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Yan, Hai

Overview:

Our research activities center on the molecular genetics and biology of cancer with a focus on the identification, characterization, and therapeutic targeting of driver mutations involved in the genesis and progression of brain cancers.  Gliomas are the most common type of primary brain tumor. Through genomic studies, we have identified mutations in IDH1 and IDH2 in 70% of progressive malignant gliomas. These are somatic missense mutations that alter a conserved arginine residue and gain a neomorphic activity. A new metabolite produced by the glioma cells impacts on chromatin modulation and genome methylation.  Malignant cells must maintain their telomeres. We identified several different tumor types exhibiting a high frequency of TERT promoter mutations, including several glioma subtypes. Conversely, we found a low frequency of TERT promoter mutations in many common epithelial tumors.  In gliomas, we found that TERT promoter mutations were mutually exclusive with ATRX alterations, which are associated with activation of the ALT pathway for telomere maintenance. These findings show that TERT promoter mutations are frequent driver events in many human cancers, particularly those that arise from tissues with low rates of self-renewal. Our long-term goal is to develop a novel molecular-based glioma classification system and a targeted therapy on the basis of IDH1 and TERT mutations. To provide novel avenues for development of anticancer therapeutics, studies involving cell line and animal models, enzymatic study, metabolome and epigenome, are being investigated to determine the consequences of IDH1 and TERT mutations on cancer cells.

Positions:

Henry S. Friedman Professor of Neuro-Oncology in the School of Medicine

Pathology
School of Medicine

Professor of Pathology

Pathology
School of Medicine

Professor of Pharmacology and Cancer Biology

Pharmacology & Cancer Biology
School of Medicine

Member of the Duke Cancer Institute

Duke Cancer Institute
School of Medicine

Education:

M.D. 1991

M.D. — Beijing Medical University (China)

Ph.D. 1997

Ph.D. — Columbia University

Research Associate, Howard Hughes Institute

Johns Hopkins University

Faculty, Research Associate, Molecular Genetics

Thomas Jefferson University

News:

Publications:

Adaptive evolution of the GDH2 allosteric domain promotes gliomagenesis by resolving IDH1(R132H) induced metabolic liabilities.

Hot-spot mutations in the isocitrate dehydrogenase 1 (IDH1) gene occur in a number of human cancers and confer a neomorphic enzyme activity that catalyzes the conversion of α-ketoglutarate (αKG) to the oncometabolite D-(2)-hydroxyglutarate (D2HG). In malignant gliomas, IDH1(R132H) expression induces widespread metabolic reprogramming, possibly requiring compensatory mechanisms to sustain the normal biosynthetic requirements of actively proliferating tumor cells. We used genetically engineered mouse models of glioma and quantitative metabolomics to investigate IDH1(R132H)-dependent metabolic reprogramming and its potential to induce biosynthetic liabilities that can be exploited for glioma therapy. In gliomagenic neural progenitor cells, IDH1(R132H) expression increased the abundance of dipeptide metabolites, depleted key tricarboxylic acid (TCA) cycle metabolites, and slowed progression of murine gliomas. Notably, expression of glutamate dehydrogenase GDH2, a hominoid-specific enzyme with relatively restricted expression to the brain, was critically involved in compensating for IDH1(R132H)-induced metabolic alterations and promoting IDH1(R132H) glioma growth. Indeed, we found that recently evolved amino acid substitutions in the GDH2 allosteric domain conferred its non-redundant, glioma-promoting properties in the presence of IDH1 mutation. Our results indicate that among the unique roles for GDH2 in the human forebrain is its ability to limit IDH1(R132H)-mediated metabolic liabilities, thus promoting glioma growth in this context. Results from this study raise the possibility that GDH2-specific inhibition may be a viable therapeutic strategy for gliomas with IDH mutations.

Authors
Waitkus, MS; Pirozzi, CJ; Moure, CJ; Diplas, BH; Hansen, LJ; Carpenter, AB; Yang, R; Wang, Z; Ingram, BO; Karoly, ED; Mohney, RP; Spasojeic, I; McLendon, RE; Friedman, HS; He, Y; Bigner, DD; Yan, H
MLA Citation
Waitkus, MS, Pirozzi, CJ, Moure, CJ, Diplas, BH, Hansen, LJ, Carpenter, AB, Yang, R, Wang, Z, Ingram, BO, Karoly, ED, Mohney, RP, Spasojeic, I, McLendon, RE, Friedman, HS, He, Y, Bigner, DD, and Yan, H. "Adaptive evolution of the GDH2 allosteric domain promotes gliomagenesis by resolving IDH1(R132H) induced metabolic liabilities." Cancer research (November 2, 2017).
PMID
29097607
Source
epmc
Published In
Cancer Research
Publish Date
2017
DOI
10.1158/0008-5472.can-17-1352

Cic Loss Promotes Gliomagenesis via Aberrant Neural Stem Cell Proliferation and Differentiation.

Inactivating mutations in the transcriptional repression factor Capicua (CIC) occur in approximately 50% of human oligodendrogliomas, but mechanistic links to pathogenesis are unclear. To address this question, we generated Cic-deficient mice and human oligodendroglioma cell models. Genetic deficiency in mice resulted in a partially penetrant embryonic or perinatal lethal phenotype, with the production of an aberrant proliferative neural population in surviving animals. In vitro cultured neural stem cells derived from Cic conditional knockout mice bypassed an EGF requirement for proliferation and displayed a defect in their potential for oligodendrocyte differentiation. Cic is known to participate in gene suppression that can be relieved by EGFR signal, but we found that cic also activated expression of a broad range of EGFR-independent genes. In an orthotopic mouse model of glioma, we found that Cic loss potentiated the formation and reduced the latency in tumor development. Collectively, our results define an important role for Cic in regulating neural cell proliferation and lineage specification, and suggest mechanistic explanations for how CIC mutations may impact the pathogenesis and therapeutic targeting of oligodendroglioma. Cancer Res; 77(22); 6097-108. ©2017 AACR.

Authors
Yang, R; Chen, LH; Hansen, LJ; Carpenter, AB; Moure, CJ; Liu, H; Pirozzi, CJ; Diplas, BH; Waitkus, MS; Greer, PK; Zhu, H; McLendon, RE; Bigner, DD; He, Y; Yan, H
MLA Citation
Yang, R, Chen, LH, Hansen, LJ, Carpenter, AB, Moure, CJ, Liu, H, Pirozzi, CJ, Diplas, BH, Waitkus, MS, Greer, PK, Zhu, H, McLendon, RE, Bigner, DD, He, Y, and Yan, H. "Cic Loss Promotes Gliomagenesis via Aberrant Neural Stem Cell Proliferation and Differentiation." Cancer research 77.22 (November 2017): 6097-6108.
PMID
28939681
Source
epmc
Published In
Cancer Research
Volume
77
Issue
22
Publish Date
2017
Start Page
6097
End Page
6108
DOI
10.1158/0008-5472.can-17-1018

Mutant IDH1 Disrupts the Mouse Subventricular Zone and Alters Brain Tumor Progression.

IDH1 mutations occur in the majority of low-grade gliomas and lead to the production of the oncometabolite, D-2-hydroxyglutarate (D-2HG). To understand the effects of tumor-associated mutant IDH1 (IDH1-R132H) on both the neural stem cell (NSC) population and brain tumorigenesis, genetically faithful cell lines and mouse model systems were generated. Here, it is reported that mouse NSCs expressing Idh1-R132H displayed reduced proliferation due to p53-mediated cell-cycle arrest as well as a decreased ability to undergo neuronal differentiation. In vivo, Idh1-R132H expression reduced proliferation of cells within the germinal zone of the subventricular zone (SVZ). The NSCs within this area were dispersed and disorganized in mutant animals, suggesting that Idh1-R132H perturbed the NSCs and the microenvironment from which gliomas arise. In addition, tumor-bearing animals expressing mutant Idh1 displayed a prolonged survival and also overexpressed Olig2, features consistent with IDH1-mutated human gliomas. These data indicate that mutant Idh1 disrupts the NSC microenvironment and the candidate cell-of-origin for glioma; thus, altering the progression of tumorigenesis. In addition, this study provides a mutant Idh1 brain tumor model that genetically recapitulates human disease, laying the foundation for future investigations on mutant IDH1-mediated brain tumorigenesis and targeted therapy.Implications: Through the use of a conditional mutant mouse model that confers a less aggressive tumor phenotype, this study reveals that mutant Idh1 impacts the candidate cell-of-origin for gliomas. Mol Cancer Res; 15(5); 507-20. ©2017 AACR.

Authors
Pirozzi, CJ; Carpenter, AB; Waitkus, MS; Wang, CY; Zhu, H; Hansen, LJ; Chen, LH; Greer, PK; Feng, J; Wang, Y; Bock, CB; Fan, P; Spasojevic, I; McLendon, RE; Bigner, DD; He, Y; Yan, H
MLA Citation
Pirozzi, CJ, Carpenter, AB, Waitkus, MS, Wang, CY, Zhu, H, Hansen, LJ, Chen, LH, Greer, PK, Feng, J, Wang, Y, Bock, CB, Fan, P, Spasojevic, I, McLendon, RE, Bigner, DD, He, Y, and Yan, H. "Mutant IDH1 Disrupts the Mouse Subventricular Zone and Alters Brain Tumor Progression." Molecular cancer research : MCR 15.5 (May 2017): 507-520.
PMID
28148827
Source
epmc
Published In
Molecular cancer research : MCR
Volume
15
Issue
5
Publish Date
2017
Start Page
507
End Page
520
DOI
10.1158/1541-7786.mcr-16-0485

The genome-wide mutational landscape of pituitary adenomas.

Authors
Song, Z-J; Reitman, ZJ; Ma, Z-Y; Chen, J-H; Zhang, Q-L; Shou, X-F; Huang, C-X; Wang, Y-F; Li, S-Q; Mao, Y; Zhou, L-F; Lian, B-F; Yan, H; Shi, Y-Y; Zhao, Y
MLA Citation
Song, Z-J, Reitman, ZJ, Ma, Z-Y, Chen, J-H, Zhang, Q-L, Shou, X-F, Huang, C-X, Wang, Y-F, Li, S-Q, Mao, Y, Zhou, L-F, Lian, B-F, Yan, H, Shi, Y-Y, and Zhao, Y. "The genome-wide mutational landscape of pituitary adenomas." Cell research 26.11 (November 2016): 1255-1259. (letter)
PMID
27670697
Source
epmc
Published In
Cell Research
Volume
26
Issue
11
Publish Date
2016
Start Page
1255
End Page
1259
DOI
10.1038/cr.2016.114

Radiolabeled inhibitors as probes for imaging mutant IDH1 expression in gliomas: Synthesis and preliminary evaluation of labeled butyl-phenyl sulfonamide analogs.

Malignant gliomas frequently harbor mutations in the isocitrate dehydrogenase 1 (IDH1) gene. Studies suggest that IDH mutation contributes to tumor pathogenesis through mechanisms that are mediated by the neomorphic metabolite of the mutant IDH1 enzyme, 2-hydroxyglutarate (2-HG). The aim of this work was to synthesize and evaluate radiolabeled compounds that bind to the mutant IDH1 enzyme with the goal of enabling noninvasive imaging of mutant IDH1 expression in gliomas by positron emission tomography (PET).A small library of nonradioactive analogs were designed and synthesized based on the chemical structure of reported butyl-phenyl sulfonamide inhibitors of mutant IDH1. Enzyme inhibition assays were conducted using purified mutant IDH1 enzyme, IDH1-R132H, to determine the IC50 and the maximal inhibitory efficiency of the synthesized compounds. Selected compounds, 1 and 4, were labeled with radioiodine ((125)I) and/or (18)F using bromo- and phenol precursors, respectively. In vivo behavior of the labeled inhibitors was studied by conducting tissue distribution studies with [(125)I]1 in normal mice. Cell uptake studies were conducted using an isogenic astrocytoma cell line that carried a native IDH1-R132H mutation to evaluate the potential uptake of the labeled inhibitors in IDH1-mutated tumor cells.Enzyme inhibition assays showed good inhibitory potency for compounds that have iodine or a fluoroethoxy substituent at the ortho position of the phenyl ring in compounds 1 and 4 with IC50 values of 1.7 μM and 2.3 μM, respectively. Compounds 1 and 4 inhibited mutant IDH1 activity and decreased the production of 2-HG in an IDH1-mutated astrocytoma cell line. Radiolabeling of 1 and 4 was achieved with an average radiochemical yield of 56.6 ± 20.1% for [(125)I]1 (n = 4) and 67.5 ± 6.6% for [(18)F]4 (n = 3). [(125)I]1 exhibited favorable biodistribution characteristics in normal mice, with rapid clearance from the blood and elimination via the hepatobiliary system by 4 h after injection. The uptake of [(125)I]1 in tumor cells positive for IDH1-R132H was significantly higher compared to isogenic WT-IDH1 controls, with a maximal uptake ratio of 1.67 at 3 h post injection. Co-incubation of the labeled inhibitors with the corresponding nonradioactive analogs, and decreasing the normal concentrations of FBS (10%) in the incubation media substantially increased the uptake of the labeled inhibitors in both the IDH1-mutant and WT-IDH1 tumor cell lines, suggesting significant non-specific binding of the synthesized labeled butyl-phenyl sulfonamide inhibitors.These data demonstrate the feasibility of developing radiolabeled probes for the mutant IDH1 enzyme based on enzyme inhibitors. Further optimization of the labeled inhibitors by modifying the chemical structure to decrease the lipophilicity and to increase potency may yield compounds with improved characteristics as probes for imaging mutant IDH1 expression in tumors.

Authors
Chitneni, SK; Reitman, ZJ; Gooden, DM; Yan, H; Zalutsky, MR
MLA Citation
Chitneni, SK, Reitman, ZJ, Gooden, DM, Yan, H, and Zalutsky, MR. "Radiolabeled inhibitors as probes for imaging mutant IDH1 expression in gliomas: Synthesis and preliminary evaluation of labeled butyl-phenyl sulfonamide analogs." European journal of medicinal chemistry 119 (August 2016): 218-230.
Website
http://hdl.handle.net/10161/12001
PMID
27163884
Source
epmc
Published In
European Journal of Medicinal Chemistry
Volume
119
Publish Date
2016
Start Page
218
End Page
230
DOI
10.1016/j.ejmech.2016.04.066

Clonality analysis of multifocal papillary thyroid carcinoma by using genetic profiles.

Papillary thyroid carcinoma (PTC) is the most common adult thyroid malignancy and often presents with multiple anatomically distinct foci within the thyroid, known as multifocal papillary thyroid carcinoma (MPTC). The widespread application of the next-generation sequencing technologies in cancer genomics research provides novel insights into determining the clonal relationship between multiple tumours within the same thyroid gland. For eight MPTC patients, we performed whole-exome sequencing and targeted region sequencing to identify the non-synonymous point mutations and gene rearrangements of distinct and spatially separated tumour foci. Among these eight MPTCs, completely discordant mutational spectra were observed in the distinct cancerous nodules of patients MPTC1 and 5, suggesting that these nodules originated from independent precursors. In another three cases (MPTC2, 6, and 8), the distinct MPTC foci of these patients had no other shared mutations except BRAF V600E, also indicating likely independent origins. Two patients (MPTC3 and 4) shared almost identical mutational spectra amongst their separate tumour nodules, suggesting a common clonal origin. MPTC patient 7 had seven cancer foci, of which two foci shared 66.7% of mutations, while the remaining cancer foci displayed no common non-synonymous mutations, indicating that MPTC7 has multiple independent origins accompanied by intraglandular disease dissemination. In this study, we found that 75% of MPTC cases arose as independent tumours, which supports the field cancerization hypothesis describing multiple malignant lesions. MPTC may also arise from intrathyroidal metastases from a single malignant clone, as well as multiple independent origins accompanied by intrathyroidal metastasis.

Authors
Lu, Z; Sheng, J; Zhang, Y; Deng, J; Li, Y; Lu, A; Zhang, J; Yu, H; Zhang, M; Xiong, Z; Yan, H; Diplas, BH; Lu, Y; Liu, B
MLA Citation
Lu, Z, Sheng, J, Zhang, Y, Deng, J, Li, Y, Lu, A, Zhang, J, Yu, H, Zhang, M, Xiong, Z, Yan, H, Diplas, BH, Lu, Y, and Liu, B. "Clonality analysis of multifocal papillary thyroid carcinoma by using genetic profiles." The Journal of pathology 239.1 (May 2016): 72-83.
PMID
27071483
Source
epmc
Published In
The Journal of Pathology
Volume
239
Issue
1
Publish Date
2016
Start Page
72
End Page
83
DOI
10.1002/path.4696

Isocitrate dehydrogenase mutations in gliomas.

Over the last decade, extraordinary progress has been made in elucidating the underlying genetic causes of gliomas. In 2008, our understanding of glioma genetics was revolutionized when mutations in isocitrate dehydrogenase 1 and 2 (IDH1/2) were identified in the vast majority of progressive gliomas and secondary glioblastomas (GBMs). IDH enzymes normally catalyze the decarboxylation of isocitrate to generate α-ketoglutarate (αKG), but recurrent mutations at Arg(132) of IDH1 and Arg(172) of IDH2 confer a neomorphic enzyme activity that catalyzes reduction of αKG into the putative oncometabolite D-2-hydroxyglutate (D2HG). D2HG inhibits αKG-dependent dioxygenases and is thought to create a cellular state permissive to malignant transformation by altering cellular epigenetics and blocking normal differentiation processes. Herein, we discuss the relevant literature on mechanistic studies of IDH1/2 mutations in gliomas, and we review the potential impact of IDH1/2 mutations on molecular classification and glioma therapy.

Authors
Waitkus, MS; Diplas, BH; Yan, H
MLA Citation
Waitkus, MS, Diplas, BH, and Yan, H. "Isocitrate dehydrogenase mutations in gliomas." Neuro-oncology 18.1 (January 2016): 16-26. (Review)
PMID
26188014
Source
epmc
Published In
Neuro-Oncology
Volume
18
Issue
1
Publish Date
2016
Start Page
16
End Page
26
DOI
10.1093/neuonc/nov136

Prevalence of deleterious ATM germline mutations in gastric cancer patients.

Besides CDH1, few hereditary gastric cancer predisposition genes have been previously reported. In this study, we discovered two germline ATM mutations (p.Y1203fs and p.N1223S) in a Chinese family with a history of gastric cancer by screening 83 cancer susceptibility genes. Using a published exome sequencing dataset, we found deleterious germline mutations of ATM in 2.7% of 335 gastric cancer patients of different ethnic origins. The frequency of deleterious ATM mutations in gastric cancer patients is significantly higher than that in general population (p=0.0000435), suggesting an association of ATM mutations with gastric cancer predisposition. We also observed biallelic inactivation of ATM in tumors of two gastric cancer patients. Further evaluation of ATM mutations in hereditary gastric cancer will facilitate genetic testing and risk assessment.

Authors
Huang, D-S; Tao, H-Q; He, X-J; Long, M; Yu, S; Xia, Y-J; Wei, Z; Xiong, Z; Jones, S; He, Y; Yan, H; Wang, X
MLA Citation
Huang, D-S, Tao, H-Q, He, X-J, Long, M, Yu, S, Xia, Y-J, Wei, Z, Xiong, Z, Jones, S, He, Y, Yan, H, and Wang, X. "Prevalence of deleterious ATM germline mutations in gastric cancer patients." Oncotarget 6.38 (December 2015): 40953-40958.
PMID
26506520
Source
epmc
Published In
Oncotarget
Volume
6
Issue
38
Publish Date
2015
Start Page
40953
End Page
40958
DOI
10.18632/oncotarget.5944

The H3.3 K27M mutation results in a poorer prognosis in brainstem gliomas than thalamic gliomas in adults.

Brainstem and thalamic gliomas are rare, and they are poorly understood in adults. Genetic aberrations that occur in these tumors are still unknown. In this study, we investigated whether thalamic gliomas have different genetic aberrations and clinical outcomes compared with brainstem gliomas in adults. Forty-three glioma samples were selected, including 28 brainstem and 15 thalamic gliomas. The frequency of the K27M mutation in adult midline gliomas was 58.1%. High-grade gliomas in the thalamus were statistically significantly more numerous than brainstem gliomas. Patients with K27M mutant brainstem gliomas had a significantly shorter overall survival than patients with wild-type tumors (P = .020) by Cox regression after adjustment for other independent risk factors. However, there was no statistical tendency toward a poorer overall survival in thalamic gliomas containing the K27M mutation compared with wild-type tumors. The presence of the K27M mutation significantly corresponded with mutations in TP53 in thalamic gliomas. Interestingly, the K27M mutation was mutually exclusive with mutations in IDH1, which was detected only in brainstem gliomas. The microarray data identified 86 differentially expressed genes between brainstem and thalamic gliomas with the K27M mutation. The cyclin-dependent kinase 6 (CDK6) gene, which plays an important role in cancer pathways, was found to be differentially expressed between brainstem and thalamic gliomas with K27M mutations. Although the K27M mutation was frequently observed in adult brainstem and thalamic gliomas, this mutation tended to be associated with a poorer prognosis in brainstem gliomas but not in thalamic gliomas. Brainstem gliomas may present different genetic aberrations from thalamic gliomas. These differences may provide guidance for therapeutic decisions for the treatment of adult brainstem and thalamic gliomas, which may have different molecular targets.

Authors
Feng, J; Hao, S; Pan, C; Wang, Y; Wu, Z; Zhang, J; Yan, H; Zhang, L; Wan, H
MLA Citation
Feng, J, Hao, S, Pan, C, Wang, Y, Wu, Z, Zhang, J, Yan, H, Zhang, L, and Wan, H. "The H3.3 K27M mutation results in a poorer prognosis in brainstem gliomas than thalamic gliomas in adults." Human pathology 46.11 (November 2015): 1626-1632.
PMID
26297251
Source
epmc
Published In
Human Pathology
Volume
46
Issue
11
Publish Date
2015
Start Page
1626
End Page
1632
DOI
10.1016/j.humpath.2015.07.002

TERT promoter mutations contribute to IDH mutations in predicting differential responses to adjuvant therapies in WHO grade II and III diffuse gliomas.

IDH mutations frequently occur in WHO grade II and III diffuse gliomas and have favorable prognosis compared to wild-type tumors. However, whether IDH mutations in WHO grade II and II diffuse gliomas predict enhanced sensitivity to adjuvant radiation (RT) or chemotherapy (CHT) is still being debated. Recent studies have identified recurrent mutations in the promoter region of telomerase reverse transcriptase (TERT) in gliomas. We previously demonstrated that TERT promoter mutations may be promising biomarkers in glioma survival prognostication when combined with IDH mutations. This study analyzed IDH and TERT promoter mutations in 295 WHO grade II and III diffuse gliomas treated with or without adjuvant therapies to explore their impact on the sensitivity of tumors to genotoxic therapies. IDH mutations were found in 216 (73.2%) patients and TERT promoter mutations were found in 112 (38%) patients. In multivariate analysis, IDH mutations (p < 0.001) were independent prognostic factors for PFS and OS in patients receiving genotoxic therapies while TERT promoter mutations were not. In univariate analysis, IDH and TERT promoter mutations were not significant prognostic factors in patients who did not receive genotoxic therapies. Adjuvant RT and CHT were factors independently impacting PFS (RT p = 0.001, CHT p = 0.026) in IDH mutated WHO grade II and III diffuse gliomas but not in IDH wild-type group. Univariate and multivariate analyses demonstrated TERT promoter mutations further stratified IDH wild-type WHO grade II and III diffuse gliomas into two subgroups with different responses to genotoxic therapies. Adjuvant RT and CHT were significant parameters influencing PFS in the IDH wt/TERT mut subgroup (RT p = 0.015, CHT p = 0.015) but not in the IDH wt/TERT wt subgroup. Our data demonstrated that IDH mutated WHO grade II and III diffuse gliomas had better PFS and OS than their IDH wild-type counterparts when genotoxic therapies were administered after surgery. Importantly, we also found that TERT promoter mutations further stratify IDH wild-type WHO grade II and III diffuse gliomas into two subgroups with different responses to adjuvant therapies. Taken together, TERT promoter mutations may predict enhanced sensitivity to genotoxic therapies in IDH wild-type WHO grade II and III diffuse gliomas and may justify intensified treatment in this subgroup.

Authors
Zhang, Z-Y; Chan, AK-Y; Ding, X-J; Qin, Z-Y; Hong, CS; Chen, L-C; Zhang, X; Zhao, F-P; Wang, Y; Wang, Y; Zhou, L-F; Zhuang, Z; Ng, H-K; Yan, H; Yao, Y; Mao, Y
MLA Citation
Zhang, Z-Y, Chan, AK-Y, Ding, X-J, Qin, Z-Y, Hong, CS, Chen, L-C, Zhang, X, Zhao, F-P, Wang, Y, Wang, Y, Zhou, L-F, Zhuang, Z, Ng, H-K, Yan, H, Yao, Y, and Mao, Y. "TERT promoter mutations contribute to IDH mutations in predicting differential responses to adjuvant therapies in WHO grade II and III diffuse gliomas." Oncotarget 6.28 (September 2015): 24871-24883.
PMID
26314843
Source
epmc
Published In
Oncotarget
Volume
6
Issue
28
Publish Date
2015
Start Page
24871
End Page
24883
DOI
10.18632/oncotarget.4549

Detecting somatic mutations in genomic sequences by means of Kolmogorov-Arnold analysis.

