD associates to epigenetic and related transcriptional changes in gene networks regulating lipid, energy and vitamin D balance. Two gene clusters responsible for lipid homeostasis (74 genes) and vitamin D and energy balance (31 genes) were investigated with regard to average epigenetic shifts within the first 1500bp next to the transcriptional start site. Three cohorts from two published genome wide driven studies that used a microarray approach were investigated including altogether 103 NAFLD and 75 liver healthy subjects. In the first two steps associations between NAFLD abundance, strength of fibrosis and methylation were investigated in two cohorts by multiple linear regression analyses, correcting for important clinical and demographic parameters. Methylation associated strength of transcription in genes showing significant NAFLD related methylation changes were studied in a third step using a third cohort and applying Pearson's correlation and robust linear regression analyses. 41 genes in gene cluster 1 and 14 genes in cluster 2 were significantly differentially methylated in dependency of NAFLD and hepatic fibrosis. We detect new genes significantly changed in methylation, including APO family members (lipid transport), NPC1L1, STARD (cholesterol transport) and GRHL (energy homeostasis). Our results allow novel insights into the hepatic epigenetic regulation of genes important for lipid and vitamin D balance in NAFLD.

Authors
Mwinyi, J; Boström, AE; Pisanu, C; Murphy, SK; Erhart, W; Schafmayer, C; Hampe, J; Moylan, C; Schiöth, HB
MLA Citation
Mwinyi, J, Boström, AE, Pisanu, C, Murphy, SK, Erhart, W, Schafmayer, C, Hampe, J, Moylan, C, and Schiöth, HB. "NAFLD is associated with methylation shifts with relevance for the expression of genes involved in lipoprotein particle composition." Biochimica et biophysica acta 1862.3 (March 2017): 314-323.
PMID
27993651
Source
epmc
Published In
Biochimica et Biophysica Acta: international journal of biochemistry and biophysics
Volume
1862
Issue
3
Publish Date
2017
Start Page
314
End Page
323
DOI
10.1016/j.bbalip.2016.12.005

Disparities in Cervical Cancer Incidence and Mortality: Can Epigenetics Contribute to Eliminating Disparities?

Screening for uterine cervical intraepithelial neoplasia (CIN) followed by aggressive treatment has reduced invasive cervical cancer (ICC) incidence and mortality. However, ICC cases and carcinoma in situ (CIS) continue to be diagnosed annually in the United States, with minorities bearing the brunt of this burden. Because ICC peak incidence and mortality are 10-15 years earlier than other solid cancers, the number of potential years of life lost to this cancer is substantial. Screening for early signs of CIN is still the mainstay of many cervical cancer control programs. However, the accuracy of existing screening tests remains suboptimal. Changes in epigenetic patterns that occur as a result of human papillomavirus infection contribute to CIN progression to cancer, and can be harnessed to improve existing screening tests. However, this requires a concerted effort to identify the epigenomic landscape that is reliably altered by HPV infection specific to ICC, distinct from transient changes.

Authors
Maguire, RL; Vidal, AC; Murphy, SK; Hoyo, C
MLA Citation
Maguire, RL, Vidal, AC, Murphy, SK, and Hoyo, C. "Disparities in Cervical Cancer Incidence and Mortality: Can Epigenetics Contribute to Eliminating Disparities?." Advances in cancer research 133 (January 2017): 129-156.
PMID
28052819
Source
epmc
Published In
Advances in cancer research
Volume
133
Publish Date
2017
Start Page
129
End Page
156
DOI
10.1016/bs.acr.2016.09.001

Environmental Influence on Preconceptional and Gestational DNA Methylation Profiles.

Authors
Murphy, SK; Keyhan, S; Guo, L; Tomins, K; Taylor, M; Joglekar, R; Huang, Z; Grenier, C; Liao, Y; Massarsky, A; Soubry, A; Lea, A; Burke, EE; Cauley, M; Hall, BJ; Lucas, JE; Hoyo, C; Di Giulio, RT; Levin, ED; Price, TM
MLA Citation
Murphy, SK, Keyhan, S, Guo, L, Tomins, K, Taylor, M, Joglekar, R, Huang, Z, Grenier, C, Liao, Y, Massarsky, A, Soubry, A, Lea, A, Burke, EE, Cauley, M, Hall, BJ, Lucas, JE, Hoyo, C, Di Giulio, RT, Levin, ED, and Price, TM. "Environmental Influence on Preconceptional and Gestational DNA Methylation Profiles." September 2016.
Source
wos-lite
Published In
Environmental and Molecular Mutagenesis
Volume
57
Publish Date
2016
Start Page
S39
End Page
S39

DNA Methylation: Basic Principles

© 2016 Elsevier Inc. All rights reserved.DNA methylation is a stable yet reversible epigenetic modification that regulates gene expression. New technologies have provided deep insights into the distribution and function of DNA methylation in humans, including the Human Roadmap Epigenome Project that defined genomewide methylation profiles across tissues and developmental stages, with the data available to anyone with Internet access. Exciting recent discoveries have revealed that 5-methylcytosine can be modified by ten-eleven translocase dioxygenases (TET1, 2, and 3) to form 5-hydroxymethylcytosine (5hmC). 5hmC is enriched in brain tissues and in embryonic stem cells and appears to have a regulatory role distinct from that of 5-methylcytosine (5mC). 5hmC also acts as a substrate for further modifications by the TET enzymes (5-formylcytosine and 5-carboxylcytosine) which undergo base excision repair by thymine DNA glycosylase (TDG) with replacement by unmethylated cytosine. These revelations present new challenges, including the need for technologies to quantify these modifications, determine their role in pathologies, and ways to target these modified bases and involved pathways to improve patient outcomes. Strategies to reverse abnormal hypermethylation of 5mC at specific loci are being developed and will eventually improve on the generalized toxicity associated with current DNA methyltransferase inhibitor therapies. Finally, exposures to endogenous and exogenous agents can lead to changes in methylation levels that increase disease risk. The sum combinatorial changes comprise what we refer to as each individual's unique "epigenoprint" that may be useful for determining risk of disease, best strategies for prevention and individualized interventions, likelihood of positive therapeutic response, and lead to improved prognoses.

Authors
Moylan, CA; Murphy, SK
MLA Citation
Moylan, CA, and Murphy, SK. "DNA Methylation: Basic Principles." Medical Epigenetics. July 1, 2016. 11-31.
Source
scopus
Publish Date
2016
Start Page
11
End Page
31
DOI
10.1016/B978-0-12-803239-8.00002-8

Suppression of ABHD2, identified through a functional genomics screen, causes anoikis resistance, chemoresistance and poor prognosis in ovarian cancer.

Anoikis resistance is a hallmark of cancer, and relates to malignant phenotypes, including chemoresistance, cancer stem like phenotypes and dissemination. The aim of this study was to identify key factors contributing to anoikis resistance in ovarian cancer using a functional genomics screen. A library of 81 000 shRNAs targeting 15 000 genes was transduced into OVCA420 cells, followed by incubation in soft agar and colony selection. We found shRNAs directed to ABHD2, ELAC2 and CYB5R3 caused reproducible anoikis resistance. These three genes are deleted in many serous ovarian cancers according to The Cancer Genome Atlas data. Suppression of ABHD2 in OVCA420 cells increased phosphorylated p38 and ERK, platinum resistance, and side population cells (p<0.01, respectively). Conversely, overexpression of ABHD2 decreased resistance to anoikis (p<0.05) and the amount of phosphorylated p38 and ERK in OVCA420 and SKOV3 cells. In clinical serous ovarian cancer specimens, low expression of ABHD2 was associated with platinum resistance and poor prognosis (p<0.05, respectively). In conclusion, we found three novel genes relevant to anoikis resistance in ovarian cancer using a functional genomics screen. Suppression of ABHD2 may promote a malignant phenotype and poor prognosis for women with serous ovarian cancer.

Authors
Yamanoi, K; Matsumura, N; Murphy, SK; Baba, T; Abiko, K; Hamanishi, J; Yamaguchi, K; Koshiyama, M; Konishi, I; Mandai, M
MLA Citation
Yamanoi, K, Matsumura, N, Murphy, SK, Baba, T, Abiko, K, Hamanishi, J, Yamaguchi, K, Koshiyama, M, Konishi, I, and Mandai, M. "Suppression of ABHD2, identified through a functional genomics screen, causes anoikis resistance, chemoresistance and poor prognosis in ovarian cancer." Oncotarget 7.30 (July 2016): 47620-47636.
PMID
27323405
Source
epmc
Published In
Oncotarget
Volume
7
Issue
30
Publish Date
2016
Start Page
47620
End Page
47636
DOI
10.18632/oncotarget.9951

Association between Prepregnancy Body Mass Index and Gestational Weight Gain with Size, Tempo, and Velocity of Infant Growth: Analysis of the Newborn Epigenetic Study Cohort.

The first 1000 days of life is a critical period of infant growth that has been linked to future adult health. Understanding prenatal factors that contribute to variation in growth during this period could inform successful prevention strategies.Prenatal and maternal characteristics, including prepregnancy obesity and gestational weight gain were evaluated in relation to weight growth trajectories during the first 24 months of life using the SuperImposition by Translation and Rotation (SITAR) method, which provides estimates of infant size, timing to peak velocity, and growth velocity. The study sample included 704 mother-infant dyads from a multiethnic prebirth cohort from the Southeastern United States. The total number of weight measures was 8670 (median number per child = 14).Several prenatal and maternal characteristics were linked with infant growth parameters. The primary findings show that compared to women with a prepregnancy BMI between 18 and 24.9, women with a prepregnancy BMI ≥40 had infants that were 8% larger during the first 24 months, a delayed tempo of around 9 days, and a slower velocity. Mothers who had greater than adequate gestational weight gain had infants that were 5% larger even after controlling for prepregnancy BMI and several other covariates.The findings contribute new data on the associations between gestational weight gain and aspects of early growth using the SITAR method, and support a growing consensus in the literature that both prepregnancy BMI and gestational weight gain relate independently to risk for greater postnatal weight growth.

Authors
Fuemmeler, BF; Wang, L; Iversen, ES; Maguire, R; Murphy, SK; Hoyo, C
MLA Citation
Fuemmeler, BF, Wang, L, Iversen, ES, Maguire, R, Murphy, SK, and Hoyo, C. "Association between Prepregnancy Body Mass Index and Gestational Weight Gain with Size, Tempo, and Velocity of Infant Growth: Analysis of the Newborn Epigenetic Study Cohort." Childhood obesity (Print) 12.3 (June 2016): 210-218.
PMID
27135650
Source
epmc
Published In
Childhood Obesity
Volume
12
Issue
3
Publish Date
2016
Start Page
210
End Page
218
DOI
10.1089/chi.2015.0253

Lead Exposure during Early Human Development and DNA Methylation of Imprinted Gene Regulatory Elements in Adulthood.

Lead exposure during early development causes neurodevelopmental disorders by unknown mechanisms. Epidemiologic studies have focused recently on determining associations between lead exposure and global DNA methylation; however, such approaches preclude the identification of loci that may alter human disease risk.The objective of this study was to determine whether maternal, postnatal, and early childhood lead exposure can alter the differentially methylated regions (DMRs) that control the monoallelic expression of imprinted genes involved in metabolism, growth, and development.Questionnaire data and serial blood lead levels were obtained from 105 participants (64 females, 41 males) of the Cincinnati Lead Study from birth to 78 months. When participants were adults, we used Sequenom EpiTYPER assays to test peripheral blood DNA to quantify CpG methylation in peripheral blood leukocytes at DMRs of 22 human imprinted genes. Statistical analyses were conducted using linear regression.Mean blood lead concentration from birth to 78 months was associated with a significant decrease in PEG3 DMR methylation (β = -0.0014; 95% CI: -0.0023, -0.0005, p = 0.002), stronger in males (β = -0.0024; 95% CI: -0.0038, -0.0009, p = 0.003) than in females (β = -0.0009; 95% CI: -0.0020, 0.0003, p = 0.1). Elevated mean childhood blood lead concentration was also associated with a significant decrease in IGF2/H19 (β = -0.0013; 95% CI: -0.0023, -0.0003, p = 0.01) DMR methylation, but primarily in females, (β = -0.0017; 95% CI: -0.0029, -0.0006, p = 0.005) rather than in males, (β = -0.0004; 95% CI: -0.0023, 0.0015, p = 0.7). Elevated blood lead concentration during the neonatal period was associated with higher PLAGL1/HYMAI DMR methylation regardless of sex (β = 0.0075; 95% CI: 0.0018, 0.0132, p = 0.01). The magnitude of associations between cumulative lead exposure and CpG methylation remained unaltered from 30 to 78 months.Our findings provide evidence that early childhood lead exposure results in sex-dependent and gene-specific DNA methylation differences in the DMRs of PEG3, IGF2/H19, and PLAGL1/HYMAI in adulthood.Li Y, Xie C, Murphy SK, Skaar D, Nye M, Vidal AC, Cecil KM, Dietrich KN, Puga A, Jirtle RL, Hoyo C. 2016. Lead exposure during early human development and DNA methylation of imprinted gene regulatory elements in adulthood. Environ Health Perspect 124:666-673; http://dx.doi.org/10.1289/ehp.1408577.

Authors
Li, Y; Xie, C; Murphy, SK; Skaar, D; Nye, M; Vidal, AC; Cecil, KM; Dietrich, KN; Puga, A; Jirtle, RL; Hoyo, C
MLA Citation
Li, Y, Xie, C, Murphy, SK, Skaar, D, Nye, M, Vidal, AC, Cecil, KM, Dietrich, KN, Puga, A, Jirtle, RL, and Hoyo, C. "Lead Exposure during Early Human Development and DNA Methylation of Imprinted Gene Regulatory Elements in Adulthood." Environmental health perspectives 124.5 (May 2016): 666-673.
PMID
26115033
Source
epmc
Published In
Environmental health perspectives
Volume
124
Issue
5
Publish Date
2016
Start Page
666
End Page
673
DOI
10.1289/ehp.1408577

Establishment of a Novel Histopathological Classification of High-Grade Serous Ovarian Carcinoma Correlated with Prognostically Distinct Gene Expression Subtypes.

Recently, The Cancer Genome Atlas data revealed four molecular subtypes of high-grade serous ovarian carcinoma (HGSOC) exhibiting distinct prognoses. We developed four novel HGSOC histopathological subtypes by focusing on tumor microenvironment: mesenchymal transition, defined by a remarkable desmoplastic reaction; immune reactive by lymphocytes infiltrating the tumor; solid and proliferative by a solid growth pattern; and papilloglandular by a papillary architecture. Unsupervised hierarchical clustering revealed four clusters correlated with histopathological subtypes in both Kyoto and Niigata HGSOC transcriptome data sets (P < 0.001). Gene set enrichment analysis revealed pathways enriched in our histopathological classification significantly overlapped with the four molecular subtypes: mesenchymal, immunoreactive, proliferative, and differentiated (P < 0.0001, respectively). In 132 HGSOC cases, progression-free survival and overall survival were best in the immune reactive, whereas overall survival was worst in the mesenchymal transition (P < 0.001, respectively), findings reproduced in 89 validation cases (P < 0.05, respectively). The CLOVAR_MES_UP single-sample gene set enrichment analysis scores representing the mesenchymal molecular subtype were higher in paclitaxel responders than nonresponders (P = 0.002) in the GSE15622 data set. Taxane-containing regimens improved survival of cases with high MES_UP scores compared with nontaxane regimens (P < 0.001) in the GSE9891 data set. Our novel histopathological classification of HGSOC correlates with distinct prognostic transcriptome subtypes. The mesenchymal transition subtype might be particularly sensitive to taxane.

Authors
Murakami, R; Matsumura, N; Mandai, M; Yoshihara, K; Tanabe, H; Nakai, H; Yamanoi, K; Abiko, K; Yoshioka, Y; Hamanishi, J; Yamaguchi, K; Baba, T; Koshiyama, M; Enomoto, T; Okamoto, A; Murphy, SK; Mori, S; Mikami, Y; Minamiguchi, S; Konishi, I
MLA Citation
Murakami, R, Matsumura, N, Mandai, M, Yoshihara, K, Tanabe, H, Nakai, H, Yamanoi, K, Abiko, K, Yoshioka, Y, Hamanishi, J, Yamaguchi, K, Baba, T, Koshiyama, M, Enomoto, T, Okamoto, A, Murphy, SK, Mori, S, Mikami, Y, Minamiguchi, S, and Konishi, I. "Establishment of a Novel Histopathological Classification of High-Grade Serous Ovarian Carcinoma Correlated with Prognostically Distinct Gene Expression Subtypes." The American journal of pathology 186.5 (May 2016): 1103-1113.
PMID
26993207
Source
epmc
Published In
The American journal of pathology
Volume
186
Issue
5
Publish Date
2016
Start Page
1103
End Page
1113
DOI
10.1016/j.ajpath.2015.12.029

Effects of Pubertal Exposure to Dietary Soy on Estrogen Receptor Activity in the Breast of Cynomolgus Macaques.

Endogenous estrogens influence mammary gland development during puberty and breast cancer risk during adulthood. Early-life exposure to dietary or environmental estrogens may alter estrogen-mediated processes. Soy foods contain phytoestrogenic isoflavones (IF), which have mixed estrogen agonist/antagonist properties. Here, we evaluated mammary gland responses over time in pubertal female cynomolgus macaques fed diets containing either casein/lactalbumin (n = 12) or soy protein containing a human-equivalent dose of 120 mg IF/day (n = 17) for approximately 4.5 years spanning menarche. We assessed estrogen receptor (ER) expression and activity, promoter methylation of ERs and their downstream targets, and markers of estrogen metabolism. Expression of ERα and classical ERα response genes (TFF1, PGR, and GREB1) decreased with maturity, independent of diet. A significant inverse correlation was observed between TFF1 mRNA and methylation of CpG sites within the TFF1 promoter. Soy effects included lower ERβ expression before menarche and lower mRNA for ERα and GREB1 after menarche. Expression of GATA-3, an epithelial differentiation marker that regulates ERα-mediated transcription, was elevated before menarche and decreased after menarche in soy-fed animals. Soy did not significantly alter expression of other ER activity markers, estrogen-metabolizing enzymes, or promoter methylation for ERs or ER-regulated genes. Our results demonstrate greater ER expression and activity during the pubertal transition, supporting the idea that this life stage is a critical window for phenotypic modulation by estrogenic compounds. Pubertal soy exposure decreases mammary ERα expression after menarche and exerts subtle effects on receptor activity and mammary gland differentiation. Cancer Prev Res; 9(5); 385-95. ©2016 AACR.

Authors
Dewi, FN; Wood, CE; Willson, CJ; Register, TC; Lees, CJ; Howard, TD; Huang, Z; Murphy, SK; Tooze, JA; Chou, JW; Miller, LD; Cline, JM
MLA Citation
Dewi, FN, Wood, CE, Willson, CJ, Register, TC, Lees, CJ, Howard, TD, Huang, Z, Murphy, SK, Tooze, JA, Chou, JW, Miller, LD, and Cline, JM. "Effects of Pubertal Exposure to Dietary Soy on Estrogen Receptor Activity in the Breast of Cynomolgus Macaques." Cancer prevention research (Philadelphia, Pa.) 9.5 (May 2016): 385-395.
PMID
27006379
Source
epmc
Published In
Cancer Prevention Research
Volume
9
Issue
5
Publish Date
2016
Start Page
385
End Page
395
DOI
10.1158/1940-6207.capr-15-0165

The BMP signaling pathway leads to enhanced proliferation in serous ovarian cancer-A potential therapeutic target.

Members of the transforming growth factor-β (TGF-β) superfamily transduce signals via SMAD proteins. SMAD2 and SMAD3 mediate TGF-β signaling, whereas SMAD1, SMAD5, and SMAD8/9 transduce bone morphogenetic protein (BMP) signals. We would like to identify the function of BMP/SMAD5 signaling in serous ovarian cancer. The protein levels of total SMAD5 and phosphorylated SMAD5 (pSMAD5) were examined by immunohistochemical analysis using clinical serous ovarian cancer samples. Following treatment with either recombinant BMP2 (rBMP2) or Dorsomorphin (DM), western blotting was performed to observe pSMAD5 protein in the cytoplasm and the nucleus, separately. Cell proliferation was detected in SMAD5 knockdown serous ovarian cancer cell lines cultured with DM or rBMP2. The impact of DM or rBMP2 on tumor growth was observed in a mouse model of serous ovarian cancer. An inverse correlation was observed between pSMAD5 levels in the nucleus and the prognosis of patients with serous ovarian cancer. The treatment of SK-OV-3 with rBMP2 stimulated pSMAD5 translocation from the cytoplasm to the nucleus, and the addition of DM inhibited this effect. The proliferation of ovarian cancer cell lines was enhanced by BMP2 and suppressed by DM via SMAD5 in vitro. In vitro and in vivo experiments clearly demonstrated BMP2-stimulated proliferation of serous ovarian cancer and inhibition of this effect by DM. Our data suggests that BMP/SMAD5 signaling plays an important role and, therefore, becomes a potential therapeutic target in serous ovarian cancer. © 2015 Wiley Periodicals, Inc.

Authors
Peng, J; Yoshioka, Y; Mandai, M; Matsumura, N; Baba, T; Yamaguchi, K; Hamanishi, J; Kharma, B; Murakami, R; Abiko, K; Murphy, SK; Konishi, I
MLA Citation
Peng, J, Yoshioka, Y, Mandai, M, Matsumura, N, Baba, T, Yamaguchi, K, Hamanishi, J, Kharma, B, Murakami, R, Abiko, K, Murphy, SK, and Konishi, I. "The BMP signaling pathway leads to enhanced proliferation in serous ovarian cancer-A potential therapeutic target." Molecular carcinogenesis 55.4 (April 2016): 335-345.
PMID
25663289
Source
epmc
Published In
Molecular Carcinogenesis
Volume
55
Issue
4
Publish Date
2016
Start Page
335
End Page
345
DOI
10.1002/mc.22283

DNA Methylation in Newborns and Maternal Smoking in Pregnancy: Genome-wide Consortium Meta-analysis.

Epigenetic modifications, including DNA methylation, represent a potential mechanism for environmental impacts on human disease. Maternal smoking in pregnancy remains an important public health problem that impacts child health in a myriad of ways and has potential lifelong consequences. The mechanisms are largely unknown, but epigenetics most likely plays a role. We formed the Pregnancy And Childhood Epigenetics (PACE) consortium and meta-analyzed, across 13 cohorts (n = 6,685), the association between maternal smoking in pregnancy and newborn blood DNA methylation at over 450,000 CpG sites (CpGs) by using the Illumina 450K BeadChip. Over 6,000 CpGs were differentially methylated in relation to maternal smoking at genome-wide statistical significance (false discovery rate, 5%), including 2,965 CpGs corresponding to 2,017 genes not previously related to smoking and methylation in either newborns or adults. Several genes are relevant to diseases that can be caused by maternal smoking (e.g., orofacial clefts and asthma) or adult smoking (e.g., certain cancers). A number of differentially methylated CpGs were associated with gene expression. We observed enrichment in pathways and processes critical to development. In older children (5 cohorts, n = 3,187), 100% of CpGs gave at least nominal levels of significance, far more than expected by chance (p value < 2.2 × 10(-16)). Results were robust to different normalization methods used across studies and cell type adjustment. In this large scale meta-analysis of methylation data, we identified numerous loci involved in response to maternal smoking in pregnancy with persistence into later childhood and provide insights into mechanisms underlying effects of this important exposure.

Authors
Joubert, BR; Felix, JF; Yousefi, P; Bakulski, KM; Just, AC; Breton, C; Reese, SE; Markunas, CA; Richmond, RC; Xu, C-J; Küpers, LK; Oh, SS; Hoyo, C; Gruzieva, O; Söderhäll, C; Salas, LA; Baïz, N; Zhang, H; Lepeule, J; Ruiz, C; Ligthart, S; Wang, T; Taylor, JA; Duijts, L; Sharp, GC; Jankipersadsing, SA; Nilsen, RM; Vaez, A; Fallin, MD; Hu, D; Litonjua, AA; Fuemmeler, BF; Huen, K; Kere, J; Kull, I; Munthe-Kaas, MC; Gehring, U; Bustamante, M; Saurel-Coubizolles, MJ; Quraishi, BM; Ren, J; Tost, J et al.
MLA Citation
Joubert, BR, Felix, JF, Yousefi, P, Bakulski, KM, Just, AC, Breton, C, Reese, SE, Markunas, CA, Richmond, RC, Xu, C-J, Küpers, LK, Oh, SS, Hoyo, C, Gruzieva, O, Söderhäll, C, Salas, LA, Baïz, N, Zhang, H, Lepeule, J, Ruiz, C, Ligthart, S, Wang, T, Taylor, JA, Duijts, L, Sharp, GC, Jankipersadsing, SA, Nilsen, RM, Vaez, A, Fallin, MD, Hu, D, Litonjua, AA, Fuemmeler, BF, Huen, K, Kere, J, Kull, I, Munthe-Kaas, MC, Gehring, U, Bustamante, M, Saurel-Coubizolles, MJ, Quraishi, BM, Ren, J, and Tost, J et al. "DNA Methylation in Newborns and Maternal Smoking in Pregnancy: Genome-wide Consortium Meta-analysis." American journal of human genetics 98.4 (April 2016): 680-696.
PMID
27040690
Source
epmc
Published In
The American Journal of Human Genetics
Volume
98
Issue
4
Publish Date
2016
Start Page
680
End Page
696
DOI
10.1016/j.ajhg.2016.02.019

Maternal B vitamins: effects on offspring weight and DNA methylation at genomically imprinted domains.

Inadequate maternal nutrition during early fetal development can create permanent alterations in the offspring, leading to poor health outcomes. While nutrients involved in one-carbon cycle metabolism are important to fetal growth, associations with specific nutrients remain inconsistent. This study estimates associations between maternal vitamins B12, B6 (pyridoxal phosphate [PLP] and 4-pyridoxic acid [PA]), and homocysteine (Hcy) concentrations, offspring weight (birth weight and 3-year weight gain), and DNA methylation at four differentially methylated regions (DMRs) known to be involved in fetal growth and development (H19, MEG3, SGCE/PEG10, and PLAGL1).Study participants (n = 496) with biomarker and birth weight data were enrolled as part of the Newborn Epigenetics STudy. Weight gain data were available for 273 offspring. Among 484 mother-infant pairs, DNA methylation at regulatory sequences of genomically imprinted genes was measured in umbilical cord blood DNA using bisulfite pyrosequencing. We used generalized linear models to estimate associations.Multivariate adjusted regression models revealed an inverse association between maternal Hcy concentration and male birth weight (β = -210.40, standard error (SE) = 102.08, p = 0.04). The offspring of the mothers in the highest quartile of B12 experienced lower weight gain between birth and 3 years compared to the offspring of the mothers in the lowest (β = -2203.03, SE = 722.49, p = 0.003). Conversely, maternal PLP was associated with higher weight gain in males; higher maternal PLP concentrations were also associated with offspring DNA methylation levels at the MEG3 DMR (p < 0.01).While maternal concentrations of B12, B6, and Hcy do not associate with birth weight overall, they may play an important role in 3-year weight gain. This is the first study to report an association between maternal PLP and methylation at the MEG3 DMR which may be an important epigenetic tag for maternal B vitamin adequacy.

Authors
McCullough, LE; Miller, EE; Mendez, MA; Murtha, AP; Murphy, SK; Hoyo, C
MLA Citation
McCullough, LE, Miller, EE, Mendez, MA, Murtha, AP, Murphy, SK, and Hoyo, C. "Maternal B vitamins: effects on offspring weight and DNA methylation at genomically imprinted domains." Clinical epigenetics 8 (January 22, 2016): 8-.
PMID
26807160
Source
epmc
Published In
Clinical Epigenetics
Volume
8
Publish Date
2016
Start Page
8
DOI
10.1186/s13148-016-0174-9

Identification through functional genomics screening of factors whose downregulation enhances the side population in ovarian cancer.

Authors
Matsumura, N; Yamanoi, K; Murphy, SK; Hamanishi, J; Abiko, K; Yamaguchi, K; Baba, T; Koshiyama, M; Konishi, I
MLA Citation
Matsumura, N, Yamanoi, K, Murphy, SK, Hamanishi, J, Abiko, K, Yamaguchi, K, Baba, T, Koshiyama, M, and Konishi, I. "Identification through functional genomics screening of factors whose downregulation enhances the side population in ovarian cancer." CLINICAL CANCER RESEARCH 22 (January 15, 2016).
Source
wos-lite
Published In
Clinical cancer research : an official journal of the American Association for Cancer Research
Volume
22
Publish Date
2016

Neighborhood and Family Environment of Expectant Mothers May Influence Prenatal Programming of Adult Cancer Risk: Discussion and an Illustrative DNA Methylation Example.

Childhood stressors including physical abuse predict adult cancer risk. Prior research portrays this finding as an indirect mechanism that operates through coping behaviors, including adult smoking, or through increased toxic exposures during childhood. Little is known about potential direct causal mechanisms between early-life stressors and adult cancer. Because prenatal conditions can affect gene expression by altering DNA methylation, with implications for adult health, we hypothesize that maternal stress may program methylation of cancer-linked genes during gametogenesis. To illustrate this hypothesis, we related maternal social resources to methylation at the imprinted MEG3 differentially methylated regulatory region, which has been linked to multiple cancer types. Mothers (n = 489) from a diverse birth cohort (Durham, North Carolina) provided newborns' cord blood and completed a questionnaire. Newborns of currently married mothers showed lower (-0.321 SD, p < .05) methylation compared to newborns of never-married mothers, who did not differ from newborns whose mothers were cohabiting and others (adjusted for demographics). MEG3 DNA methylation levels were also lower when maternal grandmothers co-resided before pregnancy (-0.314 SD, p < .05). A 1-SD increase in prenatal neighborhood disadvantage also predicted higher methylation (-0.137 SD, p < .05). In conclusion, we found that maternal social resources may result in differential methylation of MEG3, which demonstrates a potential partial mechanism priming socially disadvantaged newborns for later risk of some cancers.

Authors
King, KE; Kane, JB; Scarbrough, P; Hoyo, C; Murphy, SK
MLA Citation
King, KE, Kane, JB, Scarbrough, P, Hoyo, C, and Murphy, SK. "Neighborhood and Family Environment of Expectant Mothers May Influence Prenatal Programming of Adult Cancer Risk: Discussion and an Illustrative DNA Methylation Example." Biodemography and social biology 62.1 (January 2016): 87-104.
PMID
27050035
Source
epmc
Published In
Biodemography and Social Biology
Volume
62
Issue
1
Publish Date
2016
Start Page
87
End Page
104
DOI
10.1080/19485565.2015.1126501

Obesity-related DNA methylation at imprinted genes in human sperm: Results from the TIEGER study.

Epigenetic reprogramming in mammalian gametes resets methylation marks that regulate monoallelic expression of imprinted genes. In males, this involves erasure of the maternal methylation marks and establishment of paternal-specific methylation to appropriately guide normal development. The degree to which exogenous factors influence the fidelity of methylation reprogramming is unknown. We previously found an association between paternal obesity and altered DNA methylation in umbilical cord blood, suggesting that the father's endocrine, nutritional, or lifestyle status could potentiate intergenerational heritable epigenetic abnormalities. In these analyses, we examine the relationship between male overweight/obesity and DNA methylation status of imprinted gene regulatory regions in the gametes.Linear regression models were used to compare sperm DNA methylation percentages, quantified by bisulfite pyrosequencing, at 12 differentially methylated regions (DMRs) from 23 overweight/obese and 44 normal weight men. Our study population included 69 volunteers from The Influence of the Environment on Gametic Epigenetic Reprogramming (TIEGER) study, based in NC, USA.After adjusting for age and fertility patient status, semen from overweight or obese men had significantly lower methylation percentages at the MEG3 (β = -1.99; SE = 0.84; p = 0.02), NDN (β = -1.10; SE = 0.47; p = 0.02), SNRPN (β = -0.65; SE = 0.27; p = 0.02), and SGCE/PEG10 (β = -2.5; SE = 1.01; p = 0.01) DMRs. Our data further suggest a slight increase in DNA methylation at the MEG3-IG DMR (β = +1.22; SE = 0.59; p = 0.04) and H19 DMR (β = +1.37; SE = 0.62; p = 0.03) in sperm of overweight/obese men.Our data support that male overweight/obesity status is traceable in the sperm epigenome. Further research is needed to understand the effect of such changes and the point of origin of DNA methylation differences between lean and overweight/obese men. Together with our earlier reports on paternal obesity and epigenetic shifts in the offspring, our studies set the groundwork for future studies investigating male gametic methylation aberrations due to paternal lifestyle factors such as obesity.

Authors
Soubry, A; Guo, L; Huang, Z; Hoyo, C; Romanus, S; Price, T; Murphy, SK
MLA Citation
Soubry, A, Guo, L, Huang, Z, Hoyo, C, Romanus, S, Price, T, and Murphy, SK. "Obesity-related DNA methylation at imprinted genes in human sperm: Results from the TIEGER study." Clinical epigenetics 8 (January 2016): 51-.
PMID
27158277
Source
epmc
Published In
Clinical Epigenetics
Volume
8
Publish Date
2016
Start Page
51
DOI
10.1186/s13148-016-0217-2

A targeted analysis reveals relevant shifts in the methylation and transcription of genes responsible for bile acid homeostasis and drug metabolism in non-alcoholic fatty liver disease.

Non-alcoholic fatty liver disease (NAFLD) is associated with a high risk for liver cirrhosis and cancer. Recent studies demonstrate that NAFLD significantly impacts on the genome wide methylation and expression reporting top hit genes to be associated with e.g. diabetes mellitus. In a targeted analysis we specifically investigate to what extent NAFLD is associated with methylation and transcriptional changes in gene networks responsible for drug metabolism (DM) and bile acid (BA) homeostasis, which may trigger liver and system toxic events.We performed a systematic analysis of 73 genes responsible for BA homeostasis and DM based on liver derived methylation and expression data from three cohort studies including 103 NAFLD and 75 non-NAFLD patients. Using multiple linear regression models, we detected methylation differences in proximity to the transcriptional start site of these genes in two NAFLD cohorts and correlated the methylation of significantly changed CpG sites to transcriptional expression in a third cohort using robust multiple linear regression approaches.We detected 64 genes involved in BA homeostasis and DM to be significantly differentially methylated. In 26 of these genes, methylation significantly correlated with RNA expression, detecting i.e. genes such as CYP27A1, OSTɑ, and SLC27A5 (BA homeostasis), and SLCO2B1, SLC47A1, and several UGT and CYP genes (DM) to be NAFLD dependently modulated.NAFLD is associated with significant shifts in the methylation of key genes responsible for BA and DM that are associated with transcriptional modulations. These findings have implications for BA composition, BA regulated metabolic pathways and for drug safety and efficacy.

Authors
Schiöth, HB; Boström, A; Murphy, SK; Erhart, W; Hampe, J; Moylan, C; Mwinyi, J
MLA Citation
Schiöth, HB, Boström, A, Murphy, SK, Erhart, W, Hampe, J, Moylan, C, and Mwinyi, J. "A targeted analysis reveals relevant shifts in the methylation and transcription of genes responsible for bile acid homeostasis and drug metabolism in non-alcoholic fatty liver disease." BMC genomics 17 (January 2016): 462-.
PMID
27301979
Source
epmc
Published In
BMC Genomics
Volume
17
Publish Date
2016
Start Page
462
DOI
10.1186/s12864-016-2814-z

DNA Methylation of Regulatory Regions of Imprinted Genes at Birth and Its Relation to Infant Temperament.

DNA methylation of the differentially methylated regions (DMRs) of imprinted genes is relevant to neurodevelopment.DNA methylation status of the DMRs of nine imprinted genes in umbilical cord blood leukocytes was analyzed in relation to infant behaviors and temperament (n = 158).MEG3 DMR levels were positively associated with internalizing (β = 0.15, P = 0.044) and surgency (β = 0.19, P = 0.018) behaviors, after adjusting for birth weight, gender, gestational age at birth, maternal age at delivery, race/ethnicity, education level, smoking status, parity, and a history of anxiety or depression. Higher methylation levels at the intergenic MEG3-IG methylation regions were associated with surgency (β = 0.28, P = 0.0003) and PEG3 was positively related to externalizing (β = 0.20, P = 0.01) and negative affectivity (β = 0.18, P = 0.02).While the small sample size limits inference, these pilot data support gene-specific associations between epigenetic differences in regulatory regions of imprinted domains at birth and later infant temperament.

Authors
Fuemmeler, BF; Lee, C-T; Soubry, A; Iversen, ES; Huang, Z; Murtha, AP; Schildkraut, JM; Jirtle, RL; Murphy, SK; Hoyo, C
MLA Citation
Fuemmeler, BF, Lee, C-T, Soubry, A, Iversen, ES, Huang, Z, Murtha, AP, Schildkraut, JM, Jirtle, RL, Murphy, SK, and Hoyo, C. "DNA Methylation of Regulatory Regions of Imprinted Genes at Birth and Its Relation to Infant Temperament." Genetics & epigenetics 8 (January 2016): 59-67.
PMID
27920589
Source
epmc
Published In
Genetics and Epigenetics
Volume
8
Publish Date
2016
Start Page
59
End Page
67

Distinct Epigenetic Effects of Tobacco Smoking in Whole Blood and among Leukocyte Subtypes.

Tobacco smoke exposure dramatically alters DNA methylation in blood cells and may mediate smoking-associated complex diseases through effects on immune cell function. However, knowledge of smoking effects in specific leukocyte subtypes is limited. To better characterize smoking-associated methylation changes in whole blood and leukocyte subtypes, we used Illumina 450K arrays and Reduced Representation Bisulfite Sequencing (RRBS) to assess genome-wide DNA methylation. Differential methylation analysis in whole blood DNA from 172 smokers and 81 nonsmokers revealed 738 CpGs, including 616 previously unreported CpGs, genome-wide significantly associated with current smoking (p <1.2x10-7, Bonferroni correction). Several CpGs (MTSS1, NKX6-2, BTG2) were associated with smoking duration among heavy smokers (>22 cigarettes/day, n = 86) which might relate to long-term heavy-smoking pathology. In purified leukocyte subtypes from an independent group of 20 smokers and 14 nonsmokers we further examined methylation and gene expression for selected genes among CD14+ monocytes, CD15+ granulocytes, CD19+ B cells, and CD2+ T cells. In 10 smokers and 10 nonsmokers we used RRBS to fine map differential methylation in CD4+ T cells, CD8+ T cells, CD14+, CD15+, CD19+, and CD56+ natural killer cells. Distinct cell-type differences in smoking-associated methylation and gene expression were identified. AHRR (cg05575921), ALPPL2 (cg21566642), GFI1 (cg09935388), IER3 (cg06126421) and F2RL3 (cg03636183) showed a distinct pattern of significant smoking-associated methylation differences across cell types: granulocytes> monocytes>> B cells. In contrast GPR15 (cg19859270) was highly significant in T and B cells and ITGAL (cg09099830) significant only in T cells. Numerous other CpGs displayed distinctive cell-type responses to tobacco smoke exposure that were not apparent in whole blood DNA. Assessing the overlap between these CpG sites and differential methylated regions (DMRs) with RRBS in 6 cell types, we confirmed cell-type specificity in the context of DMRs. We identified new CpGs associated with current smoking, pack-years, duration, and revealed unique profiles of smoking-associated DNA methylation and gene expression among immune cell types, providing potential clues to hematopoietic lineage-specific effects in disease etiology.

Authors
Su, D; Wang, X; Campbell, MR; Porter, DK; Pittman, GS; Bennett, BD; Wan, M; Englert, NA; Crowl, CL; Gimple, RN; Adamski, KN; Huang, Z; Murphy, SK; Bell, DA
MLA Citation
Su, D, Wang, X, Campbell, MR, Porter, DK, Pittman, GS, Bennett, BD, Wan, M, Englert, NA, Crowl, CL, Gimple, RN, Adamski, KN, Huang, Z, Murphy, SK, and Bell, DA. "Distinct Epigenetic Effects of Tobacco Smoking in Whole Blood and among Leukocyte Subtypes." PloS one 11.12 (January 2016): e0166486-.
PMID
27935972
Source
epmc
Published In
PloS one
Volume
11
Issue
12
Publish Date
2016
Start Page
e0166486
DOI
10.1371/journal.pone.0166486

Maternal blood lead concentrations, DNA methylation of MEG3 DMR regulating the DLK1/MEG3 imprinted domain and early growth in a multiethnic cohort.

Prenatal exposure to lead (Pb) is known to decrease fetal growth; but its effects on postnatal growth and mechanistic insights linking Pb to growth are not clearly defined. Genomically imprinted genes are powerful regulators of growth and energy utilization, and may be particularly vulnerable to environmental Pb exposure. Because imprinting is established early and maintained via DNA methylation, we hypothesized that prenatal Pb exposure alters DNA methylation of imprinted genes resulting in lower birth weight and rapid growth. Pb was measured by inductively coupled plasma mass spectrometry (ICP-MS) in peripheral blood of 321 women of the Newborn Epigenetic STudy (NEST) obtained at gestation ~12 weeks. Linear and logistic regression models were used to evaluate associations between maternal Pb levels, methylation of differentially methylated regions (DMRs) regulating H19, MEG3, PEG3, and PLAGL1, measured by pyrosequencing, birth weight, and weight-for-height z score gains between birth and age 1yr, ages 1-2yrs, and 2-3yrs. Children born to women with Pb levels in the upper tertile had higher methylation of the regulatory region of the MEG3 DMR imprinted domain (β= 1.57, se= 0.82, p= 0.06). Pb levels were also associated with lower birth weight (β= -0.41, se= 0.15, p= 0.01) and rapid gains in adiposity (OR= 12.32, 95%CI=1.25-121.30, p= 0.03) by age 2-3 years. These data provide early human evidence for Pb associations with hypermethylation at the MEG3 DMR regulatory region and rapid adiposity gain-a risk factor for childhood obesity and cardiometabolic diseases in adulthood.

Authors
Nye, MD; King, KE; Darrah, TH; Maguire, R; Jima, DD; Huang, Z; Mendez, MA; Fry, RC; Jirtle, RL; Murphy, SK; Hoyo, C
MLA Citation
Nye, MD, King, KE, Darrah, TH, Maguire, R, Jima, DD, Huang, Z, Mendez, MA, Fry, RC, Jirtle, RL, Murphy, SK, and Hoyo, C. "Maternal blood lead concentrations, DNA methylation of MEG3 DMR regulating the DLK1/MEG3 imprinted domain and early growth in a multiethnic cohort." Environmental epigenetics 2.1 (January 2016).
PMID
28123784
Source
epmc
Published In
Environmental Epigenetics
Volume
2
Issue
1
Publish Date
2016
DOI
10.1093/eep/dvv009

Epigenetic silencing of Kruppel like factor-3 increases expression of pro-metastatic miR-182.

Accumulating evidence indicates that microRNAs (miRs) regulate cancer metastasis. We have shown that miR-182 drives sarcoma metastasis in vivo by coordinated regulation of multiple genes. Recently, we also demonstrated that in a subset of primary sarcomas that metastasize to the lung, miR-182 expression is elevated through binding of MyoD1 to the miR-182 promoter. However, it is not known if there are also transcription factors that inhibit miR-182 expression. Defining negative regulators of miR-182 expression may help explain why some sarcomas do not metastasize and may also identify pathways that can modulate miR-182 for therapeutic benefit. Here, we use an in silico screen, chromatin-immunoprecipitation, and luciferase reporter assays to discover that Kruppel like factor-3 (Klf-3) is a novel transcriptional repressor of miR-182. Knockdown of Klf-3 increases miR-182 expression, and stable overexpression of Klf-3, but not a DNA-binding mutant Klf-3, decreases miR-182 levels. Klf-3 expression is downregulated in both primary mouse and human metastatic sarcomas, and Klf-3 levels negatively correlate with miR-182 expression. Interestingly, Klf-3 also negatively regulates MyoD1, suggesting an alternative mechanism for Klf-3 to repress miR-182 expression in addition to direct binding of the miR-182 promoter. Using Methylation Specific PCR (MSP) and pyrosequencing assays, we found that Klf-3 is epigenetically silenced by DNA hypermethylation both in mouse and human sarcoma cells. Finally, we show the DNA methylation inhibitor 5'Azacytidine (Aza) restores Klf-3 expression while reducing miR-182 levels. Thus, our findings suggest that demethylating agents could potentially be used to modulate miR-182 levels as a therapeutic strategy.

Authors
Sachdeva, M; Dodd, RD; Huang, Z; Grenier, C; Ma, Y; Lev, DC; Cardona, DM; Murphy, SK; Kirsch, DG
MLA Citation
Sachdeva, M, Dodd, RD, Huang, Z, Grenier, C, Ma, Y, Lev, DC, Cardona, DM, Murphy, SK, and Kirsch, DG. "Epigenetic silencing of Kruppel like factor-3 increases expression of pro-metastatic miR-182." Cancer letters 369.1 (December 2015): 202-211.
PMID
26314219
Source
epmc
Published In
Cancer Letters
Volume
369
Issue
1
Publish Date
2015
Start Page
202
End Page
211
DOI
10.1016/j.canlet.2015.08.016

Chemotherapy Induces Programmed Cell Death-Ligand 1 Overexpression via the Nuclear Factor-κB to Foster an Immunosuppressive Tumor Microenvironment in Ovarian Cancer.

