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Bhattarai S, Hakkim FL, Day CA, Grigore F, Langfald A, Entin I, Hinchcliffe EH, Robinson JP. H3F3A K27M Mutations Drives a Repressive Transcriptome by Modulating Chromatin Accessibility, Independent of H3K27me3 in Diffuse Midline Glioma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.16.594522. [PMID: 38798502 PMCID: PMC11118475 DOI: 10.1101/2024.05.16.594522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Background Heterozygous histone H3.3K27M mutation is a primary oncogenic driver of Diffuse Midline Glioma (DMG). H3.3K27M inhibits the Polycomb Repressive Complex 2 (PRC2) methyltransferase complex, leading to a global reduction and redistributing of the repressive H3 lysine 27 tri-methylation. This rewiring of the epigenome is thought to promote gliomagenesis. Methods We established novel, isogenic DMG patient-derived cell lines that have been CRISPR-Cas9 edited to H3.3 WT or H3.3K27M alone and in combination with EZH2 and EZH1 co-deletion, inactivating PRC2 methyltransferase activity of PRC2 and eliminating H3K27me3. Results RNA-seq and ATAC-seq analysis of these cells revealed that K27M has a novel epigenetic effect that appears entirely independent of its effects on PRC2 function. While the loss of the PRC2 complex led to a systemic induction of gene expression (including HOX gene clusters) and upregulation of biological pathways, K27M led to a balanced gene deregulation but having an overall repressive effect on the biological pathways. Importantly, the genes uniquely deregulated by the K27M mutation, independent of methylation loss, are closely associated with changes in chromatin accessibility, with upregulated genes becoming more accessible. Notably, the PRC2- independent function of K27M appears necessary for tumorigenesis as xenografts of our H3.3K27M/EZH1/2 WT cells developed into tumors, while H3.3/EZH1/2 KO cells did not. Conclusion We demonstrate that K27M mutation alters chromatin accessibility and uniquely deregulates genes, independent of K27 methylation. We further show the mutation's role in altering biological pathways and its necessity for tumor development. Key Points We revealed genes regulated by H3.3K27M mutation and PRC2 in DMG.H3.3K27M mutation alters chromosome accessibility independent of H3K27me3.PRC2-independent effects of K27M mutation are crucial for tumor development. Importance of the Study This study is the first to demonstrate that H3F3A K27M mutations drive a repressive transcriptome by modulating chromatin accessibility independently of H3K27 trimethylation in Diffuse Midline Glioma (DMG). By isolating the effects of H3.3 K27me3 loss from those of the K27M mutation, we identified common and unique genes and pathways affected by each. We found that genes uniquely deregulated by K27M showed increased chromatin accessibility and upregulated gene expression, unlike other gene subsets affected by PRC2 knockout. Importantly, we determined the PRC2-independent function of K27M is also essential for tumorigenesis, as xenografts of H3.3 K27M/PRC2 WT cell lines formed tumors, while H3.3WT/PRC2 WT and K27M/PRC2 knockout cells did not. This research builds upon and advances prior studies, such as those identifying EZH2 as a therapeutic target in H3.3K27M DMGs, by revealing critical new pathways for gliomagenesis. The translational significance lies in identifying novel therapeutic targets against this aggressive pediatric cancer.
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Zhang L, Bordey A. Advances in glioma models using in vivo electroporation to highjack neurodevelopmental processes. Biochim Biophys Acta Rev Cancer 2023; 1878:188951. [PMID: 37433417 DOI: 10.1016/j.bbcan.2023.188951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 07/04/2023] [Accepted: 07/05/2023] [Indexed: 07/13/2023]
Abstract
Glioma is the most prevalent type of neurological malignancies. Despite decades of efforts in neurosurgery, chemotherapy and radiation therapy, glioma remains one of the most treatment-resistant brain tumors with unfavorable outcomes. Recent progresses in genomic and epigenetic profiling have revealed new concepts of genetic events involved in the etiology of gliomas in humans, meanwhile, revolutionary technologies in gene editing and delivery allows to code these genetic "events" in animals to genetically engineer glioma models. This approach models the initiation and progression of gliomas in a natural microenvironment with an intact immune system and facilitates probing therapeutic strategies. In this review, we focus on recent advances in in vivo electroporation-based glioma modeling and outline the established genetically engineered glioma models (GEGMs).