The Kolmogorov-Arnold stochasticity parameter technique is applied for the first time to the study of cancer genome sequencing, to reveal mutations. Using data generated by next-generation sequencing technologies, we have analysed the exome sequences of brain tumour patients with matched tumour and normal blood. We show that mutations contained in sequencing data can be revealed using this technique, thus providing a new methodology for determining subsequences of given length containing mutations, i.e. its value differs from those of subsequences without mutations. A potential application for this technique involves simplifying the procedure of finding segments with mutations, speeding up genomic research and accelerating its implementation in clinical diagnostics. Moreover, the prediction of a mutation associated with a family of frequent mutations in numerous types of cancers based purely on the value of the Kolmogorov function indicates that this applied marker may recognize genomic sequences that are in extremely low abundance and can be used in revealing new types of mutations.

Authors
Gurzadyan, VG; Yan, H; Vlahovic, G; Kashin, A; Killela, P; Reitman, Z; Sargsyan, S; Yegorian, G; Milledge, G; Vlahovic, B
MLA Citation
Gurzadyan, VG, Yan, H, Vlahovic, G, Kashin, A, Killela, P, Reitman, Z, Sargsyan, S, Yegorian, G, Milledge, G, and Vlahovic, B. "Detecting somatic mutations in genomic sequences by means of Kolmogorov-Arnold analysis." Royal Society open science 2.8 (August 26, 2015): 150143-.
PMID
26361546
Source
epmc
Published In
Royal Society Open Science
Volume
2
Issue
8
Publish Date
2015
Start Page
150143
DOI
10.1098/rsos.150143

193nm Lithography fabricated high sensitivity photonic crystal microcavity biosensors for plasma protein detection in patients with pancreatic cancer

© 2015 OSA. High sensitivity L13-type two-dimensional photonic crystal microcavities with nanoholes were fabricated by 193nm photolithography. 0.03 picomolar concentration pancreatic cancer biomarker in patient serum samples was experimentally detected to 10× lower dilution than ELISA.

Authors
Yang, CJ; Tang, N; Yan, H; Chakravarty, S; Li, D; Chen, RT
MLA Citation
Yang, CJ, Tang, N, Yan, H, Chakravarty, S, Li, D, and Chen, RT. "193nm Lithography fabricated high sensitivity photonic crystal microcavity biosensors for plasma protein detection in patients with pancreatic cancer." August 10, 2015.
Source
scopus
Published In
Conference on Lasers and Electro-Optics Europe - Technical Digest
Volume
2015-August
Publish Date
2015

Recurrent TERT promoter mutations identified in a large-scale study of multiple tumour types are associated with increased TERT expression and telomerase activation.

Several somatic mutation hotspots were recently identified in the telomerase reverse transcriptase (TERT) promoter region in human cancers. Large scale studies of these mutations in multiple tumour types are limited, in particular in Asian populations. This study aimed to: analyse TERT promoter mutations in multiple tumour types in a large Chinese patient cohort, investigate novel tumour types and assess the functional significance of the mutations.TERT promoter mutation status was assessed by Sanger sequencing for 13 different tumour types and 799 tumour tissues from Chinese cancer patients. Thymic epithelial tumours, gastrointestinal leiomyoma, and gastric schwannoma were included, for which the TERT promoter has not been previously sequenced. Functional studies included TERT expression by reverse-transcriptase quantitative polymerase chain reaction (RT-qPCR), telomerase activity by the telomeric repeat amplification protocol (TRAP) assay and promoter activity by the luciferase reporter assay.TERT promoter mutations were highly frequent in glioblastoma (83.9%), urothelial carcinoma (64.5%), oligodendroglioma (70.0%), medulloblastoma (33.3%) and hepatocellular carcinoma (31.4%). C228T and C250T were the most common mutations. In urothelial carcinoma, several novel rare mutations were identified. TERT promoter mutations were absent in gastrointestinal stromal tumour (GIST), thymic epithelial tumours, gastrointestinal leiomyoma, gastric schwannoma, cholangiocarcinoma, gastric and pancreatic cancer. TERT promoter mutations highly correlated with upregulated TERT mRNA expression and telomerase activity in adult gliomas. These mutations differentially enhanced the transcriptional activity of the TERT core promoter.TERT promoter mutations are frequent in multiple tumour types and have similar distributions in Chinese cancer patients. The functional significance of these mutations reflect the importance to telomere maintenance and hence tumourigenesis, making them potential therapeutic targets.

Authors
Huang, D-S; Wang, Z; He, X-J; Diplas, BH; Yang, R; Killela, PJ; Meng, Q; Ye, Z-Y; Wang, W; Jiang, X-T; Xu, L; He, X-L; Zhao, Z-S; Xu, W-J; Wang, H-J; Ma, Y-Y; Xia, Y-J; Li, L; Zhang, R-X; Jin, T; Zhao, Z-K; Xu, J; Yu, S; Wu, F; Liang, J; Wang, S; Jiao, Y; Yan, H; Tao, H-Q
MLA Citation
Huang, D-S, Wang, Z, He, X-J, Diplas, BH, Yang, R, Killela, PJ, Meng, Q, Ye, Z-Y, Wang, W, Jiang, X-T, Xu, L, He, X-L, Zhao, Z-S, Xu, W-J, Wang, H-J, Ma, Y-Y, Xia, Y-J, Li, L, Zhang, R-X, Jin, T, Zhao, Z-K, Xu, J, Yu, S, Wu, F, Liang, J, Wang, S, Jiao, Y, Yan, H, and Tao, H-Q. "Recurrent TERT promoter mutations identified in a large-scale study of multiple tumour types are associated with increased TERT expression and telomerase activation." European journal of cancer (Oxford, England : 1990) 51.8 (May 2015): 969-976.
PMID
25843513
Source
epmc
Published In
European Journal of Cancer
Volume
51
Issue
8
Publish Date
2015
Start Page
969
End Page
976
DOI
10.1016/j.ejca.2015.03.010

Genetic alterations in glioblastoma multiforme

© Cambridge University Press 2015. Glioblastoma multiforme (GBM), or Grade IV astrocytoma, is one of the most common and malignant primary tumors of the central nervous system in adults [1]. Despite years of research and advances, the average survival after diagnosis remains about 12 months [1–4] . GBM tumors can be divided into two groups: primary and secondary. Primary GBM presents de novo as GBM with no preceding lower grade tumor, representing over 90% of GBM cases [5]. On the other hand, secondary GBM first presents as a lower grade glioma and is part of a progression of increasing grade of astrocytoma: World Health Organization (WHO) Grade II diffuse astrocytoma (often called low-grade glioma), WHO Grade III anaplastic astrocytoma, and WHO Grade IV glioblastoma [5] . WHO Grade I pilocytic astrocytomas are not thought to progress [6]. Despite a similar histopathology, primary and secondary GBM each comprise a distinct combination of genetic changes and tend to occur in distinct populations. Whereas primary GBM generally occurs in older patients, usually over 60 years old [3] , secondary GBM tends to occur in middle-aged patients, of an average age of 45 years [3]. Because of these differences between primary and secondary GBM, it is entirely possible that treatments that are effective in one GBM patient population will be ineffective in others, and vice versa. The importance of understanding the genetic differences in GBM tumors from different patients is becoming increasingly clear, as genetic differences between tumors may more accurately predict prognosis than histological differences alone [7, 8] . Furthermore, because different GBM patients present with distinct combinations of genetic mutations, it is likely that therapies targeted to the specific genetic pathways that are altered in a patient's tumor will be the most efficacious way of treating this disease. However, due to the heterogeneous genome of GBM tumors, with different cells within one tumor having different mutations, tailored treatments targeting the multiple dysregulated oncogenic pathways in cancer cells of differing genotypes may achieve the most effective outcome. Identification of the genetic changes that occur in subsets of cells is critical to optimizing treatment for each patient. In this review, we focus on the genetic pathways identified as commonly altered in GBMs and the implications of changes in these pathways for prognosis and treatment.

Authors
López, GY; Samsky, M; Jones, R; Adamson, C; Yan, H
MLA Citation
López, GY, Samsky, M, Jones, R, Adamson, C, and Yan, H. "Genetic alterations in glioblastoma multiforme." Systems Biology of Cancer. January 1, 2015. 323-344.
Source
scopus
Publish Date
2015
Start Page
323
End Page
344
DOI
10.1017/9780511979811.022

Genetic dissection of leukemia-associated IDH1 and IDH2 mutants and D-2-hydroxyglutarate in Drosophila.

Gain-of-function mutations in nicotinamide adenine dinucleotide phosphate-dependent isocitrate dehydrogenase (IDH)1 and IDH2 frequently arise in human leukemias and other cancers and produce high levels of D-2-hydroxyglutarate (D-2HG). We expressed the R195H mutant of Drosophila Idh (CG7176), which is equivalent to the human cancer-associated IDH1-R132H mutant, in fly tissues using the UAS-Gal4 binary expression system. Idh-R195H caused a >25-fold elevation of D-2HG when expressed ubiquitously in flies. Expression of mutant Idh in larval blood cells (hemocytes) resulted in higher numbers of circulating blood cells. Mutant Idh expression in fly neurons resulted in neurologic and wing-expansion defects, and these phenotypes were rescued by genetic modulation of superoxide dismutase 2, p53, and apoptotic caspase cascade mediators. Idh-R163Q, which is homologous to the common leukemia-associated IDH2-R140Q mutant, resulted in moderately elevated D-2HG and milder phenotypes. We identified the fly homolog of D-2-hydroxyglutaric acid dehydrogenase (CG3835), which metabolizes D-2HG, and showed that coexpression of this enzyme with mutant Idh abolishes mutant Idh-associated phenotypes. These results provide a flexible model system to interrogate a cancer-related genetic and metabolic pathway and offer insights into the impact of IDH mutation and D-2HG on metazoan tissues.

Authors
Reitman, ZJ; Sinenko, SA; Spana, EP; Yan, H
MLA Citation
Reitman, ZJ, Sinenko, SA, Spana, EP, and Yan, H. "Genetic dissection of leukemia-associated IDH1 and IDH2 mutants and D-2-hydroxyglutarate in Drosophila." Blood 125.2 (January 2015): 336-345.
PMID
25398939
Source
epmc
Published In
Blood
Volume
125
Issue
2
Publish Date
2015
Start Page
336
End Page
345
DOI
10.1182/blood-2014-05-577940

Annexin A2 as a target endothelial cell membrane autoantigen in Behçet's disease.

Cell membrane proteins are believed to play a critical role in the pathogenesis of autoimmune diseases. However, few membrane autoantigens have been linked with Behçet's disease. Here, a cell-chip was performed to identify autoantibody target cells, and the suspected autoantigens were detected using immunoblotting. The amino acid sequences of the detected proteins were determined using LC-MALDI-TOF/TOF. Putative proteins were recombinantly expressed and purified, and a corresponding ELISA was developed and clinically validated using real clinical samples. It was found that a 36-kDa membrane protein--annexin A2--was detected in approximately one-third of the patients' blood circulation. The immunohistochemistry results showed that annexin A2 was highly expressed in vascular endothelial cells. Moreover, vascular involvement was significantly higher in the anti-annexin A2 antibody-positive group versus the anti-annexin A2 antibody-negative group among all the clinical samples analyzed, indicating that annexin A2 is a novel endothelial cell membrane antigen involved in Behçet's disease.

Authors
Chen, P; Yan, H; Tian, Y; Xun, Y; Shi, L; Bao, R; Zhang, H; Chen, G; Yang, C; Sun, S; Wang, Y; Liu, L; Zhou, Y; Zhang, C; Wang, X; Wen, Y; Bian, Y; Du, H
MLA Citation
Chen, P, Yan, H, Tian, Y, Xun, Y, Shi, L, Bao, R, Zhang, H, Chen, G, Yang, C, Sun, S, Wang, Y, Liu, L, Zhou, Y, Zhang, C, Wang, X, Wen, Y, Bian, Y, and Du, H. "Annexin A2 as a target endothelial cell membrane autoantigen in Behçet's disease." Scientific Reports 5 (January 2015): 8162-.
PMID
25641213
Source
epmc
Published In
Scientific Reports
Volume
5
Publish Date
2015
Start Page
8162
DOI
10.1038/srep08162

EGFR phosphorylation of DCBLD2 recruits TRAF6 and stimulates AKT-promoted tumorigenesis.

Aberrant activation of EGFR in human cancers promotes tumorigenesis through stimulation of AKT signaling. Here, we determined that the discoidina neuropilin-like membrane protein DCBLD2 is upregulated in clinical specimens of glioblastomas and head and neck cancers (HNCs) and is required for EGFR-stimulated tumorigenesis. In multiple cancer cell lines, EGFR activated phosphorylation of tyrosine 750 (Y750) of DCBLD2, which is located within a recently identified binding motif for TNF receptor-associated factor 6 (TRAF6). Consequently, phosphorylation of DCBLD2 Y750 recruited TRAF6, leading to increased TRAF6 E3 ubiquitin ligase activity and subsequent activation of AKT, thereby enhancing EGFR-driven tumorigenesis. Moreover, evaluation of patient samples of gliomas and HNCs revealed an association among EGFR activation, DCBLD2 phosphorylation, and poor prognoses. Together, our findings uncover a pathway in which DCBLD2 functions as a signal relay for oncogenic EGFR signaling to promote tumorigenesis and suggest DCBLD2 and TRAF6 as potential therapeutic targets for human cancers that are associated with EGFR activation.

Authors
Feng, H; Lopez, GY; Kim, CK; Alvarez, A; Duncan, CG; Nishikawa, R; Nagane, M; Su, A-JA; Auron, PE; Hedberg, ML; Wang, L; Raizer, JJ; Kessler, JA; Parsa, AT; Gao, W-Q; Kim, S-H; Minata, M; Nakano, I; Grandis, JR; McLendon, RE; Bigner, DD; Lin, H-K; Furnari, FB; Cavenee, WK; Hu, B; Yan, H; Cheng, S-Y
MLA Citation
Feng, H, Lopez, GY, Kim, CK, Alvarez, A, Duncan, CG, Nishikawa, R, Nagane, M, Su, A-JA, Auron, PE, Hedberg, ML, Wang, L, Raizer, JJ, Kessler, JA, Parsa, AT, Gao, W-Q, Kim, S-H, Minata, M, Nakano, I, Grandis, JR, McLendon, RE, Bigner, DD, Lin, H-K, Furnari, FB, Cavenee, WK, Hu, B, Yan, H, and Cheng, S-Y. "EGFR phosphorylation of DCBLD2 recruits TRAF6 and stimulates AKT-promoted tumorigenesis." The Journal of clinical investigation 124.9 (September 2014): 3741-3756.
PMID
25061874
Source
epmc
Published In
Journal of Clinical Investigation
Volume
124
Issue
9
Publish Date
2014
Start Page
3741
End Page
3756
DOI
10.1172/jci73093

EGFR phosphorylation of DCBLD2 recruits TRAF6 and stimulates AKT-promoted tumorigenesis

Authors
Feng, H; Lopez, GY; Kim, CK; Alvarez, A; Duncan, CG; Nishikawa, R; Nagane, M; Su, A-JA; Auron, PE; Hedberg, ML; Wang, L; Raizer, JJ; Kessler, JA; Parsa, AT; Gao, W-Q; Kim, S-H; Minata, M; Nakano, I; Grandis, JR; McLendon, RE; Bigner, DD; Lin, H-K; Furnari, FB; Cavenee, WK; Hu, B; Yan, H; Cheng, S-Y
MLA Citation
Feng, H, Lopez, GY, Kim, CK, Alvarez, A, Duncan, CG, Nishikawa, R, Nagane, M, Su, A-JA, Auron, PE, Hedberg, ML, Wang, L, Raizer, JJ, Kessler, JA, Parsa, AT, Gao, W-Q, Kim, S-H, Minata, M, Nakano, I, Grandis, JR, McLendon, RE, Bigner, DD, Lin, H-K, Furnari, FB, Cavenee, WK, Hu, B, Yan, H, and Cheng, S-Y. "EGFR phosphorylation of DCBLD2 recruits TRAF6 and stimulates AKT-promoted tumorigenesis." JOURNAL OF CLINICAL INVESTIGATION 124.9 (September 2014): 3741-3756.
Source
wos-lite
Published In
Journal of Clinical Investigation
Volume
124
Issue
9
Publish Date
2014
Start Page
3741
End Page
3756
DOI
10.1172/JC173093

Cancer-associated isocitrate dehydrogenase 1 (IDH1) R132H mutation and d-2-hydroxyglutarate stimulate glutamine metabolism under hypoxia.

Mutations in the cytosolic NADP(+)-dependent isocitrate dehydrogenase (IDH1) occur in several types of cancer, and altered cellular metabolism associated with IDH1 mutations presents unique therapeutic opportunities. By altering IDH1, these mutations target a critical step in reductive glutamine metabolism, the metabolic pathway that converts glutamine ultimately to acetyl-CoA for biosynthetic processes. While IDH1-mutated cells are sensitive to therapies that target glutamine metabolism, the effect of IDH1 mutations on reductive glutamine metabolism remains poorly understood. To explore this issue, we investigated the effect of a knock-in, single-codon IDH1-R132H mutation on the metabolism of the HCT116 colorectal adenocarcinoma cell line. Here we report the R132H-isobolome by using targeted (13)C isotopomer tracer fate analysis to trace the metabolic fate of glucose and glutamine in this system. We show that introduction of the R132H mutation into IDH1 up-regulates the contribution of glutamine to lipogenesis in hypoxia, but not in normoxia. Treatment of cells with a d-2-hydroxyglutarate (d-2HG) ester recapitulated these changes, indicating that the alterations observed in the knocked-in cells were mediated by d-2HG produced by the IDH1 mutant. These studies provide a dynamic mechanistic basis for metabolic alterations observed in IDH1-mutated tumors and uncover potential therapeutic targets in IDH1-mutated cancers.

Authors
Reitman, ZJ; Duncan, CG; Poteet, E; Winters, A; Yan, L-J; Gooden, DM; Spasojevic, I; Boros, LG; Yang, S-H; Yan, H
MLA Citation
Reitman, ZJ, Duncan, CG, Poteet, E, Winters, A, Yan, L-J, Gooden, DM, Spasojevic, I, Boros, LG, Yang, S-H, and Yan, H. "Cancer-associated isocitrate dehydrogenase 1 (IDH1) R132H mutation and d-2-hydroxyglutarate stimulate glutamine metabolism under hypoxia." The Journal of biological chemistry 289.34 (August 2014): 23318-23328.
PMID
24986863
Source
epmc
Published In
The Journal of biological chemistry
Volume
289
Issue
34
Publish Date
2014
Start Page
23318
End Page
23328
DOI
10.1074/jbc.m114.575183

Exome sequencing identifies somatic gain-of-function PPM1D mutations in brainstem gliomas.

Gliomas arising in the brainstem and thalamus are devastating tumors that are difficult to surgically resect. To determine the genetic and epigenetic landscape of these tumors, we performed exomic sequencing of 14 brainstem gliomas (BSGs) and 12 thalamic gliomas. We also performed targeted mutational analysis of an additional 24 such tumors and genome-wide methylation profiling of 45 gliomas. This study led to the discovery of tumor-specific mutations in PPM1D, encoding wild-type p53-induced protein phosphatase 1D (WIP1), in 37.5% of the BSGs that harbored hallmark H3F3A mutations encoding p.Lys27Met substitutions. PPM1D mutations were mutually exclusive with TP53 mutations in BSG and attenuated p53 activation in vitro. PPM1D mutations were truncating alterations in exon 6 that enhanced the ability of PPM1D to suppress the activation of the DNA damage response checkpoint protein CHK2. These results define PPM1D as a frequent target of somatic mutation and as a potential therapeutic target in brainstem gliomas.

Authors
Zhang, L; Chen, LH; Wan, H; Yang, R; Wang, Z; Feng, J; Yang, S; Jones, S; Wang, S; Zhou, W; Zhu, H; Killela, PJ; Zhang, J; Wu, Z; Li, G; Hao, S; Wang, Y; Webb, JB; Friedman, HS; Friedman, AH; McLendon, RE; He, Y; Reitman, ZJ; Bigner, DD; Yan, H
MLA Citation
Zhang, L, Chen, LH, Wan, H, Yang, R, Wang, Z, Feng, J, Yang, S, Jones, S, Wang, S, Zhou, W, Zhu, H, Killela, PJ, Zhang, J, Wu, Z, Li, G, Hao, S, Wang, Y, Webb, JB, Friedman, HS, Friedman, AH, McLendon, RE, He, Y, Reitman, ZJ, Bigner, DD, and Yan, H. "Exome sequencing identifies somatic gain-of-function PPM1D mutations in brainstem gliomas." Nature genetics 46.7 (July 2014): 726-730.
PMID
24880341
Source
epmc
Published In
Nature Genetics
Volume
46
Issue
7
Publish Date
2014
Start Page
726
End Page
730
DOI
10.1038/ng.2995

Exome sequencing identifies somatic gain-of-function PPM1D mutations in brainstem gliomas

Authors
Zhang, L; Chen, LH; Wan, H; Yang, R; Wang, Z; Feng, J; Yang, S; Jones, S; Wang, S; Zhou, W; Zhu, H; Killela, PJ; Zhang, J; Wu, Z; Li, G; Hao, S; Wang, Y; Webb, JB; Friedman, HS; Friedman, AH; McLendon, RE; He, Y; Reitman, ZJ; Bigner, DD; Yan, H
MLA Citation
Zhang, L, Chen, LH, Wan, H, Yang, R, Wang, Z, Feng, J, Yang, S, Jones, S, Wang, S, Zhou, W, Zhu, H, Killela, PJ, Zhang, J, Wu, Z, Li, G, Hao, S, Wang, Y, Webb, JB, Friedman, HS, Friedman, AH, McLendon, RE, He, Y, Reitman, ZJ, Bigner, DD, and Yan, H. "Exome sequencing identifies somatic gain-of-function PPM1D mutations in brainstem gliomas." Nature Genetics 46.7 (June 1, 2014): 726-730.
Source
crossref
Published In
Nature Genetics
Volume
46
Issue
7
Publish Date
2014
Start Page
726
End Page
730
DOI
10.1038/ng.2995

The genetic landscape of anaplastic astrocytoma.

Anaplastic astrocytoma WHO grade III (A3) is a lethal brain tumor that often occurs in middle aged patients. Clinically, it is challenging to distinguish A3 from glioblastoma multiforme (GBM) WHO grade IV. To reveal the genetic landscape of this tumor type, we sequenced the exome of a cohort of A3s (n=16). For comparison and to illuminate the genomic landscape of other glioma subtypes, we also included in our study diffuse astrocytoma WHO grade II (A2, n=7), oligoastrocytoma WHO grade II (OA2, n=2), anaplastic oligoastrocytoma WHO grade III (OA3, n=4), and GBM (n=28). Exome sequencing of A3s identified frequent mutations in IDH1 (75%, 12/16), ATRX (63%, 10/16), and TP53 (82%, 13/16). In contrast, the majority of GBMs (75%, 21/28) did not contain IDH1 or ATRX mutations, and displayed a distinct spectrum of mutations. Finally, our study also identified novel genes that were not previously linked to this tumor type. In particular, we found mutations in Notch pathway genes (NOTCH1, NOTCH2, NOTCH4, NOTCH2NL), including a recurrent NOTCH1-A465Tmutation, in 31% (5/16) of A3s. This study suggests genetic signatures will be useful for the classification of gliomas.

Authors
Killela, PJ; Pirozzi, CJ; Reitman, ZJ; Jones, S; Rasheed, BA; Lipp, E; Friedman, H; Friedman, AH; He, Y; McLendon, RE; Bigner, DD; Yan, H
MLA Citation
Killela, PJ, Pirozzi, CJ, Reitman, ZJ, Jones, S, Rasheed, BA, Lipp, E, Friedman, H, Friedman, AH, He, Y, McLendon, RE, Bigner, DD, and Yan, H. "The genetic landscape of anaplastic astrocytoma." Oncotarget 5.6 (March 30, 2014): 1452-1457.
PMID
24140581
Source
pubmed
Published In
Oncotarget
Volume
5
Issue
6
Publish Date
2014
Start Page
1452
End Page
1457
DOI
10.18632/oncotarget.1505

Mutations in IDH1, IDH2, and in the TERT promoter define clinically distinct subgroups of adult malignant gliomas.