Emerging evidence has highlighted the host immune system in modulating the patient response to chemotherapy, but the mechanism of this modulation remains unclear. The aim of this study was to analyze the effect of chemotherapy on antitumor immunity in the tumor microenvironment of ovarian cancer. Treatment of ovarian cancer cell lines with various chemotherapeutic agents resulted in upregulated expression of MHC class I and programmed cell death 1 ligand 1 (PD-L1) in a NF-κB-dependent manner and suppression of antigen-specific T-cell function in vitro. In a mouse model of ovarian cancer, treatment with paclitaxel increased CD8(+) T-cell infiltration into the tumor site, upregulated PD-L1 expression, and activated NF-κB signaling. In particular, tumor-bearing mice treated with a combination of paclitaxel and a PD-L1/PD-1 signal blockade survived longer than mice treated with paclitaxel alone. In summary, we found that chemotherapy induces local immune suppression in ovarian cancer through NF-κB-mediated PD-L1 upregulation. Thus, a combination of chemotherapy and immunotherapy targeting the PD-L1/PD-1 signaling axis may improve the antitumor response and offers a promising new treatment modality against ovarian cancer.

Authors
Peng, J; Hamanishi, J; Matsumura, N; Abiko, K; Murat, K; Baba, T; Yamaguchi, K; Horikawa, N; Hosoe, Y; Murphy, SK; Konishi, I; Mandai, M
MLA Citation
Peng, J, Hamanishi, J, Matsumura, N, Abiko, K, Murat, K, Baba, T, Yamaguchi, K, Horikawa, N, Hosoe, Y, Murphy, SK, Konishi, I, and Mandai, M. "Chemotherapy Induces Programmed Cell Death-Ligand 1 Overexpression via the Nuclear Factor-κB to Foster an Immunosuppressive Tumor Microenvironment in Ovarian Cancer." Cancer research 75.23 (December 2015): 5034-5045.
PMID
26573793
Source
epmc
Published In
Cancer Research
Volume
75
Issue
23
Publish Date
2015
Start Page
5034
End Page
5045
DOI
10.1158/0008-5472.can-14-3098

Mitochondrial Superoxide Dismutase Has a Protumorigenic Role in Ovarian Clear Cell Carcinoma.

Epithelial ovarian cancer (EOC) is the fourth leading cause of death due to cancer in women and comprises distinct histologic subtypes, which vary widely in their genetic profiles and tissues of origin. It is therefore imperative to understand the etiology of these distinct diseases. Ovarian clear cell carcinoma (OCCC), a very aggressive subtype, comprises >10% of EOCs. In the present study, we show that mitochondrial superoxide dismutase (Sod2) is highly expressed in OCCC compared with other EOC subtypes. Sod2 is an antioxidant enzyme that converts highly reactive superoxide (O2 (•-)) to hydrogen peroxide (H2O2) and oxygen (O2), and our data demonstrate that Sod2 is protumorigenic and prometastatic in OCCC. Inhibiting Sod2 expression reduces OCCC ES-2 cell tumor growth and metastasis in a chorioallantoic membrane (CAM) model. Similarly, cell proliferation, migration, spheroid attachment and outgrowth on collagen, and Akt phosphorylation are significantly decreased with reduced expression of Sod2. Mechanistically, we show that Sod2 has a dual function in supporting OCCC tumorigenicity and metastatic spread. First, Sod2 maintains highly functional mitochondria, by scavenging O2 (•-), to support the high metabolic activity of OCCC. Second, Sod2 alters the steady-state ROS balance to drive H2O2-mediated migration. While this higher steady-state H2O2 drives prometastatic behavior, it also presents a doubled-edged sword for OCCC, as it pushed the intracellular H2O2 threshold to enable more rapid killing by exogenous sources of H2O2. Understanding the complex interaction of antioxidants and ROS may provide novel therapeutic strategies to pursue for the treatment of this histologic EOC subtype.

Authors
Hemachandra, LPMP; Shin, D-H; Dier, U; Iuliano, JN; Engelberth, SA; Uusitalo, LM; Murphy, SK; Hempel, N
MLA Citation
Hemachandra, LPMP, Shin, D-H, Dier, U, Iuliano, JN, Engelberth, SA, Uusitalo, LM, Murphy, SK, and Hempel, N. "Mitochondrial Superoxide Dismutase Has a Protumorigenic Role in Ovarian Clear Cell Carcinoma." Cancer research 75.22 (November 2015): 4973-4984.
PMID
26359457
Source
epmc
Published In
Cancer Research
Volume
75
Issue
22
Publish Date
2015
Start Page
4973
End Page
4984
DOI
10.1158/0008-5472.can-14-3799

Epigenetic Regulation of GDF2 Suppresses Anoikis in Ovarian and Breast Epithelia.

Anoikis, a cell death mechanism triggered upon cell-matrix detachment, is regarded as a physiological suppressor of metastasis that can be regulated by a diverse array of signals. The protein encoded by GDF2 is BMP9 and is a member of the bone morphogenetic protein family and the transforming growth factor (TGF) β superfamily with emerging yet controversial roles in carcinogenesis. In an attempt to identify the function of growth and differentiation factor 2 (GDF2) in epithelial systems, we examined the signaling machinery that is involved and cell fate decisions in response to GDF2 in ovarian and breast epithelia. We find that GDF2 can robustly activate the SMAD1/5 signaling axis by increasing complex formation between the type I receptor serine threonine kinases activin receptor-like kinase (ALK) 3 and ALK6 and the type II receptor serine threonine kinase BMPRII. This activation is independent of cross talk with the SMAD2-transforming growth factor β pathway. By activating SMAD1/5, epithelial cells regulate anchorage-independent growth by increasing anoikis sensitivity that is dependent on GDF2's ability to sustain the activation of SMAD1/5 via ALK3 and ALK6. Consistent with a role for GDF2 in promoting anoikis susceptibility, the analysis of cell lines and patient data suggests epigenetic silencing of GDF2 in cancer cell lines and increased promoter methylation in patients. These findings collectively indicate an antimetastatic role for GDF2 in ovarian and breast cancer. The work also implicates loss of GDF2 via promoter methylation-mediated downregulation in promotion of carcinogenesis with significant relevance for the use of epigenetic drugs currently in clinical trials.

Authors
Varadaraj, A; Patel, P; Serrao, A; Bandyopadhay, T; Lee, NY; Jazaeri, AA; Huang, Z; Murphy, SK; Mythreye, K
MLA Citation
Varadaraj, A, Patel, P, Serrao, A, Bandyopadhay, T, Lee, NY, Jazaeri, AA, Huang, Z, Murphy, SK, and Mythreye, K. "Epigenetic Regulation of GDF2 Suppresses Anoikis in Ovarian and Breast Epithelia." Neoplasia (New York, N.Y.) 17.11 (November 2015): 826-838.
PMID
26678910
Source
epmc
Published In
Neoplasia (New York, N.Y.)
Volume
17
Issue
11
Publish Date
2015
Start Page
826
End Page
838
DOI
10.1016/j.neo.2015.11.003

Geographic clustering of elevated blood heavy metal levels in pregnant women.

Cadmium (Cd), lead (Pb), mercury (Hg), and arsenic (As) exposure is ubiquitous and has been associated with higher risk of growth restriction and cardiometabolic and neurodevelopmental disorders. However, cost-efficient strategies to identify at-risk populations and potential sources of exposure to inform mitigation efforts are limited. The objective of this study was to describe the spatial distribution and identify factors associated with Cd, Pb, Hg, and As concentrations in peripheral blood of pregnant women.Heavy metals were measured in whole peripheral blood of 310 pregnant women obtained at gestational age ~12 weeks. Prenatal residential addresses were geocoded and geospatial analysis (Getis-Ord Gi* statistics) was used to determine if elevated blood concentrations were geographically clustered. Logistic regression models were used to identify factors associated with elevated blood metal levels and cluster membership.Geospatial clusters for Cd and Pb were identified with high confidence (p-value for Gi* statistic <0.01). The Cd and Pb clusters comprised 10.5 and 9.2 % of Durham County residents, respectively. Medians and interquartile ranges of blood concentrations (μg/dL) for all participants were Cd 0.02 (0.01-0.04), Hg 0.03 (0.01-0.07), Pb 0.34 (0.16-0.83), and As 0.04 (0.04-0.05). In the Cd cluster, medians and interquartile ranges of blood concentrations (μg/dL) were Cd 0.06 (0.02-0.16), Hg 0.02 (0.00-0.05), Pb 0.54 (0.23-1.23), and As 0.05 (0.04-0.05). In the Pb cluster, medians and interquartile ranges of blood concentrations (μg/dL) were Cd 0.03 (0.02-0.15), Hg 0.01 (0.01-0.05), Pb 0.39 (0.24-0.74), and As 0.04 (0.04-0.05). Co-exposure with Pb and Cd was also clustered, the p-values for the Gi* statistic for Pb and Cd was <0.01. Cluster membership was associated with lower education levels and higher pre-pregnancy BMI.Our data support that elevated blood concentrations of Cd and Pb are spatially clustered in this urban environment compared to the surrounding areas. Spatial analysis of metals concentrations in peripheral blood or urine obtained routinely during prenatal care can be useful in surveillance of heavy metal exposure.

Authors
King, KE; Darrah, TH; Money, E; Meentemeyer, R; Maguire, RL; Nye, MD; Michener, L; Murtha, AP; Jirtle, R; Murphy, SK; Mendez, MA; Robarge, W; Vengosh, A; Hoyo, C
MLA Citation
King, KE, Darrah, TH, Money, E, Meentemeyer, R, Maguire, RL, Nye, MD, Michener, L, Murtha, AP, Jirtle, R, Murphy, SK, Mendez, MA, Robarge, W, Vengosh, A, and Hoyo, C. "Geographic clustering of elevated blood heavy metal levels in pregnant women." BMC public health 15 (October 9, 2015): 1035-.
PMID
26449855
Source
epmc
Published In
BMC Public Health
Volume
15
Publish Date
2015
Start Page
1035
DOI
10.1186/s12889-015-2379-9

ACLY and ACC1 Regulate Hypoxia-Induced Apoptosis by Modulating ETV4 via α-ketoglutarate.

In order to propagate a solid tumor, cancer cells must adapt to and survive under various tumor microenvironment (TME) stresses, such as hypoxia or lactic acidosis. To systematically identify genes that modulate cancer cell survival under stresses, we performed genome-wide shRNA screens under hypoxia or lactic acidosis. We discovered that genetic depletion of acetyl-CoA carboxylase (ACACA or ACC1) or ATP citrate lyase (ACLY) protected cancer cells from hypoxia-induced apoptosis. Additionally, the loss of ACLY or ACC1 reduced levels and activities of the oncogenic transcription factor ETV4. Silencing ETV4 also protected cells from hypoxia-induced apoptosis and led to remarkably similar transcriptional responses as with silenced ACLY or ACC1, including an anti-apoptotic program. Metabolomic analysis found that while α-ketoglutarate levels decrease under hypoxia in control cells, α-ketoglutarate is paradoxically increased under hypoxia when ACC1 or ACLY are depleted. Supplementation with α-ketoglutarate rescued the hypoxia-induced apoptosis and recapitulated the decreased expression and activity of ETV4, likely via an epigenetic mechanism. Therefore, ACC1 and ACLY regulate the levels of ETV4 under hypoxia via increased α-ketoglutarate. These results reveal that the ACC1/ACLY-α-ketoglutarate-ETV4 axis is a novel means by which metabolic states regulate transcriptional output for life vs. death decisions under hypoxia. Since many lipogenic inhibitors are under investigation as cancer therapeutics, our findings suggest that the use of these inhibitors will need to be carefully considered with respect to oncogenic drivers, tumor hypoxia, progression and dormancy. More broadly, our screen provides a framework for studying additional tumor cell stress-adaption mechanisms in the future.

Authors
Keenan, MM; Liu, B; Tang, X; Wu, J; Cyr, D; Stevens, RD; Ilkayeva, O; Huang, Z; Tollini, LA; Murphy, SK; Lucas, J; Muoio, DM; Kim, SY; Chi, J-T
MLA Citation
Keenan, MM, Liu, B, Tang, X, Wu, J, Cyr, D, Stevens, RD, Ilkayeva, O, Huang, Z, Tollini, LA, Murphy, SK, Lucas, J, Muoio, DM, Kim, SY, and Chi, J-T. "ACLY and ACC1 Regulate Hypoxia-Induced Apoptosis by Modulating ETV4 via α-ketoglutarate." PLoS genetics 11.10 (October 9, 2015): e1005599-.
Website
http://hdl.handle.net/10161/13614
PMID
26452058
Source
epmc
Published In
PLoS genetics
Volume
11
Issue
10
Publish Date
2015
Start Page
e1005599
DOI
10.1371/journal.pgen.1005599

Alterations of a Cellular Cholesterol Metabolism Network Are a Molecular Feature of Obesity-Related Type 2 Diabetes and Cardiovascular Disease.

Obesity is linked to type 2 diabetes (T2D) and cardiovascular diseases; however, the underlying molecular mechanisms remain unclear. We aimed to identify obesity-associated molecular features that may contribute to obesity-related diseases. Using circulating monocytes from 1,264 Multi-Ethnic Study of Atherosclerosis (MESA) participants, we quantified the transcriptome and epigenome. We discovered that alterations in a network of coexpressed cholesterol metabolism genes are a signature feature of obesity and inflammatory stress. This network included 11 BMI-associated genes related to sterol uptake (↑LDLR, ↓MYLIP), synthesis (↑SCD, FADS1, HMGCS1, FDFT1, SQLE, CYP51A1, SC4MOL), and efflux (↓ABCA1, ABCG1), producing a molecular profile expected to increase intracellular cholesterol. Importantly, these alterations were associated with T2D and coronary artery calcium (CAC), independent from cardiometabolic factors, including serum lipid profiles. This network mediated the associations between obesity and T2D/CAC. Several genes in the network harbored C-phosphorus-G dinucleotides (e.g., ABCG1/cg06500161), which overlapped Encyclopedia of DNA Elements (ENCODE)-annotated regulatory regions and had methylation profiles that mediated the associations between BMI/inflammation and expression of their cognate genes. Taken together with several lines of previous experimental evidence, these data suggest that alterations of the cholesterol metabolism gene network represent a molecular link between obesity/inflammation and T2D/CAC.

Authors
Ding, J; Reynolds, LM; Zeller, T; Müller, C; Lohman, K; Nicklas, BJ; Kritchevsky, SB; Huang, Z; de la Fuente, A; Soranzo, N; Soranzo, N; Settlage, RE; Chuang, C-C; Howard, T; Xu, N; Goodarzi, MO; Chen, Y-DI; Rotter, JI; Siscovick, DS; Parks, JS; Murphy, S; Jacobs, DR; Post, W; Tracy, RP; Wild, PS; Blankenberg, S; Hoeschele, I; Herrington, D; McCall, CE; Liu, Y
MLA Citation
Ding, J, Reynolds, LM, Zeller, T, Müller, C, Lohman, K, Nicklas, BJ, Kritchevsky, SB, Huang, Z, de la Fuente, A, Soranzo, N, Soranzo, N, Settlage, RE, Chuang, C-C, Howard, T, Xu, N, Goodarzi, MO, Chen, Y-DI, Rotter, JI, Siscovick, DS, Parks, JS, Murphy, S, Jacobs, DR, Post, W, Tracy, RP, Wild, PS, Blankenberg, S, Hoeschele, I, Herrington, D, McCall, CE, and Liu, Y. "Alterations of a Cellular Cholesterol Metabolism Network Are a Molecular Feature of Obesity-Related Type 2 Diabetes and Cardiovascular Disease." Diabetes 64.10 (October 2015): 3464-3474.
PMID
26153245
Source
epmc
Published In
Diabetes
Volume
64
Issue
10
Publish Date
2015
Start Page
3464
End Page
3474
DOI
10.2337/db14-1314

DNA Methylation Profiles of Fibrosis-Associated Gene in Blood Reflects Liver Fibrosis Severity in Human Nonalcoholic Fatty Liver Disease

Authors
Moylan, CA; Murphy, SK; Grenier, C; Abdelmalek, MF; Diehl, AM
MLA Citation
Moylan, CA, Murphy, SK, Grenier, C, Abdelmalek, MF, and Diehl, AM. "DNA Methylation Profiles of Fibrosis-Associated Gene in Blood Reflects Liver Fibrosis Severity in Human Nonalcoholic Fatty Liver Disease." October 2015.
Source
wos-lite
Published In
Hepatology
Volume
62
Publish Date
2015
Start Page
648A
End Page
649A

Genotype-Epigenotype Interaction at the IGF2 DMR.

Paternally expressed Insulin-like Growth Factor II (IGF2) encodes a gene whose protein product functions as a potent growth mitogen. Overexpression of IGF2 has been implicated in a wide number of disorders and diseases. IGF2 is regulated in part by differential methylation of the two parentally derived alleles. The differentially methylated region (DMR) located upstream of the imprinted promoters of IGF2 exhibits plasticity under environmental stress and is hypomethylated in several types of cancer. Through bisulfite pyrosequencing and confirmation by nucleotide sequencing, we discovered a CpG to CpC transversion that results in hypomethylation of one of the three CpGs comprising this DMR. The presence of the polymorphism introduces a genetic rather than an environmentally-driven epigenetic source of hypomethylation that is additive to non-genetic sources.

Authors
Murphy, SK; Erginer, E; Huang, Z; Visco, Z; Hoyo, C
MLA Citation
Murphy, SK, Erginer, E, Huang, Z, Visco, Z, and Hoyo, C. "Genotype-Epigenotype Interaction at the IGF2 DMR." Genes 6.3 (August 28, 2015): 777-789.
PMID
26343731
Source
epmc
Published In
Genes
Volume
6
Issue
3
Publish Date
2015
Start Page
777
End Page
789
DOI
10.3390/genes6030777

Abstract 2236: Emergence of epigenetic regulation of tight junction genes in recurrent serous epithelial ovarian cancer

Authors
Huang, Z; Visco, Z; Sfakianos, G; Whitaker, R; Berchuck, A; Murphy, SK
MLA Citation
Huang, Z, Visco, Z, Sfakianos, G, Whitaker, R, Berchuck, A, and Murphy, SK. "Abstract 2236: Emergence of epigenetic regulation of tight junction genes in recurrent serous epithelial ovarian cancer." August 1, 2015.
Source
crossref
Published In
Cancer Research
Volume
75
Issue
15 Supplement
Publish Date
2015
Start Page
2236
End Page
2236
DOI
10.1158/1538-7445.AM2015-2236

Maternal cadmium, iron and zinc levels, DNA methylation and birth weight.

Cadmium (Cd) is a ubiquitous and environmentally persistent toxic metal that has been implicated in neurotoxicity, carcinogenesis and obesity and essential metals including zinc (Zn) and iron (Fe) may alter these outcomes. However mechanisms underlying these relationships remain limited.We examined whether maternal Cd levels during early pregnancy were associated with offspring DNA methylation at regulatory sequences of genomically imprinted genes and weight at birth, and whether Fe and Zn altered these associations. Cd, Fe and Zn were measured in maternal blood of 319 women ≤ 12 weeks gestation. Offspring umbilical cord blood leukocyte DNA methylation at regulatory differentially methylated regions (DMRs) of 8 imprinted genes was measured using bisulfite pyrosequencing. Regression models were used to examine the relationships among Cd, Fe, Zn, and DMR methylation and birth weight.Elevated maternal blood Cd levels were associated with lower birth weight (p = 0.03). Higher maternal blood Cd levels were also associated with lower offspring methylation at the PEG3 DMR in females (β = 0.55, se = 0.17, p = 0.05), and at the MEG3 DMR in males (β = 0.72, se = 0.3, p = 0.08), however the latter association was not statistically significant. Associations between Cd and PEG3 and PLAGL1 DNA methylation were stronger in infants born to women with low concentrations of Fe (p < 0.05).Our data suggest the association between pre-natal Cd and offspring DNA methylation at regulatory sequences of imprinted genes may be sex- and gene-specific. Essential metals such as Zn may mitigate DNA methylation response to Cd exposure. Larger studies are required.

Authors
Vidal, AC; Semenova, V; Darrah, T; Vengosh, A; Huang, Z; King, K; Nye, MD; Fry, R; Skaar, D; Maguire, R; Murtha, A; Schildkraut, J; Murphy, S; Hoyo, C
MLA Citation
Vidal, AC, Semenova, V, Darrah, T, Vengosh, A, Huang, Z, King, K, Nye, MD, Fry, R, Skaar, D, Maguire, R, Murtha, A, Schildkraut, J, Murphy, S, and Hoyo, C. "Maternal cadmium, iron and zinc levels, DNA methylation and birth weight." BMC pharmacology & toxicology 16 (July 15, 2015): 20-.
PMID
26173596
Source
epmc
Published In
BMC pharmacology & toxicology
Volume
16
Publish Date
2015
Start Page
20
DOI
10.1186/s40360-015-0020-2

Systems Biology and the Epigenome

© 2015 Elsevier Inc. All rights reserved.Epigenetics can be defined as the heritable perpetuation of gene activity without modification of the DNA sequence. Epigenetic mechanisms include methylation of cytosine residues within the DNA sequence and the posttranslational modification of histone proteins. The entirety of the epigenetic features of the genome is called the epigenome. This layer of regulatory information creates a dynamic interface between environmental cues and the genome that is essential for normal development and cellular function while at the same time, providing the mechanism by which the genome can respond to the environment by altering gene expression. As such, epigenetic and epigenomic characterization has rapidly become a primary interest for scientists studying the influence of the environment on human populations. In this chapter, we introduce the two major mechanisms of epigenetic regulation, DNA methylation and histone modifications, and how these impact the structure and function of the genome.

Authors
Taylor, MM; Murphy, SK
MLA Citation
Taylor, MM, and Murphy, SK. "Systems Biology and the Epigenome." Systems Biology in Toxicology and Environmental Health. July 7, 2015. 43-56.
Source
scopus
Publish Date
2015
Start Page
43
End Page
56
DOI
10.1016/B978-0-12-801564-3.00003-1

Epigenetic regulation of Newborns’ imprinted genes related to gestational growth: patterning by parental race/ethnicity and maternal socioeconomic status

Authors
King, K; Murphy, S; Hoyo, C
MLA Citation
King, K, Murphy, S, and Hoyo, C. "Epigenetic regulation of Newborns’ imprinted genes related to gestational growth: patterning by parental race/ethnicity and maternal socioeconomic status." Journal of Epidemiology and Community Health 69.7 (July 2015): 639-647.
Source
crossref
Published In
Journal of Epidemiology and Community Health
Volume
69
Issue
7
Publish Date
2015
Start Page
639
End Page
647
DOI
10.1136/jech-2014-204781

Menstrual cyclic change of metastin/GPR54 in endometrium

© 2014, The Japanese Society for Clinical Molecular Morphology.Metastin/kisspeptin is encoded by KISS1 and functions as an endogenous ligand of GPR54. Interaction of metastin with GPR54 suppresses metastasis and also regulates release of gonadotropin-releasing hormone, which promotes secretion of estradiol (E2) and progesterone (P4). We have previously demonstrated epigenetic regulation of GPR54 in endometrial cancer and the potent role of metastin peptides in inhibiting metastasis in endometrial cancer. However, little is known about how the metastin–GPR54 axis is regulated in the endometrium, the precursor tissue of endometrial cancer. Endometrial stromal cells (ESCs) and endometrial glandular cells (EGCs) within the endometrium show morphological changes when exposed to E2 and P4. In this study, we show that metastin expression is induced in ESCs through decidualization, but is repressed in glandular components of atypical endometrial hyperplasia (AEH) and endometrial cancer relative to EGCs. The promoter of GPR54 is unmethylated in normal endometrium and in AEH. These results indicate metastin may function in decidualized endometrium to prepare for adequate placentation but this autocrine secretion of metastin is deregulated during oncogenesis to enable tumor cells to spread.

Authors
Baba, T; Kang, HS; Hosoe, Y; Kharma, B; Abiko, K; Matsumura, N; Hamanishi, J; Yamaguchi, K; Yoshioka, Y; Koshiyama, M; Mandai, M; Murphy, SK; Konishi, I
MLA Citation
Baba, T, Kang, HS, Hosoe, Y, Kharma, B, Abiko, K, Matsumura, N, Hamanishi, J, Yamaguchi, K, Yoshioka, Y, Koshiyama, M, Mandai, M, Murphy, SK, and Konishi, I. "Menstrual cyclic change of metastin/GPR54 in endometrium." Medical Molecular Morphology 48.2 (June 1, 2015): 76-84.
Source
scopus
Published In
Medical Molecular Morphology
Volume
48
Issue
2
Publish Date
2015
Start Page
76
End Page
84
DOI
10.1007/s00795-014-0081-0

Menstrual cyclic change of metastin/GPR54 in endometrium.

Metastin/kisspeptin is encoded by KISS1 and functions as an endogenous ligand of GPR54. Interaction of metastin with GPR54 suppresses metastasis and also regulates release of gonadotropin-releasing hormone, which promotes secretion of estradiol (E2) and progesterone (P4). We have previously demonstrated epigenetic regulation of GPR54 in endometrial cancer and the potent role of metastin peptides in inhibiting metastasis in endometrial cancer. However, little is known about how the metastin-GPR54 axis is regulated in the endometrium, the precursor tissue of endometrial cancer. Endometrial stromal cells (ESCs) and endometrial glandular cells (EGCs) within the endometrium show morphological changes when exposed to E2 and P4. In this study, we show that metastin expression is induced in ESCs through decidualization, but is repressed in glandular components of atypical endometrial hyperplasia (AEH) and endometrial cancer relative to EGCs. The promoter of GPR54 is unmethylated in normal endometrium and in AEH. These results indicate metastin may function in decidualized endometrium to prepare for adequate placentation but this autocrine secretion of metastin is deregulated during oncogenesis to enable tumor cells to spread.

Authors
Baba, T; Kang, HS; Hosoe, Y; Kharma, B; Abiko, K; Matsumura, N; Hamanishi, J; Yamaguchi, K; Yoshioka, Y; Koshiyama, M; Mandai, M; Murphy, SK; Konishi, I
MLA Citation
Baba, T, Kang, HS, Hosoe, Y, Kharma, B, Abiko, K, Matsumura, N, Hamanishi, J, Yamaguchi, K, Yoshioka, Y, Koshiyama, M, Mandai, M, Murphy, SK, and Konishi, I. "Menstrual cyclic change of metastin/GPR54 in endometrium." Medical molecular morphology 48.2 (June 2015): 76-84.
PMID
24908069
Source
epmc
Published In
Medical Molecular Morphology
Volume
48
Issue
2
Publish Date
2015
Start Page
76
End Page
84
DOI
10.1007/s00795-014-0081-0

Comprehensive profiling of amino acid response uncovers unique methionine-deprived response dependent on intact creatine biosynthesis.

Besides being building blocks for protein synthesis, amino acids serve a wide variety of cellular functions, including acting as metabolic intermediates for ATP generation and for redox homeostasis. Upon amino acid deprivation, free uncharged tRNAs trigger GCN2-ATF4 to mediate the well-characterized transcriptional amino acid response (AAR). However, it is not clear whether the deprivation of different individual amino acids triggers identical or distinct AARs. Here, we characterized the global transcriptional response upon deprivation of one amino acid at a time. With the exception of glycine, which was not required for the proliferation of MCF7 cells, we found that the deprivation of most amino acids triggered a shared transcriptional response that included the activation of ATF4, p53 and TXNIP. However, there was also significant heterogeneity among different individual AARs. The most dramatic transcriptional response was triggered by methionine deprivation, which activated an extensive and unique response in different cell types. We uncovered that the specific methionine-deprived transcriptional response required creatine biosynthesis. This dependency on creatine biosynthesis was caused by the consumption of S-Adenosyl-L-methionine (SAM) during creatine biosynthesis that helps to deplete SAM under methionine deprivation and reduces histone methylations. As such, the simultaneous deprivation of methionine and sources of creatine biosynthesis (either arginine or glycine) abolished the reduction of histone methylation and the methionine-specific transcriptional response. Arginine-derived ornithine was also required for the complete induction of the methionine-deprived specific gene response. Collectively, our data identify a previously unknown set of heterogeneous amino acid responses and reveal a distinct methionine-deprived transcriptional response that results from the crosstalk of arginine, glycine and methionine metabolism via arginine/glycine-dependent creatine biosynthesis.

Authors
Tang, X; Keenan, MM; Wu, J; Lin, C-A; Dubois, L; Thompson, JW; Freedland, SJ; Murphy, SK; Chi, J-T
MLA Citation
Tang, X, Keenan, MM, Wu, J, Lin, C-A, Dubois, L, Thompson, JW, Freedland, SJ, Murphy, SK, and Chi, J-T. "Comprehensive profiling of amino acid response uncovers unique methionine-deprived response dependent on intact creatine biosynthesis." PLoS genetics 11.4 (April 7, 2015): e1005158-.
PMID
25849282
Source
epmc
Published In
PLoS genetics
Volume
11
Issue
4
Publish Date
2015
Start Page
e1005158
DOI
10.1371/journal.pgen.1005158

In vitro lead exposure changes DNA methylation and expression of IGF2 and PEG1/MEST.

Epigenetic processes, such as changes in DNA methylation, likely mediate the link between environmental exposures in utero and altered gene expression. Differentially methylated regions (DMRs) that regulate imprinted genes may be especially vulnerable to environmental exposures since imprinting is established and maintained largely through DNA methylation, resulting in expression from only one parental chromosome. We used the human embryonic kidney cell line, HEK-293, to investigate the effects of exposure to physiologically relevant doses of lead acetate (Pb) on the methylation status of nine imprinted gene DMRs. We assessed mean methylation after seventy-two hours of Pb exposure (0-25 μg/dL) using bisulfite pyrosequencing. The PEG1/MEST and IGF2 DMRs had maximum methylation decreases of 9.6% (20 μg/dL; p<0.005) and 3.8% (25 μg/dL; p<0.005), respectively. Changes at the MEG3 DMRs had a maximum decrease in methylation of 2.9% (MEG3) and 1.8% (MEG3-IG) at 5 μg/dL Pb, but were not statistically significant. The H19, NNAT, PEG3, PLAGL1, and SGCE/PEG10 DMRs showed a less than 0.5% change in methylation, across the dose range used, and were deemed non-responsive to Pb in our model. Pb exposure below reportable/actionable levels increased expression of PEG1/MEST concomitant with decreased methylation. These results suggest that Pb exposure can stably alter the regulatory capacity of multiple imprinted DMRs.

Authors
Nye, MD; Hoyo, C; Murphy, SK
MLA Citation
Nye, MD, Hoyo, C, and Murphy, SK. "In vitro lead exposure changes DNA methylation and expression of IGF2 and PEG1/MEST." Toxicology in vitro : an international journal published in association with BIBRA 29.3 (April 2015): 544-550.
PMID
25596546
Source
epmc
Published In
Toxicology in Vitro
Volume
29
Issue
3
Publish Date
2015
Start Page
544
End Page
550
DOI
10.1016/j.tiv.2015.01.002

Newborns of obese parents have altered DNA methylation patterns at imprinted genes.

BACKGROUND: Several epidemiologic studies have demonstrated associations between periconceptional environmental exposures and health status of the offspring in later life. Although these environmentally related effects have been attributed to epigenetic changes, such as DNA methylation shifts at imprinted genes, little is known about the potential effects of maternal and paternal preconceptional overnutrition or obesity. OBJECTIVE: We examined parental preconceptional obesity in relation to DNA methylation profiles at multiple human imprinted genes important in normal growth and development, such as: maternally expressed gene 3 (MEG3), mesoderm-specific transcript (MEST), paternally expressed gene 3 (PEG3), pleiomorphic adenoma gene-like 1 (PLAGL1), epsilon sarcoglycan and paternally expressed gene 10 (SGCE/PEG10) and neuronatin (NNAT). METHODS: We measured methylation percentages at the differentially methylated regions (DMRs) by bisulfite pyrosequencing in DNA extracted from umbilical cord blood leukocytes of 92 newborns. Preconceptional obesity, defined as BMI ⩾30 kg m(-2), was ascertained through standardized questionnaires. RESULTS: After adjusting for potential confounders and cluster effects, paternal obesity was significantly associated with lower methylation levels at the MEST (β=-2.57; s.e.=0.95; P=0.008), PEG3 (β=-1.71; s.e.=0.61; P=0.005) and NNAT (β=-3.59; s.e.=1.76; P=0.04) DMRs. Changes related to maternal obesity detected at other loci were as follows: β-coefficient was +2.58 (s.e.=1.00; P=0.01) at the PLAGL1 DMR and -3.42 (s.e.=1.69; P=0.04) at the MEG3 DMR. CONCLUSION: We found altered methylation outcomes at multiple imprint regulatory regions in children born to obese parents, compared with children born to non-obese parents. In spite of the small sample size, our data suggest a preconceptional influence of parental life-style or overnutrition on the (re)programming of imprint marks during gametogenesis and early development. More specifically, the significant and independent association between paternal obesity and the offspring's methylation status suggests the susceptibility of the developing sperm for environmental insults. The acquired imprint instability may be carried onto the next generation and increase the risk for chronic diseases in adulthood.

Authors
Soubry, A; Murphy, SK; Wang, F; Huang, Z; Vidal, AC; Fuemmeler, BF; Kurtzberg, J; Murtha, A; Jirtle, RL; Schildkraut, JM; Hoyo, C
MLA Citation
Soubry, A, Murphy, SK, Wang, F, Huang, Z, Vidal, AC, Fuemmeler, BF, Kurtzberg, J, Murtha, A, Jirtle, RL, Schildkraut, JM, and Hoyo, C. "Newborns of obese parents have altered DNA methylation patterns at imprinted genes." Int J Obes (Lond) 39.4 (April 2015): 650-657.
PMID
24158121
Source
pubmed
Published In
International Journal of Obesity
Volume
39
Issue
4
Publish Date
2015
Start Page
650
End Page
657
DOI
10.1038/ijo.2013.193

Newborns of obese parents have altered DNA methylation patterns at imprinted genes

Background:Several epidemiologic studies have demonstrated associations between periconceptional environmental exposures and health status of the offspring in later life. Although these environmentally related effects have been attributed to epigenetic changes, such as DNA methylation shifts at imprinted genes, little is known about the potential effects of maternal and paternal preconceptional overnutrition or obesity.Objective:We examined parental preconceptional obesity in relation to DNA methylation profiles at multiple human imprinted genes important in normal growth and development, such as: maternally expressed gene 3 (MEG3), mesoderm-specific transcript (MEST), paternally expressed gene 3 (PEG3), pleiomorphic adenoma gene-like 1 (PLAGL1), epsilon sarcoglycan and paternally expressed gene 10 (SGCE/PEG10) and neuronatin (NNAT).Methods:We measured methylation percentages at the differentially methylated regions (DMRs) by bisulfite pyrosequencing in DNA extracted from umbilical cord blood leukocytes of 92 newborns. Preconceptional obesity, defined as BMI ≥30 kg m -2, was ascertained through standardized questionnaires.Results:After adjusting for potential confounders and cluster effects, paternal obesity was significantly associated with lower methylation levels at the MEST (β=-2.57; s.e.=0.95; P=0.008), PEG3 (β=-1.71; s.e.=0.61; P=0.005) and NNAT (β=-3.59; s.e.=1.76; P=0.04) DMRs. Changes related to maternal obesity detected at other loci were as follows: β-coefficient was +2.58 (s.e.=1.00; P=0.01) at the PLAGL1 DMR and -3.42 (s.e.=1.69; P=0.04) at the MEG3 DMR.Conclusion:We found altered methylation outcomes at multiple imprint regulatory regions in children born to obese parents, compared with children born to non-obese parents. In spite of the small sample size, our data suggest a preconceptional influence of parental life-style or overnutrition on the (re)programming of imprint marks during gametogenesis and early development. More specifically, the significant and independent association between paternal obesity and the offspring's methylation status suggests the susceptibility of the developing sperm for environmental insults. The acquired imprint instability may be carried onto the next generation and increase the risk for chronic diseases in adulthood.

Authors
Soubry, A; Murphy, SK; Wang, F; Huang, Z; Vidal, AC; Fuemmeler, BF; Kurtzberg, J; Murtha, A; Jirtle, RL; Schildkraut, JM; Hoyo, C
MLA Citation
Soubry, A, Murphy, SK, Wang, F, Huang, Z, Vidal, AC, Fuemmeler, BF, Kurtzberg, J, Murtha, A, Jirtle, RL, Schildkraut, JM, and Hoyo, C. "Newborns of obese parents have altered DNA methylation patterns at imprinted genes." International Journal of Obesity 39.4 (January 1, 2015): 650-657.
Source
scopus
Published In
International Journal of Obesity
Volume
39
Issue
4
Publish Date
2015
Start Page
650
End Page
657
DOI
10.1038/ijo.2013.193

Invasion of uterine cervical squamous cell carcinoma cells is facilitated by locoregional interaction with cancer-associated fibroblasts via activating transforming growth factor-beta.

OBJECTIVE: Local invasion is a common pattern of spread in uterine cervical squamous cell carcinoma (CSCC). Although transforming growth factor-beta (TGF-β) facilitates invasion of various types of cancer cells, the role of the TGF-β pathway in CSCC is unclear. In this study, we analyzed the role of TGF-β signaling in the progression of CSCC. METHODS: Immunohistochemistry was used to examine the expression of TGF-β pathway molecules in 67 CSCC samples with clinicopathological data. Activation of the TGF-β pathway was investigated following co-culture of CSCC cells and cervical cancer-associated fibroblasts (CCAFs). RESULTS: Clinicopathological analysis of CSCC samples revealed that prominent expression of TGF-β receptor-2 was more frequent in CSCC with lymphovascular space invasion (LVSI) than without LVSI (p < 0.01). Lymph node metastasis was more frequent in cases in which phosphorylated SMAD3 (pSMAD3) was localized exclusively at the boundary of tumor clusters (n = 9, p < 0.05). Recombinant TGF-β1 increased pSMAD3 expression and enhanced cellular invasion (p < 0.005) in CSCC cells, which was attenuated by an inhibitor of the TGF-β receptor (p < 0.005). Enhanced pSMAD3 expression and invasion was also observed when conditioned media from CSCC cells co-cultured with CCAFs were administered. Luciferase assays showed that this medium contained a large amount of active TGF-β. Along with TGF-β activation, thrombospondin-1 was upregulated in both CSCC cells and CCAFs, while thrombospondin-1 silencing in either CSCC cells or CCAFs repressed the activity of TGF-β. Thrombospondin-1 was prominently expressed in cases with pSMAD3 boundary staining (p < 0.05). CONCLUSIONS: These results suggest that interaction between CSCC cells and surrounding CCAFs activates TGF-β via thrombospondin-1 secretion to facilitate CSCC invasion.

Authors
Nagura, M; Matsumura, N; Baba, T; Murakami, R; Kharma, B; Hamanishi, J; Yamaguchi, K; Abiko, K; Koshiyama, M; Mandai, M; Murata, T; Murphy, SK; Konishi, I
MLA Citation
Nagura, M, Matsumura, N, Baba, T, Murakami, R, Kharma, B, Hamanishi, J, Yamaguchi, K, Abiko, K, Koshiyama, M, Mandai, M, Murata, T, Murphy, SK, and Konishi, I. "Invasion of uterine cervical squamous cell carcinoma cells is facilitated by locoregional interaction with cancer-associated fibroblasts via activating transforming growth factor-beta." Gynecologic oncology 136.1 (January 2015): 104-111.
PMID
25434636
Source
epmc
Published In
Gynecologic Oncology
Volume
136
Issue
1
Publish Date
2015
Start Page
104
End Page
111
DOI
10.1016/j.ygyno.2014.11.075

IL-10, IL-15, IL-17, and GMCSF levels in cervical cancer tissue of Tanzanian women infected with HPV16/18 vs. non-HPV16/18 genotypes.

Despite comparable screening rates for precancerous lesions, higher incidence and mortality related to cervical cancer in minority women persists. Recent evidence suggests that minority women with precancerous cervical lesions harbor a wider range of human papillomavirus (HPV) genotypes, many of these distinct from HPV16/18, those most commonly found in Caucasian women. The goal of the analysis was to determine if inflammatory cytokines and chemokines varied by HPV 16/18 versus other genotypes in cervical cancer tissues from Tanzanian women.HPV genotypes and concentrations of chemokines and cytokines were measured from homogenized fresh tumor tissue of thirty-one women with invasive cervical cancer (ICC). Risk factors for cervical cancer including age, parity, hormonal contraceptive use and cigarette smoking were obtained by questionnaire. Generalized linear models were used to evaluate differences between chemokines/cytokine levels in women infected with HPV16/18 and those infected with other HPV genotypes.After adjusting for age, parity and hormonal contraceptives, IL-17 was found significantly more frequently in invasive cervical cancer samples of women infected with HPV16/18 compared to women infected with other HPV genotypes (p = 0.033). In contrast, higher levels for granular macrophage colony-stimulating factor (p = 0.004), IL-10 (p = 0.037), and IL-15 (p = 0.041) were found in ICC tissues of women infected with genotypes other than HPV16/18 when compared to those of women infected with HPV16/18.While the small sample size limits inference, our data suggest that infection with different HPV genotypes is associated with distinct pro-inflammatory cytokine expression profiles; whether this explains some of the racial differences observed in cervical cancer is still unclear. Future studies are needed to confirm these findings.

Authors
Vidal, AC; Skaar, D; Maguire, R; Dodor, S; Musselwhite, LW; Bartlett, JA; Oneko, O; Obure, J; Mlay, P; Murphy, SK; Hoyo, C
MLA Citation
Vidal, AC, Skaar, D, Maguire, R, Dodor, S, Musselwhite, LW, Bartlett, JA, Oneko, O, Obure, J, Mlay, P, Murphy, SK, and Hoyo, C. "IL-10, IL-15, IL-17, and GMCSF levels in cervical cancer tissue of Tanzanian women infected with HPV16/18 vs. non-HPV16/18 genotypes." Infectious agents and cancer 10 (January 2015): 10-.
Website
http://hdl.handle.net/10161/12657
PMID
25810759
Source
epmc
Published In
Infectious Agents and Cancer
Volume
10
Publish Date
2015
Start Page
10
DOI
10.1186/s13027-015-0005-1

Ascites Increases Expression/Function of Multidrug Resistance Proteins in Ovarian Cancer Cells.

Chemotherapy resistance is the major reason for the failure of ovarian cancer treatment. One mechanism behind chemo-resistance involves the upregulation of multidrug resistance (MDR) genes (ABC transporters) that effectively transport (efflux) drugs out of the tumor cells. As a common symptom in stage III/IV ovarian cancer patients, ascites is associated with cancer progression. However, whether ascites drives multidrug resistance in ovarian cancer cells awaits elucidation. Here, we demonstrate that when cultured with ascites derived from ovarian cancer-bearing mice, a murine ovarian cancer cell line became less sensitive to paclitaxel, a first line chemotherapeutic agent for ovarian cancer patients. Moreover, incubation of murine ovarian cancer cells in vitro with ascites drives efflux function in these cells. Functional studies show ascites-driven efflux is suppressible by specific inhibitors of either of two ABC transporters [Multidrug Related Protein (MRP1); Breast Cancer Related Protein (BCRP)]. To demonstrate relevance of our findings to ovarian cancer patients, we studied relative efflux in human ovarian cancer cells obtained from either patient ascites or from primary tumor. Immortalized cell lines developed from human ascites show increased susceptibility to efflux inhibitors (MRP1, BCRP) compared to a cell line derived from a primary ovarian cancer, suggesting an association between ascites and efflux function in human ovarian cancer. Efflux in ascites-derived human ovarian cancer cells is associated with increased expression of ABC transporters compared to that in primary tumor-derived human ovarian cancer cells. Collectively, our findings identify a novel activity for ascites in promoting ovarian cancer multidrug resistance.

Authors
Mo, L; Pospichalova, V; Huang, Z; Murphy, SK; Payne, S; Wang, F; Kennedy, M; Cianciolo, GJ; Bryja, V; Pizzo, SV; Bachelder, RE
MLA Citation
Mo, L, Pospichalova, V, Huang, Z, Murphy, SK, Payne, S, Wang, F, Kennedy, M, Cianciolo, GJ, Bryja, V, Pizzo, SV, and Bachelder, RE. "Ascites Increases Expression/Function of Multidrug Resistance Proteins in Ovarian Cancer Cells." PloS one 10.7 (January 2015): e0131579-.
PMID
26148191
Source
epmc
Published In
PloS one
Volume
10
Issue
7
Publish Date
2015
Start Page
e0131579
DOI
10.1371/journal.pone.0131579

Associations between prenatal physical activity, birth weight, and DNA methylation at genomically imprinted domains in a multiethnic newborn cohort.