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Affiliation(s)
- Longbo Zhang
- Departments of Neurosurgery, Changde hospital, Xiangya School of Medicine, Central South University, 818 Renmin Street, Wuling District, Changde, Hunan 415003, China; Departments of Neurosurgery, and National Clinical Research Center of Geriatric Disorders, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, China; Departments of Neurosurgery, and Cellular & Molecular Physiology, Yale School of Medicine, 333 Cedar Street, New Haven, CT 06520-8082, USA.
| | - Angelique Bordey
- Departments of Neurosurgery, and Cellular & Molecular Physiology, Yale School of Medicine, 333 Cedar Street, New Haven, CT 06520-8082, USA
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Mosaab A, El-Ayadi M, Khorshed EN, Amer N, Refaat A, El-Beltagy M, Hassan Z, Soror SH, Zaghloul MS, El-Naggar S. Histone H3K27M Mutation Overrides Histological Grading in Pediatric Gliomas. Sci Rep 2020; 10:8368. [PMID: 32433577 PMCID: PMC7239884 DOI: 10.1038/s41598-020-65272-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 04/29/2020] [Indexed: 11/25/2022] Open
Abstract
Pediatric high-grade gliomas (HGG) are rare aggressive tumors that present a prognostic and therapeutic challenge. Diffuse midline glioma, H3K27M-mutant is a new entity introduced to HGG in the latest WHO classification. In this study we evaluated the presence of H3K27M mutation in 105 tumor samples histologically classified into low-grade gliomas (LGG) (n = 45), and HGG (n = 60). Samples were screened for the mutation in histone H3.3 and H3.1 variants to examine its prevalence, prognostic impact, and assess its potential clinical value in limited resource settings. H3K27M mutation was detected in 28 of 105 (26.7%) samples, and its distribution was significantly associated with midline locations (p-value < 0.0001) and HGG (p-value = 0.003). Overall and event- free survival (OS and EFS, respectively) of patients with mutant tumors did not differ significantly, neither according to histologic grade (OS p-value = 0.736, EFS p-value = 0.75) nor across anatomical sites (OS p-value = 0.068, EFS p-value = 0.153). Detection of H3K27M mutation in pediatric gliomas provides more precise risk stratification compared to traditional histopathological techniques. Hence, mutation detection should be pursued in all pediatric gliomas. Meanwhile, focusing on midline LGG can be an alternative in lower-middle-income countries to maximally optimize patients' treatment options.
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Affiliation(s)
- Amal Mosaab
- Children's Cancer Hospital Egypt 57357, Tumor Biology Research Program, Research Department, Cairo, Egypt
| | - Moatasem El-Ayadi
- Children's Cancer Hospital Egypt 57357, Department of Pediatric Oncology, Cairo, Egypt
- National Cancer Institute, Cairo University, Department of Pediatric Oncology, Cairo, Egypt
| | - Eman N Khorshed
- Children's Cancer Hospital Egypt 57357, Department of Surgical Pathology, Cairo, Egypt
- National Cancer Institute, Cairo University, Department of Surgical Pathology, Cairo, Egypt
| | - Nada Amer
- Children's Cancer Hospital Egypt 57357, Tumor Biology Research Program, Research Department, Cairo, Egypt
| | - Amal Refaat
- Children's Cancer Hospital Egypt 57357, Department of Radiology, Cairo, Egypt
- National Cancer Institute, Cairo University, Department of Radiology, Cairo, Egypt
| | - Mohamed El-Beltagy
- Children's Cancer Hospital Egypt 57357, Department of Neurosurgery, Cairo, Egypt
- Faculty of Medicine, Cairo University, Department of Neurosurgery, Cairo, Egypt
| | - Zeinab Hassan
- Faculty of Pharmacy, Helwan University, Department of Biochemistry and Molecular Biology, Cairo, Egypt
| | - Sameh H Soror
- Faculty of Pharmacy, Helwan University, Department of Biochemistry and Molecular Biology, Cairo, Egypt
| | - Mohamed Saad Zaghloul
- Children's Cancer Hospital Egypt 57357, Department of Radiotherapy, Cairo, Egypt
- National Cancer Institute, Cairo University, Department of Radiotherapy, Cairo, Egypt
| | - Shahenda El-Naggar
- Children's Cancer Hospital Egypt 57357, Tumor Biology Research Program, Research Department, Cairo, Egypt.