Frequent mutations in isocitrate dehydrogenase 1 and 2 (IDH1 and IDH2) and the promoter of telomerase reverse transcriptase (TERT) represent two significant discoveries in glioma genomics. Understanding the degree to which these two mutations co-occur or occur exclusively of one another in glioma subtypes presents a unique opportunity to guide glioma classification and prognosis. We analyzed the relationship between overall survival (OS) and the presence of IDH1/2 and TERT promoter mutations in a panel of 473 adult gliomas. We hypothesized and show that genetic signatures capable of distinguishing among several types of gliomas could be established providing clinically relevant information that can serve as an adjunct to histopathological diagnosis. We found that mutations in the TERT promoter occurred in 74.2% of glioblastomas (GBM), but occurred in a minority of Grade II-III astrocytomas (18.2%). In contrast, IDH1/2 mutations were observed in 78.4% of Grade II-III astrocytomas, but were uncommon in primary GBM. In oligodendrogliomas, TERT promoter and IDH1/2 mutations co-occurred in 79% of cases. Patients whose Grade III-IV gliomas exhibit TERT promoter mutations alone predominately have primary GBMs associated with poor median OS (11.5 months). Patients whose Grade III-IV gliomas exhibit IDH1/2 mutations alone predominately have astrocytic morphologies and exhibit a median OS of 57 months while patients whose tumors exhibit both TERT promoter and IDH1/2 mutations predominately exhibit oligodendroglial morphologies and exhibit median OS of 125 months. Analyzing gliomas based on their genetic signatures allows for the stratification of these patients into distinct cohorts, with unique prognosis and survival.

Authors
Killela, PJ; Pirozzi, CJ; Healy, P; Reitman, ZJ; Lipp, E; Rasheed, BA; Yang, R; Diplas, BH; Wang, Z; Greer, PK; Zhu, H; Wang, CY; Carpenter, AB; Friedman, H; Friedman, AH; Keir, ST; He, J; He, Y; McLendon, RE; Herndon, JE; Yan, H; Bigner, DD
MLA Citation
Killela, PJ, Pirozzi, CJ, Healy, P, Reitman, ZJ, Lipp, E, Rasheed, BA, Yang, R, Diplas, BH, Wang, Z, Greer, PK, Zhu, H, Wang, CY, Carpenter, AB, Friedman, H, Friedman, AH, Keir, ST, He, J, He, Y, McLendon, RE, Herndon, JE, Yan, H, and Bigner, DD. "Mutations in IDH1, IDH2, and in the TERT promoter define clinically distinct subgroups of adult malignant gliomas." Oncotarget 5.6 (March 2014): 1515-1525.
PMID
24722048
Source
epmc
Published In
Oncotarget
Volume
5
Issue
6
Publish Date
2014
Start Page
1515
End Page
1525

Chromatin accessibility mapping identifies mediators of basal transcription and retinoid-induced repression of OTX2 in medulloblastoma.

Despite an emerging understanding of the genetic alterations giving rise to various tumors, the mechanisms whereby most oncogenes are overexpressed remain unclear. Here we have utilized an integrated approach of genomewide regulatory element mapping via DNase-seq followed by conventional reporter assays and transcription factor binding site discovery to characterize the transcriptional regulation of the medulloblastoma oncogene Orthodenticle Homeobox 2 (OTX2). Through these studies we have revealed that OTX2 is differentially regulated in medulloblastoma at the level of chromatin accessibility, which is in part mediated by DNA methylation. In cell lines exhibiting chromatin accessibility of OTX2 regulatory regions, we found that autoregulation maintains OTX2 expression. Comparison of medulloblastoma regulatory elements with those of the developing brain reveals that these tumors engage a developmental regulatory program to drive OTX2 transcription. Finally, we have identified a transcriptional regulatory element mediating retinoid-induced OTX2 repression in these tumors. This work characterizes for the first time the mechanisms of OTX2 overexpression in medulloblastoma. Furthermore, this study establishes proof of principle for applying ENCODE datasets towards the characterization of upstream trans-acting factors mediating expression of individual genes.

Authors
Wortham, M; Guo, C; Zhang, M; Song, L; Lee, B-K; Iyer, VR; Furey, TS; Crawford, GE; Yan, H; He, Y
MLA Citation
Wortham, M, Guo, C, Zhang, M, Song, L, Lee, B-K, Iyer, VR, Furey, TS, Crawford, GE, Yan, H, and He, Y. "Chromatin accessibility mapping identifies mediators of basal transcription and retinoid-induced repression of OTX2 in medulloblastoma." PLoS ONE 9.9 (January 2014): e107156-.
Website
http://hdl.handle.net/10161/10681
PMID
25198066
Source
epmc
Published In
PloS one
Volume
9
Issue
9
Publish Date
2014
Start Page
e107156
DOI
10.1371/journal.pone.0107156

Promoting a new brain tumor mutation: TERT promoter mutations in CNS tumors.

Authors
Reitman, ZJ; Pirozzi, CJ; Yan, H
MLA Citation
Reitman, ZJ, Pirozzi, CJ, and Yan, H. "Promoting a new brain tumor mutation: TERT promoter mutations in CNS tumors." Acta Neuropathol 126.6 (December 2013): 789-792.
PMID
24217890
Source
pubmed
Published In
Acta Neuropathologica
Volume
126
Issue
6
Publish Date
2013
Start Page
789
End Page
792
DOI
10.1007/s00401-013-1207-5

Promoting a new brain tumor mutation: TERT promoter mutations in CNS tumors

Authors
Reitman, ZJ; Pirozzi, CJ; Yan, H
MLA Citation
Reitman, ZJ, Pirozzi, CJ, and Yan, H. "Promoting a new brain tumor mutation: TERT promoter mutations in CNS tumors." Acta Neuropathologica 126.6 (November 12, 2013): 789-792. (Review)
Source
scopus
Published In
Acta Neuropathologica
Volume
126
Issue
6
Publish Date
2013
Start Page
789
End Page
792
DOI
10.1007/s00401-013-1207-5

KMT2D maintains neoplastic cell proliferation and global histone H3 lysine 4 monomethylation.

KMT2D (lysine (K)-specific methyltransferase 2D), formerly named MLL2 (myeloid/lymphoid or mixed-lineage leukemia 2, also known as ALR/MLL4), is a histone methyltransferase that plays an important role in regulating gene transcription. In particular, it targets histone H3 lysine 4 (H3K4), whose methylations serve as a gene activation mark. Recently, KMT2D has emerged as one of the most frequently mutated genes in a variety of cancers and in other human diseases, including lymphoma, medulloblastoma, gastric cancer, and Kabuki syndrome. Mutations in KMT2D identified thus far point to its loss-of-function in pathogenesis and suggest its role as a tumor suppressor in various tissues. To determine the effect of a KMT2D deficiency on neoplastic cells, we used homologous recombination- and nuclease-mediated gene editing approaches to generate a panel of isogenic colorectal and medulloblastoma cancer cell lines that differ with respect to their endogenous KMT2D status. We found that a KMT2D deficiency resulted in attenuated cancer cell proliferation and defective cell migration. Analysis of histone H3 modifications revealed that KMT2D was essential for maintaining the level of global H3K4 monomethylation and that its enzymatic SET domain was directly responsible for this function. Furthermore, we found that a majority of KMT2D binding sites are located in regions of potential enhancer elements. Together, these findings revealed the role of KMT2D in regulating enhancer elements in human cells and shed light on the tumorigenic role of its deficiency. Our study supports that KMT2D has distinct roles in neoplastic cells, as opposed to normal cells, and that inhibiting KMT2D may be a viable strategy for cancer therapeutics.

Authors
Guo, C; Chen, LH; Huang, Y; Chang, C-C; Wang, P; Pirozzi, CJ; Qin, X; Bao, X; Greer, PK; McLendon, RE; Yan, H; Keir, ST; Bigner, DD; He, Y
MLA Citation
Guo, C, Chen, LH, Huang, Y, Chang, C-C, Wang, P, Pirozzi, CJ, Qin, X, Bao, X, Greer, PK, McLendon, RE, Yan, H, Keir, ST, Bigner, DD, and He, Y. "KMT2D maintains neoplastic cell proliferation and global histone H3 lysine 4 monomethylation." Oncotarget 4.11 (November 2013): 2144-2153.
PMID
24240169
Source
pubmed
Published In
Oncotarget
Volume
4
Issue
11
Publish Date
2013
Start Page
2144
End Page
2153
DOI
10.18632/oncotarget.1555

The integrated landscape of driver genomic alterations in glioblastoma.

Glioblastoma is one of the most challenging forms of cancer to treat. Here we describe a computational platform that integrates the analysis of copy number variations and somatic mutations and unravels the landscape of in-frame gene fusions in glioblastoma. We found mutations with loss of heterozygosity in LZTR1, encoding an adaptor of CUL3-containing E3 ligase complexes. Mutations and deletions disrupt LZTR1 function, which restrains the self renewal and growth of glioma spheres that retain stem cell features. Loss-of-function mutations in CTNND2 target a neural-specific gene and are associated with the transformation of glioma cells along the very aggressive mesenchymal phenotype. We also report recurrent translocations that fuse the coding sequence of EGFR to several partners, with EGFR-SEPT14 being the most frequent functional gene fusion in human glioblastoma. EGFR-SEPT14 fusions activate STAT3 signaling and confer mitogen independence and sensitivity to EGFR inhibition. These results provide insights into the pathogenesis of glioblastoma and highlight new targets for therapeutic intervention.

Authors
Frattini, V; Trifonov, V; Chan, JM; Castano, A; Lia, M; Abate, F; Keir, ST; Ji, AX; Zoppoli, P; Niola, F; Danussi, C; Dolgalev, I; Porrati, P; Pellegatta, S; Heguy, A; Gupta, G; Pisapia, DJ; Canoll, P; Bruce, JN; McLendon, RE; Yan, H; Aldape, K; Finocchiaro, G; Mikkelsen, T; Privé, GG; Bigner, DD; Lasorella, A; Rabadan, R; Iavarone, A
MLA Citation
Frattini, V, Trifonov, V, Chan, JM, Castano, A, Lia, M, Abate, F, Keir, ST, Ji, AX, Zoppoli, P, Niola, F, Danussi, C, Dolgalev, I, Porrati, P, Pellegatta, S, Heguy, A, Gupta, G, Pisapia, DJ, Canoll, P, Bruce, JN, McLendon, RE, Yan, H, Aldape, K, Finocchiaro, G, Mikkelsen, T, Privé, GG, Bigner, DD, Lasorella, A, Rabadan, R, and Iavarone, A. "The integrated landscape of driver genomic alterations in glioblastoma." Nat Genet 45.10 (October 2013): 1141-1149.
PMID
23917401
Source
pubmed
Published In
Nature Genetics
Volume
45
Issue
10
Publish Date
2013
Start Page
1141
End Page
1149
DOI
10.1038/ng.2734

Isocitrate dehydrogenase 1: what it means to the neurosurgeon: a review.

Isocitrate dehydrogenase 1 (IDH1) mutations have been discovered to be frequent and highly conserved in secondary glioblastoma multiforme and lower-grade gliomas. Although IDH1 mutations confer a unique genotype that has been associated with a favorable prognosis, the role of the mutated IDH1 enzyme and its metabolites in tumor initiation and maintenance remains unresolved. However, given that IDH1 mutations are homogeneously expressed and are limited solely to tumor tissue, targeting this mutation could potentially yield novel treatment strategies for patients with glioblastoma multiforme.

Authors
Hodges, TR; Choi, BD; Bigner, DD; Yan, H; Sampson, JH
MLA Citation
Hodges, TR, Choi, BD, Bigner, DD, Yan, H, and Sampson, JH. "Isocitrate dehydrogenase 1: what it means to the neurosurgeon: a review." J Neurosurg 118.6 (June 2013): 1176-1180. (Review)
PMID
23581583
Source
pubmed
Published In
Journal of neurosurgery
Volume
118
Issue
6
Publish Date
2013
Start Page
1176
End Page
1180
DOI
10.3171/2013.3.JNS122282

Releasing the block: setting differentiation free with mutant IDH inhibitors.

Hotspot mutations in IDH1 and IDH2 cause a differentiation block that can promote tumorigenesis. Two recent papers reported that small molecules targeting mutant IDH1 or mutant IDH2 release this differentiation block and/or impede tumor growth, providing a proof-of-concept that mutant IDHs are therapeutically targetable and that their effects are reversible.

Authors
Pirozzi, CJ; Reitman, ZJ; Yan, H
MLA Citation
Pirozzi, CJ, Reitman, ZJ, and Yan, H. "Releasing the block: setting differentiation free with mutant IDH inhibitors." Cancer Cell 23.5 (May 13, 2013): 570-572.
PMID
23680144
Source
pubmed
Published In
Cancer Cell
Volume
23
Issue
5
Publish Date
2013
Start Page
570
End Page
572
DOI
10.1016/j.ccr.2013.04.024

TERT promoter mutations occur frequently in gliomas and a subset of tumors derived from cells with low rates of self-renewal.

Malignant cells, like all actively growing cells, must maintain their telomeres, but genetic mechanisms responsible for telomere maintenance in tumors have only recently been discovered. In particular, mutations of the telomere binding proteins alpha thalassemia/mental retardation syndrome X-linked (ATRX) or death-domain associated protein (DAXX) have been shown to underlie a telomere maintenance mechanism not involving telomerase (alternative lengthening of telomeres), and point mutations in the promoter of the telomerase reverse transcriptase (TERT) gene increase telomerase expression and have been shown to occur in melanomas and a small number of other tumors. To further define the tumor types in which this latter mechanism plays a role, we surveyed 1,230 tumors of 60 different types. We found that tumors could be divided into types with low (<15%) and high (≥15%) frequencies of TERT promoter mutations. The nine TERT-high tumor types almost always originated in tissues with relatively low rates of self renewal, including melanomas, liposarcomas, hepatocellular carcinomas, urothelial carcinomas, squamous cell carcinomas of the tongue, medulloblastomas, and subtypes of gliomas (including 83% of primary glioblastoma, the most common brain tumor type). TERT and ATRX mutations were mutually exclusive, suggesting that these two genetic mechanisms confer equivalent selective growth advantages. In addition to their implications for understanding the relationship between telomeres and tumorigenesis, TERT mutations provide a biomarker that may be useful for the early detection of urinary tract and liver tumors and aid in the classification and prognostication of brain tumors.

Authors
Killela, PJ; Reitman, ZJ; Jiao, Y; Bettegowda, C; Agrawal, N; Diaz, LA; Friedman, AH; Friedman, H; Gallia, GL; Giovanella, BC; Grollman, AP; He, T-C; He, Y; Hruban, RH; Jallo, GI; Mandahl, N; Meeker, AK; Mertens, F; Netto, GJ; Rasheed, BA; Riggins, GJ; Rosenquist, TA; Schiffman, M; Shih, I-M; Theodorescu, D; Torbenson, MS; Velculescu, VE; Wang, T-L; Wentzensen, N; Wood, LD; Zhang, M; McLendon, RE; Bigner, DD; Kinzler, KW; Vogelstein, B; Papadopoulos, N; Yan, H
MLA Citation
Killela, PJ, Reitman, ZJ, Jiao, Y, Bettegowda, C, Agrawal, N, Diaz, LA, Friedman, AH, Friedman, H, Gallia, GL, Giovanella, BC, Grollman, AP, He, T-C, He, Y, Hruban, RH, Jallo, GI, Mandahl, N, Meeker, AK, Mertens, F, Netto, GJ, Rasheed, BA, Riggins, GJ, Rosenquist, TA, Schiffman, M, Shih, I-M, Theodorescu, D, Torbenson, MS, Velculescu, VE, Wang, T-L, Wentzensen, N, Wood, LD, Zhang, M, McLendon, RE, Bigner, DD, Kinzler, KW, Vogelstein, B, Papadopoulos, N, and Yan, H. "TERT promoter mutations occur frequently in gliomas and a subset of tumors derived from cells with low rates of self-renewal." Proc Natl Acad Sci U S A 110.15 (April 9, 2013): 6021-6026.
PMID
23530248
Source
pubmed
Published In
Proceedings of the National Academy of Sciences of USA
Volume
110
Issue
15
Publish Date
2013
Start Page
6021
End Page
6026
DOI
10.1073/pnas.1303607110

Exomic Sequencing of Four Rare Central Nervous System Tumor Types

Authors
Bettegowda, C; Agrawal, N; Jiao, Y; Wang, Y; Wood, LD; Rodriguez, FJ; Hruban, RH; Gallia, GL; Binder, ZA; Riggins, CJ; Salmasi, V; Riggins, GJ; Reitman, ZJ; Rasheed, A; Keir, S; Shinjo, S; Marie, S; McLendon, R; Jallo, G; Vogelstein, B; Bigner, D; Yan, H; Kinzler, KW; Papadopoulos, N
MLA Citation
Bettegowda, C, Agrawal, N, Jiao, Y, Wang, Y, Wood, LD, Rodriguez, FJ, Hruban, RH, Gallia, GL, Binder, ZA, Riggins, CJ, Salmasi, V, Riggins, GJ, Reitman, ZJ, Rasheed, A, Keir, S, Shinjo, S, Marie, S, McLendon, R, Jallo, G, Vogelstein, B, Bigner, D, Yan, H, Kinzler, KW, and Papadopoulos, N. "Exomic Sequencing of Four Rare Central Nervous System Tumor Types." ONCOTARGET 4.4 (April 2013): 572-583.
PMID
23592488
Source
wos-lite
Published In
Oncotarget
Volume
4
Issue
4
Publish Date
2013
Start Page
572
End Page
583

Reversing the Warburg effect as a treatment for glioblastoma.

Glioblastoma multiforme (GBM), like most cancers, possesses a unique bioenergetic state of aerobic glycolysis known as the Warburg effect. Here, we documented that methylene blue (MB) reverses the Warburg effect evidenced by the increasing of oxygen consumption and reduction of lactate production in GBM cell lines. MB decreases GBM cell proliferation and halts the cell cycle in S phase. Through activation of AMP-activated protein kinase, MB inactivates downstream acetyl-CoA carboxylase and decreases cyclin expression. Structure-activity relationship analysis demonstrated that toluidine blue O, an MB derivative with similar bioenergetic actions, exerts similar action in GBM cell proliferation. In contrast, two other MB derivatives, 2-chlorophenothiazine and promethazine, exert no effect on cellular bioenergetics and do not inhibit GBM cell proliferation. MB inhibits cell proliferation in both temozolomide-sensitive and -insensitive GBM cell lines. In a human GBM xenograft model, a single daily dosage of MB does not activate AMP-activated protein kinase signaling, and no tumor regression was observed. In summary, the current study provides the first in vitro proof of concept that reversal of Warburg effect might be a novel therapy for GBM.

Authors
Poteet, E; Choudhury, GR; Winters, A; Li, W; Ryou, M-G; Liu, R; Tang, L; Ghorpade, A; Wen, Y; Yuan, F; Keir, ST; Yan, H; Bigner, DD; Simpkins, JW; Yang, S-H
MLA Citation
Poteet, E, Choudhury, GR, Winters, A, Li, W, Ryou, M-G, Liu, R, Tang, L, Ghorpade, A, Wen, Y, Yuan, F, Keir, ST, Yan, H, Bigner, DD, Simpkins, JW, and Yang, S-H. "Reversing the Warburg effect as a treatment for glioblastoma." J Biol Chem 288.13 (March 29, 2013): 9153-9164.
PMID
23408428
Source
pubmed
Published In
The Journal of biological chemistry
Volume
288
Issue
13
Publish Date
2013
Start Page
9153
End Page
9164
DOI
10.1074/jbc.M112.440354

Disruption of wild-type IDH1 suppresses D-2-hydroxyglutarate production in IDH1-mutated gliomas.

Point mutations at Arg132 of the cytoplasmic NADP(+)-dependent isocitrate dehydrogenase 1 (IDH1) occur frequently in gliomas and result in a gain of function to produce the "oncometabolite" D-2-hydroxyglutarate (D-2HG). The mutated IDH1 allele is usually associated with a wild-type IDH1 allele (heterozygous) in cancer. Here, we identify 2 gliomas that underwent loss of the wild-type IDH1 allele but retained the mutant IDH1 allele following tumor progression from World Health Organization (WHO) grade III anaplastic astrocytomas to WHO grade IV glioblastomas. Intratumoral D-2HG was 14-fold lower in the glioblastomas lacking wild-type IDH1 than in glioblastomas with heterozygous IDH1 mutations. To characterize the contribution of wild-type IDH1 to cancer cell D-2HG production, we established an IDH1-mutated astrocytoma (IMA) cell line from a WHO grade III anaplastic astrocytoma. Disruption of the wild-type IDH1 allele in IMA cells by gene targeting resulted in an 87-fold decrease in cellular D-2HG levels, showing that both wild-type and mutant IDH1 alleles are required for D-2HG production in glioma cells. Expression of wild-type IDH1 was also critical for mutant IDH1-associated D-2HG production in the colorectal cancer cell line HCT116. These insights may aid in the development of therapeutic strategies to target IDH1-mutated cancers.

Authors
Jin, G; Reitman, ZJ; Duncan, CG; Spasojevic, I; Gooden, DM; Rasheed, BA; Yang, R; Lopez, GY; He, Y; McLendon, RE; Bigner, DD; Yan, H
MLA Citation
Jin, G, Reitman, ZJ, Duncan, CG, Spasojevic, I, Gooden, DM, Rasheed, BA, Yang, R, Lopez, GY, He, Y, McLendon, RE, Bigner, DD, and Yan, H. "Disruption of wild-type IDH1 suppresses D-2-hydroxyglutarate production in IDH1-mutated gliomas." Cancer Res 73.2 (January 15, 2013): 496-501.
PMID
23204232
Source
pubmed
Published In
Cancer Research
Volume
73
Issue
2
Publish Date
2013
Start Page
496
End Page
501
DOI
10.1158/0008-5472.CAN-12-2852

The integrated landscape of driver genomic alterations in glioblastoma

Glioblastoma is one of the most challenging forms of cancer to treat. Here we describe a computational platform that integrates the analysis of copy number variations and somatic mutations and unravels the landscape of in-frame gene fusions in glioblastoma. We found mutations with loss of heterozygosity in LZTR1, encoding an adaptor of CUL3-containing E3 ligase complexes. Mutations and deletions disrupt LZTR1 function, which restrains the self renewal and growth of glioma spheres that retain stem cell features. Loss-of-function mutations in CTNND2 target a neural-specific gene and are associated with the transformation of glioma cells along the very aggressive mesenchymal phenotype. We also report recurrent translocations that fuse the coding sequence of EGFR to several partners, with EGFR-SEPT14 being the most frequent functional gene fusion in human glioblastoma. EGFR-SEPT14 fusions activate STAT3 signaling and confer mitogen independence and sensitivity to EGFR inhibition. These results provide insights into the pathogenesis of glioblastoma and highlight new targets for therapeutic intervention. © 2013 Nature America, Inc. All rights reserved.

Authors
Frattini, V; Trifonov, V; Chan, JM; Castano, A; Lia, M; Abate, F; Keir, ST; Ji, AX; Zoppoli, P; Niola, F; al, E
MLA Citation
Frattini, V, Trifonov, V, Chan, JM, Castano, A, Lia, M, Abate, F, Keir, ST, Ji, AX, Zoppoli, P, Niola, F, and al, E. "The integrated landscape of driver genomic alterations in glioblastoma." Nature Genetics 45.10 (2013): 1141-1149.
Source
scival
Published In
Nature Genetics
Volume
45
Issue
10
Publish Date
2013
Start Page
1141
End Page
1149
DOI
10.1038/ng.2734

A heterozygous IDH1R132H/WT mutation induces genome-wide alterations in DNA methylation.

Monoallelic point mutations of the NADP(+)-dependent isocitrate dehydrogenases IDH1 and IDH2 occur frequently in gliomas, acute myeloid leukemias, and chondromas, and display robust association with specific DNA hypermethylation signatures. Here we show that heterozygous expression of the IDH1(R132H) allele is sufficient to induce the genome-wide alterations in DNA methylation characteristic of these tumors. Using a gene-targeting approach, we knocked-in a single copy of the most frequently observed IDH1 mutation, R132H, into a human cancer cell line and profiled changes in DNA methylation at over 27,000 CpG dinucleotides relative to wild-type parental cells. We find that IDH1(R132H/WT) mutation induces widespread alterations in DNA methylation, including hypermethylation of 2010 and hypomethylation of 842 CpG loci. We demonstrate that many of these alterations are consistent with those observed in IDH1-mutant and G-CIMP+ primary gliomas and can segregate IDH wild-type and mutated tumors as well as those exhibiting the G-CIMP phenotype in unsupervised analysis of two primary glioma cohorts. Further, we show that the direction of IDH1(R132H/WT)-mediated DNA methylation change is largely dependent upon preexisting DNA methylation levels, resulting in depletion of moderately methylated loci. Additionally, whereas the levels of multiple histone H3 and H4 methylation modifications were globally increased, consistent with broad inhibition of histone demethylation, hypermethylation at H3K9 in particular accompanied locus-specific DNA hypermethylation at several genes down-regulated in IDH1(R132H/WT) knock-in cells. These data provide insight on epigenetic alterations induced by IDH1 mutations and support a causal role for IDH1(R132H/WT) mutants in driving epigenetic instability in human cancer cells.

Authors
Duncan, CG; Barwick, BG; Jin, G; Rago, C; Kapoor-Vazirani, P; Powell, DR; Chi, J-T; Bigner, DD; Vertino, PM; Yan, H
MLA Citation
Duncan, CG, Barwick, BG, Jin, G, Rago, C, Kapoor-Vazirani, P, Powell, DR, Chi, J-T, Bigner, DD, Vertino, PM, and Yan, H. "A heterozygous IDH1R132H/WT mutation induces genome-wide alterations in DNA methylation." Genome Res 22.12 (December 2012): 2339-2355.
PMID
22899282
Source
pubmed
Published In
Genome research
Volume
22
Issue
12
Publish Date
2012
Start Page
2339
End Page
2355
DOI
10.1101/gr.132738.111

Enzyme redesign guided by cancer-derived IDH1 mutations.