Birth weight is a commonly used indicator of the fetal environment and a predictor of future health outcomes. While the etiology of birth weight extremes is likely multifactorial, epidemiologic data suggest that prenatal physical activity (PA) may play an important role. The mechanisms underlying this association remain unresolved, although epigenetics has been proposed. This study aimed to estimate associations between prenatal PA, birth weight, and newborn DNA methylation levels at differentially methylated regions (DMRs) regulating 4 imprinted genes known to be important in fetal development. Study participants (N = 1281) were enrolled as part of the Newborn Epigenetics Study. Prenatal PA was ascertained using the Pregnancy Physical Activity Questionnaire, and birth weight data obtained from hospital records. Among 484 term mother-infant pairs, imprinted gene methylation levels were measured at DMRs using bisulfite pyrosequencing. Generalized linear and logistic regression models were used to estimate associations. After adjusting for preterm birth and race/ethnicity, we found that infants born to mothers in the highest quartile of total non-sedentary time had lower birth weight compared to infants of mothers in the lowest quartile (β = -81.16, SE = 42.02, P = 0.05). These associations appeared strongest among male infants (β = -125.40, SE = 58.10, P = 0.03). Methylation at the PLAGL1 DMR was related to total non-sedentary time (P < 0.05). Our findings confirm that prenatal PA is associated with reduced birth weight, and is the first study to support a role for imprinted gene plasticity in these associations. Larger studies are required.

Authors
McCullough, LE; Mendez, MA; Miller, EE; Murtha, AP; Murphy, SK; Hoyo, C
MLA Citation
McCullough, LE, Mendez, MA, Miller, EE, Murtha, AP, Murphy, SK, and Hoyo, C. "Associations between prenatal physical activity, birth weight, and DNA methylation at genomically imprinted domains in a multiethnic newborn cohort." Epigenetics 10.7 (January 2015): 597-606.
PMID
25928716
Source
epmc
Published In
Epigenetics : official journal of the DNA Methylation Society
Volume
10
Issue
7
Publish Date
2015
Start Page
597
End Page
606
DOI
10.1080/15592294.2015.1045181

Optimizing Urine Processing Protocols for Protein and Metabolite Detection.

In urine, factors such as timing of voids, and duration at room temperature (RT) may affect the quality of recovered protein and metabolite data. Additives may aid with detection, but can add more complexity in sample collection or analysis. We aimed to identify the optimal urine processing protocol for clinically-obtained urine samples that allows for the highest protein and metabolite yields with minimal degradation.Healthy women provided multiple urine samples during the same day. Women collected their first morning (1(st) AM) void and another "random void". Random voids were aliquotted with: 1) no additive; 2) boric acid (BA); 3) protease inhibitor (PI); or 4) both BA + PI. Of these aliquots, some were immediately stored at 4°C, and some were left at RT for 4 hours. Proteins and individual metabolites were quantified, normalized to creatinine concentrations, and compared across processing conditions. Sample pools corresponding to each processing condition were analyzed using mass spectrometry to assess protein degradation.Ten Caucasian women between 35-65 years of age provided paired 1(st) morning and random voided urine samples. Normalized protein concentrations were slightly higher in 1(st) AM compared to random "spot" voids. The addition of BA did not significantly change proteins, while PI significantly improved normalized protein concentrations, regardless of whether samples were immediately cooled or left at RT for 4 hours. In pooled samples, there were minimal differences in protein degradation under the various conditions we tested. In metabolite analyses, there were significant differences in individual amino acids based on the timing of the void.For comparative translational research using urine, information about void timing should be collected and standardized. For urine samples processed in the same day, BA does not appear to be necessary while the addition of PI enhances protein yields, regardless of 4°C or RT storage temperature.

Authors
Siddiqui, NY; DuBois, LG; St John-Williams, L; Will, TJ; Grenier, C; Burke, E; Fraser, MO; Amundsen, CL; Murphy, SK
MLA Citation
Siddiqui, NY, DuBois, LG, St John-Williams, L, Will, TJ, Grenier, C, Burke, E, Fraser, MO, Amundsen, CL, and Murphy, SK. "Optimizing Urine Processing Protocols for Protein and Metabolite Detection." Journal of proteomics & bioinformatics 2015.Suppl 14 (January 2015).
PMID
27212868
Source
epmc
Published In
Journal of Proteomics and Bioinformatics
Volume
2015
Issue
Suppl 14
Publish Date
2015

Hepatocyte nuclear factor-1β (HNF-1β) promotes glucose uptake and glycolytic activity in ovarian clear cell carcinoma.

Ovarian clear cell carcinoma (OCCC) is a morphologically and biologically distinct subtype of ovarian carcinomas that often arises in ovarian endometriosis. We previously reported that a unique carcinogenic environment, especially iron-induced oxidative stress in endometriotic cysts may promote development of OCCC. We also identified a gene expression profile characteristic of OCCC (the "OCCC signature"). This 320-gene OCCC signature is enriched in genes associated with stress response and sugar metabolism. However, the biological implication of this profile is unclear. In this study, we have focused on the biological role of the HNF-1β gene within the OCCC signature, which was previously shown to be overexpressed in OCCC. Suppression of HNF-1β in the HNF-1β-overexpressing human ovarian cancer cell line RMG2 using short hairpin RNA resulted in a significant increase in proliferation. It also facilitated glucose uptake, glycolytic activity, and lactate secretion along with increased expression of the glucose transporter-1 (GLUT-1) gene and several key enzymes in the glycolytic process. Conversely, forced expression of HNF-1β in the serous ovarian cancer cell line, Hey, resulted in slowed cellular growth and repressed glycolytic activity. These data suggest that HNF-1β represses cell growth, and at the same time, it promotes aerobic glycolysis which is known as the "Warburg effect." As the Warburg effect is regarded as a characteristic metabolic process in cancer which may contribute to cell survival under hypoxic conditions or in a stressful environment, overexpression of HNF-1β may play an inevitable role in the occurrence of OCCC in stressful environment.

Authors
Okamoto, T; Mandai, M; Matsumura, N; Yamaguchi, K; Kondoh, H; Amano, Y; Baba, T; Hamanishi, J; Abiko, K; Kosaka, K; Murphy, SK; Mori, S; Konishi, I
MLA Citation
Okamoto, T, Mandai, M, Matsumura, N, Yamaguchi, K, Kondoh, H, Amano, Y, Baba, T, Hamanishi, J, Abiko, K, Kosaka, K, Murphy, SK, Mori, S, and Konishi, I. "Hepatocyte nuclear factor-1β (HNF-1β) promotes glucose uptake and glycolytic activity in ovarian clear cell carcinoma." Mol Carcinog 54.1 (January 2015): 35-49.
PMID
24105991
Source
pubmed
Published In
Molecular Carcinogenesis
Volume
54
Issue
1
Publish Date
2015
Start Page
35
End Page
49
DOI
10.1002/mc.22072

Epigenetic regulation of Newborns' imprinted genes related to gestational growth: Patterning by parental race/ethnicity and maternal socioeconomic status

© 2015 by the BMJ Publishing Group Ltd.Background Children born to parents with lower income and education are at risk for obesity and later-life risk of common chronic diseases, and epigenetics has been hypothesised to link these associations. However, epigenetic targets are unknown. We focus on a cluster of well-characterised genomically imprinted genes because their monoallelic expression is regulated by DNA methylation at differentially methylated regions (DMRs), are critical in fetal growth, and DNA methylation patterns at birth have been associated with increased risk of birth weight extremes and overweight status or obesity in early childhood. Methods We measured DNA methylation at DMRs regulating genomically imprinted domains (IGF2/H19, DLK1/MEG3, NNAT and PLAGL1) using umbilical cord blood leucocytes from 619 infants recruited in Durham, North Carolina in 2010-2011. We examined differences in DNA methylation levels by race/ethnicity of both parents, and the role that maternal socioeconomic status (SES) may play in the association between race/ethnic epigenetic differences. Results Unadjusted race/ethnic differences only were evident for DMRs regulating MEG3 and IGF2; race/ethnic differences persisted in IGF2/H19 and NNAT after accounting for income and education. Conclusions Results suggest that parental factors may not only influence DNA methylation, but also do so in ways that vary by DMR. Findings support the hypothesis that epigenetics may link the observed lower SES during the prenatal period and poor outcomes such as low birth weight; lower birth weight has previously been associated with adult-onset chronic diseases and conditions that include cardiovascular diseases, diabetes, obesity and some cancers.

Authors
King, K; Murphy, S; Hoyo, C
MLA Citation
King, K, Murphy, S, and Hoyo, C. "Epigenetic regulation of Newborns' imprinted genes related to gestational growth: Patterning by parental race/ethnicity and maternal socioeconomic status." Journal of Epidemiology and Community Health (2015).
Source
scival
Published In
Journal of Epidemiology and Community Health
Publish Date
2015
DOI
10.1136/jech-2014-204781

Hepatocyte nuclear factor-1β (HNF-1β) promotes glucose uptake and glycolytic activity in ovarian clear cell carcinoma

© 2013 Wiley Periodicals, Inc.Ovarian clear cell carcinoma (OCCC) is a morphologically and biologically distinct subtype of ovarian carcinomas that often arises in ovarian endometriosis. We previously reported that a unique carcinogenic environment, especially iron-induced oxidative stress in endometriotic cysts may promote development of OCCC. We also identified a gene expression profile characteristic of OCCC (the "OCCC signature"). This 320-gene OCCC signature is enriched in genes associated with stress response and sugar metabolism. However, the biological implication of this profile is unclear. In this study, we have focused on the biological role of the HNF-1β gene within the OCCC signature, which was previously shown to be overexpressed in OCCC. Suppression of HNF-1β in the HNF-1β-overexpressing human ovarian cancer cell line RMG2 using short hairpin RNA resulted in a significant increase in proliferation. It also facilitated glucose uptake, glycolytic activity, and lactate secretion along with increased expression of the glucose transporter-1 (GLUT-1) gene and several key enzymes in the glycolytic process. Conversely, forced expression of HNF-1β in the serous ovarian cancer cell line, Hey, resulted in slowed cellular growth and repressed glycolytic activity. These data suggest that HNF-1β represses cell growth, and at the same time, it promotes aerobic glycolysis which is known as the "Warburg effect." As the Warburg effect is regarded as a characteristic metabolic process in cancer which may contribute to cell survival under hypoxic conditions or in a stressful environment, overexpression of HNF-1β may play an inevitable role in the occurrence of OCCC in stressful environment.

Authors
Okamoto, T; Mandai, M; Matsumura, N; Yamaguchi, K; Kondoh, H; Amano, Y; Baba, T; Hamanishi, J; Abiko, K; Kosaka, K; Murphy, SK; Mori, S; Konishi, I
MLA Citation
Okamoto, T, Mandai, M, Matsumura, N, Yamaguchi, K, Kondoh, H, Amano, Y, Baba, T, Hamanishi, J, Abiko, K, Kosaka, K, Murphy, SK, Mori, S, and Konishi, I. "Hepatocyte nuclear factor-1β (HNF-1β) promotes glucose uptake and glycolytic activity in ovarian clear cell carcinoma." Molecular Carcinogenesis 54.1 (2015): 35-49.
Source
scival
Published In
Molecular Carcinogenesis
Volume
54
Issue
1
Publish Date
2015
Start Page
35
End Page
49
DOI
10.1002/mc.22072

STAT1 drives tumor progression in serous papillary endometrial cancer.

Recent studies of the interferon-induced transcription factor STAT1 have associated its dysregulation with poor prognosis in some cancers, but its mechanistic contributions are not well defined. In this study, we report that the STAT1 pathway is constitutively upregulated in type II endometrial cancers. STAT1 pathway alteration was especially prominent in serous papillary endometrial cancers (SPEC) that are refractive to therapy. Our results defined a "SPEC signature" as a molecular definition of its malignant features and poor prognosis. Specifically, we found that STAT1 regulated MYC as well as ICAM1, PD-L1, and SMAD7, as well as the capacity for proliferation, adhesion, migration, invasion, and in vivo tumorigenecity in cells with a high SPEC signature. Together, our results define STAT1 as a driver oncogene in SPEC that modulates disease progression. We propose that STAT1 functions as a prosurvival gene in SPEC, in a manner important to tumor progression, and that STAT1 may be a novel target for molecular therapy in this disease.

Authors
Kharma, B; Baba, T; Matsumura, N; Kang, HS; Hamanishi, J; Murakami, R; McConechy, MM; Leung, S; Yamaguchi, K; Hosoe, Y; Yoshioka, Y; Murphy, SK; Mandai, M; Hunstman, DG; Konishi, I
MLA Citation
Kharma, B, Baba, T, Matsumura, N, Kang, HS, Hamanishi, J, Murakami, R, McConechy, MM, Leung, S, Yamaguchi, K, Hosoe, Y, Yoshioka, Y, Murphy, SK, Mandai, M, Hunstman, DG, and Konishi, I. "STAT1 drives tumor progression in serous papillary endometrial cancer." Cancer research 74.22 (November 2014): 6519-6530.
PMID
25267067
Source
epmc
Published In
Cancer Research
Volume
74
Issue
22
Publish Date
2014
Start Page
6519
End Page
6530
DOI
10.1158/0008-5472.can-14-0847

Abstract B22: Altered methylation profiles of imprinted genes in response to prenatal exposure to cigarette smoke in the Newborn Epigenetic STudy (NEST) cohort

Authors
Nye, MD; Hoyo, C; Wang, F; Murtha, AP; Schildkraut, JM; Kurtzberg, J; Jirtle, RL; Huang, Z; Murphy, SK
MLA Citation
Nye, MD, Hoyo, C, Wang, F, Murtha, AP, Schildkraut, JM, Kurtzberg, J, Jirtle, RL, Huang, Z, and Murphy, SK. "Abstract B22: Altered methylation profiles of imprinted genes in response to prenatal exposure to cigarette smoke in the Newborn Epigenetic STudy (NEST) cohort." Cancer Epidemiology Biomarkers & Prevention 23.11 Supplement (November 2014): B22-B22.
Source
crossref
Published In
Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology
Volume
23
Issue
11 Supplement
Publish Date
2014
Start Page
B22
End Page
B22
DOI
10.1158/1538-7755.DISP13-B22

Abstract 4570: Role of ERRalpha in ovarian cancer

Authors
Stevens, EV; Whitaker, R; Guinet, A; Chang, C-Y; Grenier, C; Marks, J; McDonnell, DP; Murphy, SK; Berchuck, A; Gaillard, S
MLA Citation
Stevens, EV, Whitaker, R, Guinet, A, Chang, C-Y, Grenier, C, Marks, J, McDonnell, DP, Murphy, SK, Berchuck, A, and Gaillard, S. "Abstract 4570: Role of ERRalpha in ovarian cancer." October 1, 2014.
Source
crossref
Published In
Cancer Research
Volume
74
Issue
19 Supplement
Publish Date
2014
Start Page
4570
End Page
4570
DOI
10.1158/1538-7445.AM2014-4570

Abstract LB-123: Novel function of STAT1 pathway as a modulator of tumor progression in serous papillary endometrial cancer

Authors
Kharma, B; Baba, T; Matsumura, N; Kang, HS; Murakami, R; Yamaguchi, K; Hamanishi, J; Mandai, M; Murphy, SK; Konishi, I
MLA Citation
Kharma, B, Baba, T, Matsumura, N, Kang, HS, Murakami, R, Yamaguchi, K, Hamanishi, J, Mandai, M, Murphy, SK, and Konishi, I. "Abstract LB-123: Novel function of STAT1 pathway as a modulator of tumor progression in serous papillary endometrial cancer." October 1, 2014.
Source
crossref
Published In
Cancer Research
Volume
74
Issue
19 Supplement
Publish Date
2014
Start Page
LB-123
End Page
LB-123
DOI
10.1158/1538-7445.AM2014-LB-123

Epigenetic determinants of ovarian clear cell carcinoma biology.

Targeted approaches have revealed frequent epigenetic alterations in ovarian cancer, but the scope and relation of these changes to histologic subtype of disease is unclear. Genome-wide methylation and expression data for 14 clear cell carcinoma (CCC), 32 non-CCC and four corresponding normal cell lines were generated to determine how methylation profiles differ between cells of different histological derivations of ovarian cancer. Consensus clustering showed that CCC is epigenetically distinct. Inverse relationships between expression and methylation in CCC were identified, suggesting functional regulation by methylation, and included 22 hypomethylated (UM) genes and 276 hypermethylated (HM) genes. Categorical and pathway analyses indicated that the CCC-specific UM genes were involved in response to stress and many contain hepatocyte nuclear factor (HNF) 1-binding sites, while the CCC-specific HM genes included members of the estrogen receptor alpha (ERalpha) network and genes involved in tumor development. We independently validated the methylation status of 17 of these pathway-specific genes, and confirmed increased expression of HNF1 network genes and repression of ERalpha pathway genes in CCC cell lines and primary cancer tissues relative to non-CCC specimens. Treatment of three CCC cell lines with the demethylating agent Decitabine significantly induced expression for all five genes analyzed. Coordinate changes in pathway expression were confirmed using two primary ovarian cancer datasets (p < 0.0001 for both). Our results suggest that methylation regulates specific pathways and biological functions in CCC, with hypomethylation influencing the characteristic biology of the disease while hypermethylation contributes to the carcinogenic process.

Authors
Yamaguchi, K; Huang, Z; Matsumura, N; Mandai, M; Okamoto, T; Baba, T; Konishi, I; Berchuck, A; Murphy, SK
MLA Citation
Yamaguchi, K, Huang, Z, Matsumura, N, Mandai, M, Okamoto, T, Baba, T, Konishi, I, Berchuck, A, and Murphy, SK. "Epigenetic determinants of ovarian clear cell carcinoma biology." Int J Cancer 135.3 (August 1, 2014): 585-597.
PMID
24382740
Source
pubmed
Published In
International Journal of Cancer
Volume
135
Issue
3
Publish Date
2014
Start Page
585
End Page
597
DOI
10.1002/ijc.28701

Epigenetic determinants of ovarian clear cell carcinoma biology

Targeted approaches have revealed frequent epigenetic alterations in ovarian cancer, but the scope and relation of these changes to histologic subtype of disease is unclear. Genome-wide methylation and expression data for 14 clear cell carcinoma (CCC), 32 non-CCC and four corresponding normal cell lines were generated to determine how methylation profiles differ between cells of different histological derivations of ovarian cancer. Consensus clustering showed that CCC is epigenetically distinct. Inverse relationships between expression and methylation in CCC were identified, suggesting functional regulation by methylation, and included 22 hypomethylated (UM) genes and 276 hypermethylated (HM) genes. Categorical and pathway analyses indicated that the CCC-specific UM genes were involved in response to stress and many contain hepatocyte nuclear factor (HNF) 1-binding sites, while the CCC-specific HM genes included members of the estrogen receptor alpha (ERalpha) network and genes involved in tumor development. We independently validated the methylation status of 17 of these pathway-specific genes, and confirmed increased expression of HNF1 network genes and repression of ERalpha pathway genes in CCC cell lines and primary cancer tissues relative to non-CCC specimens. Treatment of three CCC cell lines with the demethylating agent Decitabine significantly induced expression for all five genes analyzed. Coordinate changes in pathway expression were confirmed using two primary ovarian cancer datasets (p < 0.0001 for both). Our results suggest that methylation regulates specific pathways and biological functions in CCC, with hypomethylation influencing the characteristic biology of the disease while hypermethylation contributes to the carcinogenic process. What's new? Ovarian cancer has several subtypes, and although different genetic mutations have been associated with particular subtypes, the molecular characteristics of ovarian clear cell carcinoma remain hazy. Aberrant DNA methylation can turn cells cancerous, and this study compared patterns of gene methylation in ovarian clear cell carcinomas, other ovarian cancer cells, and normal cells. They found that the clear cell carcinomas could indeed be identified by their distinctive pattern of DNA methylation. They found that this methylation pattern increased expression of certain stress response genes, while other genes, with tumor suppressive functions, were stifled. © 2013 UICC.

Authors
Yamaguchi, K; Huang, Z; Matsumura, N; Mandai, M; Okamoto, T; Baba, T; Konishi, I; Berchuck, A; Murphy, SK
MLA Citation
Yamaguchi, K, Huang, Z, Matsumura, N, Mandai, M, Okamoto, T, Baba, T, Konishi, I, Berchuck, A, and Murphy, SK. "Epigenetic determinants of ovarian clear cell carcinoma biology." International Journal of Cancer 135.3 (August 1, 2014): 585-597.
Source
scopus
Published In
International Journal of Cancer
Volume
135
Issue
3
Publish Date
2014
Start Page
585
End Page
597
DOI
10.1002/ijc.28701

Erythrocyte folate concentrations, CpG methylation at genomically imprinted domains, and birth weight in a multiethnic newborn cohort.

Epigenetic mechanisms are proposed to link maternal concentrations of methyl group donor nutrients with the risk of low birth weight. However, empirical data are lacking. We have examined the association between maternal folate and birth weight and assessed the mediating role of DNA methylation at nine differentially methylated regions (DMRs) of genomically imprinted genes in these associations. Compared with newborns of women with folate levels in the lowest quartile, birth weight was higher in newborns of mothers in the second (β = 143.2, se = 63.2, P = 0.02), third (β = 117.3, se = 64.0, P = 0.07), and fourth (β = 133.9, se = 65.2, P = 0.04) quartiles, consistent with a threshold effect. This pattern of association did not vary by race/ethnicity but was more apparent in newborns of non-obese women. DNA methylation at the PLAGL1, SGCE, DLK1/MEG3 and IGF2/H19 DMRs was associated with maternal folate levels and also birth weight, suggestive of threshold effects. MEG3 DMR methylation mediated the association between maternal folate levels and birth weight (P =0.06). While the small sample size and partial scope of examined DMRs limit our conclusions, our data suggest that, with respect to birth weight, no additional benefits may be derived from increased maternal folate concentrations, especially in non-obese women. These data also support epigenetic plasticity as a key mechanistic response to folate availability during early fetal development.

Authors
Hoyo, C; Daltveit, AK; Iversen, E; Benjamin-Neelon, SE; Fuemmeler, B; Schildkraut, J; Murtha, AP; Overcash, F; Vidal, AC; Wang, F; Huang, Z; Kurtzberg, J; Seewaldt, V; Forman, M; Jirtle, RL; Murphy, SK
MLA Citation
Hoyo, C, Daltveit, AK, Iversen, E, Benjamin-Neelon, SE, Fuemmeler, B, Schildkraut, J, Murtha, AP, Overcash, F, Vidal, AC, Wang, F, Huang, Z, Kurtzberg, J, Seewaldt, V, Forman, M, Jirtle, RL, and Murphy, SK. "Erythrocyte folate concentrations, CpG methylation at genomically imprinted domains, and birth weight in a multiethnic newborn cohort." Epigenetics 9.8 (August 2014): 1120-1130.
PMID
24874916
Source
epmc
Published In
Epigenetics : official journal of the DNA Methylation Society
Volume
9
Issue
8
Publish Date
2014
Start Page
1120
End Page
1130
DOI
10.4161/epi.29332

HPV genotypes and cervical intraepithelial neoplasia in a multiethnic cohort in the southeastern USA.

For poorly understood reasons, invasive cervical cancer (ICC) incidence and mortality rates are higher in women of African descent. Oncogenic human papillomavirus (HPV) genotypes distribution may vary between European American (EA) and African-American (AA) women and may contribute to differences in ICC incidence. The current study aimed at disentangling differences in HPV distribution among AA and EA women.Five-hundred and seventy-two women were enrolled at the time of colposcopic evaluation following an abnormal liquid-based cytology screen. HPV infections were detected using HPV linear array, and chi-squared tests and linear regression models were used to compare HPV genotypes across racial/ethnic groups by CIN status.Of the 572 participants, 494 (86 %) had detectable HPV; 245 (43 %) had no CIN lesion, 239 (42 %) had CIN1, and 88 (15 %) had CIN2/3. Seventy-three percent of all women were infected with multiple HPV genotypes. After adjusting for race, age, parity, income, oral contraception use, and current smoking, AAs were two times less likely to harbor HPV 16/18 (OR 0.48, 95 % CI 0.21-0.94, p = 0.03) when all women were considered. This association remained unchanged when only women with CIN2/3 lesions were examined (OR 0.22, 95 % CI 0.05-0.95, p = 0.04). The most frequent high-risk HPV genotypes detected among EAs were 16, 18, 56, 39, and 66, while HPV genotypes 33, 35, 45, 58, and 68 were the most frequent ones detected in AAs.Our data suggest that while HPV 16/18 are the most common genotypes among EA women with CIN, AAs may harbor different genotypes.

Authors
Vidal, AC; Smith, JS; Valea, F; Bentley, R; Gradison, M; Yarnall, KSH; Ford, A; Overcash, F; Grant, K; Murphy, SK; Hoyo, C
MLA Citation
Vidal, AC, Smith, JS, Valea, F, Bentley, R, Gradison, M, Yarnall, KSH, Ford, A, Overcash, F, Grant, K, Murphy, SK, and Hoyo, C. "HPV genotypes and cervical intraepithelial neoplasia in a multiethnic cohort in the southeastern USA." Cancer causes & control : CCC 25.8 (August 2014): 1055-1062.
PMID
24928693
Source
epmc
Published In
Cancer Causes & Control
Volume
25
Issue
8
Publish Date
2014
Start Page
1055
End Page
1062
DOI
10.1007/s10552-014-0406-2

Imprinted genes and the environment: links to the toxic metals arsenic, cadmium, lead and mercury.

Imprinted genes defy rules of Mendelian genetics with their expression tied to the parent from whom each allele was inherited. They are known to play a role in various diseases/disorders including fetal growth disruption, lower birth weight, obesity, and cancer. There is increasing interest in understanding their influence on environmentally-induced disease. The environment can be thought of broadly as including chemicals present in air, water and soil, as well as food. According to the Agency for Toxic Substances and Disease Registry (ATSDR), some of the highest ranking environmental chemicals of concern include metals/metalloids such as arsenic, cadmium, lead and mercury. The complex relationships between toxic metal exposure, imprinted gene regulation/expression and health outcomes are understudied. Herein we examine trends in imprinted gene biology, including an assessment of the imprinted genes and their known functional roles in the cell, particularly as they relate to toxic metals exposure and disease. The data highlight that many of the imprinted genes have known associations to developmental diseases and are enriched for their role in the TP53 and AhR pathways. Assessment of the promoter regions of the imprinted genes resulted in the identification of an enrichment of binding sites for two transcription factor families, namely the zinc finger family II and PLAG transcription factors. Taken together these data contribute insight into the complex relationships between toxic metals in the environment and imprinted gene biology.

Authors
Smeester, L; Yosim, AE; Nye, MD; Hoyo, C; Murphy, SK; Fry, RC
MLA Citation
Smeester, L, Yosim, AE, Nye, MD, Hoyo, C, Murphy, SK, and Fry, RC. "Imprinted genes and the environment: links to the toxic metals arsenic, cadmium, lead and mercury." Genes 5.2 (June 11, 2014): 477-496.
PMID
24921406
Source
epmc
Published In
Genes
Volume
5
Issue
2
Publish Date
2014
Start Page
477
End Page
496
DOI
10.3390/genes5020477

A paternal environmental legacy: Evidence for epigenetic inheritance through the male germ line

Literature on maternal exposures and the risk of epigenetic changes or diseases in the offspring is growing. Paternal contributions are often not considered. However, some animal and epidemiologic studies on various contaminants, nutrition, and lifestyle-related conditions suggest a paternal influence on the offspring's future health. The phenotypic outcomes may have been attributed to DNA damage or mutations, but increasing evidence shows that the inheritance of environmentally induced functional changes of the genome, and related disorders, are (also) driven by epigenetic components. In this essay we suggest the existence of epigenetic windows of susceptibility to environmental insults during sperm development. Changes in DNA methylation, histone modification, and non-coding RNAs are viable mechanistic candidates for a non-genetic transfer of paternal environmental information, from maturing germ cell to zygote. Inclusion of paternal factors in future research will ultimately improve the understanding of transgenerational epigenetic plasticity and health-related effects in future generations. © 2014 The Authors.

Authors
Soubry, A; Hoyo, C; Jirtle, RL; Murphy, SK
MLA Citation
Soubry, A, Hoyo, C, Jirtle, RL, and Murphy, SK. "A paternal environmental legacy: Evidence for epigenetic inheritance through the male germ line." BioEssays 36.4 (April 1, 2014): 359-371.
Source
scopus
Published In
Bioessays
Volume
36
Issue
4
Publish Date
2014
Start Page
359
End Page
371
DOI
10.1002/bies.201300113

A paternal environmental legacy: evidence for epigenetic inheritance through the male germ line.

Literature on maternal exposures and the risk of epigenetic changes or diseases in the offspring is growing. Paternal contributions are often not considered. However, some animal and epidemiologic studies on various contaminants, nutrition, and lifestyle-related conditions suggest a paternal influence on the offspring's future health. The phenotypic outcomes may have been attributed to DNA damage or mutations, but increasing evidence shows that the inheritance of environmentally induced functional changes of the genome, and related disorders, are (also) driven by epigenetic components. In this essay we suggest the existence of epigenetic windows of susceptibility to environmental insults during sperm development. Changes in DNA methylation, histone modification, and non-coding RNAs are viable mechanistic candidates for a non-genetic transfer of paternal environmental information, from maturing germ cell to zygote. Inclusion of paternal factors in future research will ultimately improve the understanding of transgenerational epigenetic plasticity and health-related effects in future generations.

Authors
Soubry, A; Hoyo, C; Jirtle, RL; Murphy, SK
MLA Citation
Soubry, A, Hoyo, C, Jirtle, RL, and Murphy, SK. "A paternal environmental legacy: evidence for epigenetic inheritance through the male germ line." BioEssays : news and reviews in molecular, cellular and developmental biology 36.4 (April 2014): 359-371.
PMID
24431278
Source
epmc
Published In
Bioessays
Volume
36
Issue
4
Publish Date
2014
Start Page
359
End Page
371
DOI
10.1002/bies.201300113

PEG1/MEST and IGF2 DNA methylation in CIN and in cervical cancer

Introduction: Although most invasive cervical cancer (ICC) harbor <20 human papillomavirus (HPV) genotypes, use of HPV screening to predict ICC from HPV has low specificity, resulting in multiple and costly follow-up visits and overtreatment. We examined DNA methylation at regulatory regions of imprinted genes in relation to ICC and its precursor lesions to determine if methylation profiles are associated with progression of HPV-positive lesions to ICC. Materials and methods: We enrolled 148 controls, 38 CIN and 48 ICC cases at Kilimanjaro Christian Medical Centre from 2008 to 2009. HPV was genotyped by linear array and HIV-1 serostatus was tested by two rapid HIV tests. DNA methylation was measured by bisulfite pyrosequencing at regions regulating eight imprinted domains. Logistic regression models were used to estimate odd ratios. Results: After adjusting for age, HPV infection, parity, hormonal contraceptive use, and HIV-1 serostatus, a 10 % decrease in methylation levels at an intragenic region of IGF2 was associated with higher risk of ICC (OR 2.00, 95 % CI 1.14-3.44) and cervical intraepithelial neoplasia (CIN) (OR 1.51, 95 % CI 1.00-2.50). Methylation levels at the H19 DMR and PEG1/MEST were also associated with ICC risk (OR 1.51, 95 % CI 0.90-2.53, and OR 1.44, 95 % CI 0.90-2.35, respectively). Restricting analyses to women >30 years further strengthened these associations. Conclusions: While the small sample size limits inference, these findings show that altered DNA methylation at imprinted domains including IGF2/H19 and PEG1/MEST may mediate the association between HPV and ICC risk. © 2013 The Author(s).

Authors
Vidal, AC; Henry, NM; Murphy, SK; Oneko, O; Nye, M; Bartlett, JA; Overcash, F; Huang, Z; Wang, F; Mlay, P; Obure, J; Smith, J; Vasquez, B; Swai, B; Hernandez, B; Hoyo, C
MLA Citation
Vidal, AC, Henry, NM, Murphy, SK, Oneko, O, Nye, M, Bartlett, JA, Overcash, F, Huang, Z, Wang, F, Mlay, P, Obure, J, Smith, J, Vasquez, B, Swai, B, Hernandez, B, and Hoyo, C. "PEG1/MEST and IGF2 DNA methylation in CIN and in cervical cancer." Clinical and Translational Oncology 16.3 (March 1, 2014): 266-272.
Source
scopus
Published In
Clinical and Translational Oncology
Volume
16
Issue
3
Publish Date
2014
Start Page
266
End Page
272
DOI
10.1007/s12094-013-1067-4

PEG1/MEST and IGF2 DNA methylation in CIN and in cervical cancer.

INTRODUCTION: Although most invasive cervical cancer (ICC) harbor <20 human papillomavirus (HPV) genotypes, use of HPV screening to predict ICC from HPV has low specificity, resulting in multiple and costly follow-up visits and overtreatment. We examined DNA methylation at regulatory regions of imprinted genes in relation to ICC and its precursor lesions to determine if methylation profiles are associated with progression of HPV-positive lesions to ICC. MATERIALS AND METHODS: We enrolled 148 controls, 38 CIN and 48 ICC cases at Kilimanjaro Christian Medical Centre from 2008 to 2009. HPV was genotyped by linear array and HIV-1 serostatus was tested by two rapid HIV tests. DNA methylation was measured by bisulfite pyrosequencing at regions regulating eight imprinted domains. Logistic regression models were used to estimate odd ratios. RESULTS: After adjusting for age, HPV infection, parity, hormonal contraceptive use, and HIV-1 serostatus, a 10 % decrease in methylation levels at an intragenic region of IGF2 was associated with higher risk of ICC (OR 2.00, 95 % CI 1.14-3.44) and cervical intraepithelial neoplasia (CIN) (OR 1.51, 95 % CI 1.00-2.50). Methylation levels at the H19 DMR and PEG1/MEST were also associated with ICC risk (OR 1.51, 95 % CI 0.90-2.53, and OR 1.44, 95 % CI 0.90-2.35, respectively). Restricting analyses to women >30 years further strengthened these associations. CONCLUSIONS: While the small sample size limits inference, these findings show that altered DNA methylation at imprinted domains including IGF2/H19 and PEG1/MEST may mediate the association between HPV and ICC risk.

Authors
Vidal, AC; Henry, NM; Murphy, SK; Oneko, O; Nye, M; Bartlett, JA; Overcash, F; Huang, Z; Wang, F; Mlay, P; Obure, J; Smith, J; Vasquez, B; Swai, B; Hernandez, B; Hoyo, C
MLA Citation
Vidal, AC, Henry, NM, Murphy, SK, Oneko, O, Nye, M, Bartlett, JA, Overcash, F, Huang, Z, Wang, F, Mlay, P, Obure, J, Smith, J, Vasquez, B, Swai, B, Hernandez, B, and Hoyo, C. "PEG1/MEST and IGF2 DNA methylation in CIN and in cervical cancer." Clin Transl Oncol 16.3 (March 2014): 266-272.
PMID
23775149
Source
pubmed
Published In
Clinical and Translational Oncology
Volume
16
Issue
3
Publish Date
2014
Start Page
266
End Page
272
DOI
10.1007/s12094-013-1067-4

Dasatinib (BMS-35482) interacts synergistically with docetaxel, gemcitabine, topotecan, and doxorubicin in ovarian cancer cells with high SRC pathway activation and protein expression.

PURPOSE: This study aimed to explore the activity of dasatinib in combination with docetaxel, gemcitabine, topotecan, and doxorubicin in ovarian cancer cells. METHODS: Cells with previously determined SRC pathway and protein expression (SRC pathway/SRC protein IGROV1, both high; SKOV3, both low) were treated with dasatinib in combination with the cytotoxic agents. SRC and paxillin protein expression were determined pretreatment and posttreatment. Dose-response curves were constructed, and the combination index (CI) for drug interaction was calculated. RESULTS: In the IGROV1 cells, dasatinib alone reduced phospho-SRC/total SRC 71% and p-paxillin/t-paxillin ratios 77%. Phospho-SRC (3%-33%; P = 0.002 to 0.04) and p-paxicillin (6%-19%; P = 0.01 to 0.05) levels were significantly reduced with dasatinib in combination with each cytotoxic agent. The combination of dasatinib and docetaxel, gemcitabine, or topotecan had a synergistic antiproliferative effect (CI, 0.49-0.68), whereas dasatinib combined with doxorubicin had an additive effect (CI, 1.08).In SKOV3 cells, dasatinib resulted in less pronounced reductions of phospho-SRC/total SRC (49%) and p-paxillin/t-paxillin (62%). Phospho-SRC (18%; P < 0.001) and p-paxillin levels (18%; P = 0.001; 9%; P = 0.007) were significantly decreased when dasatinib was combined with docetaxel and topotecan (p-paxillin only). Furthermore, dasatinib combined with the cytotoxics in the SKOV3 cells produced an antagonistic interaction on the proliferation of these cells (CI, 1.49-2.27). CONCLUSIONS: Dasatinib in combination with relapse chemotherapeutic agents seems to interact in a synergistic or additive manner in cells with high SRC pathway activation and protein expression. Further evaluation of dasatinib in combination with chemotherapy in ovarian cancer animal models and exploration of the use of biomarkers to direct therapy are warranted.

Authors
Secord, AA; Teoh, D; Jia, J; Nixon, AB; Grace, L; Adams, DJ; Murphy, SK
MLA Citation
Secord, AA, Teoh, D, Jia, J, Nixon, AB, Grace, L, Adams, DJ, and Murphy, SK. "Dasatinib (BMS-35482) interacts synergistically with docetaxel, gemcitabine, topotecan, and doxorubicin in ovarian cancer cells with high SRC pathway activation and protein expression." Int J Gynecol Cancer 24.2 (February 2014): 218-225.
PMID
24407585
Source
pubmed
Published In
International Journal of Gynecological Cancer
Volume
24
Issue
2
Publish Date
2014
Start Page
218
End Page
225
DOI
10.1097/IGC.0000000000000056

Hepatic gene expression profiles differentiate presymptomatic patients with mild versus severe nonalcoholic fatty liver disease.

UNLABELLED: Clinicians rely upon the severity of liver fibrosis to segregate patients with well-compensated nonalcoholic fatty liver disease (NAFLD) into subpopulations at high- versus low-risk for eventual liver-related morbidity and mortality. We compared hepatic gene expression profiles in high- and low-risk NAFLD patients to identify processes that distinguish the two groups and hence might be novel biomarkers or treatment targets. Microarray analysis was used to characterize gene expression in percutaneous liver biopsies from low-risk, "mild" NAFLD patients (fibrosis stage 0-1; n = 40) and high-risk, "severe" NAFLD patients (fibrosis stage 3-4; n = 32). Findings were validated in a second, independent cohort and confirmed by real-time polymerase chain reaction and immunohistochemistry (IHC). As a group, patients at risk for bad NAFLD outcomes had significantly worse liver injury and more advanced fibrosis (severe NAFLD) than clinically indistinguishable NAFLD patients with a good prognosis (mild NAFLD). A 64-gene profile reproducibly differentiated severe NAFLD from mild NAFLD, and a 20-gene subset within this profile correlated with NAFLD severity, independent of other factors known to influence NAFLD progression. Multiple genes involved with tissue repair/regeneration and certain metabolism-related genes were induced in severe NAFLD. Ingenuity Pathway Analysis and IHC confirmed deregulation of metabolic and regenerative pathways in severe NAFLD and revealed overlap among the gene expression patterns of severe NAFLD, cardiovascular disease, and cancer. CONCLUSION: By demonstrating specific metabolic and repair pathways that are differentially activated in livers with severe NAFLD, gene profiling identified novel targets that can be exploited to improve diagnosis and treatment of patients who are at greatest risk for NAFLD-related morbidity and mortality.

Authors
Moylan, CA; Pang, H; Dellinger, A; Suzuki, A; Garrett, ME; Guy, CD; Murphy, SK; Ashley-Koch, AE; Choi, SS; Michelotti, GA; Hampton, DD; Chen, Y; Tillmann, HL; Hauser, MA; Abdelmalek, MF; Diehl, AM
MLA Citation
Moylan, CA, Pang, H, Dellinger, A, Suzuki, A, Garrett, ME, Guy, CD, Murphy, SK, Ashley-Koch, AE, Choi, SS, Michelotti, GA, Hampton, DD, Chen, Y, Tillmann, HL, Hauser, MA, Abdelmalek, MF, and Diehl, AM. "Hepatic gene expression profiles differentiate presymptomatic patients with mild versus severe nonalcoholic fatty liver disease." Hepatology 59.2 (February 2014): 471-482.
PMID
23913408
Source
pubmed
Published In
Hepatology
Volume
59
Issue
2
Publish Date
2014
Start Page
471
End Page
482
DOI
10.1002/hep.26661

Obesity: Paternal obesity - A risk factor for autism?

Authors
Murphy, SK
MLA Citation
Murphy, SK. "Obesity: Paternal obesity - A risk factor for autism?." Nature Reviews Endocrinology 10.7 (January 1, 2014): 389-390.
Source
scopus
Published In
Nature Reviews Endocrinology
Volume
10
Issue
7
Publish Date
2014
Start Page
389
End Page
390
DOI
10.1038/nrendo.2014.81

HPV genotypes and cervical intraepithelial neoplasia in a multiethnic cohort in the southeastern USA

Purpose: For poorly understood reasons, invasive cervical cancer (ICC) incidence and mortality rates are higher in women of African descent. Oncogenic human papillomavirus (HPV) genotypes distribution may vary between European American (EA) and African-American (AA) women and may contribute to differences in ICC incidence. The current study aimed at disentangling differences in HPV distribution among AA and EA women. Methods: Five-hundred and seventy-two women were enrolled at the time of colposcopic evaluation following an abnormal liquid-based cytology screen. HPV infections were detected using HPV linear array, and chi-squared tests and linear regression models were used to compare HPV genotypes across racial/ethnic groups by CIN status. Results: Of the 572 participants, 494 (86 %) had detectable HPV; 245 (43 %) had no CIN lesion, 239 (42 %) had CIN1, and 88 (15 %) had CIN2/3. Seventy-three percent of all women were infected with multiple HPV genotypes. After adjusting for race, age, parity, income, oral contraception use, and current smoking, AAs were two times less likely to harbor HPV 16/18 (OR 0.48, 95 % CI 0.21-0.94, p = 0.03) when all women were considered. This association remained unchanged when only women with CIN2/3 lesions were examined (OR 0.22, 95 % CI 0.05-0.95, p = 0.04). The most frequent high-risk HPV genotypes detected among EAs were 16, 18, 56, 39, and 66, while HPV genotypes 33, 35, 45, 58, and 68 were the most frequent ones detected in AAs. Conclusions: Our data suggest that while HPV 16/18 are the most common genotypes among EA women with CIN, AAs may harbor different genotypes. © 2014 The Author(s).

Authors
Vidal, AC; Smith, JS; Valea, F; Bentley, R; Gradison, M; Yarnall, KSH; Ford, A; Overcash, F; Grant, K; Murphy, SK; Hoyo, C
MLA Citation
Vidal, AC, Smith, JS, Valea, F, Bentley, R, Gradison, M, Yarnall, KSH, Ford, A, Overcash, F, Grant, K, Murphy, SK, and Hoyo, C. "HPV genotypes and cervical intraepithelial neoplasia in a multiethnic cohort in the southeastern USA." Cancer Causes and Control 25.8 (January 1, 2014): 1055-1062.
Source
scopus
Published In
Cancer Causes & Control
Volume
25
Issue
8
Publish Date
2014
Start Page
1055
End Page
1062
DOI
10.1007/s10552-014-0406-2

Investigating Epigenetic Effects of Prenatal Exposure to Toxic Metals in Newborns: Challenges and Benefits.

Increasing evidence suggest that epigenetic alterations can greatly impact human health, and that epigenetic mechanisms (DNA methylation, histone modifications, and microRNAs) may be particularly relevant in responding to environmental toxicant exposure early in life. The epigenome plays a vital role in embryonic development, tissue differentiation and disease development by controlling gene expression. In this review we discuss what is currently known about epigenetic alterations in response to prenatal exposure to inorganic arsenic (iAs) and lead (Pb), focusing specifically on their effects on DNA methylation. We then describe how epigenetic alterations are being studied in newborns as potential biomarkers of in utero environmental toxicant exposure, and the benefits and challenges of this approach. In summary, the studies highlighted herein indicate how epigenetic mechanisms are impacted by early life exposure to iAs and Pb, and the research that is being done to move towards understanding the relationships between toxicant-induced epigenetic alterations and disease development. Although much remains unknown, several groups are working to understand the correlative and causal effects of early life toxic metal exposure on epigenetic changes and how these changes may result in later development of disease.

Authors
Nye, MD; Fry, RC; Hoyo, C; Murphy, SK
MLA Citation
Nye, MD, Fry, RC, Hoyo, C, and Murphy, SK. "Investigating Epigenetic Effects of Prenatal Exposure to Toxic Metals in Newborns: Challenges and Benefits." Medical epigenetics 2.1 (January 2014): 53-59.
PMID
24955086
Source
epmc
Published In
Medical Epigenetics
Volume
2
Issue
1
Publish Date
2014
Start Page
53
End Page
59
DOI
10.1159/000362336

Differential Angiogenic Gene Expression in TP53 Wild-Type and Mutant Ovarian Cancer Cell Lines.

