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Cheng, Qing

Overview:

My research has been focusing on the development of methodologies and strategies to address the general question of human cancer heterogeneity and complexity, recognizing that clinical outcomes reflect a combination of contribution from the actual tumor but also the environment in which the tumor resides. By understanding who is at risk for recurrence, who is likely to respond to a given agent or regimen, and who is likely to exhibit an adverse event associated with a particular therapy, it will be possible to tailor therapeutic strategies to the characteristics of the individual patient as opposed to relying on the results of studies with heterogeneous populations of patients.

I made the original observation that gene copy number alterations (CNAs) in malignant cells can quantitatively affect gene function (Nat Genet 2005), and the contribution of this work to the field of cancer pharmacogenomics and personalized medicine was highly recognized by a "NEWS AND VIEWS" paper of Nature Genetics, in 2005. I demonstrated that clinical phenotypes can be affected by multiple forms of alterations (methylation, mutation, CNA) (Am J Hum Genet 2006), and genome-scan of CNAs followed by pathway analysis could uncover the novel gene interactions (Nat Med 2011). We developed a methodology that compiled a large collection of genomic data (Breast Cancer Res 2012) and demonstrated that uniquely characteristic of a clinical phenotype, such as dormancy, could be accessed using gene signature, a collection of multiple genetic alterations (Breast Cancer Res 2014).

Positions:

Associate Professor in Surgery

Surgery, Surgical Sciences
School of Medicine

Member of the Duke Cancer Institute

Duke Cancer Institute
School of Medicine

Education:

Ph.D. 2001

Ph.D. — National University of Singapore

Postdoctoral Research Associate

St. Jude Children's Research Hospital

Grants:

A Molecular Framework for Understanding DCIS

Administered By
Surgery, Surgical Sciences
AwardedBy
Department of Defense
Role
Co Investigator
Start Date
September 30, 2014
End Date
September 29, 2019

Developing a HER3 Vaccine to Prevent Resistance to Endocrine Therapy

Administered By
Surgery, Surgical Sciences
AwardedBy
Department of Defense
Role
Co Investigator
Start Date
September 30, 2012
End Date
September 29, 2018

Oncogenic Signaling Networks

Administered By
Surgery, Surgical Sciences
AwardedBy
Department of Defense
Role
Co Investigator
Start Date
September 30, 2012
End Date
September 29, 2018

Advancing Immunology in Dogs with Naturally-occurring Invasive Bladder Cancer, a Relevant Model to Improve Immunotherapy Across Molecular Cancer Subtypes in Humans

Administered By
Surgery, Surgical Sciences
AwardedBy
Purdue University
Role
Co Investigator
Start Date
July 01, 2016
End Date
June 30, 2017

Automated Library Preparation System for Next-Generation Sequencing

Administered By
Biology
AwardedBy
North Carolina Biotechnology Center
Role
Major User
Start Date
September 15, 2014
End Date
September 14, 2015

Clinical Oncology Research Career Development Program

Administered By
Surgery, Surgical Sciences
AwardedBy
National Institutes of Health
Role
Research Candidate
Start Date
September 29, 2009
End Date
July 31, 2015
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Publications:

A novel integrative risk index of papillary thyroid cancer progression combining genomic alterations and clinical factors.

Although the majority of papillary thyroid cancer (PTC) is indolent, a subset of PTC behaves aggressively despite the best available treatment. A major clinical challenge is to reliably distinguish early on between those patients who need aggressive treatment from those who do not. Using a large cohort of PTC samples obtained from The Cancer Genome Atlas (TCGA), we analyzed the association between disease progression and multiple forms of genomic data, such as transcriptome, somatic mutations, and somatic copy number alterations, and found that genes related to FOXM1 signaling pathway were significantly associated with PTC progression. Integrative genomic modeling was performed, controlling for demographic and clinical characteristics, which included patient age, gender, TNM stages, histological subtypes, and history of other malignancy, using a leave-one-out elastic net model and 10-fold cross validation. For each subject, the model from the remaining subjects was used to determine the risk index, defined as a linear combination of the clinical and genomic variables from the elastic net model, and the stability of the risk index distribution was assessed through 2,000 bootstrap resampling. We developed a novel approach to combine genomic alterations and patient-related clinical factors that delineates the subset of patients who have more aggressive disease from those whose tumors are indolent and likely will require less aggressive treatment and surveillance (p = 4.62 × 10-10, log-rank test). Our results suggest that risk index modeling that combines genomic alterations with current staging systems provides an opportunity for more effective anticipation of disease prognosis and therefore enhanced precision management of PTC.

Authors
Cheng, Q; Li, X; Acharya, CR; Hyslop, T; Sosa, JA
MLA Citation
Cheng, Q, Li, X, Acharya, CR, Hyslop, T, and Sosa, JA. "A novel integrative risk index of papillary thyroid cancer progression combining genomic alterations and clinical factors." Oncotarget 8.10 (March 2017): 16690-16703.
PMID
28187428
Source
epmc
Published In
Oncotarget
Volume
8
Issue
10
Publish Date
2017
Start Page
16690
End Page
16703
DOI
10.18632/oncotarget.15128

Dormant breast cancer micrometastases reside in specific bone marrow niches that regulate their transit to and from bone.