Mutations in an enzyme can result in a neomorphic catalytic activity in cancers. We applied cancer-associated mutations from isocitrate dehydrogenases to homologous residues in the active sites of homoisocitrate dehydrogenases to derive enzymes that catalyze the conversion of 2-oxoadipate to (R)-2-hydroxyadipate, a critical step for adipic acid production. Thus, we provide a prototypic example of how insights from cancer genome sequencing and functional studies can aid in enzyme redesign.

Authors
Reitman, ZJ; Choi, BD; Spasojevic, I; Bigner, DD; Sampson, JH; Yan, H
MLA Citation
Reitman, ZJ, Choi, BD, Spasojevic, I, Bigner, DD, Sampson, JH, and Yan, H. "Enzyme redesign guided by cancer-derived IDH1 mutations." Nat Chem Biol 8.11 (November 2012): 887-889.
PMID
23001033
Source
pubmed
Published In
Nature Chemical Biology
Volume
8
Issue
11
Publish Date
2012
Start Page
887
End Page
889
DOI
10.1038/nchembio.1065

Global identification of MLL2-targeted loci reveals MLL2's role in diverse signaling pathways.

Myeloid/lymphoid or mixed-lineage leukemia (MLL)-family genes encode histone lysine methyltransferases that play important roles in epigenetic regulation of gene transcription. MLL genes are frequently mutated in human cancers. Unlike MLL1, MLL2 (also known as ALR/MLL4) and its homolog MLL3 are not well-understood. Specifically, little is known regarding the extent of global MLL2 involvement in the regulation of gene expression and the mechanism underlying its alterations in driving tumorigenesis. Here we profile the global loci targeted by MLL2. A combinatorial analysis of the MLL2 binding profile and gene expression in MLL2 wild-type versus MLL2-null isogenic cell lines identified direct transcriptional target genes and revealed the connection of MLL2 to multiple cellular signaling pathways, including the p53 pathway, cAMP-mediated signaling, and cholestasis signaling. In particular, we demonstrate that MLL2 participates in retinoic acid receptor signaling by promoting retinoic acid-responsive gene transcription. Our results present a genome-wide integrative analysis of the MLL2 target loci and suggest potential mechanisms underlying tumorigenesis driven by MLL2 alterations.

Authors
Guo, C; Chang, C-C; Wortham, M; Chen, LH; Kernagis, DN; Qin, X; Cho, Y-W; Chi, J-T; Grant, GA; McLendon, RE; Yan, H; Ge, K; Papadopoulos, N; Bigner, DD; He, Y
MLA Citation
Guo, C, Chang, C-C, Wortham, M, Chen, LH, Kernagis, DN, Qin, X, Cho, Y-W, Chi, J-T, Grant, GA, McLendon, RE, Yan, H, Ge, K, Papadopoulos, N, Bigner, DD, and He, Y. "Global identification of MLL2-targeted loci reveals MLL2's role in diverse signaling pathways." Proc Natl Acad Sci U S A 109.43 (October 23, 2012): 17603-17608.
PMID
23045699
Source
pubmed
Published In
Proceedings of the National Academy of Sciences of USA
Volume
109
Issue
43
Publish Date
2012
Start Page
17603
End Page
17608
DOI
10.1073/pnas.1208807109

Mutant IDH1 is required for IDH1 mutated tumor cell growth.

Frequent somatic hotspot mutations in isocitrate dehydrogenase 1 (IDH1) have been identified in gliomas, acute myeloid leukemias, chondrosarcomas, and other cancers, providing a likely avenue for targeted cancer therapy. However, whether mutant IDH1 protein is required for maintaining IDH1 mutated tumor cell growth remains unknown. Here, using a genetically engineered inducible system, we report that selective suppression of endogenous mutant IDH1 expression in HT1080, a fibrosarcoma cell line with a native IDH1(R132C) heterozygous mutation, significantly inhibits cell proliferation and decreases clonogenic potential. Our findings offer insights into changes that may contribute to the inhibition of cell proliferation and offer a strong preclinical rationale for utilizing mutant IDH1 as a valid therapeutic target.

Authors
Jin, G; Pirozzi, CJ; Chen, LH; Lopez, GY; Duncan, CG; Feng, J; Spasojevic, I; Bigner, DD; He, Y; Yan, H
MLA Citation
Jin, G, Pirozzi, CJ, Chen, LH, Lopez, GY, Duncan, CG, Feng, J, Spasojevic, I, Bigner, DD, He, Y, and Yan, H. "Mutant IDH1 is required for IDH1 mutated tumor cell growth." Oncotarget 3.8 (August 2012): 774-782.
PMID
22885298
Source
pubmed
Published In
Oncotarget
Volume
3
Issue
8
Publish Date
2012
Start Page
774
End Page
782
DOI
10.18632/oncotarget.577

Frequent ATRX, CIC, FUBP1 and IDH1 mutations refine the classification of malignant gliomas.

Mutations in the critical chromatin modifier ATRX and mutations in CIC and FUBP1, which are potent regulators of cell growth, have been discovered in specific subtypes of gliomas, the most common type of primary malignant brain tumors. However, the frequency of these mutations in many subtypes of gliomas, and their association with clinical features of the patients, is poorly understood. Here we analyzed these loci in 363 brain tumors. ATRX is frequently mutated in grade II-III astrocytomas (71%), oligoastrocytomas (68%), and secondary glioblastomas (57%), and ATRX mutations are associated with IDH1 mutations and with an alternative lengthening of telomeres phenotype. CIC and FUBP1 mutations occurred frequently in oligodendrogliomas (46% and 24%, respectively) but rarely in astrocytomas or oligoastrocytomas ( more than 10%). This analysis allowed us to define two highly recurrent genetic signatures in gliomas: IDH1/ATRX (I-A) and IDH1/CIC/FUBP1 (I-CF). Patients with I-CF gliomas had a significantly longer median overall survival (96 months) than patients with I-A gliomas (51 months) and patients with gliomas that did not harbor either signature (13 months). The genetic signatures distinguished clinically distinct groups of oligoastrocytoma patients, which usually present a diagnostic challenge, and were associated with differences in clinical outcome even among individual tumor types. In addition to providing new clues about the genetic alterations underlying gliomas, the results have immediate clinical implications, providing a tripartite genetic signature that can serve as a useful adjunct to conventional glioma classification that may aid in prognosis, treatment selection, and therapeutic trial design.

Authors
Jiao, Y; Killela, PJ; Reitman, ZJ; Rasheed, AB; Heaphy, CM; de Wilde, RF; Rodriguez, FJ; Rosemberg, S; Oba-Shinjo, SM; Nagahashi Marie, SK; Bettegowda, C; Agrawal, N; Lipp, E; Pirozzi, C; Lopez, G; He, Y; Friedman, H; Friedman, AH; Riggins, GJ; Holdhoff, M; Burger, P; McLendon, R; Bigner, DD; Vogelstein, B; Meeker, AK; Kinzler, KW; Papadopoulos, N; Diaz, LA; Yan, H
MLA Citation
Jiao, Y, Killela, PJ, Reitman, ZJ, Rasheed, AB, Heaphy, CM, de Wilde, RF, Rodriguez, FJ, Rosemberg, S, Oba-Shinjo, SM, Nagahashi Marie, SK, Bettegowda, C, Agrawal, N, Lipp, E, Pirozzi, C, Lopez, G, He, Y, Friedman, H, Friedman, AH, Riggins, GJ, Holdhoff, M, Burger, P, McLendon, R, Bigner, DD, Vogelstein, B, Meeker, AK, Kinzler, KW, Papadopoulos, N, Diaz, LA, and Yan, H. "Frequent ATRX, CIC, FUBP1 and IDH1 mutations refine the classification of malignant gliomas." Oncotarget 3.7 (July 2012): 709-722.
PMID
22869205
Source
pubmed
Published In
Oncotarget
Volume
3
Issue
7
Publish Date
2012
Start Page
709
End Page
722
DOI
10.18632/oncotarget.588

Apples to origins: identifying brain tumor stem cell genes by comparing transcriptomes of normal and cancer stem cells.

The mechanisms whereby medulloblastoma stem cells coordinate tumor propagation are poorly understood. Using microarray analysis, Corno and colleagues draw parallels and distinctions between medulloblastoma stem cells from the Ptch(+/-) mouse and normal neural stem cells, identifying Ebf3 as a cancer stem cell-specific transcript critical for tumor growth.

Authors
Wortham, M; Yan, H
MLA Citation
Wortham, M, and Yan, H. "Apples to origins: identifying brain tumor stem cell genes by comparing transcriptomes of normal and cancer stem cells." Cancer Discov 2.6 (June 2012): 492-494.
PMID
22684456
Source
pubmed
Published In
Cancer Discovery
Volume
2
Issue
6
Publish Date
2012
Start Page
492
End Page
494
DOI
10.1158/2159-8290.CD-12-0182

Transformation by the (R)-enantiomer of 2-hydroxyglutarate linked to EGLN activation.

The identification of succinate dehydrogenase (SDH), fumarate hydratase (FH) and isocitrate dehydrogenase (IDH) mutations in human cancers has rekindled the idea that altered cellular metabolism can transform cells. Inactivating SDH and FH mutations cause the accumulation of succinate and fumarate, respectively, which can inhibit 2-oxoglutarate (2-OG)-dependent enzymes, including the EGLN prolyl 4-hydroxylases that mark the hypoxia inducible factor (HIF) transcription factor for polyubiquitylation and proteasomal degradation. Inappropriate HIF activation is suspected of contributing to the pathogenesis of SDH-defective and FH-defective tumours but can suppress tumour growth in some other contexts. IDH1 and IDH2, which catalyse the interconversion of isocitrate and 2-OG, are frequently mutated in human brain tumours and leukaemias. The resulting mutants have the neomorphic ability to convert 2-OG to the (R)-enantiomer of 2-hydroxyglutarate ((R)-2HG). Here we show that (R)-2HG, but not (S)-2HG, stimulates EGLN activity, leading to diminished HIF levels, which enhances the proliferation and soft agar growth of human astrocytes. These findings define an enantiomer-specific mechanism by which the (R)-2HG that accumulates in IDH mutant brain tumours promotes transformation and provide a justification for exploring EGLN inhibition as a potential treatment strategy.

Authors
Koivunen, P; Lee, S; Duncan, CG; Lopez, G; Lu, G; Ramkissoon, S; Losman, JA; Joensuu, P; Bergmann, U; Gross, S; Travins, J; Weiss, S; Looper, R; Ligon, KL; Verhaak, RGW; Yan, H; Kaelin, WG
MLA Citation
Koivunen, P, Lee, S, Duncan, CG, Lopez, G, Lu, G, Ramkissoon, S, Losman, JA, Joensuu, P, Bergmann, U, Gross, S, Travins, J, Weiss, S, Looper, R, Ligon, KL, Verhaak, RGW, Yan, H, and Kaelin, WG. "Transformation by the (R)-enantiomer of 2-hydroxyglutarate linked to EGLN activation. (Published online)" Nature 483.7390 (February 15, 2012): 484-488.
PMID
22343896
Source
pubmed
Published In
Nature
Volume
483
Issue
7390
Publish Date
2012
Start Page
484
End Page
488
DOI
10.1038/nature10898

Somatic mutations in the chromatin remodeling gene ARID1A occur in several tumor types.

Mutations in the chromatin remodeling gene ARID1A have recently been identified in the majority of ovarian clear cell carcinomas (OCCCs). To determine the prevalence of mutations in other tumor types, we evaluated 759 malignant neoplasms including those of the pancreas, breast, colon, stomach, lung, prostate, brain, and blood (leukemias). We identified truncating mutations in 6% of the neoplasms studied; nontruncating somatic mutations were identified in an additional 0.4% of neoplasms. Mutations were most commonly found in gastrointestinal samples with 12 of 119 (10%) colorectal and 10 of 100 (10%) gastric neoplasms, respectively, harboring changes. More than half of the mutated colorectal and gastric cancers displayed microsatellite instability (MSI) and the mutations in these tumors were out-of-frame insertions or deletions at mononucleotide repeats. Mutations were also identified in 2-8% of tumors of the pancreas, breast, brain (medulloblastomas), prostate, and lung, and none of these tumors displayed MSI. These findings suggest that the aberrant chromatin remodeling consequent to ARID1A inactivation contributes to a variety of different types of neoplasms.

Authors
Jones, S; Li, M; Parsons, DW; Zhang, X; Wesseling, J; Kristel, P; Schmidt, MK; Markowitz, S; Yan, H; Bigner, D; Hruban, RH; Eshleman, JR; Iacobuzio-Donahue, CA; Goggins, M; Maitra, A; Malek, SN; Powell, S; Vogelstein, B; Kinzler, KW; Velculescu, VE; Papadopoulos, N
MLA Citation
Jones, S, Li, M, Parsons, DW, Zhang, X, Wesseling, J, Kristel, P, Schmidt, MK, Markowitz, S, Yan, H, Bigner, D, Hruban, RH, Eshleman, JR, Iacobuzio-Donahue, CA, Goggins, M, Maitra, A, Malek, SN, Powell, S, Vogelstein, B, Kinzler, KW, Velculescu, VE, and Papadopoulos, N. "Somatic mutations in the chromatin remodeling gene ARID1A occur in several tumor types." Hum Mutat 33.1 (January 2012): 100-103.
PMID
22009941
Source
pubmed
Published In
Human Mutation
Volume
33
Issue
1
Publish Date
2012
Start Page
100
End Page
103
DOI
10.1002/humu.21633

Aberrant Otx2 expression enhances migration and induces ectopic proliferation of hindbrain neuronal progenitor cells.

Dysregulation of Otx2 is a hallmark of the pediatric brain tumor medulloblastoma, yet its functional significance in the establishment of these tumors is unknown. Here we have sought to determine the functional consequences of Otx2 overexpression in the mouse hindbrain to characterize its potential role in medulloblastoma tumorigenesis and identify the cell types responsive to this lineage-specific oncogene. Expression of Otx2 broadly in the mouse hindbrain resulted in the accumulation of proliferative clusters of cells in the cerebellar white matter and dorsal brainstem of postnatal mice. We found that brainstem ectopia were derived from neuronal progenitors of the rhombic lip and that cerebellar ectopia were derived from granule neuron precursors (GNPs) that had migrated inwards from the external granule layer (EGL). These hyperplasias exhibited various characteristics of medulloblastoma precursor cells identified in animal models of Shh or Wnt group tumors, including aberrant localization and altered spatiotemporal control of proliferation. However, ectopia induced by Otx2 differentiated and dispersed as the animals reached adulthood, indicating that factors restricting proliferative lifespan were a limiting factor to full transformation of these cells. These studies implicate a role for Otx2 in altering the dynamics of neuronal progenitor cell proliferation.

Authors
Wortham, M; Jin, G; Sun, JL; Bigner, DD; He, Y; Yan, H
MLA Citation
Wortham, M, Jin, G, Sun, JL, Bigner, DD, He, Y, and Yan, H. "Aberrant Otx2 expression enhances migration and induces ectopic proliferation of hindbrain neuronal progenitor cells." PLoS One 7.4 (2012): e36211-.
PMID
22558385
Source
pubmed
Published In
PloS one
Volume
7
Issue
4
Publish Date
2012
Start Page
e36211
DOI
10.1371/journal.pone.0036211

Multiple CDK/CYCLIND genes are amplified in medulloblastoma and supratentorial primitive neuroectodermal brain tumor

Embryonal brain tumors, which include medulloblastoma and the more aggressive supratentorial primitive neuroectodermal tumor (sPNET), comprise one of the largest group of malignant pediatric brain tumors. We observed in high resolution array comparative genomic hybridization and polymerase chain reaction analyses that several different components of the CDK/CYCLIND/pRB regulatory complex, including the CDK4/. 6 and CCND1/. 2 loci, are targets of gene amplification in medulloblastoma and sPNET. CDK6 and CCND1 gene amplification were respectively most common and robust, and overall CDK/CYCLIND gene amplification was more commonly observed in sPNET (25%) than medulloblastoma (1-5%). CDK6 overexpression enhanced in vitro and in vivo oncogenicity and endogenous CDK6 or CCND1 knockdown decreased pRB phosphorylation and impaired cell cycle progression in both medulloblastoma and sPNET cell lines. Although animal models implicate the pRB tumor suppressor pathway in medulloblastoma and sPNET, mutations of RB1 or the related INK4 tumor suppressor loci are rare in primary human tumors. Our data suggest that CDK/CYCLIND gene amplification may represent important mechanisms for functional inactivation of pRB in medulloblastoma and sPNET. © 2012 Elsevier Inc.

Authors
Li, M; Lockwood, W; Zielenska, M; Northcott, P; Ra, YS; Bouffet, E; Yoshimoto, M; Rutka, JT; Yan, H; Taylor, MD; Eberhart, C; Hawkins, CE; Lam, W; Squire, JA; Huang, A
MLA Citation
Li, M, Lockwood, W, Zielenska, M, Northcott, P, Ra, YS, Bouffet, E, Yoshimoto, M, Rutka, JT, Yan, H, Taylor, MD, Eberhart, C, Hawkins, CE, Lam, W, Squire, JA, and Huang, A. "Multiple CDK/CYCLIND genes are amplified in medulloblastoma and supratentorial primitive neuroectodermal brain tumor." Cancer Genetics 205.5 (2012): 220-231.
PMID
22682621
Source
scival
Published In
Cancer genetics
Volume
205
Issue
5
Publish Date
2012
Start Page
220
End Page
231
DOI
10.1016/j.cancergen.2012.03.002

Isocitrate dehydrogenase mutations in gliomas: mechanisms, biomarkers and therapeutic target.

PURPOSE OF REVIEW: Isocitrate dehydrogenases, IDH1 and IDH2, decarboxylate isocitrate to α-ketoglutarate (α-KG) and reduce NADP to NADPH. Point mutations of IDH1 and IDH2 have been discovered in gliomas. IDH mutations cause loss of native enzymatic activities and confer novel activity of converting α-KG to 2-hydroxyglutarate (2-HG). The mechanisms of IDH mutations in gliomagenesis, and their value as diagnostic, prognostic marker and therapeutic target have been extensively studied. This review is to summarize the findings of these studies. RECENT FINDINGS: Crystal structural studies revealed conformation changes in mutant IDHs, which may explain the gain of function by mutant IDHs. The product of mutant IDHs, 2-HG, is an inhibitor of α-KG-dependent dioxygenases, which may cause genome-wide epigenetic changes in human gliomas. IDH mutations are a favorable prognostic factor for human glioma and can be used as biomarker for differential diagnosis and subclassification rather than predictor of response to treatment. Preliminary data suggested that inhibiting production of the substrate of mutant IDH enzymes caused slow-down of glioma cell growth. SUMMARY: As valuable diagnostic and prognostic markers of human gliomas, there is still a lack of knowledge on biological functions of mutant IDHs, making targeting IDHs in glioma both difficult and unsecured.

Authors
Guo, C; Pirozzi, CJ; Lopez, GY; Yan, H
MLA Citation
Guo, C, Pirozzi, CJ, Lopez, GY, and Yan, H. "Isocitrate dehydrogenase mutations in gliomas: mechanisms, biomarkers and therapeutic target." Curr Opin Neurol 24.6 (December 2011): 648-652. (Review)
PMID
22002076
Source
pubmed
Published In
Current Opinion in Neurology
Volume
24
Issue
6
Publish Date
2011
Start Page
648
End Page
652
DOI
10.1097/WCO.0b013e32834cd415

Mutations in CIC and FUBP1 contribute to human oligodendroglioma.

Oligodendrogliomas are the second most common malignant brain tumor in adults and exhibit characteristic losses of chromosomes 1p and 19q. To identify the molecular genetic basis for this alteration, we performed exomic sequencing of seven tumors. Among other changes, we found that the CIC gene (homolog of the Drosophila gene capicua) on chromosome 19q was somatically mutated in six cases and that the FUBP1 gene [encoding far-upstream element (FUSE) binding protein] on chromosome 1p was somatically mutated in two tumors. Examination of 27 additional oligodendrogliomas revealed 12 and 3 more tumors with mutations of CIC and FUBP1, respectively, 58% of which were predicted to result in truncations of the encoded proteins. These results suggest a critical role for these genes in the biology and pathology of oligodendrocytes.

Authors
Bettegowda, C; Agrawal, N; Jiao, Y; Sausen, M; Wood, LD; Hruban, RH; Rodriguez, FJ; Cahill, DP; McLendon, R; Riggins, G; Velculescu, VE; Oba-Shinjo, SM; Marie, SKN; Vogelstein, B; Bigner, D; Yan, H; Papadopoulos, N; Kinzler, KW
MLA Citation
Bettegowda, C, Agrawal, N, Jiao, Y, Sausen, M, Wood, LD, Hruban, RH, Rodriguez, FJ, Cahill, DP, McLendon, R, Riggins, G, Velculescu, VE, Oba-Shinjo, SM, Marie, SKN, Vogelstein, B, Bigner, D, Yan, H, Papadopoulos, N, and Kinzler, KW. "Mutations in CIC and FUBP1 contribute to human oligodendroglioma." Science 333.6048 (September 9, 2011): 1453-1455.
PMID
21817013
Source
pubmed
Published In
Science
Volume
333
Issue
6048
Publish Date
2011
Start Page
1453
End Page
1455
DOI
10.1126/science.1210557

Altered telomeres in tumors with ATRX and DAXX mutations.

The proteins encoded by ATRX and DAXX participate in chromatin remodeling at telomeres and other genomic sites. Because inactivating mutations of these genes are common in human pancreatic neuroendocrine tumors (PanNETs), we examined the telomere status of these tumors. We found that 61% of PanNETs displayed abnormal telomeres that are characteristic of a telomerase-independent telomere maintenance mechanism termed ALT (alternative lengthening of telomeres). All of the PanNETs exhibiting these abnormal telomeres had ATRX or DAXX mutations or loss of nuclear ATRX or DAXX protein. ATRX mutations also correlate with abnormal telomeres in tumors of the central nervous system. These data suggest that an alternative telomere maintenance function may operate in human tumors with alterations in the ATRX or DAXX genes.

Authors
Heaphy, CM; de Wilde, RF; Jiao, Y; Klein, AP; Edil, BH; Shi, C; Bettegowda, C; Rodriguez, FJ; Eberhart, CG; Hebbar, S; Offerhaus, GJ; McLendon, R; Rasheed, BA; He, Y; Yan, H; Bigner, DD; Oba-Shinjo, SM; Marie, SKN; Riggins, GJ; Kinzler, KW; Vogelstein, B; Hruban, RH; Maitra, A; Papadopoulos, N; Meeker, AK
MLA Citation
Heaphy, CM, de Wilde, RF, Jiao, Y, Klein, AP, Edil, BH, Shi, C, Bettegowda, C, Rodriguez, FJ, Eberhart, CG, Hebbar, S, Offerhaus, GJ, McLendon, R, Rasheed, BA, He, Y, Yan, H, Bigner, DD, Oba-Shinjo, SM, Marie, SKN, Riggins, GJ, Kinzler, KW, Vogelstein, B, Hruban, RH, Maitra, A, Papadopoulos, N, and Meeker, AK. "Altered telomeres in tumors with ATRX and DAXX mutations." Science 333.6041 (July 22, 2011): 425-.
PMID
21719641
Source
pubmed
Published In
Science
Volume
333
Issue
6041
Publish Date
2011
Start Page
425
DOI
10.1126/science.1207313

CLINICAL PATHOLOGIC DESCRIPTION OF THREE PEDIATRIC MEDULLOBLASTOMA CASES WITH MLL2/3 GENE MUTATIONS

Authors
He, Y; Lopez, G; Grant, G; Fuchs, H; Leithe, L; Gururangan, S; Bigner, D; Yan, H; Mclendon, R
MLA Citation
He, Y, Lopez, G, Grant, G, Fuchs, H, Leithe, L, Gururangan, S, Bigner, D, Yan, H, and Mclendon, R. "CLINICAL PATHOLOGIC DESCRIPTION OF THREE PEDIATRIC MEDULLOBLASTOMA CASES WITH MLL2/3 GENE MUTATIONS." May 2011.
PMID
23659599
Source
wos-lite
Published In
Neuro-Oncology
Volume
13
Publish Date
2011
Start Page
I30
End Page
I30

Genomic alterations and the pathogenesis of glioblastoma.

Authors
Duncan, CG; Yan, H
MLA Citation
Duncan, CG, and Yan, H. "Genomic alterations and the pathogenesis of glioblastoma." Cell Cycle 10.8 (April 15, 2011): 1174-1175.
PMID
21389786
Source
pubmed
Published In
Cell Cycle
Volume
10
Issue
8
Publish Date
2011
Start Page
1174
End Page
1175
DOI
10.4161/cc.10.8.15225

Profiling the effects of isocitrate dehydrogenase 1 and 2 mutations on the cellular metabolome.