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Wan YCE, Leung TCS, Ding D, Sun X, Liu J, Zhu L, Kang TZE, Yang D, Zhang Y, Zhang J, Qian C, Huen MSY, Li Q, Chow MZY, Zheng Z, Han J, Goel A, Wang X, Ishibashi T, Chan KM. Cancer-associated histone mutation H2BG53D disrupts DNA-histone octamer interaction and promotes oncogenic phenotypes. Signal Transduct Target Ther 2020; 5:27. [PMID: 32296031 PMCID: PMC7060176 DOI: 10.1038/s41392-020-0131-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 02/21/2020] [Indexed: 02/05/2023] Open
Affiliation(s)
- Yi Ching Esther Wan
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China
- Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen, China
| | - Tsz Chui Sophia Leung
- Division of Life Science, Hong Kong University of Science and Technology, Hong Kong, China
| | - Dongbo Ding
- Division of Life Science, Hong Kong University of Science and Technology, Hong Kong, China
| | - Xulun Sun
- Division of Life Science, Hong Kong University of Science and Technology, Hong Kong, China
| | - Jiaxian Liu
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China
- Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen, China
| | - Lina Zhu
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China
- Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen, China
| | - Tze Zhen Evangeline Kang
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China
- Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen, China
| | - Du Yang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Peking, China
| | - Yuchen Zhang
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China
- Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen, China
| | - Jitian Zhang
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China
- Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen, China
| | - Chengmin Qian
- School of Biomedical Sciences, The University of Hong Kong, Hong Kong, China
| | | | - Qing Li
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Peking, China
| | - Maggie Zi Ying Chow
- Ming Wai Lau Centre for Reparative Medicine, Karolinska Institutet, Hong Kong, China
| | - Zongli Zheng
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China
- Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen, China
- Ming Wai Lau Centre for Reparative Medicine, Karolinska Institutet, Hong Kong, China
| | - Junhong Han
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Sichuan, China
| | - Ajay Goel
- Department of Molecular Diagnostics and Experimental Therapeutics, Beckman Research Institute at City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Xin Wang
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China.
- Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen, China.
| | - Toyotaka Ishibashi
- Division of Life Science, Hong Kong University of Science and Technology, Hong Kong, China.
| | - Kui Ming Chan
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China.
- Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen, China.
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Yao K, Duan Z, Wang Y, Zhang M, Fan T, Wu B, Qi X. Detection of H3K27M mutation in cases of brain stem subependymoma. Hum Pathol 2019; 84:262-269. [DOI: 10.1016/j.humpath.2018.10.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/05/2018] [Revised: 10/02/2018] [Accepted: 10/11/2018] [Indexed: 10/28/2022]
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Mezquita-Pla J. Gordon H. Dixon's trace in my personal career and the quantic jump experienced in regulatory information. Syst Biol Reprod Med 2018; 64:448-468. [PMID: 30136864 DOI: 10.1080/19396368.2018.1503752] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Even before Rosalin Franklin had discovered the DNA double helix, in her impressive X-ray diffraction image pattern, Erwin Schröedinger, described, in his excellent book, What is Life, how the finding of aperiodic crystals in biological systems surprised him (an aperiodic crystal, which, in my opinion is the material carrier of life). In the 21st century and still far from being able to define life, we are attending to a quick acceleration of knowledge on regulatory information. With the discovery of new codes and punctuation marks, we will greatly increase our understanding in front of an impressive avalanche of genomic sequences. Trifonov et al. defined a genetic code as a widespread DNA sequence pattern that carries a message