Breast cancer metastatic relapse can occur years after therapy, indicating that disseminated breast cancer cells (BCCs) have a prolonged dormant phase before becoming proliferative. A major site of disease dissemination and relapse is bone, although the critical signals that allow circulating BCCs to identify bone microvasculature, enter tissue, and tether to the microenvironment are poorly understood. Using real-time in vivo microscopy of bone marrow (BM) in a breast cancer xenograft model, we show that dormant and proliferating BCCs occupy distinct areas, with dormant BCCs predominantly found in E-selectin- and stromal cell-derived factor 1 (SDF-1)-rich perisinusoidal vascular regions. We use highly specific inhibitors of E-selectin and C-X-C chemokine receptor type 4 (CXCR4) (SDF-1 receptor) to demonstrate that E-selectin and SDF-1 orchestrate opposing roles in BCC trafficking. Whereas E-selectin interactions are critical for allowing BCC entry into the BM, the SDF-1/CXCR4 interaction anchors BCCs to the microenvironment, and its inhibition induces mobilization of dormant micrometastases into circulation. Homing studies with primary BCCs also demonstrate that E-selectin regulates their entry into bone through the sinusoidal niche, and immunohistochemical staining of patient BMs shows dormant micrometastatic disease adjacent to SDF-1(+) vasculature. These findings shed light on how BCCs traffic within the host, and suggest that simultaneous blockade of CXCR4 and E-selectin in patients could molecularly excise dormant micrometastases from the protective BM environment, preventing their emergence as relapsed disease.

Authors
Price, TT; Burness, ML; Sivan, A; Warner, MJ; Cheng, R; Lee, CH; Olivere, L; Comatas, K; Magnani, J; Kim Lyerly, H; Cheng, Q; McCall, CM; Sipkins, DA
MLA Citation
Price, TT, Burness, ML, Sivan, A, Warner, MJ, Cheng, R, Lee, CH, Olivere, L, Comatas, K, Magnani, J, Kim Lyerly, H, Cheng, Q, McCall, CM, and Sipkins, DA. "Dormant breast cancer micrometastases reside in specific bone marrow niches that regulate their transit to and from bone." Science translational medicine 8.340 (May 2016): 340ra73-.
PMID
27225183
Source
epmc
Published In
Science Translational Medicine
Volume
8
Issue
340
Publish Date
2016
Start Page
340ra73
DOI
10.1126/scitranslmed.aad4059

Abstract 3212: Metastatic breast cancer cell communication within a pro-dormancy bone marrow niche

Authors
Price, TT; Lee, CH; Cheng, Q; Lyerly, HK; Fogler, WE; Magnani, JL; Sipkins, DA
MLA Citation
Price, TT, Lee, CH, Cheng, Q, Lyerly, HK, Fogler, WE, Magnani, JL, and Sipkins, DA. "Abstract 3212: Metastatic breast cancer cell communication within a pro-dormancy bone marrow niche." August 1, 2015.
Source
crossref
Published In
Cancer Research
Volume
75
Issue
15 Supplement
Publish Date
2015
Start Page
3212
End Page
3212
DOI
10.1158/1538-7445.AM2015-3212

Effect of alphavirus vaccine encoding HER2 during concurrent anti-HER2 therapies on induction of oligoclonal T cell and antibody responses against HER2.

Authors
Gwin, WR; Hobeika, A; Osada, T; Hartman, Z; Cheng, Q; Broadwater, G; Kimmick, GG; Blackwell, KL; Morse, M; Lyerly, K
MLA Citation
Gwin, WR, Hobeika, A, Osada, T, Hartman, Z, Cheng, Q, Broadwater, G, Kimmick, GG, Blackwell, KL, Morse, M, and Lyerly, K. "Effect of alphavirus vaccine encoding HER2 during concurrent anti-HER2 therapies on induction of oligoclonal T cell and antibody responses against HER2." May 20, 2015.
Source
wos-lite
Published In
Journal of Clinical Oncology
Volume
33
Issue
15
Publish Date
2015

Stevens-Johnson syndrome induced by the cross-reactivity between teicoplanin and vancomycin.

WHAT IS KNOWN AND OBJECTIVE: The glycopeptide antibiotics, vancomycin and teicoplanin, are the mainstay of therapy for severe gram-positive organisms such as methicillin-resistant Staphylococcus aureus. We report a case of Stevens-Johnson syndrome (SJS) induced by sequential therapy with teicoplanin and vancomycin, in a patient with chronic obstructive pulmonary disease (COPD). CASE SUMMARY: A 74-year-old Han Chinese with 1-year history of COPD was admitted for treatment of infective endocarditis. After teicoplanin therapy for 12 days, he developed pruritus and maculopapular over his trunk and limbs. His rash spread rapidly to most parts of the body surface area, 7 days after his anti-infection therapy was switched to vancomycin. This was stopped, but he developed SJS when teicoplanin was re-introduced. This patient recovered from his drug eruptions when both teicoplanin and vancomycin were stopped. Pharmacogenetic analyses revealed he was heterozygous with respect to two variants (rs2844682 of MUC21 and rs750332 of BAG6). WHAT IS NEW AND CONCLUSION: Cross-reactivity between vancomycin and teicoplanin is rare. SJS attributable to sequential treatment with these two antibiotics has not been reported previously. Care should be taken when prescribing vancomycin in patients with a previous documented skin eruption to teicoplanin, especially in those who carry any susceptibility alleles to SJS/TEN.

Authors
Yang, L-P; Zhang, A-L; Wang, D-D; Ke, H-X; Cheng, Q; Wang, C
MLA Citation
Yang, L-P, Zhang, A-L, Wang, D-D, Ke, H-X, Cheng, Q, and Wang, C. "Stevens-Johnson syndrome induced by the cross-reactivity between teicoplanin and vancomycin." Journal of clinical pharmacy and therapeutics 39.4 (August 2014): 442-445.
PMID
24716778
Source
epmc
Published In
Journal of Clinical Pharmacy & Therapeutics
Volume
39
Issue
4
Publish Date
2014
Start Page
442
End Page
445
DOI
10.1111/jcpt.12159

A signature of epithelial-mesenchymal plasticity and stromal activation in primary tumor modulates late recurrence in breast cancer independent of disease subtype.