Underlying mechanisms regulating angiogenesis in ovarian cancer have not been completely elucidated. Evidence suggests that the TP53 tumor suppressor pathway and tumor microenvironment play integral roles. We utilized microarray technology to study the interaction between TP53 mutational status and hypoxia on angiogenic gene expression.Affymetrix U133A arrays were analyzed for angiogenic gene expression in 19 ovarian cancer cell lines stratified both by TP53 mutation status and A2780 wild-type (wt) TP53 vs. mutated (m) TP53 cell lines after treatment under hypoxic conditions or with ionizing radiation.Twenty-eight differentially expressed angiogenic genes were identified in the mTP53 cell lines compared to wtTP53 lines. Five genes were upregulated in mTP53 cells: 40% involved in extracellular matrix (ECM) degradation [matrix metalloproteinase 10 (MMP10)/15] and 60% in angiogenesis (fibroblast growth factor receptor 3/VEGFA/ephrin receptor-B4). Twenty-three genes were upregulated in wtTP53: nearly 22% were ECM constituents or involved in ECM degradation; over 40% were growth factors or mediators of angiogenesis. Five genes were upregulated in the A2780mTP53 cells: 40% involved in ECM remodeling (MMP10, ADAMTS1), 40% with pro-angiogenic activity (EFNB2, factor 2 receptor), and 20% with anti-angiogenic properties (ADAMTS1). Three genes were upregulated in hypoxia treated cells compared to controls: one with anti-angiogenic activity (angiopoietin-like 4) and two with pro-angiogenic activity (VEGFA, EFNA3). No significant gene fold changes were noted after exposure to radiation. Four genes continued to demonstrate significant differential expression (p ≤ 0.05) after adjusting for multiple comparisons. These genes included endoglin upregulation in wt lines (pro-angiogenesis) and upregulation of FGF20 (growth factor), ADAMTS1 (anti-angiogenesis) and MMP10 (ECM degradation) in mTP53 cell lines.Our exploratory findings indicate that non-overlapping angiogenic pathways may be altered by TP53 mutations and hypoxic conditions in the tumor microenvironment. Further evaluation is needed for confirmation.

Authors
Davidson, BA; Rubatt, JM; Corcoran, DL; Teoh, DK; Bernardini, MQ; Grace, LA; Soper, WJ; Berchuck, A; Siamakpour-Reihani, S; Chen, W; Owzar, K; Murphy, SK; Secord, AA
MLA Citation
Davidson, BA, Rubatt, JM, Corcoran, DL, Teoh, DK, Bernardini, MQ, Grace, LA, Soper, WJ, Berchuck, A, Siamakpour-Reihani, S, Chen, W, Owzar, K, Murphy, SK, and Secord, AA. "Differential Angiogenic Gene Expression in TP53 Wild-Type and Mutant Ovarian Cancer Cell Lines." Frontiers in oncology 4 (January 2014): 163-.
PMID
24999452
Source
epmc
Published In
Frontiers in Oncology
Volume
4
Publish Date
2014
Start Page
163
DOI
10.3389/fonc.2014.00163

Maternal stress, preterm birth, and DNA methylation at imprint regulatory sequences in humans.

In infants exposed to maternal stress in utero, phenotypic plasticity through epigenetic events may mechanistically explain increased risk of preterm birth (PTB), which confers increased risk for neurodevelopmental disorders, cardiovascular disease, and cancers in adulthood. We examined associations between prenatal maternal stress and PTB, evaluating the role of DNA methylation at imprint regulatory regions. We enrolled women from prenatal clinics in Durham, NC. Stress was measured in 537 women at 12 weeks of gestation using the Perceived Stress Scale. DNA methylation at differentially methylated regions (DMRs) associated with H19, IGF2, MEG3, MEST, SGCE/PEG10, PEG3, NNAT, and PLAGL1 was measured from peripheral and cord blood using bisulfite pyrosequencing in a sub-sample of 79 mother-infant pairs. We examined associations between PTB and stress and evaluated differences in DNA methylation at each DMR by stress. Maternal stress was not associated with PTB (OR = 0.98; 95% CI, 0.40-2.40; P = 0.96), after adjustment for maternal body mass index (BMI), income, and raised blood pressure. However, elevated stress was associated with higher infant DNA methylation at the MEST DMR (2.8% difference, P < 0.01) after adjusting for PTB. Maternal stress may be associated with epigenetic changes at MEST, a gene relevant to maternal care and obesity. Reduced prenatal stress may support the epigenomic profile of a healthy infant.

Authors
Vidal, AC; Benjamin Neelon, SE; Liu, Y; Tuli, AM; Fuemmeler, BF; Hoyo, C; Murtha, AP; Huang, Z; Schildkraut, J; Overcash, F; Kurtzberg, J; Jirtle, RL; Iversen, ES; Murphy, SK
MLA Citation
Vidal, AC, Benjamin Neelon, SE, Liu, Y, Tuli, AM, Fuemmeler, BF, Hoyo, C, Murtha, AP, Huang, Z, Schildkraut, J, Overcash, F, Kurtzberg, J, Jirtle, RL, Iversen, ES, and Murphy, SK. "Maternal stress, preterm birth, and DNA methylation at imprint regulatory sequences in humans." Genetics & epigenetics 6 (January 2014): 37-44.
PMID
25512713
Source
epmc
Published In
Genetics and Epigenetics
Volume
6
Publish Date
2014
Start Page
37
End Page
44
DOI
10.4137/geg.s18067

Epigenetic and genetic dispositions of ovarian carcinomas.

Ovarian clear cell carcinoma has unique clinical characteristics with slow growth and a stress-resistant phenotype that is epigenetically induced during cancer progression in an inflammatory microenvironment. We refer to this as an epigenetic disposition, which is frequently associated with unique biomolecular features including prominent alterations in methylation, microsatellite instability and ARID1A mutations. This characteristic methylation profile also affects glucose metabolism, commonly known as the Warburg effect. In contrast, high-grade ovarian serous adenocarcinoma has a genetic disposition that is accompanied by rapid growth, TP53 mutations and chromosomal instability. The concept of epigenetic and genetic dispositions is applicable to various malignancies, including gastric and colorectal cancers. These disposition classifications are based on fundamental characteristics of malignancies and may provide a new vantage point for development of individualized therapies.

Authors
Yamaguchi, K; Matsumura, N; Mandai, M; Baba, T; Konishi, I; Murphy, SK
MLA Citation
Yamaguchi, K, Matsumura, N, Mandai, M, Baba, T, Konishi, I, and Murphy, SK. "Epigenetic and genetic dispositions of ovarian carcinomas." Oncoscience 1.9 (January 2014): 574-579.
PMID
25594067
Source
epmc
Published In
Oncoscience
Volume
1
Issue
9
Publish Date
2014
Start Page
574
End Page
579

PEG1/MEST and IGF2 DNA methylation in CIN and in cervical cancer

Authors
Vidal, AC; Henry, NM; Murphy, SK; Oneko, O; Nye, M; Bartlett, JA; Overcash, F; Huang, Z; Wang, F; Mlay, P; Obure, J; Smith, J; Vasquez, B; Swai, B; Hernandez, B; Hoyo, C
MLA Citation
Vidal, AC, Henry, NM, Murphy, SK, Oneko, O, Nye, M, Bartlett, JA, Overcash, F, Huang, Z, Wang, F, Mlay, P, Obure, J, Smith, J, Vasquez, B, Swai, B, Hernandez, B, and Hoyo, C. "PEG1/MEST and IGF2 DNA methylation in CIN and in cervical cancer." Clinical and Translational Oncology 16.3 (2014): 266-272.
Source
scopus
Published In
Clinical and Translational Oncology
Volume
16
Issue
3
Publish Date
2014
Start Page
266
End Page
272

What are the Implications of Distinct HPV Genotypes in Women of Different Ethnic/Racial Ancestry?

Authors
Susan K. Murphy, CH
MLA Citation
Susan K. Murphy, CH. "What are the Implications of Distinct HPV Genotypes in Women of Different Ethnic/Racial Ancestry?." Journal of Vaccines & Vaccination 05.03 (2014).
Source
crossref
Published In
Journal of Vaccines and Vaccination
Volume
05
Issue
03
Publish Date
2014
DOI
10.4172/2157-7560.1000228

Relationship between methylome and transcriptome in patients with nonalcoholic fatty liver disease.

BACKGROUND & AIMS: Cirrhosis and liver cancer are potential outcomes of advanced nonalcoholic fatty liver disease (NAFLD). It is not clear what factors determine whether patients will develop advanced or mild NAFLD, limiting noninvasive diagnosis and treatment before clinical sequelae emerge. We investigated whether DNA methylation profiles can distinguish patients with mild disease from those with advanced NAFLD, and how these patterns are functionally related to hepatic gene expression. METHODS: We collected frozen liver biopsies and clinical data from patients with biopsy-proven NAFLD (56 in the discovery cohort and 34 in the replication cohort). Samples were divided into groups based on histologic severity of fibrosis: F0-1 (mild) and F3-4 (advanced). DNA methylation profiles were determined and coupled with gene expression data from the same biopsies; differential methylation was validated in subsets of the discovery and replication cohorts. We then analyzed interactions between the methylome and transcriptome. RESULTS: Clinical features did not differ between patients known to have mild or advanced fibrosis based on biopsy analysis. There were 69,247 differentially methylated CpG sites (76% hypomethylated, 24% hypermethylated) in patients with advanced vs mild NAFLD (P < .05). Methylation at fibroblast growth factor receptor 2, methionine adenosyl methyltransferase 1A, and caspase 1 was validated by bisulfite pyrosequencing and the findings were reproduced in the replication cohort. Methylation correlated with gene transcript levels for 7% of differentially methylated CpG sites, indicating that differential methylation contributes to differences in expression. In samples with advanced NAFLD, many tissue repair genes were hypomethylated and overexpressed, and genes in certain metabolic pathways, including 1-carbon metabolism, were hypermethylated and underexpressed. CONCLUSIONS: Functionally relevant differences in methylation can distinguish patients with advanced vs mild NAFLD. Altered methylation of genes that regulate processes such as steatohepatitis, fibrosis, and carcinogenesis indicate the role of DNA methylation in progression of NAFLD.

Authors
Murphy, SK; Yang, H; Moylan, CA; Pang, H; Dellinger, A; Abdelmalek, MF; Garrett, ME; Ashley-Koch, A; Suzuki, A; Tillmann, HL; Hauser, MA; Diehl, AM
MLA Citation
Murphy, SK, Yang, H, Moylan, CA, Pang, H, Dellinger, A, Abdelmalek, MF, Garrett, ME, Ashley-Koch, A, Suzuki, A, Tillmann, HL, Hauser, MA, and Diehl, AM. "Relationship between methylome and transcriptome in patients with nonalcoholic fatty liver disease." Gastroenterology 145.5 (November 2013): 1076-1087.
PMID
23916847
Source
pubmed
Published In
Gastroenterology
Volume
145
Issue
5
Publish Date
2013
Start Page
1076
End Page
1087
DOI
10.1053/j.gastro.2013.07.047

Abstract A83: Induction of PD-L1 expression by cytotoxic agents through activation of NF-kB signal

Authors
Hamanishi, J; Matsumura, N; Jin, P; Abiko, K; Horikawa, N; Yamaguchi, K; Baba, T; Murphy, SK; Konishi, I; Mandai, M
MLA Citation
Hamanishi, J, Matsumura, N, Jin, P, Abiko, K, Horikawa, N, Yamaguchi, K, Baba, T, Murphy, SK, Konishi, I, and Mandai, M. "Abstract A83: Induction of PD-L1 expression by cytotoxic agents through activation of NF-kB signal." Clinical Cancer Research 19.19 Supplement (October 1, 2013): A83-A83.
Source
crossref
Published In
Clinical cancer research : an official journal of the American Association for Cancer Research
Volume
19
Issue
19 Supplement
Publish Date
2013
Start Page
A83
End Page
A83
DOI
10.1158/1078-0432.OVCA13-A83

Abstract B19: Functional genomics approach links anchorage-independence with tumor dormancy in ovarian cancer

Authors
Matsumura, N; Yamanoi, K; Amano, Y; Hamanishi, J; Baba, T; Murphy, SK; Konishi, I
MLA Citation
Matsumura, N, Yamanoi, K, Amano, Y, Hamanishi, J, Baba, T, Murphy, SK, and Konishi, I. "Abstract B19: Functional genomics approach links anchorage-independence with tumor dormancy in ovarian cancer." Clinical Cancer Research 19.19 Supplement (October 1, 2013): B19-B19.
Source
crossref
Published In
Clinical cancer research : an official journal of the American Association for Cancer Research
Volume
19
Issue
19 Supplement
Publish Date
2013
Start Page
B19
End Page
B19
DOI
10.1158/1078-0432.OVCA13-B19

Abstract PR08: HNF1β confers resistance to oxidative stress of ovarian clear cell carcinoma

Authors
Amano, Y; Yamaguchi, K; Mandai, M; Matsumura, N; Hamanishi, J; Baba, T; Yamanoi, K; Murphy, SK; Konishi, I
MLA Citation
Amano, Y, Yamaguchi, K, Mandai, M, Matsumura, N, Hamanishi, J, Baba, T, Yamanoi, K, Murphy, SK, and Konishi, I. "Abstract PR08: HNF1β confers resistance to oxidative stress of ovarian clear cell carcinoma." Clinical Cancer Research 19.19 Supplement (October 1, 2013): PR08-PR08.
Source
crossref
Published In
Clinical cancer research : an official journal of the American Association for Cancer Research
Volume
19
Issue
19 Supplement
Publish Date
2013
Start Page
PR08
End Page
PR08
DOI
10.1158/1078-0432.OVCA13-PR08

Associations between antibiotic exposure during pregnancy, birth weight and aberrant methylation at imprinted genes among offspring.

OBJECTIVES: Low birth weight (LBW) has been associated with common adult-onset chronic diseases, including obesity, cardiovascular disease, type II diabetes and some cancers. The etiology of LBW is multi-factorial. However, recent evidence suggests exposure to antibiotics may also increase the risk of LBW. The mechanisms underlying this association are unknown, although epigenetic mechanisms are hypothesized. In this study, we evaluated the association between maternal antibiotic use and LBW and examined the potential role of altered DNA methylation that controls growth regulatory imprinted genes in these associations. METHODS: Between 2009-2011, 397 pregnant women were enrolled and followed until delivery. Prenatal antibiotic use was ascertained through maternal self-report. Imprinted genes methylation levels were measured at differentially methylated regions (DMRs) using bisulfite pyrosequencing. Generalized linear models were used to examine associations among antibiotic use, birth weight and DMR methylation fractions. RESULTS: After adjusting for infant gender, race/ethnicity, maternal body mass index, delivery route, gestational weight gain, gestational age at delivery, folic acid intake, physical activity, maternal smoking and parity, antibiotic use during pregnancy was associated with 138 g lower birth weight compared with non-antibiotic use (β-coefficient=-132.99, s.e.=50.70, P=0.008). These associations were strongest in newborns of women who reported antibiotic use other than penicillins (β-coefficient=-135.57, s.e.=57.38, P=0.02). Methylation at five DMRs, IGF2 (P=0.05), H19 (P=0.15), PLAGL1 (P=0.01), MEG3 (P=0.006) and PEG3 (P=0.08), was associated with maternal antibiotic use; among these, only methylation at the PLAGL1 DMR was also associated with birth weight. CONCLUSION: We report an inverse association between in utero exposure to antibiotics and lower infant birth weight and provide the first empirical evidence supporting imprinted gene plasticity in these associations.

Authors
Vidal, AC; Murphy, SK; Murtha, AP; Schildkraut, JM; Soubry, A; Huang, Z; Neelon, SEB; Fuemmeler, B; Iversen, E; Wang, F; Kurtzberg, J; Jirtle, RL; Hoyo, C
MLA Citation
Vidal, AC, Murphy, SK, Murtha, AP, Schildkraut, JM, Soubry, A, Huang, Z, Neelon, SEB, Fuemmeler, B, Iversen, E, Wang, F, Kurtzberg, J, Jirtle, RL, and Hoyo, C. "Associations between antibiotic exposure during pregnancy, birth weight and aberrant methylation at imprinted genes among offspring." Int J Obes (Lond) 37.7 (July 2013): 907-913.
PMID
23609933
Source
pubmed
Published In
International Journal of Obesity
Volume
37
Issue
7
Publish Date
2013
Start Page
907
End Page
913
DOI
10.1038/ijo.2013.47

DNA methylation at imprint regulatory regions in preterm birth and infection.

OBJECTIVE: To aid in understanding long-term health consequences of intrauterine infections in preterm birth, we evaluated DNA methylation at 9 differentially methylated regions that regulate imprinted genes by type of preterm birth (spontaneous preterm labor, preterm premature rupture of membranes, or medically indicated [fetal growth restriction and preeclampsia]) and infection status (chorioamnionitis or funisitis). STUDY DESIGN: Data on type of preterm birth and infection status were abstracted from medical records and standardized pathology reports in 73 preterm infants enrolled in the Newborn Epigenetics STudy, a prospective cohort study of mother-infant dyads in Durham, NC. Cord blood was collected at birth, and infant DNA methylation levels at the H19, IGF2, MEG3, MEST, SGCE/PEG10, PEG3, NNAT, and PLAGL1 differentially methylated regions were measured using bisulfite pyrosequencing. One-way analyses of variance and logistic regression models were used to compare DNA methylation levels by type of preterm birth and infection status. RESULTS: DNA methylation levels did not differ at any of the regions (P > .20) between infants born via spontaneous preterm labor (average n = 29), preterm premature rupture of membranes (average n = 17), or medically indicated preterm birth (average n = 40). Levels were significantly increased at PLAGL1 in infants with chorioamnionitis (n = 10, 64.4%) compared with infants without chorioamnionitis (n = 63, 57.9%), P < .01. DNA methylation levels were also increased at PLAGL1 for infants with funisitis (n = 7, 63.3%) compared with infants without funisitis (n = 66, 58.3%), P < .05. CONCLUSION: Dysregulation of PLAGL1 has been associated with abnormal development and cancer. Early-life exposures, including infection/inflammation, may affect epigenetic changes that increase susceptibility to later chronic disease.

Authors
Liu, Y; Hoyo, C; Murphy, S; Huang, Z; Overcash, F; Thompson, J; Brown, H; Murtha, AP
MLA Citation
Liu, Y, Hoyo, C, Murphy, S, Huang, Z, Overcash, F, Thompson, J, Brown, H, and Murtha, AP. "DNA methylation at imprint regulatory regions in preterm birth and infection." Am J Obstet Gynecol 208.5 (May 2013): 395.e1-395.e7.
PMID
23477525
Source
pubmed
Published In
American Journal of Obstetrics & Gynecology
Volume
208
Issue
5
Publish Date
2013
Start Page
395.e1
End Page
395.e7
DOI
10.1016/j.ajog.2013.02.006

Abstract 3647: Dose-dependent alteration of CpG methylation in AHRR and GFI1 in mononuclear cell DNA of smokers.

Authors
Wang, X; Pittman, GS; Su, D; Adamski, KN; Campbell, MR; Joubert, BR; Huang, ZY; Hoyo, C; Murphy, SK; London, SA; Bell, DA
MLA Citation
Wang, X, Pittman, GS, Su, D, Adamski, KN, Campbell, MR, Joubert, BR, Huang, ZY, Hoyo, C, Murphy, SK, London, SA, and Bell, DA. "Abstract 3647: Dose-dependent alteration of CpG methylation in AHRR and GFI1 in mononuclear cell DNA of smokers." April 15, 2013.
Source
crossref
Published In
Cancer Research
Volume
73
Issue
8 Supplement
Publish Date
2013
Start Page
3647
End Page
3647
DOI
10.1158/1538-7445.AM2013-3647

Validation of ovarian cancer gene expression signatures for survival and subtype in formalin fixed paraffin embedded tissues.

INTRODUCTION: Gene expression signatures have been identified for epithelial ovarian cancer survival (TCGA) and intrinsic subtypes (Tothill et al.). One obstacle to clinical translation is that these signatures were developed using frozen tissue, whereas usually only formalin-fixed, paraffin embedded (FFPE) tissue is available. The aim of this study was to determine if gene expression signatures can be translated to fixed archival tissues. METHODS: RNA extracted from FFPE sections from 240 primary ovarian cancers was analyzed by DASL on Illumina BeadChip arrays. Concordance of expression at the individual gene level was assessed by comparing array data from the same cancers (30 frozen samples analyzed on Affymetrix arrays versus FFPE DASL). RESULTS: The correlation between FFPE and frozen survival signature estimates was 0.774. The TCGA signature using DASL was predictive of survival in 106 advanced stage high grade serous ovarian cancers (median survival 33 versus 60 months, estimated hazard ratio for death 2.30, P=0.0007). Similar to Tothill, we found using DASL that most high grade serous ovarian cancers (102/110, 93%) were assigned to subtypes 1, 2, 4 and 5, whereas most endometrioid, clear cell, mucinous and low grade serous cases (39/57, 68%) were assigned to subtypes 3 and 6 (P<10e-15). CONCLUSIONS: Although individual probe estimates of microarrays may be weakly correlated between FFPE and frozen samples, combinations of probes have robust ability to predict survival and subtype. This suggests that it may be possible to use these signatures for prognostic and predictive purposes as we seek to individualize the treatment of ovarian cancer.

Authors
Sfakianos, GP; Iversen, ES; Whitaker, R; Akushevich, L; Schildkraut, JM; Murphy, SK; Marks, JR; Berchuck, A
MLA Citation
Sfakianos, GP, Iversen, ES, Whitaker, R, Akushevich, L, Schildkraut, JM, Murphy, SK, Marks, JR, and Berchuck, A. "Validation of ovarian cancer gene expression signatures for survival and subtype in formalin fixed paraffin embedded tissues." Gynecol Oncol 129.1 (April 2013): 159-164.
PMID
23274563
Source
pubmed
Published In
Gynecologic Oncology
Volume
129
Issue
1
Publish Date
2013
Start Page
159
End Page
164
DOI
10.1016/j.ygyno.2012.12.030

Stress: A Possible Link between Genetics, Epigenetics, and Childhood Asthma

Authors
Murphy, SK; Hollingsworth, JW
MLA Citation
Murphy, SK, and Hollingsworth, JW. "Stress: A Possible Link between Genetics, Epigenetics, and Childhood Asthma." AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE 187.6 (March 15, 2013): 563-564.
PMID
23504358
Source
wos-lite
Published In
American journal of respiratory and critical care medicine
Volume
187
Issue
6
Publish Date
2013
Start Page
563
End Page
564
DOI
10.1164/rccm.201301-0178ED

Methylation at Imprinted Insulin-Like Growth Factor-2 (IGF2) Is Vulnerable to Lead Exposure in Human Embryonic Kidney Cells

Authors
Murphy, SK; Nye, MD; Hoyo, C
MLA Citation
Murphy, SK, Nye, MD, and Hoyo, C. "Methylation at Imprinted Insulin-Like Growth Factor-2 (IGF2) Is Vulnerable to Lead Exposure in Human Embryonic Kidney Cells." March 2013.
Source
wos-lite
Published In
Reproductive Sciences
Volume
20
Issue
S3
Publish Date
2013
Start Page
203A
End Page
204A

Paternal obesity is associated with IGF2 hypomethylation in newborns: results from a Newborn Epigenetics Study (NEST) cohort.

BACKGROUND: Data from epidemiological and animal model studies suggest that nutrition during pregnancy may affect the health status of subsequent generations. These transgenerational effects are now being explained by disruptions at the level of the epigenetic machinery. Besides in vitro environmental exposures, the possible impact on the reprogramming of methylation profiles at imprinted genes at a much earlier time point, such as during spermatogenesis or oogenesis, has not previously been considered. In this study, our aim was to determine associations between preconceptional obesity and DNA methylation profiles in the offspring, particularly at the differentially methylated regions (DMRs) of the imprinted Insulin-like Growth Factor 2 (IGF2) gene. METHODS: We examined DNA from umbilical cord blood leukocytes from 79 newborns, born between July 2005 and November 2006 at Duke University Hospital, Durham, NC. Their mothers participated in the Newborn Epigenetics Study (NEST) during pregnancy. Parental characteristics were obtained via standardized questionnaires and medical records. DNA methylation patterns at two DMRs were analyzed by bisulfite pyrosequencing; one DMR upstream of IGF2 (IGF2 DMR), and one DMR upstream of the neighboring H19 gene (H19 DMR). Multiple regression models were used to determine potential associations between the offspring's DNA methylation patterns and parental obesity before conception. Obesity was defined as body mass index (BMI) ≥30 kg/m². RESULTS: Hypomethylation at the IGF2 DMR was associated with paternal obesity. Even after adjusting for several maternal and newborn characteristics, we observed a persistent inverse association between DNA methylation in the offspring and paternal obesity (β-coefficient was -5.28, P = 0.003). At the H19 DMR, no significant associations were detected between methylation patterns and paternal obesity. Our data suggest an increase in DNA methylation at the IGF2 and H19 DMRs among newborns from obese mothers, but a larger study is warranted to further explore the potential effects of maternal obesity or lifestyle on the offspring's epigenome. CONCLUSIONS: While our small sample size is limited, our data indicate a preconceptional impact of paternal obesity on the reprogramming of imprint marks during spermatogenesis. Given the biological importance of imprinting fidelity, our study provides evidence for transgenerational effects of paternal obesity that may influence the offspring's future health status.

Authors
Soubry, A; Schildkraut, JM; Murtha, A; Wang, F; Huang, Z; Bernal, A; Kurtzberg, J; Jirtle, RL; Murphy, SK; Hoyo, C
MLA Citation
Soubry, A, Schildkraut, JM, Murtha, A, Wang, F, Huang, Z, Bernal, A, Kurtzberg, J, Jirtle, RL, Murphy, SK, and Hoyo, C. "Paternal obesity is associated with IGF2 hypomethylation in newborns: results from a Newborn Epigenetics Study (NEST) cohort. (Published online)" BMC Med 11 (February 6, 2013): 29-.
PMID
23388414
Source
pubmed
Published In
BMC Medicine
Volume
11
Publish Date
2013
Start Page
29
DOI
10.1186/1741-7015-11-29

Associations between birth and one year anthropometric measurements and IGF2 and IGF2R genetic variants in African American and Caucasian American infants.

Insulin-like growth factor 2 receptor (IGF2R) and insulin-like growth factor 2 (IGF2) genetic variants have been inconsistently associated with low birth weight and birth length in Caucasian and Asian infants, however few studies have included African Americans (AA). Generalized linear models and logistic regression models were used to examine associations between IGF2R single nucleotide polymorphisms (SNP) rs629849 and rs8191754, and IGF2 SNP rs680 and infant anthropometric measurements, in a racially diverse birth cohort in Durham County, North Carolina. Caucasian American (CA) carriers of the IGF2R SNP rs629849 were heavier (P = 0.02) and longer (P = 0.003) at birth, however body size at age 1 yr was similar to that of AA. Birth length significantly differed between carriers and non-carriers of the IGF2 rs680 variant in both AA (P = 0.04) and CA infants (P = 0.03). Both AA and CA carriers were 1 cm shorter at birth compared to non-carriers. We found no evidence for an association between rs8191754 and infant anthropometric measurements. Associations between SNPs andone year weight gain were only observed for rs680; CA infant carriers of rs680 variants weighed less than non-carriers at year one (P = 0.03); however, no associations were found in AA infants at year one. Larger studies using ancestral markers are required to disentangle these associations.

Authors
Vidal, AC; Overcash, F; Murphy, SK; Murtha, AP; Schildkraut, JM; Forman, MR; Demark-Wahnefried, W; Kurtzberg, J; Skaar, D; Jirtle, RL; Hoyo, C
MLA Citation
Vidal, AC, Overcash, F, Murphy, SK, Murtha, AP, Schildkraut, JM, Forman, MR, Demark-Wahnefried, W, Kurtzberg, J, Skaar, D, Jirtle, RL, and Hoyo, C. "Associations between birth and one year anthropometric measurements and IGF2 and IGF2R genetic variants in African American and Caucasian American infants." Journal of pediatric genetics 2.3 (January 2013).
PMID
26045971
Source
epmc
Published In
Journal of Pediatric Genetics
Volume
2
Issue
3
Publish Date
2013
DOI
10.3233/pge-13064

Associations between methylation of paternally expressed gene 3 (PEG3), cervical intraepithelial neoplasia and invasive cervical cancer.

Cytology-based screening for invasive cervical cancer (ICC) lacks sensitivity and specificity to discriminate between cervical intraepithelial neoplasia (CIN) likely to persist or progress from cases likely to resolve. Genome-wide approaches have been used to identify DNA methylation marks associated with CIN persistence or progression. However, associations between DNA methylation marks and CIN or ICC remain weak and inconsistent. Between 2008-2009, we conducted a hospital-based, case-control study among 213 Tanzania women with CIN 1/2/3 or ICC. We collected questionnaire data, biopsies, peripheral blood, cervical scrapes, Human papillomavirus (HPV) and HIV-1 infection status. We assessed PEG3 methylation status by bisulfite pyrosequencing. Multinomial logistic regression was used to estimate odds ratios (OR) and confidence intervals (CI 95%) for associations between PEG3 methylation status and CIN or ICC. After adjusting for age, gravidity, hormonal contraceptive use and HPV infection, a 5% increase in PEG3 DNA methylation was associated with increased risk for ICC (OR = 1.6; 95% CI 1.2-2.1). HPV infection was associated with a higher risk of CIN1-3 (OR = 15.7; 95% CI 5.7-48.6) and ICC (OR = 29.5, 95% CI 6.3-38.4). Infection with high risk HPV was correlated with mean PEG3 differentially methylated regions (DMRs) methylation (r = 0.34 p<0.0001), while the correlation with low risk HPV infection was weaker (r = 0.16 p = 0.047). Although small sample size limits inference, these data support that PEG3 methylation status has potential as a molecular target for inclusion in CIN screening to improve prediction of progression. Impact statement: We present the first evidence that aberrant methylation of the PEG3 DMR is an important co-factor in the development of Invasive cervical carcinoma (ICC), especially among women infected with high risk HPV. Our results show that a five percent increase in DNA methylation of PEG3 is associated with a 1.6-fold increase ICC risk. Suggesting PEG3 methylation status may be useful as a molecular marker for CIN screening to improve prediction of cases likely to progress.

Authors
Nye, MD; Hoyo, C; Huang, Z; Vidal, AC; Wang, F; Overcash, F; Smith, JS; Vasquez, B; Hernandez, B; Swai, B; Oneko, O; Mlay, P; Obure, J; Gammon, MD; Bartlett, JA; Murphy, SK
MLA Citation
Nye, MD, Hoyo, C, Huang, Z, Vidal, AC, Wang, F, Overcash, F, Smith, JS, Vasquez, B, Hernandez, B, Swai, B, Oneko, O, Mlay, P, Obure, J, Gammon, MD, Bartlett, JA, and Murphy, SK. "Associations between methylation of paternally expressed gene 3 (PEG3), cervical intraepithelial neoplasia and invasive cervical cancer." PLoS One 8.2 (2013): e56325-.
PMID
23418553
Source
pubmed
Published In
PloS one
Volume
8
Issue
2
Publish Date
2013
Start Page
e56325
DOI
10.1371/journal.pone.0056325

DNA methylation at imprint regulatory regions in preterm birth and infection

Objective: To aid in understanding long-term health consequences of intrauterine infections in preterm birth, we evaluated DNA methylation at 9 differentially methylated regions that regulate imprinted genes by type of preterm birth (spontaneous preterm labor, preterm premature rupture of membranes, or medically indicated [fetal growth restriction and preeclampsia]) and infection status (chorioamnionitis or funisitis). Study Design: Data on type of preterm birth and infection status were abstracted from medical records and standardized pathology reports in 73 preterm infants enrolled in the Newborn Epigenetics STudy, a prospective cohort study of mother-infant dyads in Durham, NC. Cord blood was collected at birth, and infant DNA methylation levels at the H19, IGF2, MEG3, MEST, SGCE/PEG10, PEG3, NNAT, and PLAGL1 differentially methylated regions were measured using bisulfite pyrosequencing. One-way analyses of variance and logistic regression models were used to compare DNA methylation levels by type of preterm birth and infection status. Results: DNA methylation levels did not differ at any of the regions (P >.20) between infants born via spontaneous preterm labor (average n = 29), preterm premature rupture of membranes (average n = 17), or medically indicated preterm birth (average n = 40). Levels were significantly increased at PLAGL1 in infants with chorioamnionitis (n = 10, 64.4%) compared with infants without chorioamnionitis (n = 63, 57.9%), P <.01. DNA methylation levels were also increased at PLAGL1 for infants with funisitis (n = 7, 63.3%) compared with infants without funisitis (n = 66, 58.3%), P <.05. Conclusion: Dysregulation of PLAGL1 has been associated with abnormal development and cancer. Early-life exposures, including infection/inflammation, may affect epigenetic changes that increase susceptibility to later chronic disease. © 2013 Mosby, Inc.

Authors
Liu, Y; Hoyo, C; Murphy, S; Huang, Z; Overcash, F; Thompson, J; Brown, H; Murtha, AP
MLA Citation
Liu, Y, Hoyo, C, Murphy, S, Huang, Z, Overcash, F, Thompson, J, Brown, H, and Murtha, AP. "DNA methylation at imprint regulatory regions in preterm birth and infection." American Journal of Obstetrics and Gynecology 208.5 (2013): 395.e1-395.e7.
Source
scival
Published In
American Journal of Obstetrics & Gynecology
Volume
208
Issue
5
Publish Date
2013
Start Page
395.e1
End Page
395.e7
DOI
10.1016/j.ajog.2013.02.006

Increased Intragenic IGF2 Methylation is Associated with Repression of Insulator Activity and Elevated Expression in Serous Ovarian Carcinoma.

Overexpression of insulin-like growth factor-II (IGF2) is a prominent characteristic of many epithelial ovarian malignancies. IGF2 imprinting and transcription are regulated in part through DNA methylation, which in turn regulates binding of the insulator protein CTCF within the IGF2/H19 imprint center. We have shown that IGF2 overexpression in ovarian cancer is associated with hypermethylation of CTCF binding sites within the IGF2/H19 imprint center. The aim of this study was to investigate the methylation and binding capacity of a novel putative CTCF binding motif located intragenic to IGF2 and determine how this relates to IGF2 expression. Among 35 primary serous epithelial ovarian cancer specimens, methylation of two CpGs, including one within the core binding motif and another adjacent to this motif, was higher in the 18 cancers with elevated IGF2 expression versus 10 with low expression (average 68.2 versus 38.5%; p < 0.0001). We also found that the CpG site within the CTCF binding motif is hypermethylated in male gametes (>92%; average 93.2%; N = 16). We confirmed binding of CTCF to this region in ovarian cancer cells, as well as the paralog of CTCF, Brother Of the Regulator of Imprinted Sites (BORIS), which is frequently overexpressed in cancers. The unmethylated CTCF binding motif has insulator activity in cells that express CTCF or BORIS, but not in cells that express both CTCF and BORIS. These intragenic CpG dinucleotides therefore comprise a novel paternal germline imprint mark and are located in a binding motif for the insulator protein CTCF. Methylation of the CpG dinucleotides is positively correlated with IGF2 transcription, indicating that increased methylation represses insulator function. These combined results suggest that methylation and CTCF binding at this region play important roles in regulating the level of IGF2 transcription. Our data have revealed a novel epigenetic regulatory element within the IGF2/H19 imprinted domain that is highly relevant to aberrant IGF2 expression in ovarian malignancies.

Authors
Huang, Z; Murphy, SK
MLA Citation
Huang, Z, and Murphy, SK. "Increased Intragenic IGF2 Methylation is Associated with Repression of Insulator Activity and Elevated Expression in Serous Ovarian Carcinoma. (Published online)" Front Oncol 3 (2013): 131-.
PMID
23745176
Source
pubmed
Published In
Front Oncol
Volume
3
Publish Date
2013
Start Page
131
DOI
10.3389/fonc.2013.00131

Utilization of genomic signatures to identify high-efficacy candidate drugs for chemorefractory endometrial cancers

Endometrial cancer, one of the most common gynecologic malignancies, is increasing in Japan, nearly doubling over the last decade. High-grade disease patients are often resistant to conventional chemotherapy with platinum agents; therefore, discovery of efficacious new drugs in this setting is required to benefit chemorefractory cases. The 50% growth-inhibitory (GI50) concentration of 27 clinically relevant drugs was measured in the NCI60 panel of cell lines. Gene expression data were analyzed using Bayesian binary regression, to first generate a response signature for each drug and then to calculate individual susceptibility scores using in vivo endometrial cancer data (GSE2109; http://www.ncbi.nlm.nih.gov/geo) and in vitro data (GSE25458), as well as to identify candidate drugs for chemorefractory cases. Using these candidates, cell proliferation, apoptosis and caspase assays were performed in vitro. The tumor growth-inhibitory effect of the candidate was also assessed in vivo using nude mice. Through microarray analysis, fludarabine and temsirolimus showed higher susceptibility scores in high-grade cases compared to cisplatin, doxorubicin and paclitaxel. Fludarabine significantly inhibited cell proliferation and increased apoptosis in the cisplatin-resistant endometrial cancer cell line, HEC1A, relative to HEC50B (p < 0.001). Fludarabine treatment also enhanced caspase-3/7 activity in HEC1A relative to HEC50B cells (p < 0.001), and inhibited the growth of HEC1A xenograft tumors relative to cisplatin (p < 0.05). These results support that identification and use of genomic signatures can lead to identification of new therapeutic candidates that may prove beneficial to chemoresistant cases. Fludarabine may be useful in targeting high-grade, chemorefractory endometrial cancer. © 2013 UICC.

Authors
Kharma, B; Baba, T; Mandai, M; Matsumura, N; Murphy, SK; Kang, HS; Yamanoi, K; Hamanishi, J; Yamaguchi, K; Yoshioka, Y; al, E
MLA Citation
Kharma, B, Baba, T, Mandai, M, Matsumura, N, Murphy, SK, Kang, HS, Yamanoi, K, Hamanishi, J, Yamaguchi, K, Yoshioka, Y, and al, E. "Utilization of genomic signatures to identify high-efficacy candidate drugs for chemorefractory endometrial cancers." International Journal of Cancer (2013).
PMID
23595697
Source
scival
Published In
International Journal of Cancer
Publish Date
2013
DOI
10.1002/ijc.28220

Maternal BMI, IGF-I Levels, and Birth Weight in African American and White Infants.

At birth, elevated IGF-I levels have been linked to birth weight extremes; high birth weight and low birth weight are risk factors for adult-onset chronic diseases including obesity, cardiovascular disease, and type 2 diabetes. We examined associations between plasma IGF-I levels and birth weight among infants born to African American and White obese and nonobese women. Prepregnancy weight and height were assessed among 251 pregnant women and anthropometric measurements of full term infants (≥37 weeks of gestation) were taken at birth. Circulating IGF-I was measured by ELISA in umbilical cord blood plasma. Linear regression models were utilized to examine associations between birth weight and high IGF-I, using the bottom two tertiles as referents. Compared with infants with lower IGF-I levels (≤3rd tertile), those with higher IGF-I levels (>3rd tertile) were 130 g heavier at birth, (β-coefficient = 230, se = 58.0, P = 0.0001), after adjusting for gender, race/ethnicity, gestational age, delivery route, maternal BMI and smoking. Stratified analyses suggested that these associations are more pronounced in infants born to African American women and women with BMI ≥30 kg/m(2); the cross product term for IGF-I and maternal BMI was statistically significant (P ≤ 0.0004). Our findings suggest that the association between IGF-I levels and birth weight depends more on maternal obesity than African American race/ethnicity.

Authors
Vidal, AC; Murtha, AP; Murphy, SK; Fortner, K; Overcash, F; Henry, N; Schildkraut, JM; Forman, MR; Demark-Wahnefried, W; Kurtzberg, J; Jirtle, R; Hoyo, C
MLA Citation
Vidal, AC, Murtha, AP, Murphy, SK, Fortner, K, Overcash, F, Henry, N, Schildkraut, JM, Forman, MR, Demark-Wahnefried, W, Kurtzberg, J, Jirtle, R, and Hoyo, C. "Maternal BMI, IGF-I Levels, and Birth Weight in African American and White Infants." Int J Pediatr 2013 (2013): 191472-.
PMID
23861689
Source
pubmed
Published In
International Journal of Pediatrics
Volume
2013
Publish Date
2013
Start Page
191472
DOI
10.1155/2013/191472

Bisulfite pyrosequencing.

Bisulfite pyrosequencing is a sequencing-by-synthesis method used to quantitatively determine the methylation of individual CG cytosines from PCR amplicons of a region up to 115 bases in length. The procedure relies on prior bisulfite conversion of all potentially methylated CG cytosines to either cytosine (methylated) or thymine (unmethylated) and involves the stepwise incorporation of deoxynucleotide triphosphates into the growing strand of nascent DNA. The incorporation of these dNTPs results in the proportional release of pyrophosphate, which is converted into ATP to aid in a subsequent conversion of luciferin to oxyluciferin. The amount of light released in the process is proportional to the number of nucleotides incorporated, and the procedure provides a quantitative portrait of the methylation profile for the amplicon in question.

Authors
Bassil, CF; Huang, Z; Murphy, SK
MLA Citation
Bassil, CF, Huang, Z, and Murphy, SK. "Bisulfite pyrosequencing." Methods Mol Biol 1049 (2013): 95-107.
PMID
23913212
Source
pubmed
Published In
Methods in molecular biology (Clifton, N.J.)
Volume
1049
Publish Date
2013
Start Page
95
End Page
107
DOI
10.1007/978-1-62703-547-7_9

Bisulfite sequencing of cloned alleles.

Bisulfite sequencing of cloned alleles is a widely used method for capturing the methylation profiles of single alleles. This method combines PCR amplification of the bisulfite-modified DNA with the subcloning of the amplicons into plasmids followed by transformation into bacteria and plating on selective media. The resulting colony forming units are each comprised of bacterial clones containing the same plasmid reflecting a single allele in the original PCR reaction. Following whole cell PCR and sequencing, the results provide highly detailed information about the status of each CG site within an allele. Sequencing of a large number of individual clones can provide quantitative information, assuming unbiased PCR, subcloning and clone selection. The proportion of methylated cytosine at a particular position within the sequenced alleles can be determined by counting the number of alleles showing methylation at the position of interest and dividing this by the total number of clones sequenced.

Authors
Huang, Z; Bassil, CF; Murphy, SK
MLA Citation
Huang, Z, Bassil, CF, and Murphy, SK. "Bisulfite sequencing of cloned alleles." Methods Mol Biol 1049 (2013): 83-94.
PMID
23913211
Source
pubmed
Published In
Methods in molecular biology (Clifton, N.J.)
Volume
1049
Publish Date
2013
Start Page
83
End Page
94
DOI
10.1007/978-1-62703-547-7_8

Methylation-specific PCR.

Defining DNA methylation patterns in the genome has become essential for understanding diverse biological processes including the regulation of gene expression, imprinted genes, and X chromosome inactivation and how these patterns are deregulated in human diseases. Methylation-specific (MS)-PCR is a useful tool for qualitative DNA methylation analysis with multiple advantages, including ease of design and execution, sensitivity in the ability to detect small quantities of methylated DNA, and the ability to rapidly screen a large number of samples without the need for purchase of expensive laboratory equipment. This assay requires modification of the genomic DNA by sodium bisulfite and two independent primer sets for PCR amplification, one pair designed to recognize the methylated and the other pair the unmethylated versions of the bisulfite-modified sequence. The amplicons are visualized using ethidium bromide staining following agarose gel electrophoresis. Amplicons of the expected size produced from either primer pair are indicative of the presence of DNA in the original sample with the respective methylation status.

Authors
Huang, Z; Bassil, CF; Murphy, SK
MLA Citation
Huang, Z, Bassil, CF, and Murphy, SK. "Methylation-specific PCR." Methods Mol Biol 1049 (2013): 75-82.
PMID
23913210
Source
pubmed
Published In
Methods in molecular biology (Clifton, N.J.)
Volume
1049
Publish Date
2013
Start Page
75
End Page
82
DOI
10.1007/978-1-62703-547-7_7

Main principles and outcomes of DNA methylation analysis.

Epigenetic modifications, including DNA methylation, are critically important mediators of normal cell function over the course of our lives. These modifications therefore also can play prominent roles in the development of disorders and diseases, including ovarian cancer. Genome-wide studies are now beginning to comprehensively decipher the methylome in normal and diseased tissues and cells, providing new insights into the distribution, specificity, and magnitude of modifications that occur and raising questions about these changes at specific loci. Further study of these alterations in specific tissues usually involves targeted approaches, of which there are a number available, all with distinct advantages and disadvantages. Here we provide a brief overview of DNA methylation and some of the methylation alterations that have been identified in ovarian cancer, as well as some of the technical approaches used to study these modifications.