Point mutations of the NADP(+)-dependent isocitrate dehydrogenases 1 and 2 (IDH1 and IDH2) occur early in the pathogenesis of gliomas. When mutated, IDH1 and IDH2 gain the ability to produce the metabolite (R)-2-hydroxyglutarate (2HG), but the downstream effects of mutant IDH1 and IDH2 proteins or of 2HG on cellular metabolism are unknown. We profiled >200 metabolites in human oligodendroglioma (HOG) cells to determine the effects of expression of IDH1 and IDH2 mutants. Levels of amino acids, glutathione metabolites, choline derivatives, and tricarboxylic acid (TCA) cycle intermediates were altered in mutant IDH1- and IDH2-expressing cells. These changes were similar to those identified after treatment of the cells with 2HG. Remarkably, N-acetyl-aspartyl-glutamate (NAAG), a common dipeptide in brain, was 50-fold reduced in cells expressing IDH1 mutants and 8.3-fold reduced in cells expressing IDH2 mutants. NAAG also was significantly lower in human glioma tissues containing IDH mutations than in gliomas without such mutations. These metabolic changes provide clues to the pathogenesis of tumors associated with IDH gene mutations.

Authors
Reitman, ZJ; Jin, G; Karoly, ED; Spasojevic, I; Yang, J; Kinzler, KW; He, Y; Bigner, DD; Vogelstein, B; Yan, H
MLA Citation
Reitman, ZJ, Jin, G, Karoly, ED, Spasojevic, I, Yang, J, Kinzler, KW, He, Y, Bigner, DD, Vogelstein, B, and Yan, H. "Profiling the effects of isocitrate dehydrogenase 1 and 2 mutations on the cellular metabolome." Proc Natl Acad Sci U S A 108.8 (February 22, 2011): 3270-3275.
PMID
21289278
Source
pubmed
Published In
Proceedings of the National Academy of Sciences of USA
Volume
108
Issue
8
Publish Date
2011
Start Page
3270
End Page
3275
DOI
10.1073/pnas.1019393108

2-hydroxyglutarate production, but not dominant negative function, is conferred by glioma-derived NADP-dependent isocitrate dehydrogenase mutations.

BACKGROUND: Gliomas frequently contain mutations in the cytoplasmic NADP(+)-dependent isocitrate dehydrogenase (IDH1) or the mitochondrial NADP(+)-dependent isocitrate dehydrogenase (IDH2). Several different amino acid substitutions recur at either IDH1 R132 or IDH2 R172 in glioma patients. Genetic evidence indicates that these mutations share a common gain of function, but it is unclear whether the shared function is dominant negative activity, neomorphic production of (R)-2-hydroxyglutarate (2HG), or both. METHODOLOGY/PRINCIPAL FINDINGS: We show by coprecipitation that five cancer-derived IDH1 R132 mutants bind IDH1-WT but that three cancer-derived IDH2 R172 mutants exert minimal binding to IDH2-WT. None of the mutants dominant-negatively lower isocitrate dehydrogenase activity at physiological (40 µM) isocitrate concentrations in mammalian cell lysates. In contrast to this, all of these mutants confer 10- to 100-fold higher 2HG production to cells, and glioma tissues containing IDH1 R132 or IDH2 R172 mutations contain high levels of 2HG compared to glioma tissues without IDH mutations (54.4 vs. 0.1 mg 2HG/g protein). CONCLUSIONS: Binding to, or dominant inhibition of, WT IDH1 or IDH2 is not a shared feature of the IDH1 and IDH2 mutations, and thus is not likely to be important in cancer. The fact that the gain of the enzymatic activity to produce 2HG is a shared feature of the IDH1 and IDH2 mutations suggests that this is an important function for these mutants in driving cancer pathogenesis.

Authors
Jin, G; Reitman, ZJ; Spasojevic, I; Batinic-Haberle, I; Yang, J; Schmidt-Kittler, O; Bigner, DD; Yan, H
MLA Citation
Jin, G, Reitman, ZJ, Spasojevic, I, Batinic-Haberle, I, Yang, J, Schmidt-Kittler, O, Bigner, DD, and Yan, H. "2-hydroxyglutarate production, but not dominant negative function, is conferred by glioma-derived NADP-dependent isocitrate dehydrogenase mutations. (Published online)" PLoS One 6.2 (February 4, 2011): e16812-.
PMID
21326614
Source
pubmed
Published In
PloS one
Volume
6
Issue
2
Publish Date
2011
Start Page
e16812
DOI
10.1371/journal.pone.0016812

The genetic landscape of the childhood cancer medulloblastoma.

Medulloblastoma (MB) is the most common malignant brain tumor of children. To identify the genetic alterations in this tumor type, we searched for copy number alterations using high-density microarrays and sequenced all known protein-coding genes and microRNA genes using Sanger sequencing in a set of 22 MBs. We found that, on average, each tumor had 11 gene alterations, fewer by a factor of 5 to 10 than in the adult solid tumors that have been sequenced to date. In addition to alterations in the Hedgehog and Wnt pathways, our analysis led to the discovery of genes not previously known to be altered in MBs. Most notably, inactivating mutations of the histone-lysine N-methyltransferase genes MLL2 or MLL3 were identified in 16% of MB patients. These results demonstrate key differences between the genetic landscapes of adult and childhood cancers, highlight dysregulation of developmental pathways as an important mechanism underlying MBs, and identify a role for a specific type of histone methylation in human tumorigenesis.

Authors
Parsons, DW; Li, M; Zhang, X; Jones, S; Leary, RJ; Lin, JC-H; Boca, SM; Carter, H; Samayoa, J; Bettegowda, C; Gallia, GL; Jallo, GI; Binder, ZA; Nikolsky, Y; Hartigan, J; Smith, DR; Gerhard, DS; Fults, DW; VandenBerg, S; Berger, MS; Marie, SKN; Shinjo, SMO; Clara, C; Phillips, PC; Minturn, JE; Biegel, JA; Judkins, AR; Resnick, AC; Storm, PB; Curran, T; He, Y; Rasheed, BA; Friedman, HS; Keir, ST; McLendon, R; Northcott, PA; Taylor, MD; Burger, PC; Riggins, GJ; Karchin, R; Parmigiani, G et al.
MLA Citation
Parsons, DW, Li, M, Zhang, X, Jones, S, Leary, RJ, Lin, JC-H, Boca, SM, Carter, H, Samayoa, J, Bettegowda, C, Gallia, GL, Jallo, GI, Binder, ZA, Nikolsky, Y, Hartigan, J, Smith, DR, Gerhard, DS, Fults, DW, VandenBerg, S, Berger, MS, Marie, SKN, Shinjo, SMO, Clara, C, Phillips, PC, Minturn, JE, Biegel, JA, Judkins, AR, Resnick, AC, Storm, PB, Curran, T, He, Y, Rasheed, BA, Friedman, HS, Keir, ST, McLendon, R, Northcott, PA, Taylor, MD, Burger, PC, Riggins, GJ, Karchin, R, and Parmigiani, G et al. "The genetic landscape of the childhood cancer medulloblastoma." Science 331.6016 (January 28, 2011): 435-439.
PMID
21163964
Source
pubmed
Published In
Science
Volume
331
Issue
6016
Publish Date
2011
Start Page
435
End Page
439
DOI
10.1126/science.1198056

HDMX regulates p53 activity and confers chemoresistance to 3-bis(2-chloroethyl)-1-nitrosourea.

Glioblastoma multiforme (GBM) is one of the deadliest tumors afflicting humans, and the mechanisms of its onset and progression remain largely undefined. Our attempts to elucidate its molecular pathogenesis through DNA copy-number analysis by genome-wide digital karyotyping and single nucleotide polymorphism arrays identified a dramatic focal amplification on chromosome 1q32 in 4 of 57 GBM tumors. Quantitative real-time PCR measurements revealed that HDMX is the most commonly amplified and overexpressed gene in the 1q32 locus. Further genetic screening of 284 low- and high-grade gliomas revealed that HDMX amplifications occur solely in pediatric and adult GBMs and that they are mutually exclusive of TP53 mutations and MDM2 amplifications. Here, we demonstrate that HDMX regulates p53 to promote GBM growth and attenuates tumor response to chemotherapy. In GBM cells, HDMX overexpression inhibits p53-mediated transcriptional activation of p21, releases cells from G0 to G1 phase, and enhances cellular proliferation. HDMX overexpression does not affect the expression of PUMA and BAX proapoptotic genes. While in GBM cells treated with the chemotherapeutic agent 1,3-bis(2-chloroethyl)-1-nitrosourea (BCNU), HDMX appears to stabilize p53 and promote phosphorylation of the DNA double-stranded break repair protein H2AX, up-regulate the DNA repair gene VPX, stimulate DNA repair, and confer resistance to BCNU. In summary, HDMX exhibits bona fide oncogenic properties and offers a promising molecular target for GBM therapeutic intervention.

Authors
Jin, G; Cook, S; Cui, B; Chen, WC; Keir, ST; Killela, P; Di, C; Payne, CA; Gregory, SG; McLendon, R; Bigner, DD; Yan, H
MLA Citation
Jin, G, Cook, S, Cui, B, Chen, WC, Keir, ST, Killela, P, Di, C, Payne, CA, Gregory, SG, McLendon, R, Bigner, DD, and Yan, H. "HDMX regulates p53 activity and confers chemoresistance to 3-bis(2-chloroethyl)-1-nitrosourea." Neuro Oncol 12.9 (September 2010): 956-966.
PMID
20472715
Source
pubmed
Published In
Neuro-Oncology
Volume
12
Issue
9
Publish Date
2010
Start Page
956
End Page
966
DOI
10.1093/neuonc/noq045

Integrated genomic analyses identify ERRFI1 and TACC3 as glioblastoma-targeted genes.

The glioblastoma genome displays remarkable chromosomal aberrations, which harbor critical glioblastoma-specific genes contributing to several oncogenetic pathways. To identify glioblastoma-targeted genes, we completed a multifaceted genome-wide analysis to characterize the most significant aberrations of DNA content occurring in glioblastomas. We performed copy number analysis of 111 glioblastomas by Digital Karyotyping and Illumina BeadChip assays and validated our findings using data from the TCGA (The Cancer Genome Atlas) glioblastoma project. From this study, we identified recurrent focal copy number alterations in 1p36.23 and 4p16.3. Expression analyses of genes located in the two regions revealed genes which are dysregulated in glioblastomas. Specifically, we identify EGFR negative regulator, ERRFI1, within the minimal region of deletion in 1p36.23. In glioblastoma cells with a focal deletion of the ERRFI1 locus, restoration of ERRFI1 expression slowed cell migration. Furthermore, we demonstrate that TACC3, an Aurora-A kinase substrate, on 4p16.3, displays gain of copy number, is overexpressed in a glioma-grade-specific pattern, and correlates with Aurora kinase overexpression in glioblastomas. Our multifaceted genomic evaluation of glioblastoma establishes ERRFI1 as a potential candidate tumor suppressor gene and TACC3 as a potential oncogene, and provides insight on targets for oncogenic pathway-based therapy.

Authors
Duncan, CG; Killela, PJ; Payne, CA; Lampson, B; Chen, WC; Liu, J; Solomon, D; Waldman, T; Towers, AJ; Gregory, SG; McDonald, KL; McLendon, RE; Bigner, DD; Yan, H
MLA Citation
Duncan, CG, Killela, PJ, Payne, CA, Lampson, B, Chen, WC, Liu, J, Solomon, D, Waldman, T, Towers, AJ, Gregory, SG, McDonald, KL, McLendon, RE, Bigner, DD, and Yan, H. "Integrated genomic analyses identify ERRFI1 and TACC3 as glioblastoma-targeted genes." Oncotarget 1.4 (August 2010): 265-277.
PMID
21113414
Source
pubmed
Published In
Oncotarget
Volume
1
Issue
4
Publish Date
2010
Start Page
265
End Page
277
DOI
10.18632/oncotarget.137

IDH1(R132) mutation identified in one human melanoma metastasis, but not correlated with metastases to the brain.

Isocitrate dehydrogenase 1 (IDH1) and isocitrate dehydrogenase 2 (IDH2) are enzymes which convert isocitrate to alpha-ketoglutarate while reducing nicotinamide adenine dinucleotide phosphate (NADP+to NADPH). IDH1/2 were recently identified as mutated in a large percentage of progressive gliomas. These mutations occur at IDH1(R132) or the homologous IDH2(R172). Melanomas share some genetic features with IDH1/2-mutated gliomas, such as frequent TP53 mutation. We sought to test whether melanoma is associated with IDH1/2 mutations. Seventy-eight human melanoma samples were analyzed for IDH1(R132) and IDH2(R172) mutation status. A somatic, heterozygous IDH1 c.C394T (p.R132C) mutation was identified in one human melanoma metastasis to the lung. Having identified this mutation in one metastasis, we sought to test the hypothesis that certain selective pressures in the brain environment may specifically favor the cell growth or survival of tumor cells with mutations in IDH1/2, regardless of primary tumor site. To address this, we analyzed IDH1(R132) and IDH2(R172) mutation status 53 metastatic brain tumors, including nine melanoma metastases. Results revealed no mutations in any samples. This lack of mutations would suggest that mutations in IDH1(R132) or IDH2(R172) may be necessary for the formation of tumors in a cell-lineage dependent manner, with a particularly strong selective pressure for mutations in progressive gliomas; this also suggests the lack of a particular selective pressure for growth in brain tissue in general. Studies on the cell-lineages of tumors with IDH1/2 mutations may help clarify the role of these mutations in the development of brain tumors.

Authors
Lopez, GY; Reitman, ZJ; Solomon, D; Waldman, T; Bigner, DD; McLendon, RE; Rosenberg, SA; Samuels, Y; Yan, H
MLA Citation
Lopez, GY, Reitman, ZJ, Solomon, D, Waldman, T, Bigner, DD, McLendon, RE, Rosenberg, SA, Samuels, Y, and Yan, H. "IDH1(R132) mutation identified in one human melanoma metastasis, but not correlated with metastases to the brain." Biochem Biophys Res Commun 398.3 (July 30, 2010): 585-587.
PMID
20603105
Source
pubmed
Published In
Biochemical and Biophysical Research Communications
Volume
398
Issue
3
Publish Date
2010
Start Page
585
End Page
587
DOI
10.1016/j.bbrc.2010.06.125

Isocitrate dehydrogenase 1 and 2 mutations in cancer: alterations at a crossroads of cellular metabolism.

Dysregulation of metabolism is a common phenomenon in cancer cells. The NADP(+)-dependent isocitrate dehydrogenases 1 and 2 (IDH1 and IDH2) function at a crossroads of cellular metabolism in lipid synthesis, cellular defense against oxidative stress, oxidative respiration, and oxygen-sensing signal transduction. We review the normal functions of the encoded enzymes, frequent mutations of IDH1 and IDH2 recently found in human cancers, and possible roles for the mutated enzymes in human disease. IDH1 and IDH2 mutations occur frequently in some types of World Health Organization grades 2-4 gliomas and in acute myeloid leukemias with normal karyotype. IDH1 and IDH2 mutations are remarkably specific to codons that encode conserved functionally important arginines in the active site of each enzyme. To date, all IDH1 mutations have been identified at the Arg132 codon. Mutations in IDH2 have been identified at the Arg140 codon, as well as at Arg172, which is aligned with IDH1 Arg132. IDH1 and IDH2 mutations are usually heterozygous in cancer, and they appear to confer a neomorphic enzyme activity for the enzymes to catalyze the production of D-2-hydroxyglutarate. Study of alterations in these metabolic enzymes may provide insights into the metabolism of cancer cells and uncover novel avenues for development of anticancer therapeutics.

Authors
Reitman, ZJ; Yan, H
MLA Citation
Reitman, ZJ, and Yan, H. "Isocitrate dehydrogenase 1 and 2 mutations in cancer: alterations at a crossroads of cellular metabolism." J Natl Cancer Inst 102.13 (July 7, 2010): 932-941. (Review)
PMID
20513808
Source
pubmed
Published In
Journal of the National Cancer Institute
Volume
102
Issue
13
Publish Date
2010
Start Page
932
End Page
941
DOI
10.1093/jnci/djq187

IDH1 and IDH2 hotspot mutations are not found in canine glioma.

Authors
Reitman, ZJ; Olby, NJ; Mariani, CL; Thomas, R; Breen, M; Bigner, DD; McLendon, RE; Yan, H
MLA Citation
Reitman, ZJ, Olby, NJ, Mariani, CL, Thomas, R, Breen, M, Bigner, DD, McLendon, RE, and Yan, H. "IDH1 and IDH2 hotspot mutations are not found in canine glioma." Int J Cancer 127.1 (July 1, 2010): 245-246. (Letter)
PMID
19877121
Source
pubmed
Published In
International Journal of Cancer
Volume
127
Issue
1
Publish Date
2010
Start Page
245
End Page
246
DOI
10.1002/ijc.25017

IDH1 and IDH2: not your typical oncogenes.

Oncogenes usually increase their normal function when activated. However, seemingly oncogenic mutations in IDH1 and IDH2 reduce their native enzyme activity. In this issue of Cancer Cell, Ward et al. pin down a neomorphic enzyme activity as a possible oncogenic function for these alterations.

Authors
Reitman, ZJ; Parsons, DW; Yan, H
MLA Citation
Reitman, ZJ, Parsons, DW, and Yan, H. "IDH1 and IDH2: not your typical oncogenes." Cancer Cell 17.3 (March 16, 2010): 215-216.
PMID
20227034
Source
pubmed
Published In
Cancer Cell
Volume
17
Issue
3
Publish Date
2010
Start Page
215
End Page
216
DOI
10.1016/j.ccr.2010.02.024

OTX2 is critical for the maintenance and progression of Shh-independent medulloblastomas.

OTX2 is a developmentally regulated transcription factor involved in early morphogenesis of the central nervous system. This gene is amplified and overexpressed in medulloblastoma cell lines, but the nature and extent of its genetic alterations in primary tumors have not been evaluated. Analysis of a large cohort of primary medulloblastomas revealed frequent focal copy number gain of a region minimally containing OTX2 as a single gene. OTX2 copy number gain was restricted to tumor subtypes that did not express a molecular signature of Wnt or Shh pathway activation. FISH analysis revealed copy number gain in a subset of cells within medulloblastoma samples, suggesting a late event in tumor progression. Gain of OTX2 copy number was associated with the presence of anaplastic histologic features and shorter survival in medulloblastoma patients. In support of a functional role, ectopic OTX2 expression enhanced proliferation and tumorigenicity of immortalized primary cells, whereas OTX2 knockdown in medulloblastoma cells prolonged the survival of animals bearing xenograft tumors. Mechanistic investigations revealed upregulation of MYC as a potential mechanism whereby OTX2 promotes tumor progression. Our findings define OTX2 as an important oncogenic driver in medulloblastoma.

Authors
Adamson, DC; Shi, Q; Wortham, M; Northcott, PA; Di, C; Duncan, CG; Li, J; McLendon, RE; Bigner, DD; Taylor, MD; Yan, H
MLA Citation
Adamson, DC, Shi, Q, Wortham, M, Northcott, PA, Di, C, Duncan, CG, Li, J, McLendon, RE, Bigner, DD, Taylor, MD, and Yan, H. "OTX2 is critical for the maintenance and progression of Shh-independent medulloblastomas." Cancer Res 70.1 (January 1, 2010): 181-191.
PMID
20028867
Source
pubmed
Published In
Cancer Research
Volume
70
Issue
1
Publish Date
2010
Start Page
181
End Page
191
DOI
10.1158/0008-5472.CAN-09-2331

Genetic and epigenetic inactivation of Kruppel-like factor 4 in medulloblastoma.

Although medulloblastoma is the most common pediatric malignant brain tumor, its molecular underpinnings are largely unknown. We have identified rare, recurrent homozygous deletions of Kruppel-like Factor 4 (KLF4) in medulloblastoma using high-resolution single nucleotide polymorphism arrays, digital karyotyping, and genomic real-time polymerase chain reaction (PCR). Furthermore, we show that there is loss of physiological KLF4 expression in more than 40% of primary medulloblastomas both at the RNA and protein levels. Medulloblastoma cell lines drastically increase the expression of KLF4 in response to the demethylating agent 5-azacytidine and demonstrate dense methylation of the promoter CpG island by bisulfite sequencing. Methylation-specific PCR targeting the KLF4 promoter demonstrates CpG methylation in approximately 16% of primary medulloblastomas. Reexpression of KLF4 in the D283 medulloblastoma cell line results in significant growth suppression both in vitro and in vivo. We conclude that KLF4 is inactivated by either genetic or epigenetic mechanisms in a large subset of medulloblastomas and that it likely functions as a tumor suppressor gene in the pathogenesis of medulloblastoma.

Authors
Nakahara, Y; Northcott, PA; Li, M; Kongkham, PN; Smith, C; Yan, H; Croul, S; Ra, Y-S; Eberhart, C; Huang, A; Bigner, D; Grajkowska, W; Van Meter, T; Rutka, JT; Taylor, MD
MLA Citation
Nakahara, Y, Northcott, PA, Li, M, Kongkham, PN, Smith, C, Yan, H, Croul, S, Ra, Y-S, Eberhart, C, Huang, A, Bigner, D, Grajkowska, W, Van Meter, T, Rutka, JT, and Taylor, MD. "Genetic and epigenetic inactivation of Kruppel-like factor 4 in medulloblastoma." Neoplasia 12.1 (January 2010): 20-27.
PMID
20072650
Source
pubmed
Published In
Neoplasia (New York, N.Y.)
Volume
12
Issue
1
Publish Date
2010
Start Page
20
End Page
27

A monoclonal antibody IMab-1 specifically recognizes IDH1R132H, the most common glioma-derived mutation.

IDH1 (isocitrate dehydrogenase 1) mutations have been identified as early and frequent genetic alterations in astrocytomas, oligodendrogliomas, and oligoastrocytomas as well as secondary glioblastomas. In contrast, primary glioblastomas very rarely contain IDH1 mutations, although primary and secondary glioblastomas are histologically indistinguishable. The IDH1 mutations are remarkably specific to a single codon in the conserved and functionally important Arg132 in IDH1. In gliomas, the most frequent IDH1 mutations (>90%) were G395A (R132H). In this study, we immunized mice with R132H-containing IDH1 (IDH1(R132H)) peptide. After cell fusion using Sendai virus envelope, the monoclonal antibodies (mAbs), which specifically reacted with IDH1(R132H), were screened in ELISA. One of the mAbs, IMab-1 reacted with the IDH1(R132H) peptide, but not with wild type IDH1 (IDH1(wt)) peptide in ELISA. In Western-blot analysis, IMab-1 reacted with only the IDH1(R132H) protein, not IDH1(wt) protein or the other IDH1 mutants, indicating that IMab-1 is IDH1(R132H)-specific. Furthermore, IMab-1 specifically stained the IDH1(R132H)-expressing cells in astrocytomas in immunohistochemistry, whereas it did not react with IDH1(R132H)-negative primary glioblastoma sections. In conclusion, we established an anti-IDH1(R132H)-specific monoclonal antibody IMab-1, which should be significantly useful for diagnosis and biological evaluation of mutation-bearing gliomas.

Authors
Kato, Y; Jin, G; Kuan, C-T; McLendon, RE; Yan, H; Bigner, DD
MLA Citation
Kato, Y, Jin, G, Kuan, C-T, McLendon, RE, Yan, H, and Bigner, DD. "A monoclonal antibody IMab-1 specifically recognizes IDH1R132H, the most common glioma-derived mutation." Biochem Biophys Res Commun 390.3 (December 18, 2009): 547-551.
PMID
19818334
Source
pubmed
Published In
Biochemical and Biophysical Research Communications
Volume
390
Issue
3
Publish Date
2009
Start Page
547
End Page
551
DOI
10.1016/j.bbrc.2009.10.001

Mutant metabolic enzymes are at the origin of gliomas.

Mutations of the isocitrate dehydrogenase (IDH) metabolic enzymes IDH1 and IDH2 have been found to be frequent and early genetic alterations in astrocytomas and oligodendrogliomas. All mutations identified to date affect a single amino acid located within the isocitrate binding site (R132 of IDH1 and the analogous R172 residue of IDH2). IDH1 and IDH2 mutations define a specific subtype of gliomas and may have significant utility for the diagnosis, prognosis, and treatment of patients with these tumors.

Authors
Yan, H; Bigner, DD; Velculescu, V; Parsons, DW
MLA Citation
Yan, H, Bigner, DD, Velculescu, V, and Parsons, DW. "Mutant metabolic enzymes are at the origin of gliomas." Cancer Res 69.24 (December 15, 2009): 9157-9159. (Review)
PMID
19996293
Source
pubmed
Published In
Cancer Research
Volume
69
Issue
24
Publish Date
2009
Start Page
9157
End Page
9159
DOI
10.1158/0008-5472.CAN-09-2650

Glioblastoma proto-oncogene SEC61gamma is required for tumor cell survival and response to endoplasmic reticulum stress.