Despite improvements in adjuvant therapy, late systemic recurrences remain a lethal consequence of both early- and late-stage breast cancer. A delayed recurrence is thought to arise from a state of tumor dormancy, but the mechanisms that govern tumor dormancy remain poorly understood.To address the features of breast tumors associated with late recurrence, but not confounded by variations in systemic treatment, we compiled breast tumor gene expression data from 4,767 patients and established a discovery cohort consisting of 743 lymph node-negative patients who did not receive systemic neoadjuvant or adjuvant therapy. We interrogated the gene expression profiles of the 743 tumors and identified gene expression patterns that were associated with early and late disease recurrence among these patients. We applied this classification to a subset of 46 patients for whom expression data from microdissected tumor epithelium and stroma was available, and identified a distinct gene signature in the stroma and also a corresponding tumor epithelium signature that predicted disease recurrence in the discovery cohort. This tumor epithelium signature was then validated as a predictor for late disease recurrence in the entire cohort of 4,767 patients.We identified a novel 51-gene signature from microdissected tumor epithelium associated with late disease recurrence in breast cancer independent of the molecular disease subtype. This signature correlated with gene expression alterations in the adjacent tumor stroma and describes a process of epithelial to mesenchymal transition (EMT) and tumor-stroma interactions.Our findings suggest that an EMT-related gene signature in the tumor epithelium is related to both stromal activation and escape from disease dormancy in breast cancer. The presence of a late recurrence gene signature in the primary tumor also suggests that intrinsic features of this tumor regulate the transition of disseminated tumor cells into a dormant phenotype with the ability to outgrowth as recurrent disease.

Authors
Cheng, Q; Chang, JT; Gwin, WR; Zhu, J; Ambs, S; Geradts, J; Lyerly, HK
MLA Citation
Cheng, Q, Chang, JT, Gwin, WR, Zhu, J, Ambs, S, Geradts, J, and Lyerly, HK. "A signature of epithelial-mesenchymal plasticity and stromal activation in primary tumor modulates late recurrence in breast cancer independent of disease subtype." Breast cancer research : BCR 16.4 (July 25, 2014): 407-.
PMID
25060555
Source
epmc
Published In
Breast Cancer Research
Volume
16
Issue
4
Publish Date
2014
Start Page
407
DOI
10.1186/s13058-014-0407-9

Overexpression of the EMT driver brachyury in breast carcinomas: association with poor prognosis.

The epithelial-mesenchymal transition (EMT) has been implicated as an important process in tumor cell invasion, metastasis, and drug resistance. The transcription factor brachyury has recently been described as a driver of EMT of human carcinoma cells.Brachyury mRNA and protein expression was analyzed in human breast carcinomas and benign tissues. The role of brachyury in breast tumor prognosis and drug resistance and the ability of brachyury-specific T cells to lyse human breast carcinoma cells were also evaluated. Kaplan-Meier analyses were used to evaluate the association between brachyury expression and survival. All statistical tests were two-sided.The level of brachyury expression in breast cancer cells was positively associated with their ability to invade the extracellular matrix, efficiently form mammospheres in vitro, and resist the cytotoxic effect of docetaxel. A comparison of survival among breast cancer patients treated with tamoxifen in the adjuvant setting who had tumors with high vs low brachyury mRNA expression demonstrated that high expression of brachyury is associated as an independent variable with higher risk of recurrence (hazard ratio [HR] = 7.5; 95% confidence interval [CI] = 2.4 to 23.5; P = 5.14×10(-4)) and distant metastasis (HR = 15.2; 95% CI = 3.5 to 66.3; P = 3.01×10(-4)). We also demonstrated that brachyury-specific T cells can lyse human breast carcinoma cells.The studies reported here provide the rationale for the use of a vaccine targeting brachyury for the therapy of human breast cancer, either as a monotherapy or in combination therapies.

Authors
Palena, C; Roselli, M; Litzinger, MT; Ferroni, P; Costarelli, L; Spila, A; Cavaliere, F; Huang, B; Fernando, RI; Hamilton, DH; Jochems, C; Tsang, K-Y; Cheng, Q; Lyerly, HK; Schlom, J; Guadagni, F
MLA Citation
Palena, C, Roselli, M, Litzinger, MT, Ferroni, P, Costarelli, L, Spila, A, Cavaliere, F, Huang, B, Fernando, RI, Hamilton, DH, Jochems, C, Tsang, K-Y, Cheng, Q, Lyerly, HK, Schlom, J, and Guadagni, F. "Overexpression of the EMT driver brachyury in breast carcinomas: association with poor prognosis." Journal of the National Cancer Institute 106.5 (May 9, 2014).
PMID
24815864
Source
epmc
Published In
Journal of the National Cancer Institute
Volume
106
Issue
5
Publish Date
2014
DOI
10.1093/jnci/dju054

Immunologic targeting of FOXP3 in inflammatory breast cancer cells.

The forkhead transcription factor FOXP3 is necessary for induction of regulatory T lymphocytes (Tregs) and their immunosuppressive function. We have previously demonstrated that targeting Tregs by vaccination of mice with murine FOXP3 mRNA-transfected dendritic cells (DCs) elicits FOXP3-specific T cell responses and enhances tumor immunity. It is clear that FOXP3 expression is not restricted to T-cell lineage and herein, using RT-PCR, flow cytometry, and western immunoblot we demonstrate for the first time that FOXP3 is expressed in inflammatory breast cancer (IBC) cells, SUM149 (triple negative, ErbB1-activated) and SUM190 (ErbB2-overexpressing). Importantly, FOXP3-specific T cells generated in vitro using human FOXP3 RNA-transfected DCs as stimulators efficiently lyse SUM149 cells. Interestingly, an isogenic model (rSUM149) derived from SUM149 with an enhanced anti-apoptotic phenotype was resistant to FOXP3-specific T cell mediated lysis. The MHC class I cellular processing mechanism was intact in both cell lines at the protein and transcription levels suggesting that the resistance to cytolysis by rSUM149 cells was not related to MHC class I expression or to the MHC class I antigen processing machinery in these cells. Our data suggest that FOXP3 may be an effective tumor target in IBC cells however increased anti-apoptotic signaling can lead to immune evasion.