Authors
Murphy, SK; Bassil, CF; Huang, Z
MLA Citation
Murphy, SK, Bassil, CF, and Huang, Z. "Main principles and outcomes of DNA methylation analysis." Methods Mol Biol 1049 (2013): 67-74.
PMID
23913209
Source
pubmed
Published In
Methods in molecular biology (Clifton, N.J.)
Volume
1049
Publish Date
2013
Start Page
67
End Page
74
DOI
10.1007/978-1-62703-547-7_6

Prenatal sensitization of a postnatal trigger for metabolic disease

Intrahepatic cholestasis of pregnancy (ICP), marked by elevated maternal serum bile acid levels, occurs in late pregnancy and is often associated with poor perinatal outcomes. In this issue of the JCI, Papacleovoulou et al. analyze the long-term consequences of ICP and find that teens born to mothers with ICP exhibit enhanced characteristics of metabolic syndrome relative to controls. The authors also used a new ICP mouse model to support and extend these findings, demonstrating that in utero exposure to bile acids induces persistent epigenetic alterations and abnormal placental lipogenesis, setting the stage for later metabolic dysfunction.

Authors
Murphy, SK
MLA Citation
Murphy, SK. "Prenatal sensitization of a postnatal trigger for metabolic disease." Journal of Clinical Investigation 123.7 (2013): 2786-2788.
PMID
23926602
Source
scival
Published In
Journal of Clinical Investigation
Volume
123
Issue
7
Publish Date
2013
Start Page
2786
End Page
2788
DOI
10.1172/JCI69399

Associations between antibiotic exposure during pregnancy, birth weight and aberrant methylation at imprinted genes among offspring

Objectives: Low birth weight (LBW) has been associated with common adult-onset chronic diseases, including obesity, cardiovascular disease, type II diabetes and some cancers. The etiology of LBW is multi-factorial. However, recent evidence suggests exposure to antibiotics may also increase the risk of LBW. The mechanisms underlying this association are unknown, although epigenetic mechanisms are hypothesized. In this study, we evaluated the association between maternal antibiotic use and LBW and examined the potential role of altered DNA methylation that controls growth regulatory imprinted genes in these associations. Methods: Between 2009-2011, 397 pregnant women were enrolled and followed until delivery. Prenatal antibiotic use was ascertained through maternal self-report. Imprinted genes methylation levels were measured at differentially methylated regions (DMRs) using bisulfite pyrosequencing. Generalized linear models were used to examine associations among antibiotic use, birth weight and DMR methylation fractions. Results: After adjusting for infant gender, race/ethnicity, maternal body mass index, delivery route, gestational weight gain, gestational age at delivery, folic acid intake, physical activity, maternal smoking and parity, antibiotic use during pregnancy was associated with 138 g lower birth weight compared with non-antibiotic use (β-coefficient=-132.99, s.e.=50.70, P=0.008). These associations were strongest in newborns of women who reported antibiotic use other than penicillins (β-coefficient=-135.57, s.e.=57.38, P=0.02). Methylation at five DMRs, IGF2 (P=0.05), H19 (P=0.15), PLAGL1 (P=0.01), MEG3 (P=0.006) and PEG3 (P=0.08), was associated with maternal antibiotic use; among these, only methylation at the PLAGL1 DMR was also associated with birth weight. Conclusion: We report an inverse association between in utero exposure to antibiotics and lower infant birth weight and provide the first empirical evidence supporting imprinted gene plasticity in these associations. © 2013 Macmillan Publishers Limited.

Authors
Vidal, AC; Murphy, SK; Murtha, AP; Schildkraut, JM; Soubry, A; Huang, Z; Neelon, SEB; Fuemmeler, B; Iversen, E; Wang, F; Kurtzberg, J; Jirtle, RL; Hoyo, C
MLA Citation
Vidal, AC, Murphy, SK, Murtha, AP, Schildkraut, JM, Soubry, A, Huang, Z, Neelon, SEB, Fuemmeler, B, Iversen, E, Wang, F, Kurtzberg, J, Jirtle, RL, and Hoyo, C. "Associations between antibiotic exposure during pregnancy, birth weight and aberrant methylation at imprinted genes among offspring." International Journal of Obesity 37.7 (2013): 907-913.
Source
scival
Published In
International Journal of Obesity
Volume
37
Issue
7
Publish Date
2013
Start Page
907
End Page
913
DOI
10.1038/ijo.2013.47

Utilization of genomic signatures to identify high-efficacy candidate drugs for chemorefractory endometrial cancers

Endometrial cancer, one of the most common gynecologic malignancies, is increasing in Japan, nearly doubling over the last decade. High-grade disease patients are often resistant to conventional chemotherapy with platinum agents; therefore, discovery of efficacious new drugs in this setting is required to benefit chemorefractory cases. The 50% growth-inhibitory (GI50) concentration of 27 clinically relevant drugs was measured in the NCI60 panel of cell lines. Gene expression data were analyzed using Bayesian binary regression, to first generate a response signature for each drug and then to calculate individual susceptibility scores using in vivo endometrial cancer data (GSE2109; http://www.ncbi.nlm.nih.gov/geo) and in vitro data (GSE25458), as well as to identify candidate drugs for chemorefractory cases. Using these candidates, cell proliferation, apoptosis and caspase assays were performed in vitro. The tumor growth-inhibitory effect of the candidate was also assessed in vivo using nude mice. Through microarray analysis, fludarabine and temsirolimus showed higher susceptibility scores in high-grade cases compared to cisplatin, doxorubicin and paclitaxel. Fludarabine significantly inhibited cell proliferation and increased apoptosis in the cisplatin-resistant endometrial cancer cell line, HEC1A, relative to HEC50B (p < 0.001). Fludarabine treatment also enhanced caspase-3/7 activity in HEC1A relative to HEC50B cells (p < 0.001), and inhibited the growth of HEC1A xenograft tumors relative to cisplatin (p < 0.05). These results support that identification and use of genomic signatures can lead to identification of new therapeutic candidates that may prove beneficial to chemoresistant cases. Fludarabine may be useful in targeting high-grade, chemorefractory endometrial cancer. What's new? Patients with advanced endometrial cancer need something beyond conventional therapies. Genome wide microarray analysis of these difficult-to-treat cancers has shown that they have distinctive genetic signatures. In this paper, the authors profiled drug-resistant endometrial cancer cell lines to identify potentially effective chemical therapies. From their analysis, they determined that that five of seven cancer cell lines were likely susceptible to the chemotherapy agent fludarabine. They then demonstrated fludarabine's toxicity in vitro and in vivo, suggesting the drug may have promise for treating the cancer. © 2013 UICC.

Authors
Kharma, B; Baba, T; Mandai, M; Matsumura, N; Murphy, SK; Kang, HS; Yamanoi, K; Hamanishi, J; Yamaguchi, K; Yoshioka, Y; Konishi, I
MLA Citation
Kharma, B, Baba, T, Mandai, M, Matsumura, N, Murphy, SK, Kang, HS, Yamanoi, K, Hamanishi, J, Yamaguchi, K, Yoshioka, Y, and Konishi, I. "Utilization of genomic signatures to identify high-efficacy candidate drugs for chemorefractory endometrial cancers." International Journal of Cancer 133.9 (2013): 2234-2244.
Source
scival
Published In
International Journal of Cancer
Volume
133
Issue
9
Publish Date
2013
Start Page
2234
End Page
2244
DOI
10.1002/ijc.28220

Validation of ovarian cancer gene expression signatures for survival and subtype in formalin fixed paraffin embedded tissues

Introduction Gene expression signatures have been identified for epithelial ovarian cancer survival (TCGA) and intrinsic subtypes (Tothill et al.). One obstacle to clinical translation is that these signatures were developed using frozen tissue, whereas usually only formalin-fixed, paraffin embedded (FFPE) tissue is available. The aim of this study was to determine if gene expression signatures can be translated to fixed archival tissues. Methods RNA extracted from FFPE sections from 240 primary ovarian cancers was analyzed by DASL on Illumina BeadChip arrays. Concordance of expression at the individual gene level was assessed by comparing array data from the same cancers (30 frozen samples analyzed on Affymetrix arrays versus FFPE DASL). Results The correlation between FFPE and frozen survival signature estimates was 0.774. The TCGA signature using DASL was predictive of survival in 106 advanced stage high grade serous ovarian cancers (median survival 33 versus 60 months, estimated hazard ratio for death 2.30, P = 0.0007). Similar to Tothill, we found using DASL that most high grade serous ovarian cancers (102/110, 93%) were assigned to subtypes 1, 2, 4 and 5, whereas most endometrioid, clear cell, mucinous and low grade serous cases (39/57, 68%) were assigned to subtypes 3 and 6 (P < 10e-15). Conclusions Although individual probe estimates of microarrays may be weakly correlated between FFPE and frozen samples, combinations of probes have robust ability to predict survival and subtype. This suggests that it may be possible to use these signatures for prognostic and predictive purposes as we seek to individualize the treatment of ovarian cancer. © 2012 Elsevier Inc.

Authors
Sfakianos, GP; Iversen, ES; Whitaker, R; Akushevich, L; Schildkraut, JM; Murphy, SK; Marks, JR; Berchuck, A
MLA Citation
Sfakianos, GP, Iversen, ES, Whitaker, R, Akushevich, L, Schildkraut, JM, Murphy, SK, Marks, JR, and Berchuck, A. "Validation of ovarian cancer gene expression signatures for survival and subtype in formalin fixed paraffin embedded tissues." Gynecologic Oncology 129.1 (2013): 159-164.
Source
scival
Published In
Gynecologic Oncology
Volume
129
Issue
1
Publish Date
2013
Start Page
159
End Page
164
DOI
10.1016/j.ygyno.2012.12.030

TP53 Status is Associated with Thrombospondin1 Expression In vitro.

OBJECTIVES: To elucidate the association between thrombospondin1 (THBS1) expression and TP53 status and THBS1 promoter methylation in epithelial ovarian cancer (EOC). METHODS: Epithelial ovarian cancer cell lines with known TP53 status were analyzed for THBS1 gene expression using Affymetrix U133 microarrays and promoter methylation by pyrosequencing. THBS1 mRNA expression was obtained pre- and post-exposure to radiation and hypoxia treatment in A2780 parent wild-type (wt) and mutant (m)TP53 cells. THBS1 expression was compared to tumor growth properties. RESULTS: THBS1 gene expression was higher in cells containing a wtTP53 gene or null TP53 mutation (p = 0.005) and low or absent p53 protein expression (p = 0.008) compared to those harboring a missense TP53 gene mutation and exhibiting high p53 protein expression. Following exposure to radiation, there was a 3.4-fold increase in THBS1 mRNA levels in the mTP53 versus wtTP53 A2780 cells. After exposure to hypoxia, THBS1 mRNA levels increased approximately fourfold in both wtTP53 and mTP53 A2780 cells. Promoter methylation levels were low (median = 8.6%; range = 3.5-88.8%). There was a non-significant inverse correlation between THBS1 methylation and transcript levels. There was no association between THBS1 expression and population doubling time, invasive capacity, or anchorage-independent growth. CONCLUSION: THBS1 expression may be regulated via the TP53 pathway, and induced by hypoxic tumor microenvironment conditions. Overall low levels of THBS1 promoter methylation imply that methylation is not the primary driver of THBS1 expression in EOC.

Authors
Alvarez Secord, A; Bernardini, MQ; Broadwater, G; Grace, LA; Huang, Z; Baba, T; Kondoh, E; Sfakianos, G; Havrilesky, LJ; Murphy, SK
MLA Citation
Alvarez Secord, A, Bernardini, MQ, Broadwater, G, Grace, LA, Huang, Z, Baba, T, Kondoh, E, Sfakianos, G, Havrilesky, LJ, and Murphy, SK. "TP53 Status is Associated with Thrombospondin1 Expression In vitro. (Published online)" Front Oncol 3 (2013): 269-.
PMID
24195060
Source
pubmed
Published In
Front Oncol
Volume
3
Publish Date
2013
Start Page
269
DOI
10.3389/fonc.2013.00269

DNA profiling analysis of endometrial and ovarian cell lines reveals misidentification, redundancy and contamination.

OBJECTIVES: Cell lines derived from human ovarian and endometrial cancers, and their immortalized non-malignant counterparts, are critical tools to investigate and characterize molecular mechanisms underlying gynecologic tumorigenesis, and facilitate development of novel therapeutics. To determine the extent of misidentification, contamination and redundancy, with evident consequences for the validity of research based upon these models, we undertook a systematic analysis and cataloging of endometrial and ovarian cell lines. METHODS: Profiling of cell lines by analysis of DNA microsatellite short tandem repeats (STR), p53 nucleotide polymorphisms and microsatellite instability was performed. RESULTS: Fifty-one ovarian cancer lines were profiled with ten found to be redundant and five (A2008, OV2008, C13, SK-OV-4 and SK-OV-6) identified as cervical cancer cells. Ten endometrial cell lines were analyzed, with RL-92, HEC-1A, HEC-1B, HEC-50, KLE, and AN3CA all exhibiting unique, uncontaminated STR profiles. Multiple variants of Ishikawa and ECC-1 endometrial cancer cell lines were genotyped and analyzed by sequencing of mutations in the p53 gene. The profile of ECC-1 cells did not match the EnCa-101 tumor, from which it was reportedly derived, and all ECC-1 isolates were genotyped as Ishikawa cells, MCF-7 breast cancer cells, or a combination thereof. Two normal, immortalized endometrial epithelial cell lines, HES cells and the hTERT-EEC line, were identified as HeLa cervical carcinoma and MCF-7 breast cancer cells, respectively. CONCLUSIONS: Results demonstrate significant misidentification, duplication, and loss of integrity of endometrial and ovarian cancer cell lines. Authentication by STR DNA profiling is a simple and economical method to verify and validate studies undertaken with these models.

Authors
Korch, C; Spillman, MA; Jackson, TA; Jacobsen, BM; Murphy, SK; Lessey, BA; Jordan, VC; Bradford, AP
MLA Citation
Korch, C, Spillman, MA, Jackson, TA, Jacobsen, BM, Murphy, SK, Lessey, BA, Jordan, VC, and Bradford, AP. "DNA profiling analysis of endometrial and ovarian cell lines reveals misidentification, redundancy and contamination." Gynecol Oncol 127.1 (October 2012): 241-248.
PMID
22710073
Source
pubmed
Published In
Gynecologic Oncology
Volume
127
Issue
1
Publish Date
2012
Start Page
241
End Page
248
DOI
10.1016/j.ygyno.2012.06.017

Expression QTL analysis of a gene expression signature which predicts advanced non-alcoholic fatty liver disease

Authors
Garrett, ME; Moylan, CA; Gibson, J; Yang, H; Pang, H; Dellinger, A; Suzuki, A; Tillmann, HL; Guy, CD; Abdelmalek, MF; Murphy, SK; Diehl, AM; Hauser, M; Ashley-Koch, AE
MLA Citation
Garrett, ME, Moylan, CA, Gibson, J, Yang, H, Pang, H, Dellinger, A, Suzuki, A, Tillmann, HL, Guy, CD, Abdelmalek, MF, Murphy, SK, Diehl, AM, Hauser, M, and Ashley-Koch, AE. "Expression QTL analysis of a gene expression signature which predicts advanced non-alcoholic fatty liver disease." October 2012.
Source
wos-lite
Published In
Hepatology
Volume
56
Publish Date
2012
Start Page
267A
End Page
268A

Convergent and divergent evolution of genomic imprinting in the marsupial Monodelphis domestica.

BACKGROUND: Genomic imprinting is an epigenetic phenomenon resulting in parent-of-origin specific monoallelic gene expression. It is postulated to have evolved in placental mammals to modulate intrauterine resource allocation to the offspring. In this study, we determined the imprint status of metatherian orthologues of eutherian imprinted genes. RESULTS: L3MBTL and HTR2A were shown to be imprinted in Monodelphis domestica (the gray short-tailed opossum). MEST expressed a monoallelic and a biallelic transcript, as in eutherians. In contrast, IMPACT, COPG2, and PLAGL1 were not imprinted in the opossum. Differentially methylated regions (DMRs) involved in regulating imprinting in eutherians were not found at any of the new imprinted loci in the opossum. Interestingly, a novel DMR was identified in intron 11 of the imprinted IGF2R gene, but this was not conserved in eutherians. The promoter regions of the imprinted genes in the opossum were enriched for the activating histone modification H3 Lysine 4 dimethylation. CONCLUSIONS: The phenomenon of genomic imprinting is conserved in Therians, but the marked difference in the number and location of imprinted genes and DMRs between metatherians and eutherians indicates that imprinting is not fully conserved between the two Therian infra-classes. The identification of a novel DMR at a non-conserved location as well as the first demonstration of histone modifications at imprinted loci in the opossum suggest that genomic imprinting may have evolved in a common ancestor of these two Therian infra-classes with subsequent divergence of regulatory mechanisms in the two lineages.

Authors
Das, R; Anderson, N; Koran, MI; Weidman, JR; Mikkelsen, TS; Kamal, M; Murphy, SK; Linblad-Toh, K; Greally, JM; Jirtle, RL
MLA Citation
Das, R, Anderson, N, Koran, MI, Weidman, JR, Mikkelsen, TS, Kamal, M, Murphy, SK, Linblad-Toh, K, Greally, JM, and Jirtle, RL. "Convergent and divergent evolution of genomic imprinting in the marsupial Monodelphis domestica. (Published online)" BMC Genomics 13 (August 16, 2012): 394-.
PMID
22899817
Source
pubmed
Published In
BMC Genomics
Volume
13
Publish Date
2012
Start Page
394
DOI
10.1186/1471-2164-13-394

Insulin-like growth factor 2/H19 methylation at birth and risk of overweight and obesity in children.

OBJECTIVE: To determine whether aberrant DNA methylation at differentially methylated regions (DMRs) regulating insulin-like growth factor 2 (IGF2) expression in umbilical cord blood is associated with overweight or obesity in a multiethnic cohort. STUDY DESIGN: Umbilical cord blood leukocytes of 204 infants born between 2005 and 2009 in Durham, North Carolina, were analyzed for DNA methylation at two IGF2 DMRs by using pyrosequencing. Anthropometric and feeding data were collected at age 1 year. Methylation differences were compared between children >85th percentile of the Centers for Disease Control and Prevention growth charts weight-for-age (WFA) and children ≤ 85th percentile of WFA at 1 year by using generalized linear models, adjusting for post-natal caloric intake, maternal cigarette smoking, and race/ethnicity. RESULTS: The methylation percentages at the H19 imprint center DMR was higher in infants with WFA >85th percentile (62.7%; 95% CI, 59.9%-65.5%) than in infants with WFA ≤ 85th percentile (59.3%; 95% CI, 58.2%-60.3%; P = .02). At the intragenic IGF2 DMR, methylation levels were comparable between infants with WFA ≤ 85th percentile and infants with WFA >85th percentile. CONCLUSIONS: Our findings suggest that IGF2 plasticity may be mechanistically important in early childhood overweight or obese status. If confirmed in larger studies, these findings suggest aberrant DNA methylation at sequences regulating imprinted genes may be useful identifiers of children at risk for the development of early obesity.

Authors
Perkins, E; Murphy, SK; Murtha, AP; Schildkraut, J; Jirtle, RL; Demark-Wahnefried, W; Forman, MR; Kurtzberg, J; Overcash, F; Huang, Z; Hoyo, C
MLA Citation
Perkins, E, Murphy, SK, Murtha, AP, Schildkraut, J, Jirtle, RL, Demark-Wahnefried, W, Forman, MR, Kurtzberg, J, Overcash, F, Huang, Z, and Hoyo, C. "Insulin-like growth factor 2/H19 methylation at birth and risk of overweight and obesity in children." J Pediatr 161.1 (July 2012): 31-39.
PMID
22341586
Source
pubmed
Published In
The Journal of Pediatrics
Volume
161
Issue
1
Publish Date
2012
Start Page
31
End Page
39
DOI
10.1016/j.jpeds.2012.01.015

Depression in pregnancy, infant birth weight and DNA methylation of imprint regulatory elements.

Depressed mood in pregnancy has been linked to low birth weight (LBW, < 2,500 g), a risk factor for adult-onset chronic diseases in offspring. We examined maternal depressed mood in relation to birth weight and evaluated the role of DNA methylation at regulatory sequences of imprinted genes in this association. We measured depressed mood among 922 pregnant women using the CES-D scale and obtained birth weight data from hospital records. Using bisulfite pyrosequencing of cord blood DNA from 508 infants, we measured methylation at differentially methylated regions (DMRs) regulating imprinted genes IGF2/H19, DLK1/MEG3, MEST, PEG3, PEG10/SGCE, NNAT and PLAGL1. Multiple regression models were used to examine the relationship between depressed mood, birth weight and DMR methylation levels. Depressed mood was associated with a more that 3-fold higher risk of LBW, after adjusting for delivery mode, parity, education, cigarette smoking, folic acid use and preterm birth. The association may be more pronounced in offspring of black women and female infants. Compared with infants of women without depressed mood, infants born to women with severe depressed mood had a 2.4% higher methylation at the MEG3 DMR. Whereas LBW infants had 1.6% lower methylation at the IGF2 DMR, high birth weight (> 4,500 g) infants had 5.9% higher methylation at the PLAGL1 DMR compared with normal birth weight infants. Our findings confirm that severe maternal depressed mood in pregnancy is associated with LBW, and that MEG3 and IGF2 plasticity may play important roles.

Authors
Liu, Y; Murphy, SK; Murtha, AP; Fuemmeler, BF; Schildkraut, J; Huang, Z; Overcash, F; Kurtzberg, J; Jirtle, R; Iversen, ES; Forman, MR; Hoyo, C
MLA Citation
Liu, Y, Murphy, SK, Murtha, AP, Fuemmeler, BF, Schildkraut, J, Huang, Z, Overcash, F, Kurtzberg, J, Jirtle, R, Iversen, ES, Forman, MR, and Hoyo, C. "Depression in pregnancy, infant birth weight and DNA methylation of imprint regulatory elements." Epigenetics 7.7 (July 2012): 735-746.
PMID
22677950
Source
pubmed
Published In
Epigenetics : official journal of the DNA Methylation Society
Volume
7
Issue
7
Publish Date
2012
Start Page
735
End Page
746
DOI
10.4161/epi.20734

Abstract LB-87: Methylated-mediated repression of ZNF154 in ovarian cancer is associated with poor overall survival

Authors
Okamoto, T; Yamaguchi, K; Huang, Z; Whitaker, R; Konishi, I; Berchuck, A; Murphy, SK
MLA Citation
Okamoto, T, Yamaguchi, K, Huang, Z, Whitaker, R, Konishi, I, Berchuck, A, and Murphy, SK. "Abstract LB-87: Methylated-mediated repression of ZNF154 in ovarian cancer is associated with poor overall survival." Cancer Research 72.8 Supplement (April 15, 2012): LB-87-LB-87.
Source
crossref
Published In
Cancer Research
Volume
72
Issue
8 Supplement
Publish Date
2012
Start Page
LB-87
End Page
LB-87
DOI
10.1158/1538-7445.AM2012-LB-87

Abstract 5363: Aggregation rather than monoclonal expansion explains ovarian cancer spheroid formation

Authors
Huang, Z; Lowery, WJ; Berchuck, A; Murphy, SK
MLA Citation
Huang, Z, Lowery, WJ, Berchuck, A, and Murphy, SK. "Abstract 5363: Aggregation rather than monoclonal expansion explains ovarian cancer spheroid formation." Cancer Research 72.8 Supplement (April 15, 2012): 5363-5363.
Source
crossref
Published In
Cancer Research
Volume
72
Issue
8 Supplement
Publish Date
2012
Start Page
5363
End Page
5363
DOI
10.1158/1538-7445.AM2012-5363

Association of cord blood methylation fractions at imprinted insulin-like growth factor 2 (IGF2), plasma IGF2, and birth weight.

PURPOSE: Altered methylation at Insulin-like Growth Factor 2 (IGF2) regulatory regions has previously been associated with obesity, and several malignancies including colon, esophageal, and prostate adenocarcinomas, presumably via changes in expression and/or loss of imprinting, but the functional significance of these DNA methylation marks have not been demonstrated in humans. We examined associations among DNA methylation at IGF2 differentially methylated regions (DMRs), circulating IGF2 protein concentrations in umbilical cord blood (UCB) and birth weight in newborns. METHODS: Questionnaire data were obtained from 300 pregnant women recruited between 2005 and 2009. UCB DNA methylation was measured by bisulfite pyrosequencing. UCB plasma concentrations of soluble IGF2 were measured by ELISA assays. Generalized linear regression models were used to examine the relationship between DMR methylation and IGF2 levels. RESULTS: Lower IGF2 DMR methylation was associated with elevated plasma IGF2 protein concentrations (β = -9.87, p < 0.01); an association that was stronger in infants born to obese women (pre-pregnancy BMI > 30 kg/m(2), β = -20.21, p < 0.0001). Elevated IGF2 concentrations were associated with higher birth weight (p < 0.0001) after adjusting for maternal race/ethnicity, pre-pregnancy BMI, cigarette smoking, gestational diabetes, and infant sex. These patterns of association were not apparent at the H19 DMR. CONCLUSION: Our data suggest that variation in IGF2 DMR methylation is an important mechanism by which circulating IGF2 concentrations, a putative risk factor for obesity and cancers of the colon, esophagus, and prostate, are modulated; associations that may depend on pre-pregnancy obesity.

Authors
Hoyo, C; Fortner, K; Murtha, AP; Schildkraut, JM; Soubry, A; Demark-Wahnefried, W; Jirtle, RL; Kurtzberg, J; Forman, MR; Overcash, F; Huang, Z; Murphy, SK
MLA Citation
Hoyo, C, Fortner, K, Murtha, AP, Schildkraut, JM, Soubry, A, Demark-Wahnefried, W, Jirtle, RL, Kurtzberg, J, Forman, MR, Overcash, F, Huang, Z, and Murphy, SK. "Association of cord blood methylation fractions at imprinted insulin-like growth factor 2 (IGF2), plasma IGF2, and birth weight." Cancer Causes Control 23.4 (April 2012): 635-645.
PMID
22392079
Source
pubmed
Published In
Cancer Causes & Control
Volume
23
Issue
4
Publish Date
2012
Start Page
635
End Page
645
DOI
10.1007/s10552-012-9932-y

Gender-specific methylation differences in relation to prenatal exposure to cigarette smoke.

Epigenetic alterations may mechanistically explain the developmental origins of adult disease, namely the hypothesis that many complex adult chronic diseases originate as a result of conditions encountered in utero. If true, epigenetically regulated imprinted genes, critical to normal growth and development, may partially mediate these outcomes. We determined the influence of in utero exposure to cigarette smoking on methylation at two differentially methylated regions (DMRs) regulating Insulin-like Growth Factor 2 (IGF2) and H19, and how this might relate to birth weight of infants born to 418 pregnant women. Smoking status was ascertained through self-report and medical records. Bisulfite pyrosequencing was used to measure methylation in umbilical cord blood DNAs. Least squares DNA methylation means at each DMR and birth weight were compared between infants of smokers and non-smokers, using generalized linear models. While there were no significant differences at the H19 DMR, infants born to smokers had higher methylation at the IGF2 DMR than those born to never smokers or those who quit during pregnancy (49.5%, SD=8.0 versus 46.6%, SD=5.6 and 45.8%, SD=6.3, respectively; p=0.0002). The smoking-related increase in methylation was most pronounced in male offspring (p for sex interaction=0.03), for whom approximately 20% of smoking-related low birth weight was mediated by DNA methylation at the IGF2 DMR. Our findings suggest that IGF2 DMR plasticity is an important mechanism by which in utero adjustments to environmental toxicants are conferred. Larger studies to replicate these findings are required.

Authors
Murphy, SK; Adigun, A; Huang, Z; Overcash, F; Wang, F; Jirtle, RL; Schildkraut, JM; Murtha, AP; Iversen, ES; Hoyo, C
MLA Citation
Murphy, SK, Adigun, A, Huang, Z, Overcash, F, Wang, F, Jirtle, RL, Schildkraut, JM, Murtha, AP, Iversen, ES, and Hoyo, C. "Gender-specific methylation differences in relation to prenatal exposure to cigarette smoke." Gene 494.1 (February 15, 2012): 36-43.
PMID
22202639
Source
pubmed
Published In
Gene
Volume
494
Issue
1
Publish Date
2012
Start Page
36
End Page
43
DOI
10.1016/j.gene.2011.11.062

Targeting the epigenome in ovarian cancer.

Epithelial ovarian cancer is the leading cause of death from gynecological cancers, largely owing to the development of recurrent intractable disease. Only a small number of distinct genetic mutations are known to contribute to ovarian carcinogenesis. Furthermore, understanding mechanistic genotype-phenotype links is complicated by frequent aneuploidy. Epigenetic deregulation is even more prominent, and ovarian cancers are replete with such aberrations that repress tumor suppressors and activate proto-oncogenes. Epigenetic therapies are emerging as promising agents for resensitizing platinum-resistant ovarian cancers. These drugs may also have the potential to alter epigenetic programming in cancer progenitor cells and provide a strategy for improving therapy of ovarian cancer.

Authors
Murphy, SK
MLA Citation
Murphy, SK. "Targeting the epigenome in ovarian cancer." Future Oncol 8.2 (February 2012): 151-164. (Review)
PMID
22335580
Source
pubmed
Published In
Future oncology (London, England)
Volume
8
Issue
2
Publish Date
2012
Start Page
151
End Page
164
DOI
10.2217/fon.11.152

The activated transforming growth factor-beta signaling pathway in peritoneal metastases is a potential therapeutic target in ovarian cancer.

Peritoneal dissemination including omental metastasis is the most frequent route of metastasis and an important prognostic factor in advanced ovarian cancer. We analyzed the publicly available microarray dataset (GSE2109) using binary regression and found that the transforming growth factor (TGF)-beta signaling pathway was activated in omental metastases as compared to primary sites of disease. Immunohistochemical analysis of TGF-beta receptor type 2 and phosphorylated SMAD2 indicated that both were upregulated in omental metastases as compared to primary disease sites. Treatment of the mouse ovarian cancer cell line HM-1 with recombinant TGF-β1 promoted invasiveness, cell motility and cell attachment while these were suppressed by treatment with A-83-01, an inhibitor of the TGF-β signaling pathway. Microarray analysis of HM-1 cells treated with TGF-β1 and/or A-83-01 revealed that A-83-01 efficiently inhibited transcriptional changes that are induced by TGF-β1. Using gene set enrichment analysis, we found that genes upregulated by TGF-β1 in HM-1 cells were also significantly upregulated in omental metastases compared to primary sites in the human ovarian cancer dataset, GSE2109 (false discovery rate (FDR) q = 0.086). Therapeutic effects of A-83-01 in a mouse model of peritoneal dissemination were examined. Intraperitoneal injection of A-83-01 (150 μg given three times weekly) significantly improved survival (p = 0.015). In summary, these results show that the activated TGF-β signaling pathway in peritoneal metastases is a potential therapeutic target in ovarian cancer.

Authors
Yamamura, S; Matsumura, N; Mandai, M; Huang, Z; Oura, T; Baba, T; Hamanishi, J; Yamaguchi, K; Kang, HS; Okamoto, T; Abiko, K; Mori, S; Murphy, SK; Konishi, I
MLA Citation
Yamamura, S, Matsumura, N, Mandai, M, Huang, Z, Oura, T, Baba, T, Hamanishi, J, Yamaguchi, K, Kang, HS, Okamoto, T, Abiko, K, Mori, S, Murphy, SK, and Konishi, I. "The activated transforming growth factor-beta signaling pathway in peritoneal metastases is a potential therapeutic target in ovarian cancer." Int J Cancer 130.1 (January 1, 2012): 20-28.
PMID
21503873
Source
pubmed
Published In
International Journal of Cancer
Volume
130
Issue
1
Publish Date
2012
Start Page
20
End Page
28
DOI
10.1002/ijc.25961

IGF2R genetic variants, circulating IGF2 concentrations and colon cancer risk in African Americans and Whites.

The Mannose 6 Phosphate/Insulin-like Growth Factor Receptor-2 (IGF2R) encodes a type-1 membrane protein that modulates availability of the potent mitogen, IGF2. We evaluated the associations between IGF2R non-synonymous genetic variants (c.5002G>A, Gly1619Arg(rs629849), and c.901C>G, Leu252Val(rs8191754)), circulating IGF2 levels, and colon cancer (CC) risk among African American and White participants enrolled in the North Carolina Colon Cancer Study (NCCCS). Generalized linear models were used to compare circulating levels of IGF2 among 298 African American and 518 White controls. Logistic regression models were used to estimate odds ratios (ORs) and 95% confidence intervals (CIs) for the association of IGF2R genetic variants and CC risk. Women homozygous for the IGF2R c.5002 G>A allele, had higher mean levels of circulating IGF2, 828 (SD=321) ng/ml compared to non-carriers, 595 (SD=217) ng/ml (p-value=0.01). This pattern was not apparent in individuals homozygous for the IGF2R c.901 C>G variant. Whites homozygous for the IGF2R c.901 C>G variant trended towards a higher risk of CC, OR=2.2 [95% CI(0.9-5.4)], whereas carrying the IGF2R c.5002 G>A variant was not associated with CC risk. Our findings support the hypothesis that being homozygous for the IGF2R c.5002 G>A modulates IGF2 circulating levels in a sex-specific manner, and while carrying the IGF2R c.901 C>G may increase cancer risk, the mechanism may not involve modulation of circulating IGF2.

Authors
Hoyo, C; Murphy, SK; Schildkraut, JM; Vidal, AC; Skaar, D; Millikan, RC; Galanko, J; Sandler, RS; Jirtle, R; Keku, T
MLA Citation
Hoyo, C, Murphy, SK, Schildkraut, JM, Vidal, AC, Skaar, D, Millikan, RC, Galanko, J, Sandler, RS, Jirtle, R, and Keku, T. "IGF2R genetic variants, circulating IGF2 concentrations and colon cancer risk in African Americans and Whites." Dis Markers 32.2 (2012): 133-141.
PMID
22377707
Source
pubmed
Published In
Disease markers
Volume
32
Issue
2
Publish Date
2012
Start Page
133
End Page
141
DOI
10.3233/DMA-2011-0865

Differentially methylated regions of imprinted genes in prenatal, perinatal and postnatal human tissues.

Epigenetic plasticity in relation to in utero exposures may mechanistically explain observed differences in the likelihood of developing common complex diseases including hypertension, diabetes and cardiovascular disease through the cumulative effects of subtle alterations in gene expression. Imprinted genes are essential mediators of growth and development and are characterized by differentially methylated regulatory regions (DMRs) that carry parental allele-specific methylation profiles. This theoretical 50% level of methylation provides a baseline from which endogenously- or exogenously-induced deviations in methylation can be detected. We quantified DNA methylation at imprinted gene DMRs in a large panel of human conceptal tissues, in matched buccal cell specimens collected at birth and at one year of age, and in the major cell fractions of umbilical cord blood to assess the stability of methylation at these regions. DNA methylation was measured using validated pyrosequencing assays at seven DMRs regulating the IGF2/H19, DLK1/MEG3, MEST, NNAT and SGCE/PEG10 imprinted domains. DMR methylation did not significantly differ for the H19, MEST and SGCE/PEG10 DMRs across all conceptal tissues analyzed (ANOVA p>0.10). Methylation differences at several DMRs were observed in tissues from brain (IGF2 and MEG3-IG DMRs), liver (IGF2 and MEG3 DMRs) and placenta (both DLK1/MEG3 DMRs and NNAT DMR). In most infants, methylation profiles in buccal cells at birth and at one year of age were comparable, as was methylation in the major cell fractions of umbilical cord blood. Several infants showed temporal deviations in methylation at multiple DMRs. Similarity of inter-individual and intra-individual methylation at some, but not all of the DMRs analyzed supports the possibility that methylation of these regions can serve as useful biosensors of exposure.

Authors
Murphy, SK; Huang, Z; Hoyo, C
MLA Citation
Murphy, SK, Huang, Z, and Hoyo, C. "Differentially methylated regions of imprinted genes in prenatal, perinatal and postnatal human tissues." PLoS One 7.7 (2012): e40924-.
PMID
22808284
Source
pubmed
Published In
PloS one
Volume
7
Issue
7
Publish Date
2012
Start Page
e40924
DOI
10.1371/journal.pone.0040924

The Human Imprintome: Regulatory Mechanisms, Methods of Ascertainment, and Roles in Disease Susceptibility

Authors
Skaar, DA; Li, Y; Bernal, AJ; Hoyo, C; Murphy, SK; Jirtle, RL
MLA Citation
Skaar, DA, Li, Y, Bernal, AJ, Hoyo, C, Murphy, SK, and Jirtle, RL. "The Human Imprintome: Regulatory Mechanisms, Methods of Ascertainment, and Roles in Disease Susceptibility." ILAR JOURNAL 53.3-4 (2012): 341-358.
PMID
23744971
Source
wos-lite
Published In
ILAR Journal
Volume
53
Issue
3-4
Publish Date
2012
Start Page
341
End Page
358
DOI
10.1093/ilar.53.3-4.341

Ovarian cancer progenitor/stem cells: Therapeutic potential

A number of studies provide evidence for the existence of ovarian cancer stem cells, defined by functional attributes, foremost the ability to reconstruct the heterogeneity of the original tumor in immunocompromised mice through asymmetric cell division. As satisfying as the concept of an ovarian cancer stem cell is to explain the origins of ovarian cancer, can this concept be applied universally to explain the diversity in the histologic types of epithelial ovarian cancer? Can the unique features of an ovarian cancer stem cell population be exploited to therapeutically disarm these cells? Herein we explore these questions, beginning with a brief description of cancer stem cells in general and then turning more specifically to what is known about ovarian cancer stem cells. We then explore the potential for therapeutic targeting of these cells, and what the future holds for implementation of such approaches toward improving survival of women with ovarian cancer. © 2011 Springer Science+Business Media, LLC.

Authors
Murphy, SK; Berchuck, A
MLA Citation
Murphy, SK, and Berchuck, A. "Ovarian cancer progenitor/stem cells: Therapeutic potential." (December 1, 2011): 223-244. (Chapter)
Source
scopus
Publish Date
2011
Start Page
223
End Page
244
DOI
10.1007/978-1-4419-7216-3_11

Quantitative detection of RASSF1A DNA promoter methylation in tumors and serum of patients with serous epithelial ovarian cancer.

OBJECTIVE: Detection of cell free tumor-specific DNA methylation has been proposed as a potentially useful noninvasive mechanism to detect malignancies, including ovarian cancer, and to monitor response to treatment. However, there are few easily implemented quantitative approaches available for DNA methylation analysis. Our objectives were to develop an absolute quantitative method for detection of DNA methylation using RASSF1A, a known target of promoter methylation in ovarian cancer, and test the ability to detect RASSF1A methylation in tumors and serum specimens of women with ovarian cancer. METHODS: Bisulfite modified DNAs were subjected to real time PCR using nondiscriminatory PCR primers and a probe with sequence containing a single CpG site, theoretically able to capture the methylation status of that CpG for every allele within a given specimen. Input DNA was normalized to ACTB levels detected simultaneously by assay multiplexing. Methylation levels were established by comparison to results obtained from universally methylated DNA. RESULTS: The assay was able to detect one methylated RASSF1A allele in 100,000 unmethylated alleles. RASSF1A was methylated in 54 of 106 (51%) invasive serous ovarian cancers analyzed and methylation status was concordant in 20/20 matched preoperative serum-tumor pairs. Serial serum specimens taken over the course of treatment for 8 of 9 patients showed fluctuations in RASSF1A methylation concomitant with disease status. CONCLUSIONS: This novel assay provides a real-time PCR-based method for absolute quantitation of DNA methylation. Our results support feasibility of monitoring RASSF1A methylation from serum samples taken over the course of treatment from women with ovarian cancer.

Authors
Bondurant, AE; Huang, Z; Whitaker, RS; Simel, LR; Berchuck, A; Murphy, SK
MLA Citation
Bondurant, AE, Huang, Z, Whitaker, RS, Simel, LR, Berchuck, A, and Murphy, SK. "Quantitative detection of RASSF1A DNA promoter methylation in tumors and serum of patients with serous epithelial ovarian cancer." Gynecol Oncol 123.3 (December 2011): 581-587.
PMID
21955482
Source
pubmed
Published In
Gynecologic Oncology
Volume
123
Issue
3
Publish Date
2011
Start Page
581
End Page
587
DOI
10.1016/j.ygyno.2011.08.029

Distribution of HPV genotypes in cervical intraepithelial lesions and cervical cancer in Tanzanian women.

BACKGROUND: Infection with human papillomavirus (HPV) is associated with uterine cervical intraepithelial neoplasia (CIN) and invasive cancers (ICC). Approximately 80% of ICC cases are diagnosed in under-developed countries. Vaccine development relies on knowledge of HPV genotypes characteristic of LSIL, HSIL and cancer; however, these genotypes remain poorly characterized in many African countries. To contribute to the characterization of HPV genotypes in Northeastern Tanzania, we recruited 215 women from the Reproductive Health Clinic at Kilimanjaro Christian Medical Centre. Cervical scrapes and biopsies were obtained for cytology and HPV DNA detection. RESULTS: 79 out of 215 (36.7%) enrolled participants tested positive for HPV DNA, with a large proportion being multiple infections (74%). The prevalence of HPV infection increased with lesion grade (14% in controls, 67% in CIN1 cases and 88% in CIN2-3). Among ICC cases, 89% had detectable HPV. Overall, 31 HPV genotypes were detected; the three most common HPV genotypes among ICC were HPV16, 35 and 45. In addition to these genotypes, co-infection with HPV18, 31, 33, 52, 58, 68 and 82 was found in 91% of ICC. Among women with CIN2-3, HPV53, 58 and 84/83 were the most common. HPV35, 45, 53/58/59 were the most common among CIN1 cases. CONCLUSIONS: In women with no evidence of cytological abnormalities, the most prevalent genotypes were HPV58 with HPV16, 35, 52, 66 and 73 occurring equally. Although numerical constraints limit inference, findings that 91% of ICC harbor only a small number of HPV genotypes suggests that prevention efforts including vaccine development or adjuvant screening should focus on these genotypes.

Authors
Vidal, AC; Murphy, SK; Hernandez, BY; Vasquez, B; Bartlett, JA; Oneko, O; Mlay, P; Obure, J; Overcash, F; Smith, JS; van der Kolk, M; Hoyo, C
MLA Citation
Vidal, AC, Murphy, SK, Hernandez, BY, Vasquez, B, Bartlett, JA, Oneko, O, Mlay, P, Obure, J, Overcash, F, Smith, JS, van der Kolk, M, and Hoyo, C. "Distribution of HPV genotypes in cervical intraepithelial lesions and cervical cancer in Tanzanian women. (Published online)" Infect Agent Cancer 6.1 (November 14, 2011): 20-.
Website
http://hdl.handle.net/10161/5939
PMID
22081870
Source
pubmed
Published In
Infectious Agents and Cancer
Volume
6
Issue
1
Publish Date
2011
Start Page
20
DOI
10.1186/1750-9378-6-20

The regulation of MASPIN expression in epithelial ovarian cancer: association with p53 status, and MASPIN promoter methylation: a gynecologic oncology group study.

OBJECTIVES: To elucidate the regulation of MASPIN expression in epithelial ovarian cancer (EOC) and associations with p53 status and MASPIN promoter methylation. METHODS: Seven EOC cell lines and 110 advanced stage EOC specimens were analyzed for MASPIN promoter methylation. The cell lines were treated with 5-azacytidine (5-azaC) and evaluated for MASPIN promoter methylation, protein, and mRNA expression. Wild-type (wt) p53 was transiently transfected into the mutant p53 (m p53) SKOV3 cells which were treated with 5-azaC. Phosphor imager analysis quantified the percent methylation of the MASPIN promoter. RESULTS: Of the 3 MASPIN-low m p53 cell lines 2 had greater than 5% MASPIN methylation whereas only 1 of 4 MASPIN-high wt p53 cell lines had greater than 5% MASPIN methylation. Despite the presence of aberrant MASPIN promoter methylation in SKOV3 cells, wt p53-transfection alone resulted in a 3.3-fold increase in MASPIN mRNA. The combination of 5-azaC and wt p53-transfection produced a 36% reduction in MASPIN promoter methylation and 4.5-fold increase in MASPIN transcription. Among the 110 ovarian cancer specimens analyzed for methylation of the MASPIN promoter, 81.8% were weakly methylated, 14.5% were heavily methylated and 3.6% were fully methylated. There was no relationship between promoter methylation and p53 status or MASPIN protein expression. However, MASPIN protein was 6 times more likely to be detected in cancer specimens that harbor a p53 mutation relative to cancer specimens with a wt p53 gene. CONCLUSION: The regulation of MASPIN is a complex multifactorial process that may be controlled by both p53-dependent and -independent epigenetic mechanisms.

Authors
Alvarez Secord, A; Darcy, KM; Hutson, A; Huang, Z; Lee, PS; Jewell, EL; Havrilesky, LJ; Markman, M; Muggia, F; Murphy, SK
MLA Citation
Alvarez Secord, A, Darcy, KM, Hutson, A, Huang, Z, Lee, PS, Jewell, EL, Havrilesky, LJ, Markman, M, Muggia, F, and Murphy, SK. "The regulation of MASPIN expression in epithelial ovarian cancer: association with p53 status, and MASPIN promoter methylation: a gynecologic oncology group study." Gynecol Oncol 123.2 (November 2011): 314-319.
PMID
21903246
Source
pubmed
Published In
Gynecologic Oncology
Volume
123
Issue
2
Publish Date
2011
Start Page
314
End Page
319
DOI
10.1016/j.ygyno.2011.08.003

The effects of depression and use of antidepressive medicines during pregnancy on the methylation status of the IGF2 imprinted control regions in the offspring.