Glioblastoma multiforme is the most prevalent type of adult brain tumor and one of the deadliest tumors known to mankind. The genetic understanding of glioblastoma multiforme is, however, limited, and the molecular mechanisms that facilitate glioblastoma multiforme cell survival and growth within the tumor microenvironment are largely unknown. We applied digital karyotyping and single nucleotide polymorphism arrays to screen for copy-number changes in glioblastoma multiforme samples and found that the most frequently amplified region is at chromosome 7p11.2. The high resolution of digital karyotyping and single nucleotide polymorphism arrays permits the precise delineation of amplicon boundaries and has enabled identification of the minimal region of amplification at chromosome 7p11.2, which contains two genes, EGFR and SEC61gamma. SEC61gamma encodes a subunit of a heterotrimeric protein channel located in the endoplasmic reticulum (ER). In addition to its high frequency of gene amplification in glioblastoma multiforme, SEC61gamma is also remarkably overexpressed in 77% of glioblastoma multiforme but not in lower-grade gliomas. The small interfering RNA-mediated knockdown of SEC61gamma expression in tumor cells led to growth suppression and apoptosis. Furthermore, we showed that pharmacologic ER stress agents induce SEC61gamma expression in glioblastoma multiforme cells. Together, these results indicate that aberrant expression of SEC61gamma serves significant roles in glioblastoma multiforme cell survival likely via a mechanism that is involved in the cytoprotective ER stress-adaptive response to the tumor microenvironment.

Authors
Lu, Z; Zhou, L; Killela, P; Rasheed, AB; Di, C; Poe, WE; McLendon, RE; Bigner, DD; Nicchitta, C; Yan, H
MLA Citation
Lu, Z, Zhou, L, Killela, P, Rasheed, AB, Di, C, Poe, WE, McLendon, RE, Bigner, DD, Nicchitta, C, and Yan, H. "Glioblastoma proto-oncogene SEC61gamma is required for tumor cell survival and response to endoplasmic reticulum stress." Cancer Res 69.23 (December 1, 2009): 9105-9111.
PMID
19920201
Source
pubmed
Published In
Cancer Research
Volume
69
Issue
23
Publish Date
2009
Start Page
9105
End Page
9111
DOI
10.1158/0008-5472.CAN-09-2775

Sample type bias in the analysis of cancer genomes.

There is widespread agreement that cancer gene discovery requires high-quality tumor samples. However, whether primary tumors or cultured samples are superior for cancer genomics has been a longstanding subject of debate. This debate has recently become more important because federally funded cancer genomics has been centralized under The Cancer Genome Atlas, which has chosen to focus exclusively on primary tumors. Here, we provide a data-driven "perspective" on the effect of sample type selection on cancer genomics research. We show that, in the case of glioblastoma multiforme, primary tumors and xenografts are best for the identification of amplifications, whereas xenografts and cell lines are superior for the identification of homozygous deletions. We also note that many of the most important oncogenes and tumor suppressor genes have been discovered through the use of cell lines and xenografts, and highlight the lack of published evidence supporting the dogma that ex vivo culture generates artifactual genetic lesions. Based on this analysis, we suggest that cancer genomics projects such as The Cancer Genome Atlas should include a variety of sample types such as xenografts and cell lines in their integrated genomic analysis of cancer.

Authors
Solomon, DA; Kim, J-S; Ressom, HW; Sibenaller, Z; Ryken, T; Jean, W; Bigner, D; Yan, H; Waldman, T
MLA Citation
Solomon, DA, Kim, J-S, Ressom, HW, Sibenaller, Z, Ryken, T, Jean, W, Bigner, D, Yan, H, and Waldman, T. "Sample type bias in the analysis of cancer genomes." Cancer Res 69.14 (July 15, 2009): 5630-5633.
PMID
19567670
Source
pubmed
Published In
Cancer Research
Volume
69
Issue
14
Publish Date
2009
Start Page
5630
End Page
5633
DOI
10.1158/0008-5472.CAN-09-1055

Glioblastoma multiforme: a review of therapeutic targets.

Glioblastoma is the commonest primary brain tumor, as well as the deadliest. Malignant gliomas such as glioblastoma multiforme (GBM) present some of the greatest challenges in the management of cancer patients worldwide, despite notable recent achievements in oncology. Even with aggressive surgical resections using state-of-the-art preoperative and intraoperative neuroimaging, along with recent advances in radiotherapy and chemotherapy, the prognosis for GBM patients remains dismal: survival after diagnosis is about 1 year. Established prognostic factors are limited, but include age, Karnofsky performance status, mini-mental status examination score, O6-methylguanine methyltransferase promoter methylation and extent of surgery. Standard treatment includes resection of > 95% of the tumor, followed by concurrent chemotherapy and radiotherapy. Nevertheless, GBM research is being conducted worldwide at a remarkable pace, in the laboratory and at the bedside, with some of the more recent promising studies focused on identification of aberrant genetic events and signaling pathways to develop molecular-based targeted therapies, tumor stem cell identification and characterization, modulation of tumor immunological responses and understanding of the rare long-term survivors. With this universally fatal disease, any small breakthrough will have a significant impact on survival and provide hope to the thousands of patients who receive this diagnosis annually. This review describes the epidemiology, clinical presentation, pathology and tumor immunology, with a focus on understanding the molecular biology that underlies the current targeted therapeutics being tested.

Authors
Kanu, OO; Mehta, A; Di, C; Lin, N; Bortoff, K; Bigner, DD; Yan, H; Adamson, DC
MLA Citation
Kanu, OO, Mehta, A, Di, C, Lin, N, Bortoff, K, Bigner, DD, Yan, H, and Adamson, DC. "Glioblastoma multiforme: a review of therapeutic targets." Expert Opin Ther Targets 13.6 (June 2009): 701-718. (Review)
PMID
19409033
Source
pubmed
Published In
Expert Opinion on Therapeutic Targets
Volume
13
Issue
6
Publish Date
2009
Start Page
701
End Page
718
DOI
10.1517/14728220902942348

Identification of microbial DNA in human cancer.

BACKGROUND: Microorganisms have been associated with many types of human diseases; however, a significant number of clinically important microbial pathogens remain to be discovered. METHODS: We have developed a genome-wide approach, called Digital Karyotyping Microbe Identification (DK-MICROBE), to identify genomic DNA of bacteria and viruses in human disease tissues. This method involves the generation of an experimental DNA tag library through Digital Karyotyping (DK) followed by analysis of the tag sequences for the presence of microbial DNA content using a compiled microbial DNA virtual tag library. RESULTS: To validate this technology and to identify pathogens that may be associated with human cancer pathogenesis, we used DK-MICROBE to determine the presence of microbial DNA in 58 human tumor samples, including brain, ovarian, and colorectal cancers. We detected DNA from Human herpesvirus 6 (HHV-6) in a DK library of a colorectal cancer liver metastasis and in normal tissue from the same patient. CONCLUSION: DK-MICROBE can identify previously unknown infectious agents in human tumors, and is now available for further applications for the identification of pathogen DNA in human cancer and other diseases.

Authors
Duncan, CG; Leary, RJ; Lin, JC-H; Cummins, J; Di, C; Schaefer, CF; Wang, T-L; Riggins, GJ; Edwards, J; Bigner, D; Kopelovich, L; Vogelstein, B; Kinzler, KW; Velculescu, VE; Yan, H
MLA Citation
Duncan, CG, Leary, RJ, Lin, JC-H, Cummins, J, Di, C, Schaefer, CF, Wang, T-L, Riggins, GJ, Edwards, J, Bigner, D, Kopelovich, L, Vogelstein, B, Kinzler, KW, Velculescu, VE, and Yan, H. "Identification of microbial DNA in human cancer. (Published online)" BMC Med Genomics 2 (May 8, 2009): 22-.
PMID
19426505
Source
pubmed
Published In
BMC Medical Genomics
Volume
2
Publish Date
2009
Start Page
22
DOI
10.1186/1755-8794-2-22

Glioblastoma Multiforme Oncogenomics and Signaling Pathways.

In the adult population, glioblastoma multiforme is one of the most common primary brain tumors encountered. Unfortunately, this highly malignant tumor represents over 50% of all types of primary central nervous system gliomas. The vast majority of GBMs develops quite rapidly without clinical, radiological, or morphologic evidence of a less malignant precursor lesion (primary or de novo GBMs), as compared to secondary GBMs that develop slowly by progression from diffuse low-grade astrocytomas. These GBM subtypes must be kept in mind because they may constitute distinct disease entities. Even though they look histologically quite similar, they likely involve different genetic alterations and signaling pathways. Decades of surgical therapy, radiotherapy, and chemotherapy have failed to drastically change survival. Clearly, we do not fully understand this tumor; however, the exciting genetic revolution in glioma research over the past decade is providing a promising outlook for exploring this tumor at the genetic level. Science has begun to elucidate the numerous genetic alterations and critical signaling pathways, and it has opened new exciting areas of research such as glioma stem cell biology and neoangiogenesis. This work has already begun to improve our understanding of GBM cell proliferation, migration, and invasion. Indeed, exciting novel targeted therapies are making their way to clinical trials based on this increased knowledge. This review provides the current understanding of GBM oncogenomics, signaling pathways, and glioma stem cell biology and discusses the potential new therapeutic targets on the horizon.

Authors
Kanu, OO; Hughes, B; Di, C; Lin, N; Fu, J; Bigner, DD; Yan, H; Adamson, C
MLA Citation
Kanu, OO, Hughes, B, Di, C, Lin, N, Fu, J, Bigner, DD, Yan, H, and Adamson, C. "Glioblastoma Multiforme Oncogenomics and Signaling Pathways." Clin Med Oncol 3 (April 8, 2009): 39-52.
PMID
19777070
Source
pubmed
Published In
Clinical Medicine: Oncology
Volume
3
Publish Date
2009
Start Page
39
End Page
52

IDH1 and IDH2 mutations in gliomas.

BACKGROUND: A recent genomewide mutational analysis of glioblastomas (World Health Organization [WHO] grade IV glioma) revealed somatic mutations of the isocitrate dehydrogenase 1 gene (IDH1) in a fraction of such tumors, most frequently in tumors that were known to have evolved from lower-grade gliomas (secondary glioblastomas). METHODS: We determined the sequence of the IDH1 gene and the related IDH2 gene in 445 central nervous system (CNS) tumors and 494 non-CNS tumors. The enzymatic activity of the proteins that were produced from normal and mutant IDH1 and IDH2 genes was determined in cultured glioma cells that were transfected with these genes. RESULTS: We identified mutations that affected amino acid 132 of IDH1 in more than 70% of WHO grade II and III astrocytomas and oligodendrogliomas and in glioblastomas that developed from these lower-grade lesions. Tumors without mutations in IDH1 often had mutations affecting the analogous amino acid (R172) of the IDH2 gene. Tumors with IDH1 or IDH2 mutations had distinctive genetic and clinical characteristics, and patients with such tumors had a better outcome than those with wild-type IDH genes. Each of four tested IDH1 and IDH2 mutations reduced the enzymatic activity of the encoded protein. CONCLUSIONS: Mutations of NADP(+)-dependent isocitrate dehydrogenases encoded by IDH1 and IDH2 occur in a majority of several types of malignant gliomas.

Authors
Yan, H; Parsons, DW; Jin, G; McLendon, R; Rasheed, BA; Yuan, W; Kos, I; Batinic-Haberle, I; Jones, S; Riggins, GJ; Friedman, H; Friedman, A; Reardon, D; Herndon, J; Kinzler, KW; Velculescu, VE; Vogelstein, B; Bigner, DD
MLA Citation
Yan, H, Parsons, DW, Jin, G, McLendon, R, Rasheed, BA, Yuan, W, Kos, I, Batinic-Haberle, I, Jones, S, Riggins, GJ, Friedman, H, Friedman, A, Reardon, D, Herndon, J, Kinzler, KW, Velculescu, VE, Vogelstein, B, and Bigner, DD. "IDH1 and IDH2 mutations in gliomas." N Engl J Med 360.8 (February 19, 2009): 765-773.
PMID
19228619
Source
pubmed
Published In
The New England journal of medicine
Volume
360
Issue
8
Publish Date
2009
Start Page
765
End Page
773
DOI
10.1056/NEJMoa0808710

The author and a colleague reply

Authors
Reitman, Z; Yan, H
MLA Citation
Reitman, Z, and Yan, H. "The author and a colleague reply." New England Journal of Medicine 360.21 (2009): 2249--.
Source
scival
Published In
The New England journal of medicine
Volume
360
Issue
21
Publish Date
2009
Start Page
2249-
DOI
10.1056/NEJMc090391

Mutational inactivation of PTPRD in glioblastoma multiforme and malignant melanoma.

An additional tumor suppressor gene on chromosome 9p telomeric to the CDKN2A/B locus has long been postulated to exist. Using Affymetrix 250K single nucleotide polymorphism arrays to screen for copy number changes in glioblastoma multiforme (GBM), we detected a high frequency of deletions of the PTPRD gene, which encodes a receptor protein tyrosine phosphatase at chromosome 9p23-24.1. Missense and nonsense mutations of PTPRD were identified in a subset of the samples lacking deletions, including an inherited mutation with somatic loss of the wild-type allele. We then sequenced the gene in melanoma and identified 10 somatic mutations in 7 of 57 tumors (12%). Reconstitution of PTPRD expression in GBM and melanoma cells harboring deletions or mutations led to growth suppression and apoptosis that was alleviated by both the somatic and constitutional mutations. These data implicate PTPRD in the pathogenesis of tumors of neuroectodermal origin and, when taken together with other recent reports of PTPRD mutations in adenocarcinoma of the colon and lung, suggest that PTPRD may be one of a select group of tumor suppressor genes that are inactivated in a wide range of common human tumor types.

Authors
Solomon, DA; Kim, J-S; Cronin, JC; Sibenaller, Z; Ryken, T; Rosenberg, SA; Ressom, H; Jean, W; Bigner, D; Yan, H; Samuels, Y; Waldman, T
MLA Citation
Solomon, DA, Kim, J-S, Cronin, JC, Sibenaller, Z, Ryken, T, Rosenberg, SA, Ressom, H, Jean, W, Bigner, D, Yan, H, Samuels, Y, and Waldman, T. "Mutational inactivation of PTPRD in glioblastoma multiforme and malignant melanoma." Cancer Res 68.24 (December 15, 2008): 10300-10306.
PMID
19074898
Source
pubmed
Published In
Cancer Research
Volume
68
Issue
24
Publish Date
2008
Start Page
10300
End Page
10306
DOI
10.1158/0008-5472.CAN-08-3272

An integrated genomic analysis of human glioblastoma multiforme.

Glioblastoma multiforme (GBM) is the most common and lethal type of brain cancer. To identify the genetic alterations in GBMs, we sequenced 20,661 protein coding genes, determined the presence of amplifications and deletions using high-density oligonucleotide arrays, and performed gene expression analyses using next-generation sequencing technologies in 22 human tumor samples. This comprehensive analysis led to the discovery of a variety of genes that were not known to be altered in GBMs. Most notably, we found recurrent mutations in the active site of isocitrate dehydrogenase 1 (IDH1) in 12% of GBM patients. Mutations in IDH1 occurred in a large fraction of young patients and in most patients with secondary GBMs and were associated with an increase in overall survival. These studies demonstrate the value of unbiased genomic analyses in the characterization of human brain cancer and identify a potentially useful genetic alteration for the classification and targeted therapy of GBMs.

Authors
Parsons, DW; Jones, S; Zhang, X; Lin, JC-H; Leary, RJ; Angenendt, P; Mankoo, P; Carter, H; Siu, I-M; Gallia, GL; Olivi, A; McLendon, R; Rasheed, BA; Keir, S; Nikolskaya, T; Nikolsky, Y; Busam, DA; Tekleab, H; Diaz, LA; Hartigan, J; Smith, DR; Strausberg, RL; Marie, SKN; Shinjo, SMO; Yan, H; Riggins, GJ; Bigner, DD; Karchin, R; Papadopoulos, N; Parmigiani, G; Vogelstein, B; Velculescu, VE; Kinzler, KW
MLA Citation
Parsons, DW, Jones, S, Zhang, X, Lin, JC-H, Leary, RJ, Angenendt, P, Mankoo, P, Carter, H, Siu, I-M, Gallia, GL, Olivi, A, McLendon, R, Rasheed, BA, Keir, S, Nikolskaya, T, Nikolsky, Y, Busam, DA, Tekleab, H, Diaz, LA, Hartigan, J, Smith, DR, Strausberg, RL, Marie, SKN, Shinjo, SMO, Yan, H, Riggins, GJ, Bigner, DD, Karchin, R, Papadopoulos, N, Parmigiani, G, Vogelstein, B, Velculescu, VE, and Kinzler, KW. "An integrated genomic analysis of human glioblastoma multiforme." Science 321.5897 (September 26, 2008): 1807-1812.
PMID
18772396
Source
pubmed
Published In
Science
Volume
321
Issue
5897
Publish Date
2008
Start Page
1807
End Page
1812
DOI
10.1126/science.1164382

Identification of p18 INK4c as a tumor suppressor gene in glioblastoma multiforme.

Genomic alterations leading to aberrant activation of cyclin/cyclin-dependent kinase (cdk) complexes drive the pathogenesis of many common human tumor types. In the case of glioblastoma multiforme (GBM), these alterations are most commonly due to homozygous deletion of p16(INK4a) and less commonly due to genomic amplifications of individual genes encoding cyclins or cdks. Here, we describe deletion of the p18(INK4c) cdk inhibitor as a novel genetic alteration driving the pathogenesis of GBM. Deletions of p18(INK4c) often occurred in tumors also harboring homozygous deletions of p16(INK4a). Expression of p18(INK4c) was completely absent in 43% of GBM primary tumors studied by immunohistochemistry. Lentiviral reconstitution of p18(INK4c) expression at physiologic levels in p18(INK4c)-deficient but not p18(INK4c)-proficient GBM cells led to senescence-like G(1) cell cycle arrest. These studies identify p18(INK4c) as a GBM tumor suppressor gene, revealing an additional mechanism leading to aberrant activation of cyclin/cdk complexes in this terrible malignancy.

Authors
Solomon, DA; Kim, J-S; Jenkins, S; Ressom, H; Huang, M; Coppa, N; Mabanta, L; Bigner, D; Yan, H; Jean, W; Waldman, T
MLA Citation
Solomon, DA, Kim, J-S, Jenkins, S, Ressom, H, Huang, M, Coppa, N, Mabanta, L, Bigner, D, Yan, H, Jean, W, and Waldman, T. "Identification of p18 INK4c as a tumor suppressor gene in glioblastoma multiforme." Cancer Res 68.8 (April 15, 2008): 2564-2569.
PMID
18381405
Source
pubmed
Published In
Cancer Research
Volume
68
Issue
8
Publish Date
2008
Start Page
2564
End Page
2569
DOI
10.1158/0008-5472.CAN-07-6388

Somatic mutations of GUCY2F, EPHA3, and NTRK3 in human cancers.

Tyrosine kinases are major regulators of signal transduction cascades involved in cellular proliferation and have important roles in tumorigenesis. We have recently analyzed the tyrosine kinase gene family for alterations in human colorectal cancers and identified somatic mutations in seven members of this gene family. In this study we have used high-throughput sequencing approaches to further evaluate this subset of genes for genetic alterations in other human tumors. We identified somatic mutations in GUCY2F, EPHA3, and NTRK3 in breast, lung, and pancreatic cancers. Our results implicate these tyrosine kinase genes in the pathogenesis of other tumor types and suggest that they may be useful targets for diagnostic and therapeutic intervention in selected patients.

Authors
Wood, LD; Calhoun, ES; Silliman, N; Ptak, J; Szabo, S; Powell, SM; Riggins, GJ; Wang, T-L; Yan, H; Gazdar, A; Kern, SE; Pennacchio, L; Kinzler, KW; Vogelstein, B; Velculescu, VE
MLA Citation
Wood, LD, Calhoun, ES, Silliman, N, Ptak, J, Szabo, S, Powell, SM, Riggins, GJ, Wang, T-L, Yan, H, Gazdar, A, Kern, SE, Pennacchio, L, Kinzler, KW, Vogelstein, B, and Velculescu, VE. "Somatic mutations of GUCY2F, EPHA3, and NTRK3 in human cancers." Hum Mutat 27.10 (October 2006): 1060-1061.
PMID
16941478
Source
pubmed
Published In
Human Mutation
Volume
27
Issue
10
Publish Date
2006
Start Page
1060
End Page
1061
DOI
10.1002/humu.9452

Digital karyotyping technology: exploring the cancer genome.

Identifying gene-specific alterations in cancer genomes has revealed molecules that are causal effectors of carcinogenesis and specific targets for cancer molecular diagnosis and molecular-based cancer therapies. Whole-genome analyses of many cancer genomes at the resolution of single genes is thus a desirable yet incompletely realized goal that could expedite progress in cancer diagnosis and treatment. Although methods for routine whole-genome sequencing or high-resolution epigenetic measurements are currently under development, high-resolution measurements of gene copy number, or 'gene dosage', are now underway in several laboratories. Digital karyotyping, array comparative genomic hybridization, and single nucleotide polymorphism arrays are techniques that have the potential to detect gene amplification, homozygous deletion and loss of heterozygosity at or below the average length of single genes. Recently, digital karyotyping of a small number (<20) of colon and brain cancer genomes has revealed tumor cases with significant genetic dosage alterations affecting few and, in some cases, only one complete gene. These experiments suggest that gene-specific gene dosage alterations may be sufficiently frequent to enable the identification of promising tumor gene candidates in small-scale experiments. The purpose of this review is to describe our understanding of cancer as a genetic disease, review the basic principles, methodologies and interpretational issues of traditional and high-resolution whole-genome screens, and describe the potential of our first detailed look at whole cancer genomes for progress in the understanding and treatment of cancer.

Authors
Parrett, TJ; Yan, H
MLA Citation
Parrett, TJ, and Yan, H. "Digital karyotyping technology: exploring the cancer genome." Expert Rev Mol Diagn 5.6 (November 2005): 917-925. (Review)
PMID
16255633
Source
pubmed
Published In
Expert Review of Molecular Diagnostics: new diagnostic technologies are set to revolutionise healthcare
Volume
5
Issue
6
Publish Date
2005
Start Page
917
End Page
925
DOI
10.1586/14737159.5.6.917

Identification of OTX2 as a medulloblastoma oncogene whose product can be targeted by all-trans retinoic acid.

Through digital karyotyping of permanent medulloblastoma cell lines, we found that the homeobox gene OTX2 was amplified more than 10-fold in three cell lines. Gene expression analyses showed that OTX2 transcripts were present at high levels in 14 of 15 (93%) medulloblastomas with anaplastic histopathologic features. Knockdown of OTX2 expression by siRNAs inhibited medulloblastoma cell growth in vitro, whereas pharmacologic doses of all-trans retinoic acid repressed OTX2 expression and induced apoptosis only in medulloblastoma cell lines that expressed OTX2. These observations suggest that OTX2 is essential for the pathogenesis of anaplastic medulloblastomas and that these tumors may be amenable to therapy with all-trans-retinoic acid.

Authors
Di, C; Liao, S; Adamson, DC; Parrett, TJ; Broderick, DK; Shi, Q; Lengauer, C; Cummins, JM; Velculescu, VE; Fults, DW; McLendon, RE; Bigner, DD; Yan, H
MLA Citation
Di, C, Liao, S, Adamson, DC, Parrett, TJ, Broderick, DK, Shi, Q, Lengauer, C, Cummins, JM, Velculescu, VE, Fults, DW, McLendon, RE, Bigner, DD, and Yan, H. "Identification of OTX2 as a medulloblastoma oncogene whose product can be targeted by all-trans retinoic acid." Cancer Res 65.3 (February 1, 2005): 919-924.
PMID
15705891
Source
pubmed
Published In
Cancer Research
Volume
65
Issue
3
Publish Date
2005
Start Page
919
End Page
924

Snapshot of the allele-specific variation in human gene expression.

The analysis of gene differential expression is complicated by the potentially subtle differences associated with alterations in a single allele as well as by variations between individuals that arise from environmental or physiological factors. To circumvent these analytic problems, a method, named allele-specific differential expression analysis, was developed to compare the relative expression levels of two alleles of the same gene within the same cellular sample. The studies of allele-specific expression revealed that differential expression is relatively common in the human population.

Authors
Yan, H
MLA Citation
Yan, H. "Snapshot of the allele-specific variation in human gene expression." Methods Mol Biol 311 (2005): 31-38.
PMID
16100397
Source
pubmed
Published In
Methods in molecular biology (Clifton, N.J.)
Volume
311
Publish Date
2005
Start Page
31
End Page
38
DOI
10.1385/1-59259-957-5:031

EGFR mutations and sensitivity to gefitinib.

Authors
Rich, JN; Rasheed, BKA; Yan, H
MLA Citation
Rich, JN, Rasheed, BKA, and Yan, H. "EGFR mutations and sensitivity to gefitinib." N Engl J Med 351.12 (September 16, 2004): 1260-1261. (Letter)
PMID
15376352
Source
pubmed
Published In
The New England journal of medicine
Volume
351
Issue
12
Publish Date
2004
Start Page
1260
End Page
1261

Mutations of PIK3CA in anaplastic oligodendrogliomas, high-grade astrocytomas, and medulloblastomas.

The phosphatidylinositol 3'-kinase pathway is activated in multiple advanced cancers, including glioblastomas, through inactivation of the PTEN tumor suppressor gene. Recently, mutations in PIK3CA, a member of the family of phosphatidylinositol 3'-kinase catalytic subunits, were identified in a significant fraction (25-30%) of colorectal cancers, gastric cancers, and glioblastomas and in a smaller fraction of breast and lung cancers. These mutations were found to cluster into two major "hot spots" located in the helical and catalytic domains. To determine whether PIK3CA is genetically altered in brain tumors, we performed a large-scale mutational analysis of the helical and catalytic domains. A total of 13 mutations of PIK3CA within these specific domains were identified in anaplastic oligodendrogliomas, anaplastic astrocytomas, glioblastoma multiforme, and medulloblastomas, whereas no mutations were identified in ependymomas or low-grade astrocytomas. These observations implicate PIK3CA as an oncogene in a wider spectrum of adult and pediatric brain tumors and suggest that PIK3CA may be a useful diagnostic marker or a therapeutic target in these cancers.