with an impact on biology. These patterns are largely captured in transcribed messages that give meaning and identity to the particular cells. In this review, I will go through my personal career in and after my years of work in the laboratory of Gordon H. Dixon, extending toward the impressive acquisition of new knowledge on regulatory information and genetic codes provided by remarkable scientists in the field. Abbreviations: CA II: carbonic anhydridase II (chicken); Car2: carbonic anhydridase 2 (mouse); CpG islands: short (>0.5 kb) stretches of DNA with a G+C content ≥55%; DNMT1: DNA methyltransferases 1; DNMT3b: DNA methyltransferases 3B; DSB: double-strand DNA breaks; ERT: endogenous retrotransposon; ERV: endogenous retroviruses; ES cells: embryonic stem cells; GAPDH: glyceraldehide phosphate dehydrogenase; H1: histone H1; HATs: histone acetyltransferases; HDACs: histone deacetylases; H3K4me3: histone 3 trimethylated at lys 4; H3K79me2: histone 3 dimethylated at lys 79; HMG: high mobility group proteins; HMT: histone methyltransferase; HP1: heterochromatin protein 1; HR: homologous recombination; HSE: heat-shock element; ICRs: imprinted control regions; IRF: interferon regulatory factor; LDH-A/-B: lactate dehydrogenase A/B; LTR: long terminal repeats; MeCP2: methyl CpG binding protein 2; OCT4: octamer-binding transcription factor 4; PAF1: RNA Polymerase II associated factor 1; piRNA: PIWI-interacting RNA; poly(A) tails: poly-adenine tails; PRC2: polycomb repressive complex 2; PTMs: post-translational modifications; SIRT 1: sirtuin 1, silent information regulator; STAT3: signal transducer and activator of transcription; tRNAs: transfer RNA; tRFs: tRNA-derived fragments; TSS: transcription start site; TE: transposable elements; UB I: polyubiquitin I; UB II: polyubiquitin II; UBE 2N: ubiquitin conjugating enzyme E2N; 5'-UTR: 5'-untranslated sequences; 3'-UTR: 3'-untranslated sequences.
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Affiliation(s)
- Jovita Mezquita-Pla
- a Molecular Genetics and Control of Pluripotency Laboratory, Department of Biomedicine, IDIBAPS, Faculty of Medicine , University of Barcelona , Catalonia , Spain
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7
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Finnerty BM, Gray KD, Moore MD, Zarnegar R, Fahey III TJ. Epigenetics of gastroenteropancreatic neuroendocrine tumors: A clinicopathologic perspective. World J Gastrointest Oncol 2017; 9:341-353. [PMID: 28979716 PMCID: PMC5605334 DOI: 10.4251/wjgo.v9.i9.341] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/25/2017] [Revised: 06/27/2017] [Accepted: 08/04/2017] [Indexed: 02/05/2023] Open
Abstract
Gastroenteropancreatic neuroendocrine tumors (GEP-NETs) are a heterogeneous group of rare tumors whose site-specific tumor incidence and clinical behavior vary widely. Genetic alterations associated with familial inherited syndromes have been well defined; however, the genetic profile of sporadic tumors is less clear as their tumorigenesis does not appear to be controlled by classic oncogenes such as P53, RB, or KRAS. Even within GEP-NETs, there are no common oncogenic drivers; for example, DAXX/ATRX mutations are strongly implicated in the tumorigenesis of pancreatic but not small bowel NETs. Accordingly, the dysregulation of epigenetic mechanisms has been hypothesized as a potential regulator of GEP-NET tumorigenesis and has become a major focus of recent studies. Despite the heterogeneity of tumor cohorts evaluated in these studies, it is obvious that there are methylation patterns, chromatin remodeling alterations, and microRNA and long non-coding RNA (lncRNA) differential expression profiles that are distinctive of GEP-NETs, some of which are correlated with significant differences in clinical outcomes. Several translational studies have provided convincing data identifying potential prognostic biomarkers, and some of these have demonstrated preliminary success as serum biomarkers that can be used clinically. Nevertheless, there are many opportunities to further define the mechanisms by which these epigenetic modifications influence tumorigenesis, and this will provide better insight into their prognostic and therapeutic utility. Furthermore, these findings form the foundation for future studies evaluating the clinical efficacy of epigenetic modifications as prognostic biomarkers, as well as potential therapeutic targets.