Authors
Nair, S; Aldrich, AJ; McDonnell, E; Cheng, Q; Aggarwal, A; Patel, P; Williams, MM; Boczkowski, D; Lyerly, HK; Morse, MA; Devi, GR
MLA Citation
Nair, S, Aldrich, AJ, McDonnell, E, Cheng, Q, Aggarwal, A, Patel, P, Williams, MM, Boczkowski, D, Lyerly, HK, Morse, MA, and Devi, GR. "Immunologic targeting of FOXP3 in inflammatory breast cancer cells." PLoS One 8.1 (2013): e53150-.
PMID
23341929
Source
pubmed
Published In
PloS one
Volume
8
Issue
1
Publish Date
2013
Start Page
e53150
DOI
10.1371/journal.pone.0053150

An heregulin-EGFR-HER3 autocrine signaling axis can mediate acquired lapatinib resistance in HER2+ breast cancer models.

INTRODUCTION: The human epidermal growth factor receptor 2 (HER2) receptor tyrosine kinase (RTK) oncogene is an attractive therapeutic target for the treatment of HER2-addicted tumors. Although lapatinib, an FDA-approved small-molecule HER2 and epidermal growth factor receptor (EGFR) tyrosine kinase inhibitor (TKI), represents a significant therapeutic advancement in the treatment of HER2+ breast cancers, responses to lapatinib have not been durable. Consequently, elucidation of mechanisms of acquired therapeutic resistance to HER-directed therapies is of critical importance. METHODS: Using a functional protein-pathway activation mapping strategy, along with targeted genomic knockdowns applied to a series of isogenic-matched pairs of lapatinib-sensitive and resistant cell lines, we now report an unexpected mechanism of acquired resistance to lapatinib and similar TKIs. RESULTS: The signaling analysis revealed that whereas HER2 was appropriately inhibited in lapatinib-resistant cells, EGFR tyrosine phosphorylation was incompletely inhibited. Using a targeted molecular knockdown approach to interrogate the causal molecular underpinnings of EGFR-persistent activation, we found that lapatinib-resistant cells were no longer oncogene addicted to HER2-HER3-PI3K signaling, as seen in the parental lapatinib-sensitive cell lines, but instead were dependent on a heregulin (HRG)-driven HER3-EGFR-PI3K-PDK1 signaling axis. Two FDA-approved EGFR TKIs could not overcome HRG-HER3-mediated activation of EGFR, or reverse lapatinib resistance. The ability to overcome EGFR-mediated acquired therapeutic resistance to lapatinib was demonstrated through molecular knockdown of EGFR and treatment with the irreversible pan-HER TKI neratinib, which blocked HRG-dependent phosphorylation of HER3 and EGFR, resulting in apoptosis of resistant cells. In addition, whereas HRG reversed lapatinib-mediated antitumor effects in parental HER2+ breast cancer cells, neratinib was comparatively resistant to the effects of HRG in parental cells. Finally, we showed that HRG expression is an independent negative predictor of clinical outcome in HER2+ breast cancers, providing potential clinical relevance to our findings. CONCLUSIONS: Molecular analysis of acquired therapeutic resistance to lapatinib identified a new resistance mechanism based on incomplete and "leaky" inhibition of EGFR by lapatinib. The selective pressure applied by incomplete inhibition of the EGFR drug target resulted in selection of ligand-driven feedback that sustained EGFR activation in the face of constant exposure to the drug. Inadequate target inhibition driven by a ligand-mediated autocrine feedback loop may represent a broader mechanism of therapeutic resistance to HER TKIs and suggests adopting a different strategy for selecting more effective TKIs to advance into the clinic.

Authors
Xia, W; Petricoin, EF; Zhao, S; Liu, L; Osada, T; Cheng, Q; Wulfkuhle, JD; Gwin, WR; Yang, X; Gallagher, RI; Bacus, S; Lyerly, HK; Spector, NL
MLA Citation
Xia, W, Petricoin, EF, Zhao, S, Liu, L, Osada, T, Cheng, Q, Wulfkuhle, JD, Gwin, WR, Yang, X, Gallagher, RI, Bacus, S, Lyerly, HK, and Spector, NL. "An heregulin-EGFR-HER3 autocrine signaling axis can mediate acquired lapatinib resistance in HER2+ breast cancer models." Breast Cancer Res 15.5 (2013): R85-.
PMID
24044505
Source
pubmed
Published In
Breast Cancer Research
Volume
15
Issue
5
Publish Date
2013
Start Page
R85
DOI
10.1186/bcr3480

Amplification and high-level expression of heat shock protein 90 marks aggressive phenotypes of human epidermal growth factor receptor 2 negative breast cancer.