Authors
Broderick, DK; Di, C; Parrett, TJ; Samuels, YR; Cummins, JM; McLendon, RE; Fults, DW; Velculescu, VE; Bigner, DD; Yan, H
MLA Citation
Broderick, DK, Di, C, Parrett, TJ, Samuels, YR, Cummins, JM, McLendon, RE, Fults, DW, Velculescu, VE, Bigner, DD, and Yan, H. "Mutations of PIK3CA in anaplastic oligodendrogliomas, high-grade astrocytomas, and medulloblastomas." Cancer Res 64.15 (August 1, 2004): 5048-5050.
PMID
15289301
Source
pubmed
Published In
Cancer Research
Volume
64
Issue
15
Publish Date
2004
Start Page
5048
End Page
5050
DOI
10.1158/0008-5472.CAN-04-1170

Mutational analysis of the tyrosine phosphatome in colorectal cancers.

Tyrosine phosphorylation, regulated by protein tyrosine phosphatases (PTPs) and kinases (PTKs), is important in signaling pathways underlying tumorigenesis. A mutational analysis of the tyrosine phosphatase gene superfamily in human cancers identified 83 somatic mutations in six PTPs (PTPRF, PTPRG, PTPRT, PTPN3, PTPN13, PTPN14), affecting 26% of colorectal cancers and a smaller fraction of lung, breast, and gastric cancers. Fifteen mutations were nonsense, frameshift, or splice-site alterations predicted to result in truncated proteins lacking phosphatase activity. Five missense mutations in the most commonly altered PTP (PTPRT) were biochemically examined and found to reduce phosphatase activity. Expression of wild-type but not a mutant PTPRT in human cancer cells inhibited cell growth. These observations suggest that the mutated tyrosine phosphatases are tumor suppressor genes, regulating cellular pathways that may be amenable to therapeutic intervention.

Authors
Wang, Z; Shen, D; Parsons, DW; Bardelli, A; Sager, J; Szabo, S; Ptak, J; Silliman, N; Peters, BA; van der Heijden, MS; Parmigiani, G; Yan, H; Wang, T-L; Riggins, G; Powell, SM; Willson, JKV; Markowitz, S; Kinzler, KW; Vogelstein, B; Velculescu, VE
MLA Citation
Wang, Z, Shen, D, Parsons, DW, Bardelli, A, Sager, J, Szabo, S, Ptak, J, Silliman, N, Peters, BA, van der Heijden, MS, Parmigiani, G, Yan, H, Wang, T-L, Riggins, G, Powell, SM, Willson, JKV, Markowitz, S, Kinzler, KW, Vogelstein, B, and Velculescu, VE. "Mutational analysis of the tyrosine phosphatome in colorectal cancers." Science 304.5674 (May 21, 2004): 1164-1166.
PMID
15155950
Source
pubmed
Published In
Science
Volume
304
Issue
5674
Publish Date
2004
Start Page
1164
End Page
1166
DOI
10.1126/science.1096096

High frequency of mutations of the PIK3CA gene in human cancers.

Authors
Samuels, Y; Wang, Z; Bardelli, A; Silliman, N; Ptak, J; Szabo, S; Yan, H; Gazdar, A; Powell, SM; Riggins, GJ; Willson, JKV; Markowitz, S; Kinzler, KW; Vogelstein, B; Velculescu, VE
MLA Citation
Samuels, Y, Wang, Z, Bardelli, A, Silliman, N, Ptak, J, Szabo, S, Yan, H, Gazdar, A, Powell, SM, Riggins, GJ, Willson, JKV, Markowitz, S, Kinzler, KW, Vogelstein, B, and Velculescu, VE. "High frequency of mutations of the PIK3CA gene in human cancers." Science 304.5670 (April 23, 2004): 554-.
PMID
15016963
Source
pubmed
Published In
Science
Volume
304
Issue
5670
Publish Date
2004
Start Page
554
DOI
10.1126/science.1096502

Detection of allelic variations of human gene expression by polymerase colonies.

BACKGROUND: Quantification of variations of human gene expression is complicated by the small differences between different alleles. Recent work has shown that variations do exist in the relative allelic expression levels in certain genes of heterozygous individuals. Herein, we describe the application of an immobilized polymerase chain reaction technique as an alternative approach to measure relative allelic differential expression. RESULTS: Herein, we report a novel assay, based on immobilized polymerase colonies, that accurately quantifies the relative expression levels of two alleles in a given sample. Mechanistically, this was accomplished by PCR amplifying a gene in a cDNA library in a thin polyacrylamide gel. By immobilizing the PCR, it is ensured that each transcript gives rise to only a single immobilized PCR colony, or "polony". Once polony amplified, the two alleles of the gene were differentially labeled by performing in situ sequencing with fluorescently labeled nucleotides. For these sets of experiments, silent single nucleotide polymorphisms (SNPs) were used to discriminate the two alleles. Finally, a simple count was then performed on the differentially labeled polonies in order to determine the relative expression levels of the two alleles. To validate this technique, the relative expression levels of PKD2 in a family of heterozygous patients bearing the 4208G/A SNP were examined and compared to the literature. CONCLUSIONS: We were able to reproduce the results of allelic variation in gene expression using an accurate technology known as polymerase colonies. Therefore, we have demonstrated the utility of this method in human gene expression analysis.

Authors
Butz, JA; Yan, H; Mikkilineni, V; Edwards, JS
MLA Citation
Butz, JA, Yan, H, Mikkilineni, V, and Edwards, JS. "Detection of allelic variations of human gene expression by polymerase colonies. (Published online)" BMC Genet 5 (February 16, 2004): 3-.
PMID
15040815
Source
pubmed
Published In
BMC Genetics
Volume
5
Publish Date
2004
Start Page
3
DOI
10.1186/1471-2156-5-3

Allelic variations in gene expression.

PURPOSE OF REVIEW: Genetic variants determine phenotypic variability. Many genetic studies suggest that protein structural variations predispose the population to more than 1000 different hereditary diseases. Unfortunately, despite the study of genetic polymorphisms for many decades, the milder phenotypic variations believed to account for most human physical and behavioral differences and underlying the most common human genetic diseases (including cancers) cannot be accounted for easily by these variations in the protein coding sequences. Thus, it has been hypothesized that the study of natural differential expression presenting within and among populations may enhance understanding of human phenotypic variation. RECENT FINDINGS: During the last year, reports identifying variations in gene expression in different organisms and finding subtle changes of gene expression associated with common genetic disease have pointed to variations in gene expression as playing a central role in molecular evolution and human disease. Advances in the functional analysis of gene regulatory networks-in particular, new methods for distinguishing cis-acting components from trans-acting factors-have provided the impetus for these discoveries. SUMMARY: This review represents current knowledge about allelic variation in gene expression and its increasingly important role in understanding the genotype-phenotype relation. Characterization of these allelic variations may open largely uncharted territory in genomics for biomedical researchers and may eventually lead to the discovery of the causative genes of common hereditary diseases and their mechanism of action.

Authors
Yan, H; Zhou, W
MLA Citation
Yan, H, and Zhou, W. "Allelic variations in gene expression." Curr Opin Oncol 16.1 (January 2004): 39-43. (Review)
PMID
14685091
Source
pubmed
Published In
Current Opinion in Oncology
Volume
16
Issue
1
Publish Date
2004
Start Page
39
End Page
43

EGFR mutations and sensitivity to gefitinib [3] (multiple letters)

Authors
Sorscher, SM; Rich, JN; Rasheed, BKA; Yan, H; Rossi, G; Marchioni, A; Longo, L; Haber, DA; Bell, DW; Lynch, TJ
MLA Citation
Sorscher, SM, Rich, JN, Rasheed, BKA, Yan, H, Rossi, G, Marchioni, A, Longo, L, Haber, DA, Bell, DW, and Lynch, TJ. "EGFR mutations and sensitivity to gefitinib [3] (multiple letters)." New England Journal of Medicine 351.12 (2004): 1260-1261.
PMID
15371587
Source
scival
Published In
New England Journal of Medicine
Volume
351
Issue
12
Publish Date
2004
Start Page
1260
End Page
1261
DOI
10.1056/NEJM200409163511221

Transforming single DNA molecules into fluorescent magnetic particles for detection and enumeration of genetic variations.

Many areas of biomedical research depend on the analysis of uncommon variations in individual genes or transcripts. Here we describe a method that can quantify such variation at a scale and ease heretofore unattainable. Each DNA molecule in a collection of such molecules is converted into a single magnetic particle to which thousands of copies of DNA identical in sequence to the original are bound. This population of beads then corresponds to a one-to-one representation of the starting DNA molecules. Variation within the original population of DNA molecules can then be simply assessed by counting fluorescently labeled particles via flow cytometry. This approach is called BEAMing on the basis of four of its principal components (beads, emulsion, amplification, and magnetics). Millions of individual DNA molecules can be assessed in this fashion with standard laboratory equipment. Moreover, specific variants can be isolated by flow sorting and used for further experimentation. BEAMing can be used for the identification and quantification of rare mutations as well as to study variations in gene sequences or transcripts in specific populations or tissues.

Authors
Dressman, D; Yan, H; Traverso, G; Kinzler, KW; Vogelstein, B
MLA Citation
Dressman, D, Yan, H, Traverso, G, Kinzler, KW, and Vogelstein, B. "Transforming single DNA molecules into fluorescent magnetic particles for detection and enumeration of genetic variations." Proc Natl Acad Sci U S A 100.15 (July 22, 2003): 8817-8822.
PMID
12857956
Source
pubmed
Published In
Proceedings of the National Academy of Sciences of USA
Volume
100
Issue
15
Publish Date
2003
Start Page
8817
End Page
8822
DOI
10.1073/pnas.1133470100

Allelic variation in human gene expression.

Authors
Yan, H; Yuan, W; Velculescu, VE; Vogelstein, B; Kinzler, KW
MLA Citation
Yan, H, Yuan, W, Velculescu, VE, Vogelstein, B, and Kinzler, KW. "Allelic variation in human gene expression." Science 297.5584 (August 16, 2002): 1143-.
PMID
12183620
Source
pubmed
Published In
Science
Volume
297
Issue
5584
Publish Date
2002
Start Page
1143
DOI
10.1126/science.1072545

Allele separation facilitates interpretation of potential splicing alterations and genomic rearrangements.

Mutations that alter normal splice patterns and genomic rearrangements are common causes of hereditary diseases including hereditary nonpolyposis colorectal cancer. However, abnormal transcripts can be difficult to detect and interpret because splicing patterns are often heterogeneous even in normal cells. Standard techniques including sequencing and Southern hybridization fail to detect some genomic rearrangements. We show here that separation of alleles in somatic cell hybrids, through "conversion" technology, considerably facilitates the interpretation of abnormal splicing patterns and the detection of genomic rearrangements. We detected novel mutations in MLH1 in each of four hereditary nonpolyposis colorectal cancer patients. The genomic mutations were CAG>CAA predicting Q346Q; GAG>AAG predicting E102K; a>g at nucleotide 1559-2 at intron 13, and a tandem duplication involving exons 7-12. By separating the two alleles, we showed that one allele produced only abnormal transcript or no transcript whereas the other allele produced only normal transcript. These results allowed pathogenicity to be unambiguously assigned to the mutations and increased the sensitivity of genomic testing.

Authors
Nakagawa, H; Yan, H; Lockman, J; Hampel, H; Kinzler, KW; Vogelstein, B; De La Chapelle, A
MLA Citation
Nakagawa, H, Yan, H, Lockman, J, Hampel, H, Kinzler, KW, Vogelstein, B, and De La Chapelle, A. "Allele separation facilitates interpretation of potential splicing alterations and genomic rearrangements." Cancer Res 62.16 (August 15, 2002): 4579-4582.
PMID
12183410
Source
pubmed
Published In
Cancer Research
Volume
62
Issue
16
Publish Date
2002
Start Page
4579
End Page
4582

Stat2 binding to the interferon-alpha receptor 2 subunit is not required for interferon-alpha signaling.

The interferon-alpha (IFNalpha) receptor consists of two subunits, the IFNalpha receptor 1 (IFNaR1) and 2 (IFNaR2) chains. Following ligand binding, IFNaR1 is phosphorylated on tyrosine 466, and this site recruits Stat2 via its SH2 domain. In contrast, IFNaR2 binds Stat2 constitutively. In this study we have characterized the Stat2-IFNaR2 interaction and examined its role in IFNalpha signaling. Stat2 binds the major IFNaR2 protein but not a variant containing a shorter cytoplasmic domain. The interaction does not require a STAT SH2 domain. Both tyrosine-phosphorylated and non-phosphorylated Stat2 bind IFNaR2 in vitro; however, relatively little phosphorylated Stat2 associates with IFNaR2 in vivo. In vitro binding assays defined IFNaR2 residues 418-444 as the minimal interaction domain and site-specific mutation of conserved acidic residues within this domain disrupted in vitro and in vivo binding. An IFNaR2 construct carrying these mutations was either (i) overexpressed in 293T cells or (ii) used to complement IFNaR2-deficient U5A cells. Unexpectedly, the activity of an IFNalpha-dependent reporter gene was not reduced but, instead, was enhanced up to 2-fold. This suggests that this particular IFNaR2-Stat2 interaction is not required for IFNalpha signaling, but might act to negatively inhibit signaling. Finally, a doubly truncated recombinant fragment of Stat2, spanning residues 136-702, associated with IFNaR2 in vitro, indicating that the interaction with IFNaR2 is direct and occurs in a central region of Stat2 marked by a hydrophobic core.

Authors
Nguyen, V-P; Saleh, AZM; Arch, AE; Yan, H; Piazza, F; Kim, J; Krolewski, JJ
MLA Citation
Nguyen, V-P, Saleh, AZM, Arch, AE, Yan, H, Piazza, F, Kim, J, and Krolewski, JJ. "Stat2 binding to the interferon-alpha receptor 2 subunit is not required for interferon-alpha signaling." J Biol Chem 277.12 (March 22, 2002): 9713-9721.
PMID
11786546
Source
pubmed
Published In
The Journal of biological chemistry
Volume
277
Issue
12
Publish Date
2002
Start Page
9713
End Page
9721
DOI
10.1074/jbc.M111161200

Small changes in expression affect predisposition to tumorigenesis.

We have used quantitative measures of gene expression to show that constitutional 50% decreases in expression of one adenomatous polyposis coli tumor suppressor gene (APC) allele can lead to the development of familial adenomatous polyposis.

Authors
Yan, H; Dobbie, Z; Gruber, SB; Markowitz, S; Romans, K; Giardiello, FM; Kinzler, KW; Vogelstein, B
MLA Citation
Yan, H, Dobbie, Z, Gruber, SB, Markowitz, S, Romans, K, Giardiello, FM, Kinzler, KW, and Vogelstein, B. "Small changes in expression affect predisposition to tumorigenesis." Nat Genet 30.1 (January 2002): 25-26.
PMID
11743581
Source
pubmed
Published In
Nature Genetics
Volume
30
Issue
1
Publish Date
2002
Start Page
25
End Page
26
DOI
10.1038/ng799

Phenotypic analysis of hMSH2 mutations in mouse cells carrying human chromosomes.

Conversion of diploidy to haploidy is a method that allows the generation of stable murine/human hybrid cell lines carrying selected human chromosomes in only a single copy. In this setting, it is possible to detect genetic mutations with greater sensitivity and reliability than in diploid cells. Using this method, we were able to identify mutations in the human mismatch repair (MMR) gene hMSH2 in hereditary nonpolyposis colon cancer families, which have escaped detection by the conventional methods. In this report, we show that such hybrid cell lines can also be a valuable tool in the study of the mutated MMR proteins, in particular the variants found in hereditary nonpolyposis colon cancer families that carry missense mutations and where it is unclear whether they predispose to colon cancer. This analysis is made possible by the fact that the human hMSH2 protein is able to complement the MMR defect in the host murine cell line.

Authors
Marra, G; D'Atri, S; Yan, H; Perrera, C; Cannavo', E; Vogelstein, B; Jiricny, J
MLA Citation
Marra, G, D'Atri, S, Yan, H, Perrera, C, Cannavo', E, Vogelstein, B, and Jiricny, J. "Phenotypic analysis of hMSH2 mutations in mouse cells carrying human chromosomes." Cancer Res 61.21 (November 1, 2001): 7719-7721.
PMID
11691782
Source
pubmed
Published In
Cancer Research
Volume
61
Issue
21
Publish Date
2001
Start Page
7719
End Page
7721

The role of hPMS1 and hPMS2 in predisposing to colorectal cancer.

Hereditary nonpolyposis colorectal cancer (HNPCC) is attributable to a deficiency of mismatch repair. Inactivation of DNA mismatch repair underlies the genesis of microsatellite instability in colorectal cancer. Germline mutations in three DNA mismatch repair genes, hMSH2, hMLH1, and hMSH6, have been found to segregate in HNPCC and HNPCC-like families. The two DNA mismatch repair genes hPMS1 and hPMS2 have also been suggested to predispose to HNPCC. In this study, 84 HNPCC and HNPCC-like kindreds without known mutations in the other three known DNA mismatch repair genes were screened for germline mutations in the hPMS1 or hPMS2 gene. No clear-cut pathogenic mutations were identified. Conversion technology was used to detect a large hMSH2 deletion in two affected members of the kindred in which the hPMS1 mutation was originally reported, whereas the hPMS1 mutation was only present in one of these two individuals. Since the hPMS1 and hPMS2 genes were first reported, germline mutations in hPMS2 have been demonstrated primarily in patients with Turcot's syndrome. However, no mutation in any of the two genes has been found to segregate in HNPCC families. Until there is better evidence for an increased colorectal cancer risk associated with germline mutations in these genes, a conservative interpretation of the role of mutations in these genes is advised.

Authors
Liu, T; Yan, H; Kuismanen, S; Percesepe, A; Bisgaard, ML; Pedroni, M; Benatti, P; Kinzler, KW; Vogelstein, B; Ponz de Leon, M; Peltomäki, P; Lindblom, A
MLA Citation
Liu, T, Yan, H, Kuismanen, S, Percesepe, A, Bisgaard, ML, Pedroni, M, Benatti, P, Kinzler, KW, Vogelstein, B, Ponz de Leon, M, Peltomäki, P, and Lindblom, A. "The role of hPMS1 and hPMS2 in predisposing to colorectal cancer." Cancer Res 61.21 (November 1, 2001): 7798-7802.
PMID
11691795
Source
pubmed
Published In
Cancer Research
Volume
61
Issue
21
Publish Date
2001
Start Page
7798
End Page
7802

Facilitating haplotype analysis by fully automated analysis of all chromosomes in human-mouse hybrid cell lines.

Recent evidence suggests that haplotype analysis is essential in recognizing genetic factors involved in the tendency toward a particular disease or pharmacogenetic phenotype, as well as to identify genes involved in multigenic disorders. Because of the increasing need for efficient haplotype tests, a new hybrid system, called conversion technology, was developed. Conversion technology aims at converting the diploid chromosome content into a haploid state so that hybrids contain a single copy of any desired chromosome. A number of mutations can now be identified easily, as they are no longer obscured by the normal sequence present on the other copy of the chromosome. However, the efficient use of this hybrid system depends on a complete analysis of both human and mouse chromosome complements in order to assess the stability of the hybrid cells and to accurately determine their human chromosome content. We describe a new multicolor FISH-based method capable of analyzing both genomes simultaneously in a single hybridization. This new technique should become an instrumental part of inexpensive, reliable haplotype tests.

Authors
Langer, S; Jentsch, I; Gangnus, R; Yan, H; Lengauer, C; Speicher, MR
MLA Citation
Langer, S, Jentsch, I, Gangnus, R, Yan, H, Lengauer, C, and Speicher, MR. "Facilitating haplotype analysis by fully automated analysis of all chromosomes in human-mouse hybrid cell lines." Cytogenet Cell Genet 93.1-2 (2001): 11-15.
PMID
11474169
Source
pubmed
Published In
Cytogenetics and cell genetics
Volume
93
Issue
1-2
Publish Date
2001
Start Page
11
End Page
15
DOI
10.1159/000056938

Tech.sight. Genetic testing--present and future.

Authors
Yan, H; Kinzler, KW; Vogelstein, B
MLA Citation
Yan, H, Kinzler, KW, and Vogelstein, B. "Tech.sight. Genetic testing--present and future." Science 289.5486 (September 15, 2000): 1890-1892. (Review)
PMID
11012364
Source
pubmed
Published In
Science
Volume
289
Issue
5486
Publish Date
2000
Start Page
1890
End Page
1892

Conversion of diploidy to haploidy.

Authors
Yan, H; Papadopoulos, N; Marra, G; Perrera, C; Jiricny, J; Boland, CR; Lynch, HT; Chadwick, RB; de la Chapelle, A; Berg, K; Eshleman, JR; Yuan, W; Markowitz, S; Laken, SJ; Lengauer, C; Kinzler, KW; Vogelstein, B
MLA Citation
Yan, H, Papadopoulos, N, Marra, G, Perrera, C, Jiricny, J, Boland, CR, Lynch, HT, Chadwick, RB, de la Chapelle, A, Berg, K, Eshleman, JR, Yuan, W, Markowitz, S, Laken, SJ, Lengauer, C, Kinzler, KW, and Vogelstein, B. "Conversion of diploidy to haploidy." Nature 403.6771 (February 17, 2000): 723-724.
PMID
10693791
Source
pubmed
Published In
Nature
Volume
403
Issue
6771
Publish Date
2000
Start Page
723
End Page
724
DOI
10.1038/35001659

Genetic testing - Present and future

Authors
Yan, H; Kinzler, KW; Vogelstein, B
MLA Citation
Yan, H, Kinzler, KW, and Vogelstein, B. "Genetic testing - Present and future." Science 289.5486 (2000): 1890-1892.
Source
scival
Published In
Science
Volume
289
Issue
5486
Publish Date
2000
Start Page
1890
End Page
1892
DOI
10.1126/science.289.5486.1890

Definition of the interferon-alpha receptor-binding domain on the TYK2 kinase.

Interferons and cytokines modulate gene expression via a simple, direct signaling pathway containing receptors, JAK tyrosine kinases, and STAT transcription factors. The interferon-alpha pathway is a model for these cascades. Two receptors, IFNaR1 and IFNaR2, associate exclusively in a constitutive manner with two JAK proteins, TYK2 and JAK1, respectively. Defining the molecular interface between JAK proteins and their receptors is critical to understanding the signaling pathway and may contribute to the development of novel therapeutics. This report defines the IFNaR1 interaction domain on TYK2. In vitro binding studies demonstrate that the amino-terminal half of TYK2, which is approximately 600 amino acids long and contains JAK homology (JH) domains 3-7, comprises the maximal binding domain for IFNaR1. A fragment containing amino acids 171-601 (JH3-6) also binds IFNaR1, but with reduced affinity. Glutathione S-transferase-TYK2 fusion proteins approximating either the JH6 or JH3 domain affinity-precipitate IFNaR1, suggesting that these are major sites of interaction within the larger binding domain. TYK2 amino acids 1-601 act in a dominant manner to inhibit the transcription of an interferon-alpha-dependent reporter gene, presumably by displacing endogenous TYK2 from the receptor. This same fragment inhibits interferon-alpha-dependent tyrosine phosphorylation of TYK2, STAT1, and STAT2.

Authors
Yan, H; Piazza, F; Krishnan, K; Pine, R; Krolewski, JJ
MLA Citation
Yan, H, Piazza, F, Krishnan, K, Pine, R, and Krolewski, JJ. "Definition of the interferon-alpha receptor-binding domain on the TYK2 kinase." J Biol Chem 273.7 (February 13, 1998): 4046-4051.
PMID
9461596
Source
pubmed
Published In
The Journal of biological chemistry
Volume
273
Issue
7
Publish Date
1998
Start Page
4046
End Page
4051

Definition of the interferon-α receptor-binding domain on the TYK2 kinase

Interferons and cytokines modulate gene expression via a simple, direct signaling pathway containing receptors, JAK tyrosine kinases, and STAT transcription factors. The interferon-α pathway is a model for these cascades. Two receptors, IFNaR1 and IFNaR2, associate exclusively in a constitutive manner with two JAK proteins, TYK2 and JAK1, respectively. Defining the molecular interface between JAK proteins and their receptors is critical to understanding the signaling pathway and may contribute to the development of novel therapeutics. This report defines the IFNaR1 interaction domain on TYK2. In vitro binding studies demonstrate that the amino-terminal half of TYK2, which is ~600 amino acids long and contains JAK homology (JH) domains 3-7, comprises the maximal binding domain for IFNaR1. A fragment containing amino acids 171-601 (JH3-6) also binds IFNaR1, but with reduced affinity. Glutathione S-transferase-TYK2 fusion proteins approximating either the JH6 or JH3 domain affinity-precipitate FNaR1, suggesting that these are major sites of interaction within the larger binding domain. TYK2 amino acids 1-601 act in a dominant manner to inhibit the transcription of an interferon- α-dependent reporter gene, presumably by displacing endogenous TYK2 from the receptor. This same fragment inhibits interferon-α-dependent tyrosine phosphorylation of TYK2, STAT1, and STAT2.