In utero exposures to environmental factors may result in persistent epigenetic modifications affecting normal development and susceptibility to chronic diseases in later life. We explored the relationship between exposure of the growing fetus to maternal depression or antidepressants and DNA methylation at two differentially methylated regions (DMRs) of the imprinted Insulin-like Growth Factor 2 (IGF2) gene. Aberrant DNA methylation at the IGF2 and neighboring H19 DMRs has been associated with deregulated IGF2 expression, childhood cancers and several chronic diseases during adulthood. Our study population is comprised of pregnant mothers and their newborns (n = 436), as part of the Newborn Epigenetics Study (NEST). A standardized questionnaire was completed and medical record data were abstracted to ascertain maternal depression and antidepressive drug use. DMR methylation levels in umbilical cord blood leukocytes were quantified using pyrosequencing. From the 436 newborns, laboratory data were obtained for 356 individuals at the IGF2 DMRs, and for 411 individuals at the H19 DMRs; about half of each group was African American or Caucasian. While overall no association between depression and methylation profiles was found, we observed a significant hypermethylation of the H19 DMRs in newborns of African American (n = 177) but not Caucasian (n = 168) mothers who reported the use of antidepressive drugs during pregnancy (β = +6.89, p = 0.01). Of note, our data reveal a race-independent association between smoking during pregnancy and methylation at the IGF2 DMR (+3.05%, p = 0.01). In conclusion, our findings suggest a race-dependent response related to maternal use of antidepressants at one of the IGF2 DMRs in the offspring.

Authors
Soubry, A; Murphy, S; Huang, Z; Murtha, A; Schildkraut, J; Jirtle, R; Wang, F; Kurtzberg, J; Demark-Wahnefried, W; Forman, M; Hoyo, C
MLA Citation
Soubry, A, Murphy, S, Huang, Z, Murtha, A, Schildkraut, J, Jirtle, R, Wang, F, Kurtzberg, J, Demark-Wahnefried, W, Forman, M, and Hoyo, C. "The effects of depression and use of antidepressive medicines during pregnancy on the methylation status of the IGF2 imprinted control regions in the offspring. (Published online)" Clin Epigenetics 3 (October 26, 2011): 2-.
PMID
22414206
Source
pubmed
Published In
Clinical Epigenetics
Volume
3
Publish Date
2011
Start Page
2
DOI
10.1186/1868-7083-3-2

Novel retrotransposed imprinted locus identified at human 6p25.

Differentially methylated regions (DMRs) are stable epigenetic features within or in proximity to imprinted genes. We used this feature to identify candidate human imprinted loci by quantitative DNA methylation analysis. We discovered a unique DMR at the 5'-end of FAM50B at 6p25.2. We determined that sense transcripts originating from the FAM50B locus are expressed from the paternal allele in all human tissues investigated except for ovary, in which expression is biallelic. Furthermore, an antisense transcript, FAM50B-AS, was identified to be monoallelically expressed from the paternal allele in a variety of tissues. Comparative phylogenetic analysis showed that FAM50B orthologs are absent in chicken and platypus, but are present and biallelically expressed in opossum and mouse. These findings indicate that FAM50B originated in Therians after divergence from Prototherians via retrotransposition of a gene on the X chromosome. Moreover, our data are consistent with acquisition of imprinting during Eutherian evolution after divergence of Glires from the Euarchonta mammals. FAM50B expression is deregulated in testicular germ cell tumors, and loss of imprinting occurs frequently in testicular seminomas, suggesting an important role for FAM50B in spermatogenesis and tumorigenesis. These results also underscore the importance of accounting for parental origin in understanding the mechanism of 6p25-related diseases.

Authors
Zhang, A; Skaar, DA; Li, Y; Huang, D; Price, TM; Murphy, SK; Jirtle, RL
MLA Citation
Zhang, A, Skaar, DA, Li, Y, Huang, D, Price, TM, Murphy, SK, and Jirtle, RL. "Novel retrotransposed imprinted locus identified at human 6p25." Nucleic Acids Res 39.13 (July 2011): 5388-5400.
PMID
21421564
Source
pubmed
Published In
Nucleic Acids Research
Volume
39
Issue
13
Publish Date
2011
Start Page
5388
End Page
5400
DOI
10.1093/nar/gkr108

Methylation variation at IGF2 differentially methylated regions and maternal folic acid use before and during pregnancy.

Folic acid (FA) supplementation before and during pregnancy has been associated with decreased risk of neural tube defects although recent reports suggest it may also increase the risk of other chronic diseases. We evaluated exposure to maternal FA supplementation before and during pregnancy in relation to aberrant DNA methylation at two differentially methylated regions (DMRs) regulating Insulin-like Growth Factor 2 (IGF2) expression in infants. Aberrant methylation at these regions has been associated with IGF2 deregulation and increased susceptibility to several chronic diseases. Using a self-administered questionnaire, we assessed FA intake before and during pregnancy in 438 pregnant women. Pyrosequencing was used to measure methylation at two IGF2 DMRs in umbilical cord blood leukocytes. Mixed models were used to determine relationships between maternal FA supplementation before or during pregnancy and DNA methylation levels at birth. Average methylation at the H19 DMR was 61.2%. Compared to infants born to women reporting no FA intake before or during pregnancy, methylation levels at the H19 DMR decreased with increasing FA intake (2.8%, p=0.03, and 4.9%, p=0.04, for intake before and during pregnancy, respectively). This methylation decrease was most pronounced in male infants (p=0.01). Methylation alterations at the H19 DMR are likely an important mechanism by which FA risks and/or benefits are conferred in utero. Because stable methylation marks at DMRs regulating imprinted genes are acquired before gastrulation, they may serve as archives of early exposures with the potential to improve our understanding of developmental origins of adult disease.

Authors
Hoyo, C; Murtha, AP; Schildkraut, JM; Jirtle, RL; Demark-Wahnefried, W; Forman, MR; Iversen, ES; Kurtzberg, J; Overcash, F; Huang, Z; Murphy, SK
MLA Citation
Hoyo, C, Murtha, AP, Schildkraut, JM, Jirtle, RL, Demark-Wahnefried, W, Forman, MR, Iversen, ES, Kurtzberg, J, Overcash, F, Huang, Z, and Murphy, SK. "Methylation variation at IGF2 differentially methylated regions and maternal folic acid use before and during pregnancy." Epigenetics 6.7 (July 2011): 928-936.
PMID
21636975
Source
pubmed
Published In
Epigenetics : official journal of the DNA Methylation Society
Volume
6
Issue
7
Publish Date
2011
Start Page
928
End Page
936

Abstract 3014: Quantitative accuracy of Illumina HumanMethylation27 Infinium BeadChip data assessed by pyrosequencing

Authors
Huang, Z; Yamaguchi, K; Berchuck, A; Murphy, SK
MLA Citation
Huang, Z, Yamaguchi, K, Berchuck, A, and Murphy, SK. "Abstract 3014: Quantitative accuracy of Illumina HumanMethylation27 Infinium BeadChip data assessed by pyrosequencing." Cancer Research 71.8 Supplement (April 15, 2011): 3014-3014.
Source
crossref
Published In
Cancer Research
Volume
71
Issue
8 Supplement
Publish Date
2011
Start Page
3014
End Page
3014
DOI
10.1158/1538-7445.AM2011-3014

Abstract 2754: Maternal use of antidepressants in pregnancy is associated with hypermethylation at the IGF2 imprinted control regions in the offspring in a race-dependent fashion

Authors
Soubry, A; Murphy, SK; Huang, Z; Murtha, A; Schildkraut, JM; Jirtle, RL; Wang, F; Kurtzberg, J; Demark-Wahnefried, W; Forman, M; Hoyo, C
MLA Citation
Soubry, A, Murphy, SK, Huang, Z, Murtha, A, Schildkraut, JM, Jirtle, RL, Wang, F, Kurtzberg, J, Demark-Wahnefried, W, Forman, M, and Hoyo, C. "Abstract 2754: Maternal use of antidepressants in pregnancy is associated with hypermethylation at the IGF2 imprinted control regions in the offspring in a race-dependent fashion." Cancer Research 71.8 Supplement (April 15, 2011): 2754-2754.
Source
crossref
Published In
Cancer Research
Volume
71
Issue
8 Supplement
Publish Date
2011
Start Page
2754
End Page
2754
DOI
10.1158/1538-7445.AM2011-2754

GPR54 is a target for suppression of metastasis in endometrial cancer.

Invasion into deep myometrium and/or lymphovascular space is a well-known risk factor for endometrial cancer metastasis, resulting in poor prognosis. It is therefore clinically important to identify novel molecules that suppress tumor invasion. Reduced expression of the metastasis suppressor, kisspeptin (KISS1), and its endogenous receptor, GPR54, has been reported in several cancers, but the significance of the KISS1/GPR54 axis in endometrial cancer metastasis has not been clarified. Metastin-10 is the minimal bioactive sequence of genetic products of KISS1. Clinicopathological analysis of 92 endometrial cancers revealed overall survival is improved in cancers with high expression of GPR54 (P < 0.05) and that GPR54 expression is associated with known prognostic factors including FIGO stage, grade, and deep myometrial invasion. Through RNAi and microarray analyses, metastin-10 was predicted to suppress metastasis of GPR54-expressing endometrial cancers in vivo. Methylation analysis revealed GPR54 is epigenetically regulated. Metastin-GPR54 axis function was restored following treatment with the DNA hypomethylating agent 5-aza-DC. These data suggest that metastin-10 may be effective at inhibiting the metastatic spread of endometrial cancers in combination with demethylating agents to induce GPR54 expression.

Authors
Kang, HS; Baba, T; Mandai, M; Matsumura, N; Hamanishi, J; Kharma, B; Kondoh, E; Yoshioka, Y; Oishi, S; Fujii, N; Murphy, SK; Konishi, I
MLA Citation
Kang, HS, Baba, T, Mandai, M, Matsumura, N, Hamanishi, J, Kharma, B, Kondoh, E, Yoshioka, Y, Oishi, S, Fujii, N, Murphy, SK, and Konishi, I. "GPR54 is a target for suppression of metastasis in endometrial cancer." Mol Cancer Ther 10.4 (April 2011): 580-590.
PMID
21282360
Source
pubmed
Published In
Molecular cancer therapeutics
Volume
10
Issue
4
Publish Date
2011
Start Page
580
End Page
590
DOI
10.1158/1535-7163.MCT-10-0763

Dasatinib (BMS-35482) has synergistic activity with paclitaxel and carboplatin in ovarian cancer cells.

PURPOSE: To explore the activity of dasatinib alone and in combination with paclitaxel and carboplatin in ovarian cancer cells and to determine if dasatinib activity can be predicted based on evaluation of the SRC pathway. EXPERIMENTAL DESIGN: Microarray analysis was performed for IGROV1, OVCAR3, A2780 and SKOV3 ovarian cancer cells and the status of the genomic SRC signature pathway was determined. Cells were treated with carboplatin, paclitaxel and dasatinib individually and in combination. Pre- and post-treatment phospho-SRC (pSRC) and SRC protein expression was determined. Dose-response curves were constructed, and drug interaction was assessed by the Combination Index (CI) method. RESULTS: SRC protein expression levels reflected the SRC pathway genomic signature in the cell lines with the lowest (SKOV3) and highest (IGROV1) pathway expression, but not in those with intermediate expression (OVCAR3, A2780). Dasatinib treatment caused loss of pSRC in all cell lines, with 50% growth inhibition for IGROV1 at 70 nM, OVCAR3 at 34 nM, A2780 at 4.1 μM and SKOV3 at 530 nM. Dasatinib combined with cytotoxics yielded a synergistic effect (CI=0.46 to 0.79) in all cell lines except SKOV3. CONCLUSION: Dasatinib in combination with standard chemotherapeutic agents appears to interact in a synergistic manner in some ovarian cancer cell lines. Further research is needed to evaluate tumor cell characteristics which predict response to dasatinib.

Authors
Teoh, D; Ayeni, TA; Rubatt, JM; Adams, DJ; Grace, L; Starr, MD; Barry, WT; Berchuck, A; Murphy, SK; Secord, AA
MLA Citation
Teoh, D, Ayeni, TA, Rubatt, JM, Adams, DJ, Grace, L, Starr, MD, Barry, WT, Berchuck, A, Murphy, SK, and Secord, AA. "Dasatinib (BMS-35482) has synergistic activity with paclitaxel and carboplatin in ovarian cancer cells." Gynecol Oncol 121.1 (April 2011): 187-192.
PMID
21208651
Source
pubmed
Published In
Gynecologic Oncology
Volume
121
Issue
1
Publish Date
2011
Start Page
187
End Page
192
DOI
10.1016/j.ygyno.2010.11.017

Folic acid supplementation before and during pregnancy in the Newborn Epigenetics STudy (NEST).

BACKGROUND: Folic acid (FA) added to foods during fortification is 70-85% bioavailable compared to 50% of folate occurring naturally in foods. Thus, if FA supplements also are taken during pregnancy, both mother and fetus can be exposed to FA exceeding the Institute of Medicine's recommended tolerable upper limit (TUL) of 1,000 micrograms per day (μg/d) for adult pregnant women. The primary objective is to estimate the proportion of women taking folic acid (FA) doses exceeding the TUL before and during pregnancy, and to identify correlates of high FA use. METHODS: During 2005-2008, pre-pregnancy and pregnancy-related data on dietary supplementation were obtained by interviewing 539 pregnant women enrolled at two obstetrics-care facilities in Durham County, North Carolina. RESULTS: Before pregnancy, 51% of women reported FA supplementation and 66% reported this supplementation during pregnancy. Before pregnancy, 11.9% (95% CI = 9.2%-14.6%) of women reported supplementation with FA doses above the TUL of 1,000 μg/day, and a similar proportion reported this intake prenatally. Before pregnancy, Caucasian women were more likely to take FA doses above the TUL (OR = 2.99; 95% = 1.28-7.00), compared to African American women, while women with chronic conditions were less likely to take FA doses above the TUL (OR = 0.48; 95%CI = 0.21-0.97). Compared to African American women, Caucasian women were also more likely to report FA intake in doses exceeding the TUL during pregnancy (OR = 5.09; 95%CI = 2.07-12.49). CONCLUSIONS: Fifty-one percent of women reported some FA intake before and 66% during pregnancy, respectively, and more than one in ten women took FA supplements in doses that exceeded the TUL. Caucasian women were more likely to report high FA intake. A study is ongoing to identify possible genetic and non-genotoxic effects of these high doses.

Authors
Hoyo, C; Murtha, AP; Schildkraut, JM; Forman, MR; Calingaert, B; Demark-Wahnefried, W; Kurtzberg, J; Jirtle, RL; Murphy, SK
MLA Citation
Hoyo, C, Murtha, AP, Schildkraut, JM, Forman, MR, Calingaert, B, Demark-Wahnefried, W, Kurtzberg, J, Jirtle, RL, and Murphy, SK. "Folic acid supplementation before and during pregnancy in the Newborn Epigenetics STudy (NEST). (Published online)" BMC Public Health 11.1 (January 21, 2011): 46-.
PMID
21255390
Source
pubmed
Published In
BMC Public Health
Volume
11
Issue
1
Publish Date
2011
Start Page
46
DOI
10.1186/1471-2458-11-46

Epigenetic suppression of the TGF-beta pathway revealed by transcriptome profiling in ovarian cancer.

Epithelial ovarian cancer is the leading cause of death among gynecologic malignancies. Diagnosis usually occurs after metastatic spread, largely reflecting vague symptoms of early disease combined with lack of an effective screening strategy. Epigenetic mechanisms of gene regulation, including DNA methylation, are fundamental to normal cellular function and also play a major role in carcinogenesis. To elucidate the biological and clinical relevance of DNA methylation in ovarian cancer, we conducted expression microarray analysis of 39 cell lines and 17 primary culture specimens grown in the presence or absence of DNA methyltransferase (DNMT) inhibitors. Two parameters, induction of expression and standard deviation among untreated samples, identified 378 candidate methylated genes, many relevant to TGF-beta signaling. We analyzed 43 of these genes and they all exhibited methylation. Treatment with DNMT inhibitors increased TGF-beta pathway activity. Hierarchical clustering of ovarian cancers using the 378 genes reproducibly generated a distinct gene cluster strongly correlated with TGF-beta pathway activity that discriminates patients based on age. These data suggest that accumulation of age-related epigenetic modifications leads to suppression of TGF-beta signaling and contributes to ovarian carcinogenesis.

Authors
Matsumura, N; Huang, Z; Mori, S; Baba, T; Fujii, S; Konishi, I; Iversen, ES; Berchuck, A; Murphy, SK
MLA Citation
Matsumura, N, Huang, Z, Mori, S, Baba, T, Fujii, S, Konishi, I, Iversen, ES, Berchuck, A, and Murphy, SK. "Epigenetic suppression of the TGF-beta pathway revealed by transcriptome profiling in ovarian cancer." Genome Res 21.1 (January 2011): 74-82.
PMID
21156726
Source
pubmed
Published In
Genome research
Volume
21
Issue
1
Publish Date
2011
Start Page
74
End Page
82
DOI
10.1101/gr.108803.110

Mouse models of epigenetic inheritance

This chapter discusses the mouse models of epigenetic inheritance. The increasing evidence implicates epigenetic changes as a primary impetus in disease development. The epigenetic regulation alters gene expression to promote compensatory adjustments in metabolism. These early adaptive epigenetic changes have consequences later in life when the metabolic changes no longer coincide with the external environment, resulting in pathologies such as coronary heart disease and obesity. The abnormal paternal epigenetic inheritance indicates that another epigenetic mark aside from DNA methylation is incompletely cleared in the heterozygous knockout offspring and leads to epigenetic inheritance and phenotypic change. Mouse models have become powerful tools for examining transgenerational inheritance of epigenetic marks as well as unique biosensors for early developmental exposures to nutritional supplements and chemical contaminants that disrupt epigenetic programming. With the increased utility of these models, our understanding of epigenetic mark inheritance at metastable epialleles and imprinted genes, and across the genome, will expand. As the model is more completely defined, the possibilities increase for their expanded use to address a broad array of research questions involved in complex human disease such as diabetes, neurological disorders, and cancer. © 2011 Elsevier Inc. All rights reserved.

Authors
Bernal, AJ; Murphy, SK; Jirtle, RL
MLA Citation
Bernal, AJ, Murphy, SK, and Jirtle, RL. "Mouse models of epigenetic inheritance." Handbook of Epigenetics (2011): 233-249.
Source
scival
Published In
Handbook of Epigenetics
Publish Date
2011
Start Page
233
End Page
249
DOI
10.1016/B978-0-12-375709-8.00015-0

Sorafenib efficacy in ovarian clear cell carcinoma revealed by transcriptome profiling.

The purpose of this study was to investigate a new modality of therapy against ovarian clear cell carcinoma (OCCC), a chemoresistant subtype of ovarian cancer. Microarray datasets of ovarian cancer cell lines and cancer tissues were analyzed using bioinformatic tools. The gene expression profile of OCCC was similar to that of renal cell carcinoma (RCC). This similarity was at least partially due to hepatocyte nuclear factor 1 pathway activation common to both malignancies. In addition, oncogenic pathway alterations were characteristic of OCCC including hypoxia inducible factor 1 alpha subunit and relatively high Ras activities. Therefore, we predicted that the multi-kinase inhibitor sorafenib, which is approved for RCC and suppresses Ras activity, would also be effective against OCCC. Orally administered sorafenib (40 mg/kg per day) significantly inhibited tumor growth in nude mice when it was given after inoculation with the OCCC cell line RMG-2 (P = 0.002). Furthermore, sorafenib significantly reduced tumor size when it was administered to established RMG-2 tumors (P = 0.0002), while intraperitoneal injection of cisplatin (5 mg/kg per week) did not. In conclusion, the prominent anti-tumor effect of sorafenib against OCCC indicates that sorafenib is a promising candidate drug and supports the need for clinical trials using sorafenib against OCCC. This report demonstrates a method to utilize genome-wide information to facilitate translational research for treatments against less common subtypes of cancers.

Authors
Matsumura, N; Mandai, M; Okamoto, T; Yamaguchi, K; Yamamura, S; Oura, T; Baba, T; Hamanishi, J; Kang, HS; Matsui, S; Mori, S; Murphy, SK; Konishi, I
MLA Citation
Matsumura, N, Mandai, M, Okamoto, T, Yamaguchi, K, Yamamura, S, Oura, T, Baba, T, Hamanishi, J, Kang, HS, Matsui, S, Mori, S, Murphy, SK, and Konishi, I. "Sorafenib efficacy in ovarian clear cell carcinoma revealed by transcriptome profiling." Cancer Sci 101.12 (December 2010): 2658-2663.
PMID
21040214
Source
pubmed
Published In
Cancer Science
Volume
101
Issue
12
Publish Date
2010
Start Page
2658
End Page
2663
DOI
10.1111/j.1349-7006.2010.01736.x

Expression signatures of TP53 mutations in serous ovarian cancers.

BACKGROUND: Mutations in the TP53 gene are extremely common and occur very early in the progression of serous ovarian cancers. Gene expression patterns that relate to mutational status may provide insight into the etiology and biology of the disease. METHODS: The TP53 coding region was sequenced in 89 frozen serous ovarian cancers, 40 early stage (I/II) and 49 advanced stage (III/IV). Affymetrix U133A expression data was used to define gene expression patterns by mutation, type of mutation, and cancer stage. RESULTS: Missense or chain terminating (null) mutations in TP53 were found in 59/89 (66%) ovarian cancers. Early stage cancers had a significantly higher rate of null mutations than late stage disease (38% vs. 8%, p < 0.03). In advanced stage cases, mutations were more prevalent in short term survivors than long term survivors (81% vs. 30%, p = 0.0004). Gene expression patterns had a robust ability to predict TP53 status within training data. By using early versus late stage disease for out of sample predictions, the signature derived from early stage cancers could accurately (86%) predict mutation status of late stage cancers. CONCLUSIONS: This represents the first attempt to define a genomic signature of TP53 mutation in ovarian cancer. Patterns of gene expression characteristic of TP53 mutation could be discerned and included several genes that are known p53 targets or have been described in the context of expression signatures of TP53 mutation in breast cancer.

Authors
Bernardini, MQ; Baba, T; Lee, PS; Barnett, JC; Sfakianos, GP; Secord, AA; Murphy, SK; Iversen, E; Marks, JR; Berchuck, A
MLA Citation
Bernardini, MQ, Baba, T, Lee, PS, Barnett, JC, Sfakianos, GP, Secord, AA, Murphy, SK, Iversen, E, Marks, JR, and Berchuck, A. "Expression signatures of TP53 mutations in serous ovarian cancers. (Published online)" BMC Cancer 10 (May 26, 2010): 237-.
Website
http://hdl.handle.net/10161/4356
PMID
20504346
Source
pubmed
Published In
BMC Cancer
Volume
10
Publish Date
2010
Start Page
237
DOI
10.1186/1471-2407-10-237

Targeting slow-proliferating ovarian cancer cells.

Advanced ovarian cancer has a high rate of recurrence and mortality despite relative chemosensitivity at the time of initial treatment. Conventional chemotherapeutic agents typically target rapidly dividing cells. Disease relapse may therefore result from the survival and later emergence of latent slow-proliferating and/or quiescent cancer cells. We sought to identify drugs that target this cell population and to investigate the influence of these cells on outcome of patients in remission from advanced ovarian cancer. Drugs with increased efficacy against slower proliferating cells were identified using correlation-based screening of 44,657 compounds tested on the NCI-60 panel of cancer cell lines. Validation of candidates was performed in comparison with Cisplatin or Paclitaxel and by manipulation of proliferation rates by serum deprivation. Cytostatic and cytocidal effects were evaluated using MTT assays and active caspase-3 immunocytochemistry. Ki-67 proliferation indices were determined for tumors from 104 patients in remission. UCN-01 efficacy was correlated with longer doubling time among the NCI-60 cell lines (R = 0.54, p < 0.0001) and in a panel of 24 ovarian cancer cell lines (R = 0.42, p = 0.04), whereas this was not the case for Cisplatin (R = -0.10, p = 0.65) and Paclitaxel efficacy correlated with shorter doubling time (R = -0.52, p = 0.009). Cytostatic and cytocidal effects of UCN-01 were increased in serum-deprived cells. A low proliferation index was associated with presence of persistent disease at second-look surgery (p = 0.01) and poor survival (disease-free survival, p = 0.002; overall survival, p = 0.04). These results suggest that targeting quiescent ovarian cancer cells may be a worthwhile therapeutic approach to improving survival of women with ovarian cancer.

Authors
Kondoh, E; Mori, S; Yamaguchi, K; Baba, T; Matsumura, N; Cory Barnett, J; Whitaker, RS; Konishi, I; Fujii, S; Berchuck, A; Murphy, SK
MLA Citation
Kondoh, E, Mori, S, Yamaguchi, K, Baba, T, Matsumura, N, Cory Barnett, J, Whitaker, RS, Konishi, I, Fujii, S, Berchuck, A, and Murphy, SK. "Targeting slow-proliferating ovarian cancer cells." Int J Cancer 126.10 (May 15, 2010): 2448-2456.
PMID
19795452
Source
pubmed
Published In
International Journal of Cancer
Volume
126
Issue
10
Publish Date
2010
Start Page
2448
End Page
2456
DOI
10.1002/ijc.24919

Identification of an ovarian clear cell carcinoma gene signature that reflects inherent disease biology and the carcinogenic processes.

Ovarian clear cell carcinoma (OCCC) shows unique clinical features including an association with endometriosis and poor prognosis. We previously reported that the contents of endometriotic cysts, especially high concentrations of free iron, are a possible cause of OCCC carcinogenesis through iron-induced persistent oxidative stress. In this study, we conducted gene expression microarray analysis using 38 ovarian cancer cell lines and identified genes commonly expressed in both OCCC cell lines and clinical samples, which comprise an OCCC gene signature. The OCCC signature reproducibly predicts OCCC specimens in other microarray data sets, suggesting that this gene profile reflects the inherent biological characteristics of OCCC. The OCCC signature contains known markers of OCCC, such as hepatocyte nuclear factor-1beta (HNF-1beta) and versican (VCAN), and other genes that reflect oxidative stress. Expression of OCCC signature genes was induced by treatment of immortalized ovarian surface epithelial cells with the contents of endometriotic cysts, indicating that the OCCC signature is largely dependent on the tumor microenvironment. Induction of OCCC signature genes is at least in part epigenetically regulated, as we found hypomethylation of HNF-1beta and VCAN in OCCC cell lines. This genome-wide study indicates that the tumor microenvironment induces specific gene expression profiles that contribute to the development of distinct cancer subtypes.

Authors
Yamaguchi, K; Mandai, M; Oura, T; Matsumura, N; Hamanishi, J; Baba, T; Matsui, S; Murphy, SK; Konishi, I
MLA Citation
Yamaguchi, K, Mandai, M, Oura, T, Matsumura, N, Hamanishi, J, Baba, T, Matsui, S, Murphy, SK, and Konishi, I. "Identification of an ovarian clear cell carcinoma gene signature that reflects inherent disease biology and the carcinogenic processes." Oncogene 29.12 (March 25, 2010): 1741-1752.
PMID
20062075
Source
pubmed
Published In
Oncogene: Including Oncogene Reviews
Volume
29
Issue
12
Publish Date
2010
Start Page
1741
End Page
1752
DOI
10.1038/onc.2009.470

Elevated MAL expression is accompanied by promoter hypomethylation and platinum resistance in epithelial ovarian cancer.

We previously found that the gene encoding the Myelin and Lymphocyte protein, MAL, was among the most highly expressed genes in serous ovarian cancers from short-term survivors (<3 years) relative to those of long-term survivors (>7 years). In the present study, we have found that this difference in expression is partially attributable to differences in DNA methylation at a specific region within the MAL promoter CpG island. While MAL was largely unmethylated at the transcription start site (Region 1; -48 to +73 bp) in primary serous ovarian cancers, methylation of an upstream region (Region 2; -452 to -266 bp) was inversely correlated with MAL transcription in the primary cancers (R = -0.463) and ovarian cancer cell lines (R = -0.444). Following treatment of the OVCA432 cell line with 5-azacytidine, methylation of Region 2 decreased from 73.3% to 34.7% (p = 0.007) while Region 1 was unaffected. This was accompanied by a 10-fold increase in MAL expression. Since MAL transcripts are elevated in tumors from short-term survivors, all of whom were treated with platinum-based therapy, MAL may have a role in cisplatin response. We therefore determined the 50% growth inhibitory dose of cisplatin in 30 ovarian cancer cell lines and compared this to MAL expression. MAL transcript levels were higher in the resistant ovarian cell lines (p = 0.04). MAL methylation status may therefore serve as a marker of platinum sensitivity while MAL protein may be a target for development of novel therapies aimed at enhancing sensitivity to platinum-based drugs in ovarian cancer.

Authors
Lee, PS; Teaberry, VS; Bland, AE; Huang, Z; Whitaker, RS; Baba, T; Fujii, S; Secord, AA; Berchuck, A; Murphy, SK
MLA Citation
Lee, PS, Teaberry, VS, Bland, AE, Huang, Z, Whitaker, RS, Baba, T, Fujii, S, Secord, AA, Berchuck, A, and Murphy, SK. "Elevated MAL expression is accompanied by promoter hypomethylation and platinum resistance in epithelial ovarian cancer." Int J Cancer 126.6 (March 15, 2010): 1378-1389.
PMID
19642140
Source
pubmed
Published In
International Journal of Cancer
Volume
126
Issue
6
Publish Date
2010
Start Page
1378
End Page
1389
DOI
10.1002/ijc.24797

Ovarian cancer tumor infiltrating T-regulatory (T(reg)) cells are associated with a metastatic phenotype.

OBJECTIVE: The objective of this study was to examine the clinicopathologic correlates of T-regulatory (T(reg)) cell infiltration in serous ovarian cancers and to define gene signatures associated with high T(reg)s. METHODS: Tumor infiltrating T(reg) and cytotoxic T-cells (CTLs) were quantitated in 232 primary serous ovarian cancers by immunostaining for FOXP3 and CD8. Expression microarray analysis was performed in a subset of 48 advanced cancers with the highest and lowest numbers of infiltrating T(reg)s and a genomic signature was developed using binary regression. ANOVA analysis was performed to assess the most differentially expressed genes and these genes were further assessed using Ingenuity Pathway Analysis (IPA) software. RESULTS: High T(reg) infiltration in ovarian cancers was associated with high grade (p<0.0001), advanced stage (p=0.004) and suboptimal debulking (p<0.04), but not with survival. In contrast, high tumor infiltrating CD8 CTL infiltration was associated with favorable survival (median survival 48.7 vs. 34.6 months, p=0.01). A microarray-based genomic signature for high tumor-infiltrating T(reg) cells had a 77% predictive accuracy using leave-one-out cross-validation. ANOVA of microarray data revealed the antigen presentation pathway as the most differentially expressed canonical pathway (p<0.00001) between cancers with high and low T(reg) cells. CONCLUSIONS: These data suggest that there may be an association between increased T(reg) cell infiltration in ovarian cancers and advanced stage. Increased T(reg) infiltration is characterized by a genomic signature enriched with several immunologic pathway genes. Therapeutic strategies that reduce tumor infiltrating T(reg) cells are under investigation and may prove useful in ovarian cancers with high numbers of these cells.

Authors
Barnett, JC; Bean, SM; Whitaker, RS; Kondoh, E; Baba, T; Fujii, S; Marks, JR; Dressman, HK; Murphy, SK; Berchuck, A
MLA Citation
Barnett, JC, Bean, SM, Whitaker, RS, Kondoh, E, Baba, T, Fujii, S, Marks, JR, Dressman, HK, Murphy, SK, and Berchuck, A. "Ovarian cancer tumor infiltrating T-regulatory (T(reg)) cells are associated with a metastatic phenotype." Gynecol Oncol 116.3 (March 2010): 556-562.
PMID
20006900
Source
pubmed
Published In
Gynecologic Oncology
Volume
116
Issue
3
Publish Date
2010
Start Page
556
End Page
562
DOI
10.1016/j.ygyno.2009.11.020

Targeting ovarian cancer-initiating cells.

Evidence supports that a variety of cancers are sparked by the growth of cells that exhibit characteristics of stem cells. Such cancer-initiating cells are capable of populating a tumor with a heterogeneous group of daughter cells while still maintaining the ability to self-renew. Several groups have recently reported the identification of cancer-initiating cells in ovarian cancer, the most lethal gynecologic malignancy. Epithelial ovarian cancer comprises 90% of cancers of the ovary and consists of four major histologic types, each bearing some resemblance to tissues in the peritoneal cavity. Although epithelial ovarian cancer has traditionally been thought to originate from the single layer of cells surrounding each ovary, new findings suggest that many of these cancers derive from Müllerian epithelium. This raises questions about the origin of ovarian cancer-initiating cells, and if there may be more than one source. Despite the initial effectiveness of primary therapy against advanced stage ovarian cancer, most of these cases recur, months to years following diagnosis. The cause of disease recurrence is unknown, but may involve cancer-initiating cells that survive chemotherapy and enter a period of dormancy while residing in as-yet undefined niches within the body before being triggered to initiate renewed growth. Herein the nature of these cells is explored as well as novel approaches for therapeutic targeting.

Authors
Murphy, SK
MLA Citation
Murphy, SK. "Targeting ovarian cancer-initiating cells." Anticancer Agents Med Chem 10.2 (February 2010): 157-163. (Review)
PMID
20184540
Source
pubmed
Published In
Anti-Cancer Agents in Medicinal Chemistry
Volume
10
Issue
2
Publish Date
2010
Start Page
157
End Page
163

High poly(adenosine diphosphate-ribose) polymerase expression and poor survival in advanced-stage serous ovarian cancer.

OBJECTIVE: To estimate the range of poly(adenosine diphosphate [ADP]-ribose) polymerase expression in serous ovarian cancers and to determine whether expression is associated with response to therapy and outcome. METHODS: Immunostaining for poly(ADP-ribose) polymerase was performed in 186 paraffin-embedded, serous ovarian cancers. Nuclear poly(ADP-ribose) polymerase expression was quantified using a scoring system that assesses both staining intensity and percentage of cells staining. Kaplan-Meier analysis was performed to evaluate the relationship between poly(ADP-ribose) polymerase expression and overall survival. RESULTS: High poly(ADP-ribose) polymerase expression was present in 54% of serous cancers but was not associated with stage or grade. There was no difference in the rate of complete clinical response to primary chemotherapy between cases with low poly(ADP-ribose) polymerase expression (70%) compared with those with high poly(ADP-ribose) polymerase expression (71%). However, high poly(ADP-ribose) polymerase expression was associated with significantly worse median overall survival (36 compared with 43 months, P=.04, hazard ratio 0.71). CONCLUSION: Expression of poly(ADP-ribose) polymerase in ovarian cancers is heterogeneous, and high expression in serous ovarian cancers is associated with worse overall survival. These data suggest that evaluation of poly(ADP-ribose) polymerase expression in the primary cancer could potentially allow selective use of poly(ADP-ribose) polymerase inhibitors in patients most likely to respond. LEVEL OF EVIDENCE: III.

Authors
Barnett, JC; Bean, SM; Nakayama, JM; Kondoh, E; Murphy, SK; Berchuck, A
MLA Citation
Barnett, JC, Bean, SM, Nakayama, JM, Kondoh, E, Murphy, SK, and Berchuck, A. "High poly(adenosine diphosphate-ribose) polymerase expression and poor survival in advanced-stage serous ovarian cancer." Obstet Gynecol 115.1 (January 2010): 49-54.
PMID
20027033
Source
pubmed
Published In
Obstetrics and Gynecology
Volume
115
Issue
1
Publish Date
2010
Start Page
49
End Page
54
DOI
10.1097/AOG.0b013e3181c2d294

IGF2R polymorphisms and risk of esophageal and gastric adenocarcinomas.

The mannose-6-phosphate/insulin-like growth factor 2 receptor (M6P/IGF2R) encodes a protein that plays a critical role in tumor suppression, in part by modulating bioavailability of a potent mitogen, insulin-like growth factor-2 (IGF2). We tested the hypothesis that the common nonsynonymous genetic variants in M6P/IGF2R c.901C > G (Leu > Val) in exon 6 and c.5002G > A (Gly > Arg) in exon 34 are associated with risk of esophageal and gastric cancers. Study participants in this population-based study comprise 197 controls and 182 cases, including 105 with esophageal-gastric cardia adenocarcinoma (EGA), 57 with noncardia gastric adenocarcinoma and 20 with esophageal squamous (ES) cell carcinoma. Among white males, odds ratios (ORs) were elevated in relation to carrying at least 1 c.901C > G allele for EGA [OR = 1.9; 95% confidence intervals (CIs) = 1.0-3.6] and noncardia gastric cancer (OR = 2.5; 95% CI = 1.2-5.5), but not ES. Exploratory subgroup analyses suggested that associations between EGA and this variant were stronger among irregular or nonusers of nonsteroidal anti-inflammatory drugs (NSAIDs) (OR = 2.3; 95% CI = 1.2-4.2) and cigarette smokers (OR = 2.1; 95% CI = 1.0-4.2). An association between carrying the c.5002G > A genotype and EGA was not evident. These findings suggest that nonsynonymous polymorphisms in M6P/IGF2R may contribute to the risks of EGA and noncardia adenocarcinomas. Larger studies are required to confirm these findings.

Authors
Hoyo, C; Schildkraut, JM; Murphy, SK; Chow, W-H; Vaughan, TL; Risch, H; Marks, JR; Jirtle, RL; Calingaert, B; Mayne, S; Fraumeni, J; Gammon, MD
MLA Citation
Hoyo, C, Schildkraut, JM, Murphy, SK, Chow, W-H, Vaughan, TL, Risch, H, Marks, JR, Jirtle, RL, Calingaert, B, Mayne, S, Fraumeni, J, and Gammon, MD. "IGF2R polymorphisms and risk of esophageal and gastric adenocarcinomas." Int J Cancer 125.11 (December 1, 2009): 2673-2678.
PMID
19626700
Source
pubmed
Published In
International Journal of Cancer
Volume
125
Issue
11
Publish Date
2009
Start Page
2673
End Page
2678
DOI
10.1002/ijc.24623

Genomic and epigenetic evidence for oxytocin receptor deficiency in autism.

BACKGROUND: Autism comprises a spectrum of behavioral and cognitive disturbances of childhood development and is known to be highly heritable. Although numerous approaches have been used to identify genes implicated in the development of autism, less than 10% of autism cases have been attributed to single gene disorders. METHODS: We describe the use of high-resolution genome-wide tilepath microarrays and comparative genomic hybridization to identify copy number variants within 119 probands from multiplex autism families. We next carried out DNA methylation analysis by bisulfite sequencing in a proband and his family, expanding this analysis to methylation analysis of peripheral blood and temporal cortex DNA of autism cases and matched controls from independent datasets. We also assessed oxytocin receptor (OXTR) gene expression within the temporal cortex tissue by quantitative real-time polymerase chain reaction (PCR). RESULTS: Our analysis revealed a genomic deletion containing the oxytocin receptor gene, OXTR (MIM accession no.: 167055), previously implicated in autism, was present in an autism proband and his mother who exhibits symptoms of obsessive-compulsive disorder. The proband's affected sibling did not harbor this deletion but instead may exhibit epigenetic misregulation of this gene through aberrant gene silencing by DNA methylation. Further DNA methylation analysis of the CpG island known to regulate OXTR expression identified several CpG dinucleotides that show independent statistically significant increases in the DNA methylation status in the peripheral blood cells and temporal cortex in independent datasets of individuals with autism as compared to control samples. Associated with the increase in methylation of these CpG dinucleotides is our finding that OXTR mRNA showed decreased expression in the temporal cortex tissue of autism cases matched for age and sex compared to controls. CONCLUSION: Together, these data provide further evidence for the role of OXTR and the oxytocin signaling pathway in the etiology of autism and, for the first time, implicate the epigenetic regulation of OXTR in the development of the disorder.See the related commentary by Gurrieri and Neri: http://www.biomedcentral.com/1741-7015/7/63.

Authors
Gregory, SG; Connelly, JJ; Towers, AJ; Johnson, J; Biscocho, D; Markunas, CA; Lintas, C; Abramson, RK; Wright, HH; Ellis, P; Langford, CF; Worley, G; Delong, GR; Murphy, SK; Cuccaro, ML; Persico, A; Pericak-Vance, MA
MLA Citation
Gregory, SG, Connelly, JJ, Towers, AJ, Johnson, J, Biscocho, D, Markunas, CA, Lintas, C, Abramson, RK, Wright, HH, Ellis, P, Langford, CF, Worley, G, Delong, GR, Murphy, SK, Cuccaro, ML, Persico, A, and Pericak-Vance, MA. "Genomic and epigenetic evidence for oxytocin receptor deficiency in autism. (Published online)" BMC Med 7 (October 22, 2009): 62-.
PMID
19845972
Source
pubmed
Published In
BMC Medicine
Volume
7
Publish Date
2009
Start Page
62
DOI
10.1186/1741-7015-7-62

Imprint regulatory elements as epigenetic biosensors of exposure in epidemiological studies.

Authors
Hoyo, C; Murphy, SK; Jirtle, RL
MLA Citation
Hoyo, C, Murphy, SK, and Jirtle, RL. "Imprint regulatory elements as epigenetic biosensors of exposure in epidemiological studies." J Epidemiol Community Health 63.9 (September 2009): 683-684.
PMID
19679714
Source
pubmed
Published In
Journal of Epidemiology and Community Health
Volume
63
Issue
9
Publish Date
2009
Start Page
683
End Page
684
DOI
10.1136/jech.2009.090803

Anchorage-independent cell growth signature identifies tumors with metastatic potential.

The oncogenic phenotype is complex, resulting from the accumulation of multiple somatic mutations that lead to the deregulation of growth regulatory and cell fate controlling activities and pathways. The ability to dissect this complexity, so as to reveal discrete aspects of the biology underlying the oncogenic phenotype, is critical to understanding the various mechanisms of disease as well as to reveal opportunities for novel therapeutic strategies. Previous work has characterized the process of anchorage-independent growth of cancer cells in vitro as a key aspect of the tumor phenotype, particularly with respect to metastatic potential. Nevertheless, it remains a major challenge to translate these cell biology findings into the context of human tumors. We previously used DNA microarray assays to develop expression signatures, which have the capacity to identify subtle distinctions in biological states and can be used to connect in vitro and in vivo states. Here we describe the development of a signature of anchorage-independent growth, show that the signature exhibits characteristics of deregulated mitochondrial function and then demonstrate that the signature identifies human tumors with the potential for metastasis.

Authors
Mori, S; Chang, JT; Andrechek, ER; Matsumura, N; Baba, T; Yao, G; Kim, JW; Gatza, M; Murphy, S; Nevins, JR
MLA Citation
Mori, S, Chang, JT, Andrechek, ER, Matsumura, N, Baba, T, Yao, G, Kim, JW, Gatza, M, Murphy, S, and Nevins, JR. "Anchorage-independent cell growth signature identifies tumors with metastatic potential." Oncogene 28.31 (August 6, 2009): 2796-2805.
PMID
19483725
Source
pubmed
Published In
Oncogene: Including Oncogene Reviews
Volume
28
Issue
31
Publish Date
2009
Start Page
2796
End Page
2805
DOI
10.1038/onc.2009.139

MLH1 expression sensitises ovarian cancer cells to cell death mediated by XIAP inhibition.

BACKGROUND: The X-linked inhibitor of apoptosis protein (XIAP), an endogenous apoptosis suppressor, can determine the level of caspase accumulation and the resultant response to apoptosis-inducing agents such as cisplatin in epithelial ovarian cancer (EOC). In addition, the mismatch repair protein, hMLH1, has been linked to DNA damage-induced apoptosis by cisplatin by both p53-dependent and -independent mechanisms. METHODS: In this study, hMLH1 expression was correlated with clinical response to platinum drugs and survival in advanced stage (III-IV) EOC patients. We then investigated whether MLH1 loss was a determinant in anti-apoptosis response to cisplatin mediated by XIAP in isogenic and established EOC cell lines with differential p53 status. RESULTS: The percentage of cells undergoing cisplatin-induced cell killing was higher in MLH1-proficient cells than in MLH1-defective cells. In addition, the presence of wild-type hMLH1 or hMLH1 re-expression significantly increased sensitivity to 6-thioguanine, a MMR-dependent agent. Cell-death response to 6-thioguanine and cisplatin was associated with significant proteolysis of MLH1, with XIAP destabilisation and increased caspase-3 activity. The siRNA-mediated inhibition of XIAP increased MLH1 proteolysis and cell death in MLH1-proficient cells but not in MLH1-defective cells. CONCLUSION: These data suggest that XIAP inhibitors may prove to be an effective means of sensitising EOC to MLH1-dependent apoptosis.