INTRODUCTION: Although human epidermal growth factor receptor 2 (HER2) positive or estrogen receptor (ER) positive breast cancers are treated with clinically validated anti-HER2 or anti-estrogen therapies, intrinsic and acquired resistance to these therapies appears in a substantial proportion of breast cancer patients and new therapies are needed. Identification of additional molecular factors, especially those characterized by aggressive behavior and poor prognosis, could prioritize interventional opportunities to improve the diagnosis and treatment of breast cancer. METHODS: We compiled a collection of 4,010 breast tumor gene expression data derived from 23 datasets that have been posted on the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO) database. We performed a genome-scale survival analysis using Cox-regression survival analyses, and validated using Kaplan-Meier Estimates survival and Cox Proportional-Hazards Regression survival analyses. We conducted a genome-scale analysis of chromosome alteration using 481 breast cancer samples obtained from The Cancer Genome Atlas (TCGA), from which combined expression and copy number data were available. We assessed the correlation between somatic copy number alterations and gene expression using analysis of variance (ANOVA). RESULTS: Increased expression of each of the heat shock protein (HSP) 90 isoforms, as well as HSP transcriptional factor 1 (HSF1), was correlated with poor prognosis in different subtypes of breast cancer. High-level expression of HSP90AA1 and HSP90AB1, two cytoplasmic HSP90 isoforms, was driven by chromosome coding region amplifications and were independent factors that led to death from breast cancer among patients with triple-negative (TNBC) and HER2-/ER+ subtypes, respectively. Furthermore, amplification of HSF1 was correlated with higher HSP90AA1 and HSP90AB1 mRNA expression among the breast cancer cells without amplifications of these two genes. A collection of HSP90AA1, HSP90AB1 and HSF1 amplifications defined a subpopulation of breast cancer with up-regulated HSP90 gene expression, and up-regulated HSP90 expression independently elevated the risk of recurrence of TNBC and poor prognosis of HER2-/ER+ breast cancer. CONCLUSIONS: Up-regulated HSP90 mRNA expression represents a confluence of genomic vulnerability that renders HER2 negative breast cancers more aggressive, resulting in poor prognosis. Targeting breast cancer with up-regulated HSP90 may potentially improve the effectiveness of clinical intervention in this disease.

Authors
Cheng, Q; Chang, JT; Geradts, J; Neckers, LM; Haystead, T; Spector, NL; Lyerly, HK
MLA Citation
Cheng, Q, Chang, JT, Geradts, J, Neckers, LM, Haystead, T, Spector, NL, and Lyerly, HK. "Amplification and high-level expression of heat shock protein 90 marks aggressive phenotypes of human epidermal growth factor receptor 2 negative breast cancer. (Published online)" Breast Cancer Res 14.2 (April 17, 2012): R62-.
PMID
22510516
Source
pubmed
Published In
Breast Cancer Research
Volume
14
Issue
2
Publish Date
2012
Start Page
R62
DOI
10.1186/bcr3168

Somatic deletions of genes regulating MSH2 protein stability cause DNA mismatch repair deficiency and drug resistance in human leukemia cells.

DNA mismatch repair enzymes (for example, MSH2) maintain genomic integrity, and their deficiency predisposes to several human cancers and to drug resistance. We found that leukemia cells from a substantial proportion of children (∼11%) with newly diagnosed acute lymphoblastic leukemia have low or undetectable MSH2 protein levels, despite abundant wild-type MSH2 mRNA. Leukemia cells with low levels of MSH2 contained partial or complete somatic deletions of one to four genes that regulate MSH2 degradation (FRAP1 (also known as MTOR), HERC1, PRKCZ and PIK3C2B); we also found these deletions in individuals with adult acute lymphoblastic leukemia (16%) and sporadic colorectal cancer (13.5%). Knockdown of these genes in human leukemia cells recapitulated the MSH2 protein deficiency by enhancing MSH2 degradation, leading to substantial reduction in DNA mismatch repair and increased resistance to thiopurines. These findings reveal a previously unrecognized mechanism whereby somatic deletions of genes regulating MSH2 degradation result in undetectable levels of MSH2 protein in leukemia cells, DNA mismatch repair deficiency and drug resistance.

Authors
Diouf, B; Cheng, Q; Krynetskaia, NF; Yang, W; Cheok, M; Pei, D; Fan, Y; Cheng, C; Krynetskiy, EY; Geng, H; Chen, S; Thierfelder, WE; Mullighan, CG; Downing, JR; Hsieh, P; Pui, C-H; Relling, MV; Evans, WE
MLA Citation
Diouf, B, Cheng, Q, Krynetskaia, NF, Yang, W, Cheok, M, Pei, D, Fan, Y, Cheng, C, Krynetskiy, EY, Geng, H, Chen, S, Thierfelder, WE, Mullighan, CG, Downing, JR, Hsieh, P, Pui, C-H, Relling, MV, and Evans, WE. "Somatic deletions of genes regulating MSH2 protein stability cause DNA mismatch repair deficiency and drug resistance in human leukemia cells. (Published online)" Nat Med 17.10 (September 25, 2011): 1298-1303.
PMID
21946537
Source
pubmed
Published In
Nature Medicine
Volume
17
Issue
10
Publish Date
2011
Start Page
1298
End Page
1303
DOI
10.1038/nm.2430

Epigenetic regulation of human gamma-glutamyl hydrolase activity in acute lymphoblastic leukemia cells.

Gamma-glutamyl hydrolase (GGH) catalyzes degradation of the active polyglutamates of natural folates and the antifolate methotrexate (MTX). We found that GGH activity is directly related to GGH messenger RNA expression in acute lymphoblastic leukemia (ALL) cells of patients with a wild-type germline GGH genotype. We identified two CpG islands (CpG1 and CpG2) in the region extending from the GGH promoter through the first exon and into intron 1 and showed that methylation of both CpG islands in the GGH promoter (seen in leukemia cells from approximately 15% of patients with nonhyperdiploid B-lineage ALL) is associated with significantly reduced GGH mRNA expression and catalytic activity and with significantly higher accumulation of MTX polyglutamates (MTXPG(4-7)) in ALL cells. Furthermore, methylation of CpG1 was leukemia-cell specific and had a pronounced effect on GGH expression, whereas methylation of CpG2 was common in leukemia cells and normal leukocytes but did not significantly alter GGH expression. These findings indicate that GGH activity in human leukemia cells is regulated by epigenetic changes, in addition to previously recognized genetic polymorphisms and karyotypic abnormalities, which collectively determine interindividual differences in GGH activity and influence MTXPG accumulation in leukemia cells.