Authors
Yan, H; Piazza, F; Krishnan, K; Pine, R; Krolewski, JJ
MLA Citation
Yan, H, Piazza, F, Krishnan, K, Pine, R, and Krolewski, JJ. "Definition of the interferon-α receptor-binding domain on the TYK2 kinase." Journal of Biological Chemistry 273.7 (1998): 4045-4051.
Source
scival
Published In
Journal of Biological Chemistry
Volume
273
Issue
7
Publish Date
1998
Start Page
4045
End Page
4051

A region of the beta subunit of the interferon alpha receptor different from box 1 interacts with Jak1 and is sufficient to activate the Jak-Stat pathway and induce an antiviral state.

Coexpression of the alpha and betaL subunits of the human interferon alpha (IFNalpha) receptor is required for the induction of an antiviral state by human IFNalpha. To explore the role of the different domains of the betaL subunit in IFNalpha signaling, we coexpressed wild-type alpha subunit and truncated forms of the betaL chain in L-929 cells. Our results demonstrated that the first 82 amino acids (AAs) (AAs 265-346) of the cytoplasmic domain of the betaL chain are sufficient to activate the Jak-Stat pathway and trigger an antiviral state after IFNalpha2 binding to the receptor. This region of the betaL chain, required for Jak1 binding and activation, contains the Box 1 motif that is important for the interaction of some cytokine receptors with Jak kinases. However, using glutathione S-transferase fusion proteins containing amino- and carboxyl-terminal deletions of the betaL cytoplasmic domain, we demonstrate that the main Jak1-binding region (corresponding to AAs 300-346 on the beta subunit) is distinct from the Box 1 domain (AAs 287-295).

Authors
Domanski, P; Fish, E; Nadeau, OW; Witte, M; Platanias, LC; Yan, H; Krolewski, J; Pitha, P; Colamonici, OR
MLA Citation
Domanski, P, Fish, E, Nadeau, OW, Witte, M, Platanias, LC, Yan, H, Krolewski, J, Pitha, P, and Colamonici, OR. "A region of the beta subunit of the interferon alpha receptor different from box 1 interacts with Jak1 and is sufficient to activate the Jak-Stat pathway and induce an antiviral state." J Biol Chem 272.42 (October 17, 1997): 26388-26393.
PMID
9334213
Source
pubmed
Published In
The Journal of biological chemistry
Volume
272
Issue
42
Publish Date
1997
Start Page
26388
End Page
26393

Dimerization of a chimeric CD4-interferon-alpha receptor reconstitutes the signaling events preceding STAT phosphorylation.

Interferon-alpha induces the rapid tyrosine phosphorylation of a number of molecules, including the cognate receptors, JAK-family kinases (Jak1 and tyk2), and latent transcription factors (STATs 1 and 2). Here, we describe the use of chimeric molecules composed of the extracellular domain of CD4 fused to the intracellular domain of the interferon-alpha receptor subunit 1 (IFNaR1). Antibody mediated crosslinking dimerizes the transfected chimeras, activates tyk2 and induces a tyk2-dependent tyrosine phosphorylation of the intracellular domain of the chimera. We further define the major site of IFNaR1 phosphorylation, and show that phosphorylation of this site is required for association with STAT2. Finally, we show that homodimerization of IFNaR1 is not sufficient to activate the STATs, suggesting a role for the IFNaR2 subunit and Jak1 in the transduction of the interferon-alpha signal.

Authors
Krishnan, K; Yan, H; Lim, JT; Krolewski, JJ
MLA Citation
Krishnan, K, Yan, H, Lim, JT, and Krolewski, JJ. "Dimerization of a chimeric CD4-interferon-alpha receptor reconstitutes the signaling events preceding STAT phosphorylation." Oncogene 13.1 (July 4, 1996): 125-133.
PMID
8700538
Source
pubmed
Published In
Oncogene: Including Oncogene Reviews
Volume
13
Issue
1
Publish Date
1996
Start Page
125
End Page
133

Molecular characterization of an alpha interferon receptor 1 subunit (IFNaR1) domain required for TYK2 binding and signal transduction.

Binding of alpha interferon (IFNalpha) to its receptors induces rapid tyrosine phosphorylation of the receptor subunits IFNaR1 and IFNaR2, the TYK2 and JAK1 tyrosine kinases, and the Stat1 and Stat2 transcription factors. Previous studies have demonstrated that TYK2 directly and specifically binds to and tyrosine phosphorylates IFNaR1 in vitro. We now report a detailed analysis of the TYK2 binding domain on the IFNaR1 subunit. First, we used an in vitro binding assay to identify the TYK2 binding motif in IFNaR1 as well as the critical residues within this region. The most striking feature is the importance of a number of hydrophobic and acidic residues. A minor role is also ascribed to a region resembling the proline-rich "box 1" sequence. In addition, mutations which disrupt in vitro binding also disrupt the coimmunoprecipitation of the receptor and TYK2. We also provide direct evidence that the binding region is both necessary and sufficient to activate TYK2 in vivo. Specifically, mutations in the binding domain act in a dominant-negative fashion to inhibit the IFNalpha-induced tyrosine phosphorylation of TYK2 and Stat2. Further, introduction of dimerized glutathione S-transferase-IFNaR1 fusion proteins into permeabilized cells is sufficient to induce phosphorylation of TYK2 and the receptor, confirming the role of the binding domain in IFNalpha signal transduction. These studies provide clues to the sequences determining the specificity of the association between JAK family tyrosine kinases and cytokine receptors as well as the functional role of these kinases in cytokine signal transduction.

Authors
Yan, H; Krishnan, K; Lim, JT; Contillo, LG; Krolewski, JJ
MLA Citation
Yan, H, Krishnan, K, Lim, JT, Contillo, LG, and Krolewski, JJ. "Molecular characterization of an alpha interferon receptor 1 subunit (IFNaR1) domain required for TYK2 binding and signal transduction." Mol Cell Biol 16.5 (May 1996): 2074-2082.
PMID
8628273
Source
pubmed
Published In
Molecular and Cellular Biology
Volume
16
Issue
5
Publish Date
1996
Start Page
2074
End Page
2082

The SH2 domains of Stat1 and Stat2 mediate multiple interactions in the transduction of IFN-alpha signals.

Analysis of the ability of IFN-alpha to rapidly stimulate genes has led to the identification of a new family of signal transducing factors (STFs). The STF activated by IFN-alpha consists of two members of the STAT (Signal Transducers and Activators of Transcription) family of signaling proteins, Stat1 and Stat2. Sequence comparison of these STATs has determined that they share several conserved domains, the most notable of which is an SH2 domain. Recently, studies have determined that these SH2 domains can mediate a specific association between a STAT and the cytoplasmic domain of the appropriate receptor. Once associated with the receptor, the STATs become activated by an associated tyrosine kinase, whereupon they dissociate from the receptor and dimerize to form active STFs. The SH2 domain has also been implicated in the formation of STAT dimers found in STFs, suggesting it may play multiple roles in signaling. We have carried out a detailed analysis on the role of the Stat1 and Stat2 SH2 domains in the mediation of IFN-alpha stimulated signals. These studies, which have determined that the SH2 domain of Stat1 and Stat2 can mediate homo- as well as heterodimerization, suggest that a single SH2 domain-phosphotyrosyl interaction is sufficient for dimerization. Moreover, they provide the first direct evidence that the target of the SH2 domain is the STAT tyrosine activation site. In addition, these studies implicate the SH2 domain in another step in the signaling cascade, namely mediation of the interaction between STATs and their activating kinases (i.e. the JAKs).

Authors
Gupta, S; Yan, H; Wong, LH; Ralph, S; Krolewski, J; Schindler, C
MLA Citation
Gupta, S, Yan, H, Wong, LH, Ralph, S, Krolewski, J, and Schindler, C. "The SH2 domains of Stat1 and Stat2 mediate multiple interactions in the transduction of IFN-alpha signals." EMBO J 15.5 (March 1, 1996): 1075-1084.
PMID
8605877
Source
pubmed
Published In
EMBO Journal
Volume
15
Issue
5
Publish Date
1996
Start Page
1075
End Page
1084

Phosphorylated interferon-alpha receptor 1 subunit (IFNaR1) acts as a docking site for the latent form of the 113 kDa STAT2 protein.

Interferon-alpha (IFN alpha) induces rapid tyrosine phosphorylation of its receptors, two JAK kinases and three STAT transcription factors. One kinase, p135tyk2, is complexed with the IFNaR1 receptor, and may catalyze some of these phosphorylation events. We demonstrate that, in vitro, p135tyk2 phosphorylates two tyrosines on IFNaR1. A phosphopeptide corresponding to the major phosphorylation site (Tyr466) binds STAT2, but not STAT1, in an SH-2-dependent manner. Furthermore, only latent, non-phosphorylated STAT2 interacts with this phosphopeptide. When this phosphopeptide is introduced into permeabilized cells, the IFN alpha-dependent tyrosine phosphorylation of both STATs is blocked. Finally, mutant versions of IFNaR1, in which Tyr466 is changed to phenylalanine, can act in a dominant negative manner to inhibit phosphorylation of STAT2. These observations are consistent with a model in which IFNaR1 mediates the interaction between JAK kinases and the STAT transcription factors.

Authors
Yan, H; Krishnan, K; Greenlund, AC; Gupta, S; Lim, JT; Schreiber, RD; Schindler, CW; Krolewski, JJ
MLA Citation
Yan, H, Krishnan, K, Greenlund, AC, Gupta, S, Lim, JT, Schreiber, RD, Schindler, CW, and Krolewski, JJ. "Phosphorylated interferon-alpha receptor 1 subunit (IFNaR1) acts as a docking site for the latent form of the 113 kDa STAT2 protein." EMBO J 15.5 (March 1, 1996): 1064-1074.
PMID
8605876
Source
pubmed
Published In
EMBO Journal
Volume
15
Issue
5
Publish Date
1996
Start Page
1064
End Page
1074

A mutant form of p135tyk2, an interferon-alpha inducible tyrosine kinase, suppresses the transformed phenotype of Daudi cells.

The type I interferons induce an anti-viral state and suppress cell growth. The p135tyk2 non-receptor tyrosine kinase appears to initiate, at least in part, the type I interferon signal transduction pathway, and thereby activates type I interferon-dependent gene expression. To determine if p135tyk2 can suppress growth and/or tumorigenesis, derivatives of the tyk2 gene were introduced into the tumorigenic cell line Daudi. Transfectants expressing a tyk2 construct missing the carboxy-terminal 22 amino acids cloned with a greatly reduced efficiency in soft agar and displayed a partial decrease in the ability to form tumors in athymic mice. In addition, transfectants producing a kinase deficient version of tyk2 show an increase in both growth rate and agar cloning efficiency, suggesting that the inactive kinase can act in a dominant-negative manner. Surprisingly, the carboxyl-terminal deleted protein lacks both auto-kinase activity, and activity towards a putative substrate, even though it induces a phenotype which is precisely the opposite of that produced by another kinase-deficient tyk2 mutant containing an altered ATP binding site. Thus, while these results add tyk2 to a growing list of interferon-alpha regulated proteins that might be able to suppress tumor formation, the biochemical basis of this activity remains unknown.

Authors
Davis, E; Krishnan, K; Yan, H; Newcomb, EW; Krolewski, JJ
MLA Citation
Davis, E, Krishnan, K, Yan, H, Newcomb, EW, and Krolewski, JJ. "A mutant form of p135tyk2, an interferon-alpha inducible tyrosine kinase, suppresses the transformed phenotype of Daudi cells." Leukemia 10.3 (March 1996): 543-551.
PMID
8642873
Source
pubmed
Published In
Leukemia
Volume
10
Issue
3
Publish Date
1996
Start Page
543
End Page
551

Interferon a receptor 1 subunit (IFNaRI) binds to TYK2 and acts as a docking site for STAT2

Interferon a induces rapid tyrosine phosphorylation of its receptor, JAK1 and TYK2 tyrosine kinases, and STAT1 and STAT2 latent transcription factors. We have provided substantial direct evidence that STAT2 can bind to a phosphorylated tyrosine residue of IFNaRI in a SH2 dependent manner. Further, we have generated data suggesting that STATs dimerization drives the release of the phosphorylated STAT from the docking site. In addition, we independently confirmed the findings that the STAT2 and STAT1 are phosphorylated sequentially in the IFNa signaling pathway. We have also demonstrated the direct binding and phosphorylation of IFNaRI by TYK2 tyrosine kinase and provided the first detailed characterization of a JAK kinase binding site on a cytokine receptor and receptor binding site on the kinase. With this data, we are able to provide the first demonstration that point mutations which disrupt kinase-receptor binding also disrupt signaling. These observations are consistent with a model in which IFNaRI participates in initiating the IFNa signaling by mediating the interaction between JAK kinases and the STAT transcription factors.

Authors
Yan, H; Krishnan, K; Lim, JTE; Krolewski, J
MLA Citation
Yan, H, Krishnan, K, Lim, JTE, and Krolewski, J. "Interferon a receptor 1 subunit (IFNaRI) binds to TYK2 and acts as a docking site for STAT2." FASEB Journal 10.6 (1996): A1516-.
Source
scival
Published In
The FASEB journal : official publication of the Federation of American Societies for Experimental Biology
Volume
10
Issue
6
Publish Date
1996
Start Page
A1516

Homodimerization and intermolecular tyrosine phosphorylation of the Tyk-2 tyrosine kinase.

The Jak kinases and Stat transcription factors play a major role in signaling of various cytokines including IFN alpha. In this report we show a ligand-independent interaction between Tyk-2 and Jak-1 kinases. We also demonstrate that the Tyk-2 kinase forms a homodimer that has the ability to undergo intermolecular tyrosine phosphorylation. The formation of the Tyk-2 homodimer is independent of both tyrosine phosphorylation and the presence of the tyrosine kinase domain.

Authors
Domanski, P; Yan, H; Witte, MM; Krolewski, J; Colamonici, OR
MLA Citation
Domanski, P, Yan, H, Witte, MM, Krolewski, J, and Colamonici, OR. "Homodimerization and intermolecular tyrosine phosphorylation of the Tyk-2 tyrosine kinase." FEBS Lett 374.3 (November 6, 1995): 317-322.
PMID
7589562
Source
pubmed
Published In
FEBS Letters
Volume
374
Issue
3
Publish Date
1995
Start Page
317
End Page
322

Glutathione S-transferase fusion proteins mimic receptor dimerization in permeabilized cells.

Authors
Yan, H; Lim, JT; Contillo, LG; Krolewski, JJ
MLA Citation
Yan, H, Lim, JT, Contillo, LG, and Krolewski, JJ. "Glutathione S-transferase fusion proteins mimic receptor dimerization in permeabilized cells." Anal Biochem 231.2 (November 1, 1995): 455-458.
PMID
8595002
Source
pubmed
Published In
Analytical Biochemistry
Volume
231
Issue
2
Publish Date
1995
Start Page
455
End Page
458
DOI
10.1006/abio.1995.0080

Stat recruitment by tyrosine-phosphorylated cytokine receptors: an ordered reversible affinity-driven process.

Herein, we demonstrate that purified Stat1 binds to its tyrosine-phosphorylated docking site on the IFN gamma receptor alpha chain in a direct, specific, and reversible manner. Using surface plasmon resonance, we determine the affinity (KD = 137 nM) and specificity of the interaction and define the minimum affinity needed for receptor-mediated Stat1 activation. In addition, we quantitate the relative ability of purified Stat1 to interact with tyrosine-phosphorylated binding sites on other Stat proteins. Finally, we describe experiments that imply that the unidirectional release of activated Stat1 from the IFN gamma receptor reflects the preference of free tyrosine-phosphorylated Stat1 monomers to form high avidity reciprocal homodimers rather than reassociating with the receptor binding site. Our results demonstrate that IFN gamma-induced Stat1 activation is an ordered and affinity-driven process and we propose that this process may serve as a paradigm for Stat activation by other cytokine receptors.

Authors
Greenlund, AC; Morales, MO; Viviano, BL; Yan, H; Krolewski, J; Schreiber, RD
MLA Citation
Greenlund, AC, Morales, MO, Viviano, BL, Yan, H, Krolewski, J, and Schreiber, RD. "Stat recruitment by tyrosine-phosphorylated cytokine receptors: an ordered reversible affinity-driven process." Immunity 2.6 (June 1995): 677-687.
PMID
7796299
Source
pubmed
Published In
Immunity
Volume
2
Issue
6
Publish Date
1995
Start Page
677
End Page
687

Direct binding to and tyrosine phosphorylation of the alpha subunit of the type I interferon receptor by p135tyk2 tyrosine kinase.

Binding of type I interferons (IFNs) to their receptors induces rapid tyrosine phosphorylation of multiple proteins, including the alpha and beta subunits of the receptor, the polypeptides that form the transcriptional activator ISGF3 alpha (Stat113, Stat84, and Stat91), and the p135tyk2 and Jak-1 tyrosine kinases. In this report, we demonstrate that the alpha subunit of the type I IFN receptor (IFN-R) corresponds to the product of a previously cloned receptor subunit cDNA and, further, that the p135tyk2 tyrosine kinase directly binds and tyrosine phosphorylates this receptor subunit. Glutathione S-transferase (GST) fusion proteins encoding the different regions of the cytoplasmic domain of the alpha subunit can bind the p135tyk2 contained in human cell lysates. The association between the alpha subunit and Tyk2 was demonstrated by immunoblotting with anti-Tyk2 and antiphosphotyrosine antibodies and by using an in vitro kinase assay. Analogous experiments were then performed with recombinant baculoviruses encoding constitutively active Jak family tyrosine kinases. In this case, p135tyk2, but not Jak-1 or Jak-2 protein, binds to the GST-IFN-R proteins, suggesting that the interaction between these two proteins is both direct and specific. We also demonstrate that Tyk2, from extracts of either IFN alpha-treated human cells or insect cells infected with the recombinant baculoviruses, can catalyze in vitro phosphorylation of GST-IFN-R protein in a specific manner. Deletion mutants of the GST-IFN-R protein were used to localize both the binding and tyrosine phosphorylation site(s) to a 46-amino-acid juxtamembrane region of the alpha subunit, which shows sequence homology to functionally similar regions of other cytokine receptor proteins. These data support the hypothesis that the Tyk2 protein functions as part of a receptor complex to initiate intracellular signaling in response to type I IFNs.

Authors
Colamonici, O; Yan, H; Domanski, P; Handa, R; Smalley, D; Mullersman, J; Witte, M; Krishnan, K; Krolewski, J
MLA Citation
Colamonici, O, Yan, H, Domanski, P, Handa, R, Smalley, D, Mullersman, J, Witte, M, Krishnan, K, and Krolewski, J. "Direct binding to and tyrosine phosphorylation of the alpha subunit of the type I interferon receptor by p135tyk2 tyrosine kinase." Mol Cell Biol 14.12 (December 1994): 8133-8142.
PMID
7526154
Source
pubmed
Published In
Molecular and Cellular Biology
Volume
14
Issue
12
Publish Date
1994
Start Page
8133
End Page
8142

p135tyk2, an interferon-alpha-activated tyrosine kinase, is physically associated with an interferon-alpha receptor.

Recent genetic studies have linked the tyk2 gene, which encodes a novel type of non-receptor tyrosine kinase, to the interferon-alpha intracellular signaling pathway. In this report, biochemical evidence is presented which supports this proposed function for the tyk2 tyrosine kinase and further defines its role in the interferon-alpha signaling cascade. Specifically, the tyk2 gene is shown to encode a 135-kDa protein which is rapidly phosphorylated on tyrosine in response to interferon-alpha treatment. Indirect evidence suggests that the tyrosine phosphorylation of p135tyk2 is the result of autokinase activity, implying that the Tyk2 tyrosine kinase is activated by interferon-alpha treatment. Two complementary methods demonstrate a physical association between p135tyk2 and the alpha-subunit of the interferon-alpha receptor. First, immunoblots show that monoclonal antibodies against the alpha-subunit of the interferon-alpha receptor can co-immunoprecipitate p135tyk2. Second, interferon-alpha receptor proteins which have been labeled by affinity cross-linking with 125I-interferon-alpha 2 can be co-immunoprecipitated using anti-tyk2 antisera. Taken together, these data suggest that an interferon-alpha receptor-p135tyk2 complex functions, in a manner analogous to the CD4-lck tyrosine kinase complex, to initiate the interferon-alpha signaling cascade.

Authors
Colamonici, OR; Uyttendaele, H; Domanski, P; Yan, H; Krolewski, JJ
MLA Citation
Colamonici, OR, Uyttendaele, H, Domanski, P, Yan, H, and Krolewski, JJ. "p135tyk2, an interferon-alpha-activated tyrosine kinase, is physically associated with an interferon-alpha receptor." J Biol Chem 269.5 (February 4, 1994): 3518-3522.
PMID
8106393
Source
pubmed
Published In
The Journal of biological chemistry
Volume
269
Issue
5
Publish Date
1994
Start Page
3518
End Page
3522
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Research Areas:

  • Adaptor Proteins, Signal Transducing
  • Adenocarcinoma
  • Adenocarcinoma, Clear Cell
  • Adenoma
  • Adenosine Triphosphatases
  • Adenosine Triphosphate
  • Adipates
  • Aged
  • Aged, 80 and over
  • Alcohol Oxidoreductases
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  • Alternative Splicing
  • Amino Acid Sequence
  • Animals
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  • Astrocytoma
  • Base Pair Mismatch
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  • Binding Sites
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  • Brain Neoplasms
  • Burkitt Lymphoma
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  • Catalytic Domain
  • Cell Differentiation
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  • Cell Growth Processes
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  • Cells, Cultured
  • Central Nervous System Neoplasms
  • Cerebellar Neoplasms
  • Cerebellum
  • Chromatin
  • Chromatin Assembly and Disassembly
  • Chromatin Immunoprecipitation
  • Chromosome Aberrations
  • Chromosome Painting
  • Chromosomes
  • Chromosomes, Human, Pair 1
  • Chromosomes, Human, Pair 19
  • Chromosomes, Human, Pair 2
  • Chromosomes, Human, Pair 9
  • Cloning, Molecular
  • Codon
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  • Computational Biology
  • CpG Islands
  • Cyclin-Dependent Kinase Inhibitor p18
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  • Genes, APC
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  • Genetic Complementation Test
  • Genetic Loci
  • Genetic Techniques
  • Genetic Variation
  • Genetics, Medical
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  • Genomics
  • Genotype
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  • Humans
  • Hybridomas
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  • Immunoprecipitation
  • In Situ Hybridization, Fluorescence
  • Interferon Type I
  • Interferon-alpha
  • Interferon-gamma
  • Isocitrate Dehydrogenase
  • Isocitrates
  • Janus Kinase 1
  • Kaplan-Meier Estimate
  • Karyotyping
  • Ketoglutaric Acids
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  • Methylene Blue
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  • Neoplasms, Experimental
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  • Oligodendroglioma
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  • Otx Transcription Factors
  • Phenotype
  • Phenylurea Compounds
  • Phosphatidylinositol 3-Kinases
  • Phosphoric Monoester Hydrolases
  • Phosphotyrosine
  • Physical Chromosome Mapping
  • Point Mutation
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  • Polymorphism, Genetic
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  • Procollagen-Proline Dioxygenase
  • Prognosis
  • Promoter Regions, Genetic
  • Protein Biosynthesis
  • Protein Conformation
  • Protein Engineering
  • Protein Kinases
  • Protein Processing, Post-Translational
  • Protein Structure, Tertiary
  • Protein Tyrosine Phosphatase, Non-Receptor Type 13
  • Protein Tyrosine Phosphatase, Non-Receptor Type 3
  • Protein Tyrosine Phosphatases
  • Protein-Tyrosine Kinases
  • Proto-Oncogene Proteins
  • RNA Interference
  • RNA, Messenger
  • RNA, Small Interfering
  • Real-Time Polymerase Chain Reaction
  • Receptor Protein-Tyrosine Kinases
  • Receptor, Epidermal Growth Factor
  • Receptor, Interferon alpha-beta
  • Receptor, Notch2
  • Receptor, trkC
  • Receptor-Like Protein Tyrosine Phosphatases, Class 2
  • Receptor-Like Protein Tyrosine Phosphatases, Class 5
  • Receptors, Cell Surface
  • Receptors, Cytokine
  • Receptors, Interferon
  • Recombinant Fusion Proteins
  • Repressor Proteins
  • Reverse Transcriptase Polymerase Chain Reaction
  • Rhombencephalon
  • Risk Factors
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  • STAT1 Transcription Factor
  • STAT2 Transcription Factor
  • Saccharomyces cerevisiae
  • Sequence Analysis, DNA
  • Sequence Deletion
  • Signal Transduction
  • Spodoptera
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  • Stomach Neoplasms
  • Streptolysins
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  • Survival Rate
  • TYK2 Kinase
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  • Tumor Suppressor Proteins
  • Tunicamycin
  • Tyrosine
  • Up-Regulation
  • Xenograft Model Antitumor Assays
  • Young Adult
  • src Homology Domains