Authors
Ding, X; Mohd, AB; Huang, Z; Baba, T; Bernardini, MQ; Lyerly, HK; Berchuck, A; Murphy, SK; Buermeyer, AB; Devi, GR
MLA Citation
Ding, X, Mohd, AB, Huang, Z, Baba, T, Bernardini, MQ, Lyerly, HK, Berchuck, A, Murphy, SK, Buermeyer, AB, and Devi, GR. "MLH1 expression sensitises ovarian cancer cells to cell death mediated by XIAP inhibition." Br J Cancer 101.2 (July 21, 2009): 269-277.
PMID
19603033
Source
pubmed
Published In
British Journal of Cancer
Volume
101
Issue
2
Publish Date
2009
Start Page
269
End Page
277
DOI
10.1038/sj.bjc.6605180

CTCF binding at a novel intragenic binding site is associated with elevated IGF2 expression in serous epithelial ovarian cancer

Authors
Huang, Z; Wen, Y; Simel, L; Price, T; Berchuck, A; Murphy, SK
MLA Citation
Huang, Z, Wen, Y, Simel, L, Price, T, Berchuck, A, and Murphy, SK. "CTCF binding at a novel intragenic binding site is associated with elevated IGF2 expression in serous epithelial ovarian cancer." CANCER RESEARCH 69 (May 1, 2009).
Source
wos-lite
Published In
Cancer Research
Volume
69
Publish Date
2009

Microarray analysis of early stage serous ovarian cancers shows profiles predictive of favorable outcome.

PURPOSE: Although few women with advanced serous ovarian cancer are cured, detection of the disease at an early stage is associated with a much higher likelihood of survival. We previously used gene expression array analysis to distinguish subsets of advanced cancers based on disease outcome. In the present study, we report on gene expression of early-stage cancers and validate our prognostic model for advanced-stage cancers. EXPERIMENTAL DESIGN: Frozen specimens from 39 stage I/II, 42 stage III/IV, and 20 low malignant potential cancers were obtained from four different sites. A linear discriminant model was used to predict survival based upon array data. RESULTS: We validated the late-stage survival model and show that three of the most differentially expressed genes continue to be predictive of outcome. Most early-stage cancers (38 of 39 invasive, 15 of 20 low malignant potential) were classified as long-term survivors (median probabilities 0.97 and 0.86). MAL, the most differentially expressed gene, was further validated at the protein level and found to be an independent predictor of poor survival in an unselected group of advanced serous cancers (P = 0.0004). CONCLUSIONS: These data suggest that serous ovarian cancers detected at an early stage generally have a favorable underlying biology similar to advanced-stage cases that are long-term survivors. Conversely, most late-stage ovarian cancers seem to have a more virulent biology. This insight suggests that if screening approaches are to succeed it will be necessary to develop approaches that are able to detect these virulent cancers at an early stage.

Authors
Berchuck, A; Iversen, ES; Luo, J; Clarke, JP; Horne, H; Levine, DA; Boyd, J; Alonso, MA; Secord, AA; Bernardini, MQ; Barnett, JC; Boren, T; Murphy, SK; Dressman, HK; Marks, JR; Lancaster, JM
MLA Citation
Berchuck, A, Iversen, ES, Luo, J, Clarke, JP, Horne, H, Levine, DA, Boyd, J, Alonso, MA, Secord, AA, Bernardini, MQ, Barnett, JC, Boren, T, Murphy, SK, Dressman, HK, Marks, JR, and Lancaster, JM. "Microarray analysis of early stage serous ovarian cancers shows profiles predictive of favorable outcome." Clin Cancer Res 15.7 (April 1, 2009): 2448-2455.
PMID
19318476
Source
pubmed
Published In
Clinical cancer research : an official journal of the American Association for Cancer Research
Volume
15
Issue
7
Publish Date
2009
Start Page
2448
End Page
2455
DOI
10.1158/1078-0432.CCR-08-2430

Stress affects uterine receptivity through an ovarian-independent pathway.

BACKGROUND: Although stress is known to disturb natural fertility through the inhibition of the hypothalamic-pituitary-gonadal (HPG) axis, the impact of stress on infertile women who receive exogenous gonadal hormones is not well defined. This is probably due to lack of experimental models for evaluating the impacts of stress through an ovarian-independent pathway. The objective of this study was to investigate the possible impact of stress on uterine receptivity, independent of HPG axis dysfunction, using a mouse implantation model maintained with hormone supplementation. METHODS: Blastocysts from donor mice were transferred into the uterine lumen of ovariectomized (OVX) Balb/c female recipient mice following supplementation with estradiol and progesterone. The recipients were divided into two groups: those exposed (stress group) or not exposed (control group) to intermittent sonic exposure prior to embryo transfer (ET). The number of implantation sites (IS) was compared between these groups. Microarray analysis was performed to elucidate stress-induced molecular alterations in uteri during the implantation period. Sequential gene expression of leukemia inhibitory factor (Lif), an estradiol-inducible gene, was also analyzed using real-time PCR. RESULTS: A non-mating OVX model with satisfactory implantation rates was established. The number of IS in the stress group (n = 20) was significantly less than that in the control group (n = 18) (Mann-Whitney test, P = 0.0375). Implantation-related genes and ovarian-hormone-responsive genes were repressed in the stress group despite ovarian hormone supplementation. The expression of Lif was suppressed in the stress group. CONCLUSIONS: Stress can cause decreased uterine receptivity through an ovarian-independent pathway.

Authors
Kondoh, E; Okamoto, T; Higuchi, T; Tatsumi, K; Baba, T; Murphy, SK; Takakura, K; Konishi, I; Fujii, S
MLA Citation
Kondoh, E, Okamoto, T, Higuchi, T, Tatsumi, K, Baba, T, Murphy, SK, Takakura, K, Konishi, I, and Fujii, S. "Stress affects uterine receptivity through an ovarian-independent pathway." Hum Reprod 24.4 (April 2009): 945-953.
PMID
19098291
Source
pubmed
Published In
Human Reproduction
Volume
24
Issue
4
Publish Date
2009
Start Page
945
End Page
953
DOI
10.1093/humrep/den461

Methylation of THBS1, the Gene Encoding Thrombospondin-1 in Uterine Fibroids and Myometrium

Authors
Murphy, SK; Jayes, FL; Feng, L; Huang, Z; Leppert, PC
MLA Citation
Murphy, SK, Jayes, FL, Feng, L, Huang, Z, and Leppert, PC. "Methylation of THBS1, the Gene Encoding Thrombospondin-1 in Uterine Fibroids and Myometrium." March 2009.
Source
wos-lite
Published In
Reproductive Sciences
Volume
16
Issue
3
Publish Date
2009
Start Page
214A
End Page
214A

Altered IGF2/H19 Imprint Center Methylation in Uterine Fibroids but Not in Adjacent Myometrium

Authors
Murphy, SK; Jayes, FL; Feng, L; Huang, Z; Leppert, PC
MLA Citation
Murphy, SK, Jayes, FL, Feng, L, Huang, Z, and Leppert, PC. "Altered IGF2/H19 Imprint Center Methylation in Uterine Fibroids but Not in Adjacent Myometrium." March 2009.
Source
wos-lite
Published In
Reproductive Sciences
Volume
16
Issue
3
Publish Date
2009
Start Page
216A
End Page
216A

Inactivation of the MAL gene in breast cancer is a common event that predicts benefit from adjuvant chemotherapy.

Dysregulation of MAL (myelin and lymphocyte protein) has been implicated in several malignancies including esophageal, ovarian, and cervical cancers. The MAL protein functions in apical transport in polarized epithelial cells; therefore, its disruption may lead to loss of organized polarity characteristic of most solid malignancies. Bisulfite sequencing of the MAL promoter CpG island revealed hypermethylation in breast cancer cell lines and 69% of primary tumors analyzed compared with normal breast epithelial cells. Differential methylation between normal and cancer DNA was confined to the proximal promoter region. In a subset of breast cancer cell lines including T47D and MCF7 cells, promoter methylation correlated with transcriptional silencing that was reversible with the methylation inhibitor 5-aza-2'-deoxycytidine. In addition, expression of MAL reduced motility and resulted in a redistribution of lipid raft components in MCF10A cells. MAL protein expression measured by immunohistochemistry revealed no significant correlation with clinicopathologic features. However, in patients who did not receive adjuvant chemotherapy, reduced MAL expression was a significant predictive factor for disease-free survival. These data implicate MAL as a commonly altered gene in breast cancer with implications for response to chemotherapy.

Authors
Horne, HN; Lee, PS; Murphy, SK; Alonso, MA; Olson, JA; Marks, JR
MLA Citation
Horne, HN, Lee, PS, Murphy, SK, Alonso, MA, Olson, JA, and Marks, JR. "Inactivation of the MAL gene in breast cancer is a common event that predicts benefit from adjuvant chemotherapy." Mol Cancer Res 7.2 (February 2009): 199-209.
PMID
19208741
Source
pubmed
Published In
Molecular cancer research : MCR
Volume
7
Issue
2
Publish Date
2009
Start Page
199
End Page
209
DOI
10.1158/1541-7786.MCR-08-0314

Yin yang 1 modulates taxane response in epithelial ovarian cancer.

Survival of ovarian cancer patients is largely dictated by their response to chemotherapy, which depends on underlying molecular features of the malignancy. We previously identified YIN YANG 1 (YY1) as a gene whose expression is positively correlated with ovarian cancer survival. Herein, we investigated the mechanistic basis of this association. Epigenetic and genetic characteristics of YY1 in serous epithelial ovarian cancer were analyzed along with YY1 mRNA and protein. Patterns of gene expression in primary serous epithelial ovarian cancer and in the NCI60 database were investigated using computational methods. YY1 function and modulation of chemotherapeutic response in vitro was studied using small interfering RNA knockdown. Microarray analysis showed strong positive correlation between expression of YY1 and genes with YY1 and transcription factor E2F binding motifs in ovarian cancer and in the NCI60 cancer cell lines. Clustering of microarray data for these genes revealed that high YY1/E2F3 activity positively correlates with survival of patients treated with the microtubule-stabilizing drug paclitaxel. Increased sensitivity to taxanes, but not to DNA cross-linking platinum agents, was also characteristic of NCI60 cancer cell lines with a high YY1/E2F signature. YY1 knockdown in ovarian cancer cell lines results in inhibition of anchorage-independent growth, motility, and proliferation but also increases resistance to taxanes, with no effect on cisplatin sensitivity. These results, together with the prior demonstration of augmentation of microtubule-related genes by E2F3, suggest that enhanced taxane sensitivity in tumors with high YY1/E2F activity may be mediated by modulation of putative target genes with microtubule function.

Authors
Matsumura, N; Huang, Z; Baba, T; Lee, PS; Barnett, JC; Mori, S; Chang, JT; Kuo, W-L; Gusberg, AH; Whitaker, RS; Gray, JW; Fujii, S; Berchuck, A; Murphy, SK
MLA Citation
Matsumura, N, Huang, Z, Baba, T, Lee, PS, Barnett, JC, Mori, S, Chang, JT, Kuo, W-L, Gusberg, AH, Whitaker, RS, Gray, JW, Fujii, S, Berchuck, A, and Murphy, SK. "Yin yang 1 modulates taxane response in epithelial ovarian cancer." Mol Cancer Res 7.2 (February 2009): 210-220.
PMID
19208743
Source
pubmed
Published In
Molecular cancer research : MCR
Volume
7
Issue
2
Publish Date
2009
Start Page
210
End Page
220
DOI
10.1158/1541-7786.MCR-08-0255

High poly (ADP-ribose) polymerase (PARP) expression is associated with poor survival in advanced-stage serous ovarian cancer

Authors
Barnett, JC; Kondoh, E; Whitaker, R; Murphy, SK; Berchuck, A
MLA Citation
Barnett, JC, Kondoh, E, Whitaker, R, Murphy, SK, and Berchuck, A. "High poly (ADP-ribose) polymerase (PARP) expression is associated with poor survival in advanced-stage serous ovarian cancer." GYNECOLOGIC ONCOLOGY 112.2 (February 2009): S107-S107.
Source
wos-lite
Published In
Gynecologic Oncology
Volume
112
Issue
2
Publish Date
2009
Start Page
S107
End Page
S107

7-hydroxystaurosporine (UCN-01) is effective in targeting ovarian cancer spheroids

Authors
Kondoh, E; Baba, T; Malsumura, N; Konishi, I; Fujii, S; Berchuck, A; Murphy, SK
MLA Citation
Kondoh, E, Baba, T, Malsumura, N, Konishi, I, Fujii, S, Berchuck, A, and Murphy, SK. "7-hydroxystaurosporine (UCN-01) is effective in targeting ovarian cancer spheroids." GYNECOLOGIC ONCOLOGY 112.2 (February 2009): S161-S162.
Source
wos-lite
Published In
Gynecologic Oncology
Volume
112
Issue
2
Publish Date
2009
Start Page
S161
End Page
S162

Gene signature specific for ovarian clear cell carcinoma is induced by the contents of endometriotic cysts

Authors
Yamaguchi, K; Mandai, M; Matsumura, N; Baba, T; Oura, T; Matsui, S; Murphy, SK; Berchuck, A; Fujii, S; Konishi, I
MLA Citation
Yamaguchi, K, Mandai, M, Matsumura, N, Baba, T, Oura, T, Matsui, S, Murphy, SK, Berchuck, A, Fujii, S, and Konishi, I. "Gene signature specific for ovarian clear cell carcinoma is induced by the contents of endometriotic cysts." GYNECOLOGIC ONCOLOGY 112.2 (February 2009): S132-S132.
Source
wos-lite
Published In
Gynecologic Oncology
Volume
112
Issue
2
Publish Date
2009
Start Page
S132
End Page
S132

Ovarian cancer tumor-infiltrating regulatory T cells are associated with a metastatic phenotype

Authors
Barnett, JC; Whitaker, R; Kondoh, E; Baba, T; Murphy, SK; Berchuck, A
MLA Citation
Barnett, JC, Whitaker, R, Kondoh, E, Baba, T, Murphy, SK, and Berchuck, A. "Ovarian cancer tumor-infiltrating regulatory T cells are associated with a metastatic phenotype." GYNECOLOGIC ONCOLOGY 112.2 (February 2009): S11-S11.
Source
wos-lite
Published In
Gynecologic Oncology
Volume
112
Issue
2
Publish Date
2009
Start Page
S11
End Page
S11

Loss of GPR54 correlates with stem cell activity in high-grade endometrial cancer

Authors
Baba, T; Kang, HS; Matsumura, N; Hamanishi, J; Mandai, M; Berchuck, A; Murphy, SK; Konishi, I
MLA Citation
Baba, T, Kang, HS, Matsumura, N, Hamanishi, J, Mandai, M, Berchuck, A, Murphy, SK, and Konishi, I. "Loss of GPR54 correlates with stem cell activity in high-grade endometrial cancer." GYNECOLOGIC ONCOLOGY 112.2 (February 2009): S78-S78.
Source
wos-lite
Published In
Gynecologic Oncology
Volume
112
Issue
2
Publish Date
2009
Start Page
S78
End Page
S78

Intragenic methylation at a novel CTCF binding site is associated with elevated IGF2 expression in serous epithelial ovarian cancer

Authors
Murphy, SK; Huang, Z; Wen, Y; Simel, LR; Price, TM; Berchuck, A
MLA Citation
Murphy, SK, Huang, Z, Wen, Y, Simel, LR, Price, TM, and Berchuck, A. "Intragenic methylation at a novel CTCF binding site is associated with elevated IGF2 expression in serous epithelial ovarian cancer." GYNECOLOGIC ONCOLOGY 112.2 (February 2009): S138-S138.
Source
wos-lite
Published In
Gynecologic Oncology
Volume
112
Issue
2
Publish Date
2009
Start Page
S138
End Page
S138

Validation of the MAL gene as a predictor of survival in advanced-stage high-grade serous ovarian cancer

Authors
Barnett, JC; Iverson, E; Dressman, H; Whitaker, R; Murphy, SK; Lancaster, J; Berchuck, A
MLA Citation
Barnett, JC, Iverson, E, Dressman, H, Whitaker, R, Murphy, SK, Lancaster, J, and Berchuck, A. "Validation of the MAL gene as a predictor of survival in advanced-stage high-grade serous ovarian cancer." GYNECOLOGIC ONCOLOGY 112.2 (February 2009): S123-S124.
Source
wos-lite
Published In
Gynecologic Oncology
Volume
112
Issue
2
Publish Date
2009
Start Page
S123
End Page
S124

Imprinted Neuronatin: A potential epigenetie biomarker of ovarian cancer

Authors
Murphy, SK; Chen, L
MLA Citation
Murphy, SK, and Chen, L. "Imprinted Neuronatin: A potential epigenetie biomarker of ovarian cancer." GYNECOLOGIC ONCOLOGY 112.2 (February 2009): S135-S135.
Source
wos-lite
Published In
Gynecologic Oncology
Volume
112
Issue
2
Publish Date
2009
Start Page
S135
End Page
S135

MiRNA patterns in ovarian cancer cell lines: Correlation with serum studies

Authors
Resnick, KE; Alder, H; Secord, AA; Whitaker, R; Richardson, DL; Heaphy, C; Murphy, SK; Baba, T; Croce, C; Colin, DE
MLA Citation
Resnick, KE, Alder, H, Secord, AA, Whitaker, R, Richardson, DL, Heaphy, C, Murphy, SK, Baba, T, Croce, C, and Colin, DE. "MiRNA patterns in ovarian cancer cell lines: Correlation with serum studies." GYNECOLOGIC ONCOLOGY 112.2 (February 2009): S115-S116.
Source
wos-lite
Published In
Gynecologic Oncology
Volume
112
Issue
2
Publish Date
2009
Start Page
S115
End Page
S116

Epigenetic regulation of CD133 and tumorigenicity of CD133+ ovarian cancer cells.

The cancer stem cell hypothesis posits that malignant growth arises from a rare population of progenitor cells within a tumor that provide it with unlimited regenerative capacity. Such cells also possess increased resistance to chemotherapeutic agents. Resurgence of chemoresistant disease after primary therapy typifies epithelial ovarian cancer and may be attributable to residual cancer stem cells, or cancer-initiating cells, that survive initial treatment. As the cell surface marker CD133 identifies cancer-initiating cells in a number of other malignancies, we sought to determine the potential role of CD133+ cells in epithelial ovarian cancer. We detected CD133 on ovarian cancer cell lines, in primary cancers and on purified epithelial cells from ascitic fluid of ovarian cancer patients. We found CD133+ ovarian cancer cells generate both CD133+ and CD133- daughter cells, whereas CD133- cells divide symmetrically. CD133+ cells exhibit enhanced resistance to platinum-based therapy, drugs commonly used as first-line agents for the treatment of ovarian cancer. Sorted CD133+ ovarian cancer cells also form more aggressive tumor xenografts at a lower inoculum than their CD133- progeny. Epigenetic changes may be integral to the behavior of cancer progenitor cells and their progeny. In this regard, we found that CD133 transcription is controlled by both histone modifications and promoter methylation. Sorted CD133- ovarian cancer cells treated with DNA methyltransferase and histone deacetylase inhibitors show a synergistic increase in cell surface CD133 expression. Moreover, DNA methylation at the ovarian tissue active P2 promoter is inversely correlated with CD133 transcription. We also found that promoter methylation increases in CD133- progeny of CD133+ cells, with CD133+ cells retaining a less methylated or unmethylated state. Taken together, our results show that CD133 expression in ovarian cancer is directly regulated by epigenetic modifications and support the idea that CD133 demarcates an ovarian cancer-initiating cell population. The activity of these cells may be epigenetically detected and such cells might serve as pertinent chemotherapeutic targets for reducing disease recurrence.

Authors
Baba, T; Convery, PA; Matsumura, N; Whitaker, RS; Kondoh, E; Perry, T; Huang, Z; Bentley, RC; Mori, S; Fujii, S; Marks, JR; Berchuck, A; Murphy, SK
MLA Citation
Baba, T, Convery, PA, Matsumura, N, Whitaker, RS, Kondoh, E, Perry, T, Huang, Z, Bentley, RC, Mori, S, Fujii, S, Marks, JR, Berchuck, A, and Murphy, SK. "Epigenetic regulation of CD133 and tumorigenicity of CD133+ ovarian cancer cells." Oncogene 28.2 (January 15, 2009): 209-218.
PMID
18836486
Source
pubmed
Published In
Oncogene: Including Oncogene Reviews
Volume
28
Issue
2
Publish Date
2009
Start Page
209
End Page
218
DOI
10.1038/onc.2008.374

Stem cell marker CD133 (PROMININ-1) is epigenetically regulated in ovarian cancer

Authors
Baba, T; Convery, PA; Matsumura, N; Whitaker, RS; Perry, T; Huang, Z; Mori, S; Kondoh, E; Bentley, RC; Fujii, S; Marks, JR; Berchuck, A; Murphy, SK
MLA Citation
Baba, T, Convery, PA, Matsumura, N, Whitaker, RS, Perry, T, Huang, Z, Mori, S, Kondoh, E, Bentley, RC, Fujii, S, Marks, JR, Berchuck, A, and Murphy, SK. "Stem cell marker CD133 (PROMININ-1) is epigenetically regulated in ovarian cancer." March 2008.
Source
wos-lite
Published In
Gynecologic Oncology
Volume
108
Issue
3
Publish Date
2008
Start Page
S104
End Page
S104

Targeting dormant ovarian cancer cells

Authors
Kondoh, E; Baba, T; Matsurnura, N; Fujii, S; Berchuck, A; Murphy, SK
MLA Citation
Kondoh, E, Baba, T, Matsurnura, N, Fujii, S, Berchuck, A, and Murphy, SK. "Targeting dormant ovarian cancer cells." GYNECOLOGIC ONCOLOGY 108.3 (March 2008): S13-S14.
Source
wos-lite
Published In
Gynecologic Oncology
Volume
108
Issue
3
Publish Date
2008
Start Page
S13
End Page
S14

Methylation in ovarian cancer is related to poor prognosis and suppression of the transforming growth factor signaling pathway

Authors
Matsumura, N; Huang, Z; Perry, T; Kroyer, D; Baba, T; Mori, S; Fujii, S; Berchuck, A; Murphy, SK
MLA Citation
Matsumura, N, Huang, Z, Perry, T, Kroyer, D, Baba, T, Mori, S, Fujii, S, Berchuck, A, and Murphy, SK. "Methylation in ovarian cancer is related to poor prognosis and suppression of the transforming growth factor signaling pathway." GYNECOLOGIC ONCOLOGY 108.3 (March 2008): S104-S104.
Source
wos-lite
Published In
Gynecologic Oncology
Volume
108
Issue
3
Publish Date
2008
Start Page
S104
End Page
S104

Microarray analysis defines patterns of gene expression associated with mutation of TP53 in ovarian cancer

Authors
Bernardini, MQ; Lee, P; Baba, T; Whitaker, RS; Murphy, SK; Berchuck, A
MLA Citation
Bernardini, MQ, Lee, P, Baba, T, Whitaker, RS, Murphy, SK, and Berchuck, A. "Microarray analysis defines patterns of gene expression associated with mutation of TP53 in ovarian cancer." GYNECOLOGIC ONCOLOGY 108.3 (March 2008): S84-S84.
Source
wos-lite
Published In
Gynecologic Oncology
Volume
108
Issue
3
Publish Date
2008
Start Page
S84
End Page
S84

Microarray analysis identifies NSC668814 as a potentially active chemotherapeutic agent for platinum-resistant ovarian cancers with TP53 mutations

Authors
Baba, T; Mori, S; Matsumura, N; Bernardini, M; Fujii, S; Berchuck, A; Murphy, SK
MLA Citation
Baba, T, Mori, S, Matsumura, N, Bernardini, M, Fujii, S, Berchuck, A, and Murphy, SK. "Microarray analysis identifies NSC668814 as a potentially active chemotherapeutic agent for platinum-resistant ovarian cancers with TP53 mutations." GYNECOLOGIC ONCOLOGY 108.3 (March 2008): S72-S72.
Source
wos-lite
Published In
Gynecologic Oncology
Volume
108
Issue
3
Publish Date
2008
Start Page
S72
End Page
S72

MAL, a gene associated with survival in epithelial ovarian cancer, is epigenetically regulated

Authors
Lee, PS; Teaberry, V; Bland, AE; Huang, Z; Secord, AA; Berchuck, A; Murphy, SK
MLA Citation
Lee, PS, Teaberry, V, Bland, AE, Huang, Z, Secord, AA, Berchuck, A, and Murphy, SK. "MAL, a gene associated with survival in epithelial ovarian cancer, is epigenetically regulated." GYNECOLOGIC ONCOLOGY 108.3 (March 2008): S125-S125.
Source
wos-lite
Published In
Gynecologic Oncology
Volume
108
Issue
3
Publish Date
2008
Start Page
S125
End Page
S125

Stem cell marker CD133 (PROMININ-1) is epigenetically regulated in ovarian cancer

Authors
Baba, T; Convey, P; Matsumura, N; Whitaker, RS; Perry, T; Huang, Z; Mori, S; Kondoh, E; Bentley, RC; Fujii, S; Berchuck, A; Murphy, SK; Marks, JR
MLA Citation
Baba, T, Convey, P, Matsumura, N, Whitaker, RS, Perry, T, Huang, Z, Mori, S, Kondoh, E, Bentley, RC, Fujii, S, Berchuck, A, Murphy, SK, and Marks, JR. "Stem cell marker CD133 (PROMININ-1) is epigenetically regulated in ovarian cancer." 2008.
Source
wos-lite
Published In
Cancer biomarkers : section A of Disease markers
Volume
4
Issue
3
Publish Date
2008
Start Page
175
End Page
176

Imprinted expression of the canine IGF2R, in the absence of an anti-sense transcript or promoter methylation.

Imprinted genes are epigenetically modified in a parent of origin-dependent manner, and as a consequence, are differentially expressed. Although the evolution of genomic imprinting is a subject of intense debate, imprinted genes have been studied primarily in mice and humans and in a small number of marsupial mammals. Comparative studies involving rodents and primates are of limited value, as they belong to the same superordinal group of eutherian mammals (Euarchontoglires). On the other hand, comparisons involving marsupials may not be informative, due to phylogenetic distance. Canis familiaris belongs to Laurasiatheria, a sister-group of Euarchontoglires, and should prove useful in comparative studies of imprinted genes. Using RT-PCR we demonstrate monoallelic expression of the canine IGF2R in several tissues, including uterus and umbilical cord. In the case of umbilical cord, we identify the expressed allele as maternally derived. The canine IGF2R is thus an imprinted gene. Using bisulfite sequencing, we show that the canine IGF2R resembles the imprinted mouse Igf2r in having a CpG island in intron 2 that is hemi-methylated. However, it differs from the mouse gene in that maintenance of the monoallelic expression of canine IGF2R does not require expression of an anti-sense transcript from the paternally derived allele, or methylation of the repressed IGF2R promoter. In these two important features, the imprinted canine gene resembles the imprinted opossum IGF2R. Our data suggest that these features were properties of the ancestral imprinted IGF2R and that the anti-sense transcript (Air) and promoter methylation observed in mouse are derived features of the mouse Igf2r locus.

Authors
O'Sullivan, FM; Murphy, SK; Simel, LR; McCann, A; Callanan, JJ; Nolan, CM
MLA Citation
O'Sullivan, FM, Murphy, SK, Simel, LR, McCann, A, Callanan, JJ, and Nolan, CM. "Imprinted expression of the canine IGF2R, in the absence of an anti-sense transcript or promoter methylation." Evol Dev 9.6 (November 2007): 579-589.
PMID
17976054
Source
pubmed
Published In
Evolution and Development
Volume
9
Issue
6
Publish Date
2007
Start Page
579
End Page
589
DOI
10.1111/j.1525-142X.2007.00198.x

Trophinin is a potent prognostic marker of ovarian cancer involved in platinum sensitivity.

Ovarian cancer is the leading cause of death in women with gynecological malignancies, with prognosis of advanced stage tumors determined by chemotherapeutic response and the success of tumor resection. Since aberrant RAS pathway activation is frequent in ovarian cancer, study of in vitro RAS-induced transformation and accompanying genomic expression changes in ovarian surface epithelial cells is imperative for development of new therapeutic modalities and for understanding tumorigenesis. cDNA microarray analysis revealed TROPHONIN (TRO), a homophilic adhesion molecule involved in blastocyst implantation, was among the genes most downregulated by RAS induction. TRO expression is higher in cisplatin-sensitive cancer cell lines and positively correlates with prognoses in ovarian cancers. TRO knockdown by RNA interference conferred cisplatin resistance and led to increased invasiveness of cultured ovarian cancer cells. These findings underscore the importance of TRO in tumorigenesis, and suggest that TRO may be a useful biomarker for cisplatin sensitivity and invasive potential.

Authors
Baba, T; Mori, S; Matsumura, N; Kariya, M; Murphy, SK; Kondoh, E; Kusakari, T; Kuroda, H; Mandai, M; Higuchi, T; Takakura, K; Fukuda, MN; Fujii, S
MLA Citation
Baba, T, Mori, S, Matsumura, N, Kariya, M, Murphy, SK, Kondoh, E, Kusakari, T, Kuroda, H, Mandai, M, Higuchi, T, Takakura, K, Fukuda, MN, and Fujii, S. "Trophinin is a potent prognostic marker of ovarian cancer involved in platinum sensitivity." Biochem Biophys Res Commun 360.2 (August 24, 2007): 363-369.
PMID
17597582
Source
pubmed
Published In
Biochemical and Biophysical Research Communications
Volume
360
Issue
2
Publish Date
2007
Start Page
363
End Page
369
DOI
10.1016/j.bbrc.2007.06.070

Loss of betaglycan expression in ovarian cancer: role in motility and invasion.

The transforming growth factor-beta (TGF-beta) superfamily members, TGF-beta, activin, and inhibin, all have prominent roles in regulating normal ovarian function. Betaglycan, or the type III TGF-beta receptor, is a coreceptor that regulates TGF-beta, activin, and inhibin signaling. Here, we show that betaglycan expression is frequently decreased or lost in epithelial derived ovarian cancer at both the mRNA and protein level, with the degree of loss correlating with tumor grade. Treatment of ovarian cancer cell lines with the methyltransferase inhibitor 5-aza-2-deoxycytidine and the histone deacetylase inhibitor trichostatin A resulted in significant synergistic induction of betaglycan message levels and increased betaglycan protein expression, indicating that epigenetic silencing may play a role in the loss of betaglycan expression observed in ovarian cancer. Although restoring betaglycan expression in Ovca429 ovarian cancer cells is not sufficient to restore TGF-beta-mediated inhibition of proliferation, betaglycan significantly inhibits ovarian cancer cell motility and invasiveness. Furthermore, betaglycan specifically enhances the antimigratory effects of inhibin and the ability of inhibin to repress matrix metalloproteinase levels in these cells. These results show, for the first time, epigenetic regulation of betaglycan expression in ovarian cancer, and a novel role for betaglycan in regulating ovarian cancer motility and invasiveness.

Authors
Hempel, N; How, T; Dong, M; Murphy, SK; Fields, TA; Blobe, GC
MLA Citation
Hempel, N, How, T, Dong, M, Murphy, SK, Fields, TA, and Blobe, GC. "Loss of betaglycan expression in ovarian cancer: role in motility and invasion." Cancer Res 67.11 (June 1, 2007): 5231-5238.
PMID
17522389
Source
pubmed
Published In
Cancer Research
Volume
67
Issue
11
Publish Date
2007
Start Page
5231
End Page
5238
DOI
10.1158/0008-5472.CAN-07-0035

Regulation of the metastasis suppressor gene MKK4 in ovarian cancer.

OBJECTIVES: MKK4 is a metastasis suppressor that is downregulated in some ovarian cancers. We sought to investigate whether promoter methylation, loss of heterozygosity, or changes in phosphorylation are involved in MKK4 dysregulation during ovarian carcinogenesis. METHODS: Bisulfite sequencing was used to determine MKK4 promoter methylation. PCR analysis of tumor/normal DNA was performed to determine LOH at the MKK4 locus. Normal human ovarian surface epithelium (HOSE) and SKOV-3 cells were serum starved and treated with EGF, TGFbeta, or wortmannin. Western blotting was performed using antibodies that detect total and phosphorylated MKK4. RESULTS: No MKK4 promoter hypermethylation was detected in 21 ovarian cancers. LOH was detected at the MKK4 intragenic marker D17S969 in 35% of cases and at D17S1303 in 20%. MKK4 protein was detected in 97% of ovarian tumors. The inactivated phosphoserine 80 (ser-80) form comprised 62% of phosphorylated MKK4 protein in ovarian tumors. Treatment of HOSE or SKOV-3 cells with EGF induced a 1.7- to 4.2-fold increase in phosphorylation of ser-80 MKK4 without altering total MKK4 protein. TGFbeta increased MKK4 ser-80 phosphorylation by 5.4-fold above baseline. The PI3K/Akt pathway inhibitor wortmannin decreased the amount of ser-80 MKK4 by 50%, and inhibited EGF stimulation of MKK4 ser-80 phosphorylation by 60%. CONCLUSIONS: LOH of MKK4 occurs in some ovarian cancers, but without loss of MKK4 protein. MKK4 expression does not appear to be downregulated by promoter methylation. Peptide growth factors induce MKK4 ser-80 phosphorylation, which downregulates its activity. PI3K/Akt pathway inhibitors can partially block ser-80 phosphorylation and this may have therapeutic implications.

Authors
Spillman, MA; Lacy, J; Murphy, SK; Whitaker, RS; Grace, L; Teaberry, V; Marks, JR; Berchuck, A
MLA Citation
Spillman, MA, Lacy, J, Murphy, SK, Whitaker, RS, Grace, L, Teaberry, V, Marks, JR, and Berchuck, A. "Regulation of the metastasis suppressor gene MKK4 in ovarian cancer." Gynecol Oncol 105.2 (May 2007): 312-320.
PMID
17276500
Source
pubmed
Published In
Gynecologic Oncology
Volume
105
Issue
2
Publish Date
2007
Start Page
312
End Page
320
DOI
10.1016/j.ygyno.2006.12.017

Perspectives: the possible influence of assisted reproductive technologies on transgenerational reproductive effects of environmental endocrine disruptors.

Demasculinization by environmental endocrine-disrupting chemicals (EDCs) is observed in many animal species but less evident in humans. Rodent studies with gestational exposure to either the fungicide vinclozolin or the insecticide methoxychlor demonstrate impaired male fertility with abnormal DNA methylation patterns in spermatozoa. Once established, these epigenetic changes may be permanent and thus paternally passed to subsequent generations. Conclusive evidence of a similar phenomenon in humans has not been established, but several observations bring up the possibility. Some, but not all, studies show an increase in male genital abnormalities after prenatal EDC exposure. Other studies demonstrate sperm abnormalities in males with EDC contact, although it is unclear as to whether this is due to prenatal or postnatal exposure. Although not examined in males with EDC exposure, one study shows gamete DNA methylation abnormalities in males with severe oligospermia. A subsequent study failed to corroborate these findings. The use of assisted reproductive techniques including intracytoplasmic sperm injection has removed natural selection barriers thus enabling reproduction in males that would otherwise be sterile. This review explores the hypothesis that prenatal EDC exposure results in transgenerational male reproductive abnormalities propagated by the use of assisted reproductive technologies.

Authors
Price, TM; Murphy, SK; Younglai, EV
MLA Citation
Price, TM, Murphy, SK, and Younglai, EV. "Perspectives: the possible influence of assisted reproductive technologies on transgenerational reproductive effects of environmental endocrine disruptors." Toxicol Sci 96.2 (April 2007): 218-226. (Review)
PMID
17190972
Source
pubmed
Published In
Toxicological Sciences (Elsevier)
Volume
96
Issue
2
Publish Date
2007
Start Page
218
End Page
226
DOI
10.1093/toxsci/kfl196

Global expression analysis of cancer/testis genes in uterine cancers reveals a high incidence of BORIS expression.

PURPOSE: Cancer/testis (CT) genes predominantly expressed in the testis (germ cells) and generally not in other normal tissues are aberrantly expressed in human cancers. This highly restricted expression provides a unique opportunity to use these CT genes for diagnostics, immunotherapeutic, or other targeted therapies. The purpose of this study was to identify those CT genes with the greatest incidence of expression in uterine cancers. EXPERIMENTAL DESIGN: We queried the expression of known and putative CT gene transcripts (representing 79 gene loci) using whole genome gene expression arrays. Specifically, the global gene expressions of uterine cancers (n = 122) and normal uteri (n = 10) were determined using expression data from the Affymetrix HG-U133A and HG-U133B chips. Additionally, we also examined the brother of the regulator of imprinted sites (BORIS) transcript by reverse transcription-PCR and quantitative PCR because its transcript was not represented on the array. RESULTS: Global microarray analysis detected many CT genes expressed in various uterine cancers; however, no individual CT gene was expressed in more than 25% of all cancers. The expression of the two most commonly expressed CT genes on the arrays, MAGEA9 (24 of 122 cancers and 0 of 10 normal tissues) and Down syndrome critical region 8 (DSCR8)/MMA1 (16 if 122 cancers and 0 of 10 normal tissues), was confirmed by reverse transcription-PCR methods, validating the array screening approach. In contrast to the relatively low incidence of expression of the other CT genes, BORIS expression was detected in 73 of 95 (77%) endometrial cancers and 24 of 31 (77%) uterine mixed mesodermal tumors. CONCLUSIONS: These data provide the first extensive survey of multiple CT genes in uterine cancers. Importantly, we detected a high frequency of BORIS expression in uterine cancers, suggesting its potential as an immunologic or diagnostic target for these cancers. Given the high incidence of BORIS expression and its possible regulatory role, an examination of BORIS function in the etiology of these cancers is warranted.

Authors
Risinger, JI; Chandramouli, GVR; Maxwell, GL; Custer, M; Pack, S; Loukinov, D; Aprelikova, O; Litzi, T; Schrump, DS; Murphy, SK; Berchuck, A; Lobanenkov, V; Barrett, JC
MLA Citation
Risinger, JI, Chandramouli, GVR, Maxwell, GL, Custer, M, Pack, S, Loukinov, D, Aprelikova, O, Litzi, T, Schrump, DS, Murphy, SK, Berchuck, A, Lobanenkov, V, and Barrett, JC. "Global expression analysis of cancer/testis genes in uterine cancers reveals a high incidence of BORIS expression." Clin Cancer Res 13.6 (March 15, 2007): 1713-1719.
PMID
17363524
Source
pubmed
Published In
Clinical cancer research : an official journal of the American Association for Cancer Research
Volume
13
Issue
6
Publish Date
2007
Start Page
1713
End Page
1719
DOI
10.1158/1078-0432.CCR-05-2569

Trinucleotide repeat polymorphisms in the androgen receptor gene and risk of ovarian cancer.

INTRODUCTION: Androgens may play a role in the development of ovarian cancers. Two trinucleotide repeat polymorphisms have been described in exon 1 of the androgen receptor (AR) gene that may affect its function. Previous studies of ovarian cancer and AR repeat polymorphisms have been inconsistent. METHODS: We analyzed CAG and GGC repeat length polymorphisms in the AR gene using data from a population-based case-control study of ovarian cancer that included 594 cases and 681 controls. Repeat lengths were determined by fluorescent DNA fragment analysis using ABI GeneScan software. Change point models were used to determine appropriate repeat length cutoff points by race (African American versus Caucasian) for both the shorter and longer CAG and GGC repeats. RESULTS: No relationship was observed between CAG repeat length and ovarian cancer among Caucasians. Among African Americans, having a short repeat length on either allele was associated with a 2-fold increase in ovarian cancer risk (age-adjusted odds ratio, 2.2; 95% confidence interval, 1.1-4.1). Having short CAG repeat lengths for both alleles was associated with a 5-fold increased risk for developing ovarian cancer (age-adjusted odds ratio, 5.4; 95% confidence interval, 1.4-1.7). No relationship with the GGC repeat length polymorphisms was observed. CONCLUSION: These results suggest that having a short CAG repeat length in AR increases ovarian cancer risk in African Americans. The failure to observe this relationship in Caucasians may be due to the rarity of such short CAG alleles in this population or could reflect racial differences in disease etiology.

Authors
Schildkraut, JM; Murphy, SK; Palmieri, RT; Iversen, E; Moorman, PG; Huang, Z; Halabi, S; Calingaert, B; Gusberg, A; Marks, JR; Berchuck, A
MLA Citation
Schildkraut, JM, Murphy, SK, Palmieri, RT, Iversen, E, Moorman, PG, Huang, Z, Halabi, S, Calingaert, B, Gusberg, A, Marks, JR, and Berchuck, A. "Trinucleotide repeat polymorphisms in the androgen receptor gene and risk of ovarian cancer." Cancer Epidemiol Biomarkers Prev 16.3 (March 2007): 473-480.
PMID
17372242
Source
pubmed
Published In
Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology
Volume
16
Issue
3
Publish Date
2007
Start Page
473
End Page
480
DOI
10.1158/1055-9965.EPI-06-0868

Genomic sweeping for hypermethylated genes.

MOTIVATION: Genes silenced by the aberrent methylation of nearby CpG islands can contribute to the onset or progression of cancer and represent potential biomarkers for diagnosis and prognosis. Relatively few have thus far been validated as hypermethylated in cancer among over 14,000 candidates with promoter region CpG islands. A descriptive set of genes known to be unmethylated in cancer does not exist. This lack of a negative set and a large number of candidates necessitated the development of a new approach to identify novel genes hypermethylated in cancer. RESULTS: We developed a general method, cluster_boost, that in an imbalanced data setting predicts new minority class members given limited known samples and a large set of unlabeled samples. Synthetic datasets modeled after the hypermethylated genes data show that cluster_boost can successfully identify minority samples within unlabeled data. Using genome sequence features, cluster_boost predicted candidate hypermethylated genes among 14,000 genes of unknown status. In primary ovarian cancers, we determined the methylation status for 15 genes with different levels of support for being hypermethlyated. Results indicate cluster_boost can accurately identify novel genes hypermethylated in cancer. AVAILABILITY: Software and datasets are freely available at http://labs.genome.duke.edu/FureyLab/cluster_boost.php. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Authors
Goh, L; Murphy, SK; Muhkerjee, S; Furey, TS
MLA Citation
Goh, L, Murphy, SK, Muhkerjee, S, and Furey, TS. "Genomic sweeping for hypermethylated genes." Bioinformatics 23.3 (February 1, 2007): 281-288.
PMID
17148511
Source
pubmed
Published In
Bioinformatics
Volume
23
Issue
3
Publish Date
2007
Start Page
281
End Page
288
DOI
10.1093/bioinformatics/btl620

Cancer susceptibility: epigenetic manifestation of environmental exposures.

Cancer is a disease that results from both genetic and epigenetic changes. Discordant phenotypes and varying incidences of complex diseases such as cancer in monozygotic twins as well as genetically identical laboratory animals have long been attributed to differences in environmental exposures. Accumulating evidence indicates, however, that disparities in gene expression resulting from variable modifications in DNA methylation and chromatin structure in response to the environment also play a role in differential susceptibility to disease. Despite a growing consensus on the importance of epigenetics in the etiology of chronic human diseases, the genes most prone to epigenetic dysregulation are incompletely defined. Moreover, neither the environmental agents most strongly affecting the epigenome nor the critical windows of vulnerability to environmentally induced epigenetic alterations are adequately characterized. These major deficits in knowledge markedly impair our ability to understand fully the etiology of cancer and the importance of the epigenome in diagnosing and preventing this devastating disease.

Authors
Weidman, JR; Dolinoy, DC; Murphy, SK; Jirtle, RL
MLA Citation
Weidman, JR, Dolinoy, DC, Murphy, SK, and Jirtle, RL. "Cancer susceptibility: epigenetic manifestation of environmental exposures." Cancer J 13.1 (January 2007): 9-16. (Review)
PMID
17464241
Source
pubmed
Published In
Cancer Journal
Volume
13
Issue
1
Publish Date
2007
Start Page
9
End Page
16
DOI
10.1097/PPO.0b013e31803c71f2

Frequent IGF2/H19 domain epigenetic alterations and elevated IGF2 expression in epithelial ovarian cancer.

Overexpression of the imprinted insulin-like growth factor-II (IGF2) is a prominent characteristic of gynecologic malignancies. The purpose of this study was to determine whether IGF2 loss of imprinting (LOI), aberrant H19 expression, and/or epigenetic deregulation of the IGF2/H19 imprinted domain contributes to elevated IGF2 expression in serous epithelial ovarian tumors. IGF2 LOI was observed in 5 of 23 informative serous epithelial ovarian cancers, but this did not correlate with elevated expression of IGF2 H19 RNA expression levels were also found not to correlate with IGF2 transcript levels. However, we identified positive correlations between elevated IGF2 expression and hypermethylation of CCCTC transcription factor binding sites 1 and 6 at the H19 proximal imprint center (P = 0.05 and 0.02, respectively). Hypermethylation of CCCTC transcription factor sites 1 and 6 was observed more frequently in cancer DNA compared with lymphocyte DNA obtained from women without malignancy (P < 0.0001 for both sites 1 and 6). Ovarian cancers were also more likely to exhibit maternal allele-specific hypomethylation upstream of the imprinted IGF2 promoters when compared with normal lymphocyte DNA (P = 0.004). This is the same region shown previously to be hypomethylated in colon cancers with IGF2 LOI, but this was not associated with LOI in ovarian cancers. Elevated IGF2 expression is a frequent event in serous ovarian cancer and this occurs in the absence of IGF2 LOI. These data indicate that the epigenetic changes observed in these cancers at the imprint center may contribute to IGF2 overexpression in a novel mechanistic manner.