Authors
Cheng, Q; Cheng, C; Crews, KR; Ribeiro, RC; Pui, C-H; Relling, MV; Evans, WE
MLA Citation
Cheng, Q, Cheng, C, Crews, KR, Ribeiro, RC, Pui, C-H, Relling, MV, and Evans, WE. "Epigenetic regulation of human gamma-glutamyl hydrolase activity in acute lymphoblastic leukemia cells." Am J Hum Genet 79.2 (August 2006): 264-274.
PMID
16826517
Source
pubmed
Published In
The American Journal of Human Genetics
Volume
79
Issue
2
Publish Date
2006
Start Page
264
End Page
274
DOI
10.1086/505645

Cancer pharmacogenomics may require both qualitative and quantitative approaches.

Resistance to chemotherapy is a major cause of mortality in patients receiving treatment for most types of cancer, and overcoming drug resistance has become an important focus of current research. A major clinical challenge is the fact that most anticancer drugs have a narrow therapeutic range, that is, their effective dose is relatively close to that associated with substantial toxicity. Significant advances have been achieved in event-free survival of patients with many types of cancer (most dramatically childhood acute lymphoblastic leukemia, ALL) through a better understanding of the pathobiology of human cancers, the cellular mechanisms of cancer chemotherapy, and the determinants of inter-individual differences in drug effects and treatment response. It is anticipated that expanding our knowledge of these areas will lead to the development of new anticancer agents and to more effective use of existing cancer chemotherapy. Pharmacogenomics research aims to elucidate the genetics determinants of drug efficacy and toxicity. Results of recent studies indicate that both qualitative and quantitative genomic analyses may be required for precise pharmacogenomic characterization of some types of human cancer.

Authors
Cheng, Q; Evans, WE
MLA Citation
Cheng, Q, and Evans, WE. "Cancer pharmacogenomics may require both qualitative and quantitative approaches." Cell Cycle 4.11 (November 2005): 1506-1509. (Review)
PMID
16258271
Source
pubmed
Published In
Cell Cycle
Volume
4
Issue
11
Publish Date
2005
Start Page
1506
End Page
1509
DOI
10.4161/cc.4.11.2160

Karyotypic abnormalities create discordance of germline genotype and cancer cell phenotypes.

The nature of mendelian inheritance assumes that all tissues in which a phenotype of interest is expressed have a uniform diploid karyotype, which is often not the case in cancer cells. Owing to nonrandom gains of chromosomes, trisomies are present in many cases of leukemia and other malignances. We used polymorphisms in the genes encoding thiopurine S-methyltransferase (TPMT), gamma-glutamyl hydrolase (GGH) and the reduced folate carrier (SLC19A1) to assess the nature of chromosomal acquisition and its influence on genotype-phenotype concordance in cancer cells. TPMT and GGH activities in somatic cells were concordant with germline genotypes, whereas activities in leukemia cells were determined by chromosomal number and whether the acquired chromosomes contained a wild-type or variant allele. Leukemia cells that had acquired an additional chromosome containing a wild-type TPMT or GGH allele had significantly lower accumulation of thioguanine nucleotides or methotrexate polyglutamates, respectively. Among these genes, there was a comparable number of acquired chromosomes with wild-type and variant alleles. Therefore, chromosomal gain can alter the concordance of germline genotype and cancer cell phenotypes, indicating that allele-specific quantitative genotyping may be required to define cancer pharmacogenomics unequivocally.

Authors
Cheng, Q; Yang, W; Raimondi, SC; Pui, C-H; Relling, MV; Evans, WE
MLA Citation
Cheng, Q, Yang, W, Raimondi, SC, Pui, C-H, Relling, MV, and Evans, WE. "Karyotypic abnormalities create discordance of germline genotype and cancer cell phenotypes." Nat Genet 37.8 (August 2005): 878-882.
PMID
16041371
Source
pubmed
Published In
Nature Genetics
Volume
37
Issue
8
Publish Date
2005
Start Page
878
End Page
882
DOI
10.1038/ng1612

Folate pathway gene expression differs in subtypes of acute lymphoblastic leukemia and influences methotrexate pharmacodynamics.

The ability of leukemia cells to accumulate methotrexate polyglutamate (MTXPG) is an important determinant of the antileukemic effects of methotrexate (MTX). We measured in vivo MTXPG accumulation in leukemia cells from 101 children with acute lymphoblastic leukemia (ALL) and established that B-lineage ALL with either TEL-AML1 or E2A-PBX1 gene fusion, or T-lineage ALL, accumulates significantly lower MTXPG compared with B-lineage ALL without these genetic abnormalities or compared with hyperdiploid (fewer than 50 chromosomes) ALL. To elucidate mechanisms underlying these differences in MTXPG accumulation, we used oligonucleotide microarrays to analyze expression of 32 folate pathway genes in diagnostic leukemia cells from 197 children. This revealed ALL subtype-specific patterns of folate pathway gene expression that were significantly related to MTXPG accumulation. We found significantly lower expression of the reduced folate carrier (SLC19A1, an MTX uptake transporter) in E2A-PBX1 ALL, significantly higher expression of breast cancer resistance protein (ABCG2, an MTX efflux transporter) in TEL-AML1 ALL, and lower expression of FPGS (which catalyzes formation of MTXPG) in T-lineage ALL, consistent with lower MTXPG accumulation in these ALL subtypes. These findings reveal distinct mechanisms of subtype-specific differences in MTXPG accumulation and point to new strategies to overcome these potential causes of treatment failure in childhood ALL.

Authors
Kager, L; Cheok, M; Yang, W; Zaza, G; Cheng, Q; Panetta, JC; Pui, C-H; Downing, JR; Relling, MV; Evans, WE
MLA Citation
Kager, L, Cheok, M, Yang, W, Zaza, G, Cheng, Q, Panetta, JC, Pui, C-H, Downing, JR, Relling, MV, and Evans, WE. "Folate pathway gene expression differs in subtypes of acute lymphoblastic leukemia and influences methotrexate pharmacodynamics." J Clin Invest 115.1 (January 2005): 110-117.
PMID
15630450
Source
pubmed
Published In
Journal of Clinical Investigation
Volume
115
Issue
1
Publish Date
2005
Start Page
110
End Page
117
DOI
10.1172/JCI22477

A substrate specific functional polymorphism of human gamma-glutamyl hydrolase alters catalytic activity and methotrexate polyglutamate accumulation in acute lymphoblastic leukaemia cells.