Authors
Murphy, SK; Huang, Z; Wen, Y; Spillman, MA; Whitaker, RS; Simel, LR; Nichols, TD; Marks, JR; Berchuck, A
MLA Citation
Murphy, SK, Huang, Z, Wen, Y, Spillman, MA, Whitaker, RS, Simel, LR, Nichols, TD, Marks, JR, and Berchuck, A. "Frequent IGF2/H19 domain epigenetic alterations and elevated IGF2 expression in epithelial ovarian cancer." Mol Cancer Res 4.4 (April 2006): 283-292.
PMID
16603642
Source
pubmed
Published In
Molecular cancer research : MCR
Volume
4
Issue
4
Publish Date
2006
Start Page
283
End Page
292
DOI
10.1158/1541-7786.MCR-05-0138

Callipyge mutation affects gene expression in cis: a potential role for chromatin structure.

Muscular hypertrophy in callipyge sheep results from a single nucleotide substitution located in the genomic interval between the imprinted Delta, Drosophila, Homolog-like 1 (DLK1) and Maternally Expressed Gene 3 (MEG3). The mechanism linking the mutation to muscle hypertrophy is unclear but involves DLK1 overexpression. The mutation is contained within CLPG1 transcripts produced from this region. Herein we show that CLPG1 is expressed prenatally in the hypertrophy-responsive longissimus dorsi muscle by all four possible genotypes, but postnatal expression is restricted to sheep carrying the mutation. Surprisingly, the mutation results in nonimprinted monoallelic transcription of CLPG1 from only the mutated allele in adult sheep, whereas it is expressed biallelically during prenatal development. We further demonstrate that local CpG methylation is altered by the presence of the mutation in longissimus dorsi of postnatal sheep. For 10 CpG sites flanking the mutation, methylation is similar prenatally across genotypes, but doubles postnatally in normal sheep. This normal postnatal increase in methylation is significantly repressed in sheep carrying one copy of the mutation, and repressed even further in sheep with two mutant alleles. The attenuation in methylation status in the callipyge sheep correlates with the onset of the phenotype, continued CLPG1 transcription, and high-level expression of DLK1. In contrast, normal sheep exhibit hypermethylation of this locus after birth and CLPG1 silencing, which coincides with DLK1 transcriptional repression. These data are consistent with the notion that the callipyge mutation inhibits perinatal nucleation of regional chromatin condensation resulting in continued elevated transcription of prenatal DLK1 levels in adult callipyge sheep. We propose a model incorporating these results that can also account for the enigmatic normal phenotype of homozygous mutant sheep.

Authors
Murphy, SK; Nolan, CM; Huang, Z; Kucera, KS; Freking, BA; Smith, TPL; Leymaster, KA; Weidman, JR; Jirtle, RL
MLA Citation
Murphy, SK, Nolan, CM, Huang, Z, Kucera, KS, Freking, BA, Smith, TPL, Leymaster, KA, Weidman, JR, and Jirtle, RL. "Callipyge mutation affects gene expression in cis: a potential role for chromatin structure." Genome Res 16.3 (March 2006): 340-346.
PMID
16415109
Source
pubmed
Published In
Genome research
Volume
16
Issue
3
Publish Date
2006
Start Page
340
End Page
346
DOI
10.1101/gr.4389306

High throughput detection of M6P/IGF2R intronic hypermethylation and LOH in ovarian cancer.

Cell surface mannose 6-phosphate/insulin-like growth factor II receptors (M6P/IGF2R) bind and target exogenous insulin-like growth factor II (IGF2) to the prelysosomes where it is degraded. Loss of heterozygosity (LOH) for M6P/IGF2R is found in cancers, with mutational inactivation of the remaining allele. We exploited the normal allele-specific differential methylation of the M6P/IGF2R intron 2 CpG island to rapidly evaluate potential LOH in ovarian cancers, since every normal individual is informative. To this end, we developed a method for bisulfite modification of genomic DNA in 96-well format that allows for rapid methylation profiling. We identified ovarian cancers with M6P/IGF2R LOH, but unexpectedly also found frequent abnormal acquisition of methylation on the paternally inherited allele at intron 2. These results demonstrate the utility of our high-throughput method of bisulfite modification for analysis of large sample numbers. They further show that the methylation status of the intron 2 CpG island may be a useful indicator of LOH and biomarker of disease.

Authors
Huang, Z; Wen, Y; Shandilya, R; Marks, JR; Berchuck, A; Murphy, SK
MLA Citation
Huang, Z, Wen, Y, Shandilya, R, Marks, JR, Berchuck, A, and Murphy, SK. "High throughput detection of M6P/IGF2R intronic hypermethylation and LOH in ovarian cancer. (Published online)" Nucleic Acids Res 34.2 (2006): 555-563.
PMID
16432260
Source
pubmed
Published In
Nucleic Acids Research
Volume
34
Issue
2
Publish Date
2006
Start Page
555
End Page
563
DOI
10.1093/nar/gkj468

Patterns of gene expression that characterize long-term survival in advanced stage serous ovarian cancers.

PURPOSE: A better understanding of the underlying biology of invasive serous ovarian cancer is critical for the development of early detection strategies and new therapeutics. The objective of this study was to define gene expression patterns associated with favorable survival. EXPERIMENTAL DESIGN: RNA from 65 serous ovarian cancers was analyzed using Affymetrix U133A microarrays. This included 54 stage III/IV cases (30 short-term survivors who lived <3 years and 24 long-term survivors who lived >7 years) and 11 stage I/II cases. Genes were screened on the basis of their level of and variability in expression, leaving 7,821 for use in developing a predictive model for survival. A composite predictive model was developed that combines Bayesian classification tree and multivariate discriminant models. Leave-one-out cross-validation was used to select and evaluate models. RESULTS: Patterns of genes were identified that distinguish short-term and long-term ovarian cancer survivors. The expression model developed for advanced stage disease classified all 11 early-stage ovarian cancers as long-term survivors. The MAL gene, which has been shown to confer resistance to cancer therapy, was most highly overexpressed in short-term survivors (3-fold compared with long-term survivors, and 29-fold compared with early-stage cases). These results suggest that gene expression patterns underlie differences in outcome, and an examination of the genes that provide this discrimination reveals that many are implicated in processes that define the malignant phenotype. CONCLUSIONS: Differences in survival of advanced ovarian cancers are reflected by distinct patterns of gene expression. This biological distinction is further emphasized by the finding that early-stage cancers share expression patterns with the advanced stage long-term survivors, suggesting a shared favorable biology.

Authors
Berchuck, A; Iversen, ES; Lancaster, JM; Pittman, J; Luo, J; Lee, P; Murphy, S; Dressman, HK; Febbo, PG; West, M; Nevins, JR; Marks, JR
MLA Citation
Berchuck, A, Iversen, ES, Lancaster, JM, Pittman, J, Luo, J, Lee, P, Murphy, S, Dressman, HK, Febbo, PG, West, M, Nevins, JR, and Marks, JR. "Patterns of gene expression that characterize long-term survival in advanced stage serous ovarian cancers." Clin Cancer Res 11.10 (May 15, 2005): 3686-3696.
PMID
15897565
Source
pubmed
Published In
Clinical cancer research : an official journal of the American Association for Cancer Research
Volume
11
Issue
10
Publish Date
2005
Start Page
3686
End Page
3696
DOI
10.1158/1078-0432.CCR-04-2398

Transforming growth factor beta receptor I polyalanine repeat polymorphism does not increase ovarian cancer risk.

OBJECTIVES: It has been suggested that the 6A allele of the type I TGFbeta receptor (TGFbetaR1) polyalanine repeat tract polymorphism may increase susceptibility to various types of cancer including ovarian cancer. METHODS: The TGFbetaR1 polyalanine polymorphism was genotyped in 588 ovarian cancer cases and 614 controls from a population-based case-control study in North Carolina. RESULTS: Significant racial differences in the frequency of the 6A allele were observed between Caucasian (10.7%) and African-American (2.4%) controls (P < 0.001). One or two copies of the 6A allele of the TGFbetaR1 polyalanine polymorphism was carried by 18% of all controls and 19% of cases, and there was no association with ovarian cancer risk (OR = 1.07, 95% CI 0.80-1.44). The odds ratio for 6A homozygotes was 1.81 (95% CI 0.655.06), but these comprised only 0.98% of controls and 1.70% of cases. CONCLUSIONS: The 6A allele of the TGFbetaR1 polyalanine polymorphism does not appear to increase ovarian cancer risk. Larger studies would be needed to exclude the possibility that the small fraction of individuals who are 6A homozygotes have an increased risk of ovarian or other cancers.

Authors
Spillman, MA; Schildkraut, JM; Halabi, S; Moorman, P; Calingaert, B; Bentley, RC; Marks, JR; Murphy, S; Berchuck, A
MLA Citation
Spillman, MA, Schildkraut, JM, Halabi, S, Moorman, P, Calingaert, B, Bentley, RC, Marks, JR, Murphy, S, and Berchuck, A. "Transforming growth factor beta receptor I polyalanine repeat polymorphism does not increase ovarian cancer risk." Gynecol Oncol 97.2 (May 2005): 543-549.
PMID
15863158
Source
pubmed
Published In
Gynecologic Oncology
Volume
97
Issue
2
Publish Date
2005
Start Page
543
End Page
549
DOI
10.1016/j.ygyno.2005.01.025

Analysis of methylation-sensitive transcriptome identifies GADD45a as a frequently methylated gene in breast cancer.

Treatment of the breast cancer cell line, MDAMB468 with the DNA methylation inhibitor, 5-azacytidine (5-AzaC) results in growth arrest, whereas the growth of the normal breast epithelial line DU99 (telomerase immortalized) is relatively unaffected. Comparing gene expression profiles of these two lines after 5-AzaC treatment, we identified 36 genes that had relatively low basal levels in MDAMB468 cells compared to the DU99 line and were induced in the cancer cell line but not in the normal breast epithelial line. Of these genes, 33 have associated CpG islands greater than 300 bp in length but only three have been previously described as targets for aberrant methylation in human cancer. Northern blotting for five of these genes (alpha-Catenin, DTR, FYN, GADD45a, and Zyxin) verified the array results. Further analysis of one of these genes, GADD45a, showed that 5-AzaC induced expression in five additional breast cancer cell lines with little or no induction in three additional lines derived from normal breast epithelial cells. The CpG island associated with GADD45a was analysed by bisulfite sequencing, sampling over 100 CpG dinucleotides. We found that four CpG's, located approximately 700 bp upstream of the transcriptional start site are methylated in the majority of breast cancer cell lines and primary tumors but not in DNA from normal breast epithelia or matched lymphocytes from cancer patients. Therefore, this simple method of dynamic transcriptional profiling yielded a series of novel methylation-sensitive genes in breast cancer including the BRCA1 and p53 responsive gene, GADD45a.

Authors
Wang, W; Huper, G; Guo, Y; Murphy, SK; Olson, JA; Marks, JR
MLA Citation
Wang, W, Huper, G, Guo, Y, Murphy, SK, Olson, JA, and Marks, JR. "Analysis of methylation-sensitive transcriptome identifies GADD45a as a frequently methylated gene in breast cancer." Oncogene 24.16 (April 14, 2005): 2705-2714.
PMID
15735726
Source
pubmed
Published In
Oncogene: Including Oncogene Reviews
Volume
24
Issue
16
Publish Date
2005
Start Page
2705
End Page
2714
DOI
10.1038/sj.onc.1208464

Abnormal postnatal maintenance of elevated DLK1 transcript levels in callipyge sheep.

The underlying mechanism of the callipyge muscular hypertrophy phenotype in sheep (Ovis aries) is not presently understood. This phenotype, characterized by increased glycolytic type II muscle proportion and cell size accompanied by decreased adiposity, is not visibly detectable until approximately three to eight weeks after birth. The muscular hypertrophy results from a single nucleotide change located at the telomeric end of ovine Chromosome 18, in the region between the imprinted MATERNALLY EXPRESSED GENE 3 (MEG3) and DELTA, DROSOPHILA, HOMOLOG-LIKE 1 (DLK1) genes. The callipyge phenotype is evident only when the mutation is paternally inherited by a heterozygous individual. We have examined the pre- and postnatal expression of MEG3 and DLK1 in sheep of all four possible genotypes in affected and unaffected muscles as well as in liver. Here we show that the callipyge phenotype correlates with abnormally high DLK1 expression during the postnatal period in the affected sheep and that this elevation is specific to the hypertrophy-responsive fast-twitch muscles. These results are the first to show anomalous gene expression that coincides with both the temporal and spatial distribution of the callipyge phenotype. They suggest that the effect of the callipyge mutation is to interfere with the normal postnatal downregulation of DLK1 expression.

Authors
Murphy, SK; Freking, BA; Smith, TPL; Leymaster, K; Nolan, CM; Wylie, AA; Evans, HK; Jirtle, RL
MLA Citation
Murphy, SK, Freking, BA, Smith, TPL, Leymaster, K, Nolan, CM, Wylie, AA, Evans, HK, and Jirtle, RL. "Abnormal postnatal maintenance of elevated DLK1 transcript levels in callipyge sheep." Mamm Genome 16.3 (March 2005): 171-183.
PMID
15834634
Source
pubmed
Published In
Mammalian Genome
Volume
16
Issue
3
Publish Date
2005
Start Page
171
End Page
183
DOI
10.1007/s00335-004-2421-1

Phylogenetic footprint analysis of IGF2 in extant mammals.

Genomic imprinting results in monoallelic gene transcription that is directed by cis-acting regulatory elements epigenetically marked in a parent-of-origin-dependent manner. We performed phylogenetic sequence and epigenetic comparisons of IGF2 between the nonimprinted platypus (Ornithorhynchus anatinus) and imprinted opossum (Didelphis virginiana), mouse (Mus musculus), and human (Homo sapiens) to determine if their divergent imprint status would reflect differences in the conservation of genomic elements important in the regulation of imprinting. We report herein that IGF2 imprinting does not correlate evolutionarily with differential intragenic methylation, nor is it associated with motif 13, a reported IGF2-specific "imprint signature" located in the coding region. Instead, IGF2 imprinting is strongly associated with both the lack of short interspersed transposable elements (SINEs) and an intragenic conserved inverted repeat that contains candidate CTCF-binding sites, a role not previously ascribed to this particular sequence element. Our results are the first to demonstrate that comparative footprint analysis of species from evolutionarily distant mammalian clades, and exhibiting divergent imprint status is a powerful bioinformatics-based approach for identifying cis-acting elements potentially involved not only in the origins of genomic imprinting, but also in its maintenance in humans.

Authors
Weidman, JR; Murphy, SK; Nolan, CM; Dietrich, FS; Jirtle, RL
MLA Citation
Weidman, JR, Murphy, SK, Nolan, CM, Dietrich, FS, and Jirtle, RL. "Phylogenetic footprint analysis of IGF2 in extant mammals." Genome Res 14.9 (September 2004): 1726-1732.
PMID
15342558
Source
pubmed
Published In
Genome research
Volume
14
Issue
9
Publish Date
2004
Start Page
1726
End Page
1732
DOI
10.1101/gr.2774804

Epigenetic detection of human chromosome 14 uniparental disomy.

The recent demonstration of genomic imprinting of DLK1 and MEG3 on human chromosome 14q32 indicates that these genes might contribute to the discordant phenotypes associated with uniparental disomy (UPD) of chromosome 14. Regulation of imprinted expression of DLK1 and MEG3 involves a differentially methylated region (DMR) that encompasses the MEG3 promoter. We exploited the normal differential methylation of the DLK1/MEG3 region to develop a rapid diagnostic PCR assay based upon an individual's epigenetic profile. We used methylation-specific multiplex PCR in a retrospective analysis to amplify divergent lengths of the methylated and unmethylated MEG3 DMR in a single reaction and accurately identified normal, maternal UPD14, and paternal UPD14 in bisulfite converted DNA samples. This approach, which is based solely on differential epigenetic profiles, may be generally applicable for rapidly and economically screening for other imprinting defects associated with uniparental disomy, determining loss of heterozygosity of imprinted tumor suppressor genes, and identifying gene-specific hypermethylation events associated with neoplastic progression.

Authors
Murphy, SK; Wylie, AA; Coveler, KJ; Cotter, PD; Papenhausen, PR; Sutton, VR; Shaffer, LG; Jirtle, RL
MLA Citation
Murphy, SK, Wylie, AA, Coveler, KJ, Cotter, PD, Papenhausen, PR, Sutton, VR, Shaffer, LG, and Jirtle, RL. "Epigenetic detection of human chromosome 14 uniparental disomy." Hum Mutat 22.1 (July 2003): 92-97.
PMID
12815599
Source
pubmed
Published In
Human Mutation
Volume
22
Issue
1
Publish Date
2003
Start Page
92
End Page
97
DOI
10.1002/humu.10237

Imprinting evolution and the price of silence.

In contrast to the biallelic expression of most genes, expression of genes subject to genomic imprinting is monoallelic and based on the sex of the transmitting parent. Possession of only a single active allele can lead to deleterious health consequences in humans. Aberrant expression of imprinted genes, through either genetic or epigenetic alterations, can result in developmental failures, neurodevelopmental and neurobehavioral disorders and cancer. The evolutionary emergence of imprinting occurred in a common ancestor to viviparous mammals after divergence from the egg-laying monotremes. Current evidence indicates that imprinting regulation in metatherian mammals differs from that in eutherian mammals. This suggests that imprinting mechanisms are evolving from those that were established 150 million years ago. Therefore, comparing genomic sequence of imprinted domains from marsupials and eutherians with those of orthologous regions in monotremes offers a potentially powerful bioinformatics approach for identifying novel imprinted genes and their regulatory elements. Such comparative studies will also further our understanding of the molecular evolution and phylogenetic distribution of imprinted genes.

Authors
Murphy, SK; Jirtle, RL
MLA Citation
Murphy, SK, and Jirtle, RL. "Imprinting evolution and the price of silence." Bioessays 25.6 (June 2003): 577-588. (Review)
PMID
12766947
Source
pubmed
Published In
Bioessays
Volume
25
Issue
6
Publish Date
2003
Start Page
577
End Page
588
DOI
10.1002/bies.10277

Exclusion of maternal uniparental disomy of chromosome 14 in patients referred for Prader-Willi syndrome using a multiplex methylation polymerase chain reaction assay.

Authors
Dietz, LG; Wylie, AA; Rauen, KA; Murphy, SK; Jirtle, RL; Cotter, PD
MLA Citation
Dietz, LG, Wylie, AA, Rauen, KA, Murphy, SK, Jirtle, RL, and Cotter, PD. "Exclusion of maternal uniparental disomy of chromosome 14 in patients referred for Prader-Willi syndrome using a multiplex methylation polymerase chain reaction assay." J Med Genet 40.4 (April 2003): e46-. (Letter)
PMID
12676919
Source
pubmed
Published In
Journal of medical genetics
Volume
40
Issue
4
Publish Date
2003
Start Page
e46

Identification of the single base change causing the callipyge muscle hypertrophy phenotype, the only known example of polar overdominance in mammals.

A small genetic region near the telomere of ovine chromosome 18 was previously shown to carry the mutation causing the callipyge muscle hypertrophy phenotype in sheep. Expression of this phenotype is the only known case in mammals of paternal polar overdominance gene action. A region surrounding two positional candidate genes was sequenced in animals of known genotype. Mutation detection focused on an inbred ram of callipyge phenotype postulated to have inherited chromosome segments identical-by-descent with exception of the mutated position. In support of this hypothesis, this inbred ram was homozygous over 210 Kb of sequence, except for a single heterozygous base position. This single polymorphism was genotyped in multiple families segregating the callipyge locus (CLPG), providing 100% concordance with animals of known CLPG genotype, and was unique to descendants of the founder animal. The mutation lies in a region of high homology among mouse, sheep, cattle, and humans, but not in any previously identified expressed transcript. A substantial open reading frame exists in the sheep sequence surrounding the mutation, although this frame is not conserved among species. Initial functional analysis indicates sequence encompassing the mutation is part of a novel transcript expressed in sheep fetal muscle we have named CLPG1.

Authors
Freking, BA; Murphy, SK; Wylie, AA; Rhodes, SJ; Keele, JW; Leymaster, KA; Jirtle, RL; Smith, TPL
MLA Citation
Freking, BA, Murphy, SK, Wylie, AA, Rhodes, SJ, Keele, JW, Leymaster, KA, Jirtle, RL, and Smith, TPL. "Identification of the single base change causing the callipyge muscle hypertrophy phenotype, the only known example of polar overdominance in mammals." Genome Res 12.10 (October 2002): 1496-1506.
PMID
12368241
Source
pubmed
Published In
Genome research
Volume
12
Issue
10
Publish Date
2002
Start Page
1496
End Page
1506
DOI
10.1101/gr.571002

Exclusion of maternal uniparental disomy of chromosome 14 in Prader-Willi syndrome referrals using a rapid methylation PCR assay.

Authors
Dietz, L; Wylie, AA; Rauen, KA; Murphy, SK; Jirtle, RL; Cotter, PD
MLA Citation
Dietz, L, Wylie, AA, Rauen, KA, Murphy, SK, Jirtle, RL, and Cotter, PD. "Exclusion of maternal uniparental disomy of chromosome 14 in Prader-Willi syndrome referrals using a rapid methylation PCR assay." October 2002.
Source
wos-lite
Published In
The American Journal of Human Genetics
Volume
71
Issue
4
Publish Date
2002
Start Page
553
End Page
553

An imprinted PEG1/MEST antisense expressed predominantly in human testis and in mature spermatozoa

PEG1 (or MEST) is an imprinted gene located on human chromosome 7q32 that is expressed predominantly from the paternal allele. In the mouse, Peg1/Mest is associated with embryonic growth and maternal behavior. Human PEG1 is transcribed from two promoters; the transcript from promoter P1 is derived from both parental alleles, and the transcript from P2 is exclusively from the paternal allele. We characterized the P1 and P2 transcripts in various normal and neoplastic tissues. In the normal tissues, PEG1 was transcribed from both promoters P1 and P2, whereas in six of eight neoplastic tissues, PEG1 was transcribed exclusively from promoter P1. Bisulfite sequencing demonstrated high levels of CpG methylation in the P2 region of DNA from a lung tumor. In the region between P1 and P2, we identified a novel transcript, PEG1-AS, in an antisense orientation to PEG1. PEG1-AS is a spliced transcript and was detected as a strong 2.4-kilobase band on a Northern blot. PEG1-AS and PEG1 P2-sense transcript were expressed exclusively from the paternal allele. Fragments of DNA from within the 1.5-kilobase region between PEG1-AS and the P2 exon were ligated to a pGL3 luciferase reporter vector and transfected into NCI H23 cells. This DNA exhibited strong promoter activity in both the sense and antisense directions, indicating that PEG1-AS and P2 exon share a common promoter region. Treatment of the transfected DNA fragments with CpG methylase abolished the promoter activity. Of interest, PEG1-AS was expressed predominantly in testis and in mature motile spermatozoa, indicating a possible role for this transcript in human sperm physiology and fertilization.

Authors
Li, T; Vu, TH; Lee, K-O; Yang, Y; Nguyen, CV; Bui, HQ; Zeng, Z-L; Nguyen, BT; Hu, J-F; Murphy, SK; Jirtle, RL; Hoffman, AR
MLA Citation
Li, T, Vu, TH, Lee, K-O, Yang, Y, Nguyen, CV, Bui, HQ, Zeng, Z-L, Nguyen, BT, Hu, J-F, Murphy, SK, Jirtle, RL, and Hoffman, AR. "An imprinted PEG1/MEST antisense expressed predominantly in human testis and in mature spermatozoa." Journal of Biological Chemistry 277.16 (2002): 13518-13527.
PMID
11821432
Source
scival
Published In
The Journal of biological chemistry
Volume
277
Issue
16
Publish Date
2002
Start Page
13518
End Page
13527
DOI
10.1074/jbc.M200458200

Development and characterization of a conditional M6p/Igf2r knockout mouse.

Authors
Murphy, SK; Wylie, AA; McVie-Wylie, AJ; Pulford, D; Nolan, CM; Orton, TC; Jirtle, RL
MLA Citation
Murphy, SK, Wylie, AA, McVie-Wylie, AJ, Pulford, D, Nolan, CM, Orton, TC, and Jirtle, RL. "Development and characterization of a conditional M6p/Igf2r knockout mouse." AMERICAN JOURNAL OF HUMAN GENETICS 69.4 (October 2001): 363-363.
Source
wos-lite
Published In
The American Journal of Human Genetics
Volume
69
Issue
4
Publish Date
2001
Start Page
363
End Page
363

NNATresides in a micro-imprinted domain on human chromosome 20q11.2.

Authors
Evans, HK; Wylie, AA; Murphy, SK; Jirtle, RL
MLA Citation
Evans, HK, Wylie, AA, Murphy, SK, and Jirtle, RL. "NNATresides in a micro-imprinted domain on human chromosome 20q11.2." AMERICAN JOURNAL OF HUMAN GENETICS 69.4 (October 2001): 346-346.
Source
wos-lite
Published In
The American Journal of Human Genetics
Volume
69
Issue
4
Publish Date
2001
Start Page
346
End Page
346

The neuronatin gene resides in a "micro-imprinted" domain on human chromosome 20q11.2.

A small fraction of the genome contains genes that are imprinted and thus expressed exclusively from one parental allele. We report here that the human neuronatin gene (NNAT) on chromosome 20q11.2 is imprinted and transcribed specifically from the paternal allele. The region containing NNAT has multiple CpG islands, and methylation analysis showed that a 1.8-kb CpG island in its promoter region exhibits differential methylation in all tissues examined. This finding is consistent with the island acting as a component of the NNAT imprint control domain. NNAT lies within the singular 8.5-kb intron of the gene encoding bladder cancer-associated protein (BLCAP), which, as we demonstrate, is not imprinted. This study provides the first example, to our knowledge, in humans of an imprinted gene contained within the genomic structure of a nonimprinted gene. Thus, NNAT is in an imprinted "microdomain," making this locus uniquely suited for the investigation of mechanisms of localized imprint regulation.

Authors
Evans, HK; Wylie, AA; Murphy, SK; Jirtle, RL
MLA Citation
Evans, HK, Wylie, AA, Murphy, SK, and Jirtle, RL. "The neuronatin gene resides in a "micro-imprinted" domain on human chromosome 20q11.2." Genomics 77.1-2 (September 2001): 99-104.
PMID
11543638
Source
pubmed
Published In
Genomics
Volume
77
Issue
1-2
Publish Date
2001
Start Page
99
End Page
104
DOI
10.1006/geno.2001.6612

RNA replication from the simian virus 5 antigenomic promoter requires three sequence-dependent elements separated by sequence-independent spacer regions.

We have previously shown for the paramyxovirus simian virus 5 (SV5) that a functional promoter for RNA replication requires proper spacing between two discontinuous elements: a 19-base segment at the 3' terminus (conserved region I [CRI]) and an 18-base internal region (CRII) that is contained within the coding region of the L protein gene. In the work described here, we have used a reverse-genetics system to determine if the 53-base segment between CRI and CRII contains additional sequence-specific signals required for optimal replication or if this segment functions solely as a sequence-independent spacer region. A series of copyback defective interfering minigenome analogs were constructed to contain substitutions of nonviral sequences in place of bases 21 to 72 of the antigenomic promoter, and the relative level of RNA replication was measured by Northern blot analysis. The results from our mutational analysis indicate that in addition to CRI and CRII, optimal replication from the SV5 antigenomic promoter requires a third sequence-dependent element located 51 to 66 bases from the 3' end of the RNA. Minigenome RNA replication was not affected by changes in the either the position of this element in relation to CRI and CRII or the predicted hexamer phase of NP encapsidation. Thus, optimal RNA replication from the SV5 antigenomic promoter requires three sequence-dependent elements, CRI, CRII and bases 51 to 66.

Authors
Keller, MA; Murphy, SK; Parks, GD
MLA Citation
Keller, MA, Murphy, SK, and Parks, GD. "RNA replication from the simian virus 5 antigenomic promoter requires three sequence-dependent elements separated by sequence-independent spacer regions." J Virol 75.8 (April 2001): 3993-3998.
PMID
11264390
Source
pubmed
Published In
Journal of virology
Volume
75
Issue
8
Publish Date
2001
Start Page
3993
End Page
3998
DOI
10.1128/JVI.75.8.3993-3998.2001

Imprinting of PEG3, the human homologue of a mouse gene involved in nurturing behavior.

The paternally expressed Peg3 gene in mice encodes an unusual Krüppel-type zinc finger protein implicated in critical cellular and behavioral functions including growth, apoptosis, and maternal nurturing behavior. Methylation and expression analyses were used to determine whether PEG3 on chromosome 19q13.4 is imprinted in humans. The PEG3 promoter is encompassed within a large CpG-rich region that is differentially methylated in fetal tissues. Furthermore, expression studies demonstrate that PEG3 is ubiquitously imprinted throughout development and postnatally. Multiple isoforms of the PEG3 gene, including a novel transcript, are paternally expressed. These results are the first to show that human chromosome 19q13.4 contains an imprinted region. The imprinted status of PEG3 throughout life coupled with its neural expression and putative roles in regulating cell growth suggests that PEG3 may be a susceptibility locus for cancer as well as neurobehavioral deficits.

Authors
Murphy, SK; Wylie, AA; Jirtle, RL
MLA Citation
Murphy, SK, Wylie, AA, and Jirtle, RL. "Imprinting of PEG3, the human homologue of a mouse gene involved in nurturing behavior." Genomics 71.1 (January 1, 2001): 110-117.
PMID
11161803
Source
pubmed
Published In
Genomics
Volume
71
Issue
1
Publish Date
2001
Start Page
110
End Page
117
DOI
10.1006/geno.2000.6419

Novel imprinted DLK1/GTL2 domain on human chromosome 14 contains motifs that mimic those implicated in IGF2/H19 regulation.

The evolution of genomic imprinting in mammals occurred more than 100 million years ago, and resulted in the formation of genes that are functionally haploid because of parent-of-origin-dependent expression. Despite ample evidence from studies in a number of species suggesting the presence of imprinted genes on human chromosome 14, their identity has remained elusive. Here we report the identification of two reciprocally imprinted genes, GTL2 and DLK1, which together define a novel imprinting cluster on human chromosome 14q32. The maternally expressed GTL2 (gene trap locus 2) gene encodes for a nontranslated RNA. DLK1 (delta, Drosophila, homolog-like 1) is a paternally expressed gene that encodes for a transmembrane protein containing six epidermal growth factor (EGF) repeat motifs closely related to those present in the delta/notch/serrate family of signaling molecules. The paternal expression, chromosomal localization, and biological function of DLK1 also make it a likely candidate gene for the callipyge phenotype in sheep. Many of the predicted structural and regulatory features of the DLK1/GTL2 domain are highly analogous to those implicated in IGF2/H19 imprint regulation, including two hemimethylated consensus binding sites for the vertebrate enhancer blocking protein, CTCF. These results provide evidence that a common mechanism and domain organization may be used for juxtapositioned, reciprocally imprinted genes.

Authors
Wylie, AA; Murphy, SK; Orton, TC; Jirtle, RL
MLA Citation
Wylie, AA, Murphy, SK, Orton, TC, and Jirtle, RL. "Novel imprinted DLK1/GTL2 domain on human chromosome 14 contains motifs that mimic those implicated in IGF2/H19 regulation." Genome Res 10.11 (November 2000): 1711-1718.
PMID
11076856
Source
pubmed
Published In
Genome research
Volume
10
Issue
11
Publish Date
2000
Start Page
1711
End Page
1718

Identification of a novel imprinted domain at human chromosome 14q32.

Authors
Wylie, AA; Murphy, SK; Orton, TC; Jirtle, RL
MLA Citation
Wylie, AA, Murphy, SK, Orton, TC, and Jirtle, RL. "Identification of a novel imprinted domain at human chromosome 14q32." AMERICAN JOURNAL OF HUMAN GENETICS 67.4 (October 2000): 190-190.
Source
wos-lite
Published In
The American Journal of Human Genetics
Volume
67
Issue
4
Publish Date
2000
Start Page
190
End Page
190

Imprinting of PEG3, the human homolog of a gene involved in nurturing behaviour.

Authors
Murphy, SK; Wylie, AA; Jirtle, RL
MLA Citation
Murphy, SK, Wylie, AA, and Jirtle, RL. "Imprinting of PEG3, the human homolog of a gene involved in nurturing behaviour." AMERICAN JOURNAL OF HUMAN GENETICS 67.4 (October 2000): 189-189.
Source
wos-lite
Published In
The American Journal of Human Genetics
Volume
67
Issue
4
Publish Date
2000
Start Page
189
End Page
189

Imprinted genes as potential genetic and epigenetic toxicologic targets.

Genomic imprinting is an epigenetic phenomenon in eutherian mammals that results in the differential expression of the paternally and maternally inherited alleles of a gene. Imprinted genes are necessary for normal mammalian development. This requirement has been proposed to have evolved because of an interparental genetic battle for the utilization of maternal resources during gestation and postnatally. The nonrandom requisite for monoallelic expression of a subset of genes has also resulted in the formation of susceptibility loci for neurobehavioral disorders, developmental disorders, and cancer. Since imprinting involves both cytosine methylation within CpG islands and changes in chromatin structure, imprinted genes are potential targets for dysregulation by epigenetic toxicants that modify DNA methylation and histone acetylation.

Authors
Murphy, SK; Jirtle, RL
MLA Citation
Murphy, SK, and Jirtle, RL. "Imprinted genes as potential genetic and epigenetic toxicologic targets." Environ Health Perspect 108 Suppl 1 (March 2000): 5-11. (Review)
PMID
10698719
Source
pubmed
Published In
Environmental health perspectives
Volume
108 Suppl 1
Publish Date
2000
Start Page
5
End Page
11

RNA replication for the paramyxovirus simian virus 5 requires an internal repeated (CGNNNN) sequence motif.

A functional RNA replication promoter for the paramyxovirus simian virus 5 (SV5) requires two essential and discontinuous elements: 19 bases at the 3' terminus (conserved region I) and an 18-base internal region (conserved region II [CRII]) that is contained within the coding region of the L protein gene. A reverse-genetics system was used to determine the sequence requirements for the internal CRII element to function in RNA replication. A series of copyback defective interfering (DI) RNA analogs were constructed to contain point mutations in the 18 nucleotides composing CRII, and their relative replication levels were analyzed. The results indicated that SV5 DI RNA replication was reduced by substitutions for two CG dinucleotides, which in the nucleocapsid template are in the first two positions of the first two hexamers of CRII nucleotides. Substitutions for other bases within CRII did not reduce RNA synthesis. Thus, two consecutive 5'-CGNNNN-3' hexamers form an important sequence in the SV5 CRII promoter element. The position of the CG dinucleotide within the SV5 leader and antitrailer promoters was highly conserved among other members of the Rubulavirus genus, but this motif differed significantly in both sequence and position from that previously identified for Sendai virus. The possible roles of the CRII internal promoter element in paramyxovirus RNA replication are discussed.

Authors
Murphy, SK; Parks, GD
MLA Citation
Murphy, SK, and Parks, GD. "RNA replication for the paramyxovirus simian virus 5 requires an internal repeated (CGNNNN) sequence motif." J Virol 73.1 (January 1999): 805-809.
PMID
9847393
Source
pubmed
Published In
Journal of virology
Volume
73
Issue
1
Publish Date
1999
Start Page
805
End Page
809

A functional antigenomic promoter for the paramyxovirus simian virus 5 requires proper spacing between an essential internal segment and the 3' terminus.

A previous analysis of naturally occurring defective interfering (DI) RNA genomes of the prototypic paramyxovirus simian virus 5 (SV5) indicated that 113 bases at the 3' terminus of the antigenome were sufficient to direct RNA encapsidation and replication. A nucleotide sequence alignment of the antigenomic 3'-terminal 113 bases of members of the Rubulavirus genus of the Paramyxoviridae family identified two regions of sequence identity: bases 1 to 19 at the 3' terminus (conserved region I [CRI]) and a more distal region consisting of antigenome bases 73 to 90 (CRII) that was contained within the 3' coding region of the L protein gene. To determine whether these regions of the antigenome were essential for SV5 RNA replication, a reverse genetics system was used to analyze the replication of copyback DI RNA analogs that contained a foreign gene (GL, encoding green fluorescence protein) flanked by 113 5'-terminal bases and various amounts of SV5 3'-terminal antigenomic sequences. Results from a deletion analysis showed that efficient encapsidation and replication of SV5-GL DI RNA analogs occurred when the 90 3'-terminal bases of the SV5 antigenomic RNA were retained, but replication was reduced approximately 5- to 14-fold in the case of truncated antigenomes that lacked the 3'-end CRII sequences. A chimeric copyback DI RNA containing the 3'-terminal 98 bases including the CRI and CRII sequences from the human parainfluenza virus type 2 (HPIV2) antigenome in place of the corresponding SV5 sequences was efficiently replicated by SV5 cDNA-derived components. However, replication was reduced approximately 20-fold for a truncated SV5-HPIV2 chimeric RNA that lacked the HPIV2 CRII sequences between antigenome bases 72 and 90. Progressive deletions of 6 to 18 bases in the region located between the SV5 antigenomic CRI and CRII segments (3'-end nucleotides 21 to 38) resulted in a approximately 25-fold decrease in SV5-GL RNA synthesis. Surprisingly, replication was restored to wild-type levels when these length alterations between CRI and CRII were corrected by replacing the deleted bases with nonviral sequences. Together, these data suggest that a functional SV5 antigenomic promoter requires proper spacing between an essential internal region and the 3' terminus. A model is presented for the structure of the 3' end of the SV5 antigenome which proposes that positioning of CRI and CRII along the same face of the helical nucleocapsid is an essential feature of a functional antigenomic promoter.

Authors
Murphy, SK; Ito, Y; Parks, GD
MLA Citation
Murphy, SK, Ito, Y, and Parks, GD. "A functional antigenomic promoter for the paramyxovirus simian virus 5 requires proper spacing between an essential internal segment and the 3' terminus." J Virol 72.1 (January 1998): 10-19.
PMID
9420195
Source
pubmed
Published In
Journal of virology
Volume
72
Issue
1
Publish Date
1998
Start Page
10
End Page
19

Genome nucleotide lengths that are divisible by six are not essential but enhance replication of defective interfering RNAs of the paramyxovirus simian virus 5.

For some members of the Paramyxoviridae family of negative strand RNA viruses, efficient genome replication only occurs when the total genome length is a multiple of six (6N length, where N is any integer). To determine if this "rule of six" requirement applied to the replication of the prototype paramyxovirus simian virus 5 (SV5), defective interfering (DI) RNA genomes were generated by sequential undiluted passage of virus in tissue culture. Molecular cloning and nucleotide sequence analysis of 10 RNA genomes revealed a series of copyback DI RNAs with chain lengths between 449 and 1365 bases, but only 4 of the 10 naturally occurring RNA genomes were of 6N length. Many of the cloned DI genomes could be grouped into two distinct nested sets, with the members of each set having the same polymerase crossover junctions and extent of terminal complementarity but differing from each other by internal deletions. One of these nested sets of genomes consisted of novel DI RNAs that contained a pentameric stretch of nontemplated adenosine residues inserted precisely at the polymerase crossover junction. A reverse genetics system was established in which SV5 DI genomes were replicated in vivo entirely by cDNA-derived components. Using this system, two naturally occurring SV5 DI RNAs were examined in a mutational analysis to determine the role of genome length on SV5 RNA replication. The progressive insertion of one to six nucleotides into a 6N length DI genome (852 bases) resulted in a reduction in replication for RNAs that contained one to four additional bases (approximately 35-50% of WT levels), followed by an increase back to WT replication levels for genomes that were altered by five and six base insertions (approximately 70 and 100% of WT levels, respectively). An insertion of five nucleotides into a second non-6N length DI RNA (499 total bases) created a genome length that was a multiple of six (504 bases) and led to a approximately 10-fold stimulation of replication over that of the unaltered genome. Together, these results indicate that there was a clear influence of 6N genome length on SV5 DI RNA replication, but the stringency of this replication requirement appeared to be less than that found previously for other paramyxoviruses. This work completes the testing of the rule of six replication requirement for representatives of each of the four genera of the Paramyxoviridae family and indicates that the preference for replication of 6N length RNA genomes varies between the individual paramyxoviruses.

Authors
Murphy, SK; Parks, GD
MLA Citation
Murphy, SK, and Parks, GD. "Genome nucleotide lengths that are divisible by six are not essential but enhance replication of defective interfering RNAs of the paramyxovirus simian virus 5." Virology 232.1 (May 26, 1997): 145-157.
PMID
9185598
Source
pubmed
Published In
Virology
Volume
232
Issue
1
Publish Date
1997
Start Page
145
End Page
157
DOI
10.1006/viro.1997.8530

Effects of temperature abuse on survival of Vibrio vulnificus in oysters

Opaque and translucent morphotypes of a TnphoA-containing strain of Vibrio vulnificus were fed to oysters, which were subsequently stored at temperatures ranging from 0.5 to 22°C for 10 days. Samples of oysters were homogenized and plated at intervals to determine the cell density of V. vulnificus and total aerobic population of bacteria present. At all temperatures, the numbers of V. vulnificus (both morphotypes) declined over the 10-day study period. The same observation was made with a lower inoculum of V. vulnificus. Identical experiments with shucked oysters showed a more rapid decrease in V. vulnificus. Identical experiments with shucked oysters showed a more rapid decrease in V. vulnificus to levels below limits of detection. Little change in the total bacterial counts was observed in shellstock oysters at any of the test temperatures, whereas incubation at the higher temperatures (17 and 22°C) resulted in large increases in total counts in shucked oysters. These data suggest that temperature abuse of oysters may not be a factor in increasing the public health risk of V. vulnificus through raw oyster consumption. However, the data also suggest that even with proper storage, indigenous levels of V. vulnificus may remain sufficiently high in shellstock oysters to produce infection in compromised hosts.

Authors
Murphy, SK; Oliver, JD
MLA Citation
Murphy, SK, and Oliver, JD. "Effects of temperature abuse on survival of Vibrio vulnificus in oysters." Applied and Environmental Microbiology 58.9 (1992): 2771-2775.
PMID
1332610
Source
scival
Published In
Applied and Environmental Microbiology
Volume
58
Issue
9
Publish Date
1992
Start Page
2771
End Page
2775

450K epigenome-wide scan identifies differential DNA methylation in newborns related to maternal smoking during pregnancy.

BACKGROUND: Epigenetic modifications, such as DNA methylation, due to in utero exposures may play a critical role in early programming for childhood and adult illness. Maternal smoking is a major risk factor for multiple adverse health outcomes in children, but the underlying mechanisms are unclear. OBJECTIVE: We investigated epigenome-wide methylation in cord blood of newborns in relation to maternal smoking during pregnancy. METHODS: We examined maternal plasma cotinine (an objective biomarker of smoking) measured during pregnancy in relation to DNA methylation at 473,844 CpG sites (CpGs) in 1,062 newborn cord blood samples from the Norwegian Mother and Child Cohort Study (MoBa) using the Infinium HumanMethylation450 BeadChip (450K). RESULTS: We found differential DNA methylation at epigenome-wide statistical significance (p-value < 1.06 × 10-7) for 26 CpGs mapped to 10 genes. We replicated findings for CpGs in AHRR, CYP1A1, and GFI1 at strict Bonferroni-corrected statistical significance in a U.S. birth cohort. AHRR and CYP1A1 play a key role in the aryl hydrocarbon receptor signaling pathway, which mediates the detoxification of the components of tobacco smoke. GFI1 is involved in diverse developmental processes but has not previously been implicated in responses to tobacco smoke. CONCLUSIONS: We identified a set of genes with methylation changes present at birth in children whose mothers smoked during pregnancy. This is the first study of differential methylation across the genome in relation to maternal smoking during pregnancy using the 450K platform. Our findings implicate epigenetic mechanisms in the pathogenesis of the adverse health outcomes associated with this important in utero exposure.

Authors
Joubert, BR; Håberg, SE; Nilsen, RM; Wang, X; Vollset, SE; Murphy, SK; Huang, Z; Hoyo, C; Midttun, Ø; Cupul-Uicab, LA; Ueland, PM; Wu, MC; Nystad, W; Bell, DA; Peddada, SD; London, SJ
MLA Citation
Joubert, BR, Håberg, SE, Nilsen, RM, Wang, X, Vollset, SE, Murphy, SK, Huang, Z, Hoyo, C, Midttun, Ø, Cupul-Uicab, LA, Ueland, PM, Wu, MC, Nystad, W, Bell, DA, Peddada, SD, and London, SJ. "450K epigenome-wide scan identifies differential DNA methylation in newborns related to maternal smoking during pregnancy." Environ Health Perspect 120.10: 1425-1431.
PMID
22851337
Source
pubmed
Published In
Environmental health perspectives
Volume
120
Issue
10
Start Page
1425
End Page
1431
DOI
10.1289/ehp.1205412
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