We found a significant inverse relationship between gamma-glutamyl hydrolase (GGH) activity and the accumulation of long-chain methotrexate polyglutamates (MTXPG4-7) in non-hyperdiploid B-lineage acute lymphoblastic leukaemia (ALL) cells after uniform treatment with high-dose methotrexate (HDMTX) (1 g/m i.v.). To identify genetic polymorphisms that alter the function of human GGH, we sequenced the GGH exons of genomic DNA from children with ALL, who had a 7.8-fold range of GGH activity in their ALL cells at diagnosis. A single nucleotide polymorphism (452C>T, T127I) was found among patients with low GGH activity, but not found in patients with high GGH activity. Computational modelling indicated that the T127I substitution alters the molecular surface conformation at the catalytic cleft-tail on GGH, which is predicted to alter binding affinity with long chain but not short-chain methotrexate polyglutamates. Enzyme kinetic analysis of heterologously expressed GGH revealed a significantly higher Km (2.7-fold) and lower catalytic efficiency (Vmax/Km reduced 67%) of the T127I variant compared to wild-type GGH using long-chain MTXPG5 as substrate, but not a significant change with short-chain MTXPG2. The 452C>T single nucleotide polymorphism (SNP) was also associated with lower GGH activity in hyperdiploid B-lineage and T lineage ALL cells. Caucasians [10.0%; 95% confidence interval (CI) 6.7-13.3%; n = 155] were found to have a significantly higher frequency of the Ile allele than African-Americans (4.4%; 95% CI 1.2-7.5%; n = 80) (P = 0.033). These studies demonstrate a substrate specific functional SNP (452C>T) in the human GGH gene that is associated with lower catalytic activity and higher accumulation of long-chain MTX-PG in leukaemia cells of patients treated with HDMTX.

Authors
Cheng, Q; Wu, B; Kager, L; Panetta, JC; Zheng, J; Pui, C-H; Relling, MV; Evans, WE
MLA Citation
Cheng, Q, Wu, B, Kager, L, Panetta, JC, Zheng, J, Pui, C-H, Relling, MV, and Evans, WE. "A substrate specific functional polymorphism of human gamma-glutamyl hydrolase alters catalytic activity and methotrexate polyglutamate accumulation in acute lymphoblastic leukaemia cells." Pharmacogenetics 14.8 (August 2004): 557-567.
PMID
15284538
Source
pubmed
Published In
Pharmacogenetics and Genomics
Volume
14
Issue
8
Publish Date
2004
Start Page
557
End Page
567

Identification and characterization of genes involved in the carcinogenesis of human squamous cell cervical carcinoma.

We utilized RT-PCR differential display and cDNA microarrays to identify cellular genes involved in the multi-step carcinogenesis of squamous cell cervical carcinoma. Thirty-eight cervical cancer patients in various stages of the disease and 5 non-cervical cancer patients were studied. Twenty-five cDNA clones were identified and these were subsequently demonstrated to be consistently over-expressed in squamous cell cervical carcinoma biopsies of various FIGO stages. To further evaluate the possible role that these genes may play in the progression of disease, we performed Northern blot analysis and RNA-RNA in situ hybridization studies using cervical cancer biopsies of various FIGO stages. Of particular interest are the 2 clones G32C4B and G30CC that have been identified to be the NADH dehydrogenase 4 gene and the gene that encodes ribosomal protein S12 respectively when compared to sequences available in the GenBank database. Increased expression of these 2 genes were detected in the matched normal tissues collected together with the late FIGO stages of cervical cancer biopsies. In comparison, upregulation of these 2 genes was not detected in cervical squamous epithelium collected from patients admitted for surgery for non-malignant conditions, suggesting that expression of these 2 genes may have altered in the adjacent histopathologically "normal" cervical squamous epithelial tissue from cervical cancer patients. The ribosomal protein S12 and the NADH dehydrogenase 4 genes may therefore be potentially useful as early pre-transformation diagnostic markers for human cervical cancer.

Authors
Cheng, Q; Lau, WM; Tay, SK; Chew, SH; Ho, TH; Hui, KM
MLA Citation
Cheng, Q, Lau, WM, Tay, SK, Chew, SH, Ho, TH, and Hui, KM. "Identification and characterization of genes involved in the carcinogenesis of human squamous cell cervical carcinoma." Int J Cancer 98.3 (March 20, 2002): 419-426.
PMID
11920594
Source
pubmed
Published In
International Journal of Cancer
Volume
98
Issue
3
Publish Date
2002
Start Page
419
End Page
426

Identification of molecular markers for the early detection of human squamous cell carcinoma of the uterine cervix.

To identify novel cellular genes that could potentially act as predictive molecular markers for human cervical cancer, we employed RT--PCR differential display, reverse Northern and Northern blot analysis to compare the gene expression profiles between squamous cell carcinoma biopsies and adjacent histo-pathological normal epithelium tissues. Twenty-eight cDNA clones were isolated that were demonstrated to be consistently over-expressed in squamous cell cervical cancer biopsies of FIGO stages 1B to 3B. Most importantly, it was observed that, in addition to their over-expression in cancer lesions, some of these genes are upregulated in the presumably histo-pathological normal adjacent tissues. Of particular interest is clone G30CC that has been identified to be the gene that encodes S12 ribosomal protein. When employed for RNA--RNA in situ hybridization experiments, expression of G30CC could be detected in the immature basal epithelial cells of histo-pathological normal tissues collected from cervical cancer patients of early FIGO stages. In comparison, the expression of G30CC was not detected in cervical tissues collected from patients admitted for surgery of non-malignant conditions. These results allow the distinct possibility of employing the ribosomal protein S12 gene as an early molecular diagnostic identifier for the screening of human cervical cancer and a potential target employed for cancer gene therapy trials.

Authors
Cheng, Q; Lau, WM; Chew, SH; Ho, TH; Tay, SK; Hui, KM
MLA Citation
Cheng, Q, Lau, WM, Chew, SH, Ho, TH, Tay, SK, and Hui, KM. "Identification of molecular markers for the early detection of human squamous cell carcinoma of the uterine cervix." Br J Cancer 86.2 (January 21, 2002): 274-281.
PMID
11870519
Source
pubmed
Published In
British Journal of Cancer
Volume
86
Issue
2
Publish Date
2002
Start Page
274
End Page
281
DOI
10.1038/sj.bjc.6600038

Characterization of tumor-specific cytotoxic effector cells with a novel CD3-/Thy-1+ phenotype

The introduction and expression of allogeneic MHC class I genes in tumors can generate tumor-specific immunity which subsequently results in the regression of parental tumors. Immunization of naive (AKR/J x C57BL/6)F1 mice with H-2K(b)-transformed K36 tumor cells was found to render recipient mice immune to a subsequent challenge by parental K36 tumor cells. Two types of cytotoxic T effector cells were demonstrated in these immune mice. One of the cytotoxic effector cells generated against the K36 tumor cells is the conventional CD3+ cells, and these account for approximately one-third of the total observed tumor-specific cytotoxicity in vitro. The other cytotoxic effector cell generated following the immunization of (AKR/J x C57BL/6)F1 mice with the H-2K(b)-transformed K36 cells had the CD3-/Thy-1+ phenotype, and accounted for the remaining two-thirds of the observed tumor-specific cytotoxicity in vitro. These CD3-/Thy-1+ cells can lyse parental K36 tumor cells in a tumor-specific fashion, and tumor-specific immunity can be adoptively transferred to naive animals via the CD3-/Thy-1+ cells. In contrast to CD3+ CTL, CD3-/Thy-1+ cells express CD45RB(low) Ly-6C(high), and HSA molecules. Although the CD3-/Thy-1+ cells can be activated in vitro by IL-2, TPA, and ionomycin, they cannot be propagated in vitro. The CD3-/Thy-1+ cells undergo apoptosis following prolonged culture in vitro. At present, the exact mechanism(s) by which CD3-/Thy-1+ cells can mediate tumor-specific cell lysis in the absence of identifiable T cell receptor molecules is unknown; nevertheless, these data suggest the existence of a novel T cell type to combat tumors.

Authors
Sabapathy, TK; Cheng, Q; Hui, KM
MLA Citation
Sabapathy, TK, Cheng, Q, and Hui, KM. "Characterization of tumor-specific cytotoxic effector cells with a novel CD3-/Thy-1+ phenotype." Cellular Immunology 166.1 (1995): 141-153.
PMID
7585974
Source
scival
Published In
Cellular Immunology
Volume
166
Issue
1
Publish Date
1995
Start Page
141
End Page
153
DOI
10.1006/cimm.1995.0016

Expression of three forms of melanoma growth stimulating activity (MGSA)/gro in human retinal pigment epithelial cells.

PURPOSE: To characterize mRNA expression and protein production of the cytokine MGSA/gro in human retinal pigment epithelial (RPE) cells and to determine whether expression of MGSA/gro is modulated by serum and the cytokines interleukin 1 beta (IL-1 beta), tumor necrosis factor alpha (TNF alpha), or transforming growth factor beta (TGF beta) mediators implicated in proliferative vitreoretinopathy (PVR). METHODS: Reverse-transcription polymerase chain reaction was used to determine the steady-state mRNA expression of three forms of MGSA/gro, alpha, beta, and gamma, by cultured human RPE cells in the presence or absence of recombinant IL-1 beta, TNF alpha, or TGF beta, or when serum-starved cells were re-fed with medium containing serum. Immunocytochemistry was used to characterize RPE cell-associated MGSA/gro protein, and immunoprecipitation of MGSA/gro from cell-conditioned medium was used to demonstrate MGSA/gro secretion. RESULTS: MGSA/gro mRNA was expressed minimally under basal conditions. Expression for all three forms of MGSA/gro mRNA was induced in a dose- and time-dependent manner after exposure to IL-1 beta, to a lesser extent after exposure to TNF alpha, but not after exposure to TGF beta. Serum induced MGSA/gro alpha and gamma transcripts, but not beta transcripts. Cell-associated MGSA/gro was identified on RPE cells grown in the absence of cytokines, but MGSA/gro was not secreted under these conditions. Exposure to IL-1 beta did not consistently cause increased cell-associated MGSA/gro; however, IL-1 beta induced secretion of MGSA/gro in a time-dependent manner. CONCLUSION: MGSA/gro is produced by human RPE in response to mediators implicated in PVR. Because MGSA/gro is a pleiotropic modulator of cell proliferation and inflammation, it may contribute to the intraocular wound healing response that characterizes PVR.

Authors
Jaffe, GJ; Richmond, A; Van Le, L; Shattuck, RL; Cheng, QC; Wong, F; Roberts, W
MLA Citation
Jaffe, GJ, Richmond, A, Van Le, L, Shattuck, RL, Cheng, QC, Wong, F, and Roberts, W. "Expression of three forms of melanoma growth stimulating activity (MGSA)/gro in human retinal pigment epithelial cells." Invest Ophthalmol Vis Sci 34.9 (August 1993): 2776-2785.
PMID
8344798
Source
pubmed
Published In
Investigative Ophthalmology and Visual Science
Volume
34
Issue
9
Publish Date
1993
Start Page
2776
End Page
2785
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