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Affiliation(s)
- Brendan M Finnerty
- Department of Surgery, New York Presbyterian Hospital, Weill Cornell Medicine, New York, NY 10065, United States
| | - Katherine D Gray
- Department of Surgery, New York Presbyterian Hospital, Weill Cornell Medicine, New York, NY 10065, United States
| | - Maureen D Moore
- Department of Surgery, New York Presbyterian Hospital, Weill Cornell Medicine, New York, NY 10065, United States
| | - Rasa Zarnegar
- Department of Surgery, New York Presbyterian Hospital, Weill Cornell Medicine, New York, NY 10065, United States
| | - Thomas J Fahey III
- Department of Surgery, New York Presbyterian Hospital, Weill Cornell Medicine, New York, NY 10065, United States
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8
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Feng Z, Wang L, Sun Y, Jiang Z, Domsic J, An C, Xing B, Tian J, Liu X, Metz DC, Yang X, Marmorstein R, Ma X, Hua X. Menin and Daxx Interact to Suppress Neuroendocrine Tumors through Epigenetic Control of the Membrane Metallo-Endopeptidase. Cancer Res 2017; 77:401-411. [PMID: 27872097 PMCID: PMC5243199 DOI: 10.1158/0008-5472.can-16-1567] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Revised: 09/22/2016] [Accepted: 10/06/2016] [Indexed: 01/06/2023]
Abstract
Neuroendocrine tumors (NET) often harbor loss-of-function mutations in the MEN1 and DAXX tumor suppressor genes. Here, we report that the products of these genes, menin and Daxx, interact directly with each other to suppress the proliferation of NET cells, to a large degree by inhibiting expression of the membrane metallo-endopeptidase (MME). Menin and Daxx were required to enhance histone H3 lysine9 trimethylation (H3K9me3) at the MME promoter, as mediated partly by the histone H3 methyltransferase SUV39H1. Notably, the menin T429K mutation associated with a NET syndrome reduced Daxx binding, MME repression, and proliferation of NET cells. Conversely, inhibition of MME in NET cells repressed proliferation and tumor growth in vivo Our findings reveal a previously unappreciated cross-talk between two crucial tumor suppressor genes thought to work by independent pathways, focusing on MME as a common target of menin/Daxx to treat NET. Cancer Res; 77(2); 401-11. ©2016 AACR.
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Affiliation(s)
- Zijie Feng
- Shenzhen University College of Medicine, Medical Center and Diabetes Center, Shenzhen, China
- Department of Cancer Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
- Abramson Family Cancer Research Institute (AFCRI), Abramson Cancer Center, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Lei Wang
- Department of Cancer Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
- Abramson Family Cancer Research Institute (AFCRI), Abramson Cancer Center, University of Pennsylvania, Philadelphia, Pennsylvania
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Yanmei Sun
- Shenzhen University College of Medicine, Medical Center and Diabetes Center, Shenzhen, China
| | - Zongzhe Jiang
- Shenzhen University College of Medicine, Medical Center and Diabetes Center, Shenzhen, China
| | - John Domsic
- Abramson Family Cancer Research Institute (AFCRI), Abramson Cancer Center, University of Pennsylvania, Philadelphia, Pennsylvania
- Department of Biochemistry and Biophysics, AFCRI, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Chiying An
- Department of Cancer Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
- Abramson Family Cancer Research Institute (AFCRI), Abramson Cancer Center, University of Pennsylvania, Philadelphia, Pennsylvania
- Department of Endocrinology and Metabolism, the First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Bowen Xing
- Shenzhen University College of Medicine, Medical Center and Diabetes Center, Shenzhen, China
| | - Jingjing Tian
- Shenzhen University College of Medicine, Medical Center and Diabetes Center, Shenzhen, China
| | - Xiuheng Liu
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, China
| | - David C Metz
- Abramson Family Cancer Research Institute (AFCRI), Abramson Cancer Center, University of Pennsylvania, Philadelphia, Pennsylvania
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Xiaolu Yang
- Department of Cancer Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
- Abramson Family Cancer Research Institute (AFCRI), Abramson Cancer Center, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Ronen Marmorstein
- Abramson Family Cancer Research Institute (AFCRI), Abramson Cancer Center, University of Pennsylvania, Philadelphia, Pennsylvania
- Department of Biochemistry and Biophysics, AFCRI, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Xiaosong Ma
- Shenzhen University College of Medicine, Medical Center and Diabetes Center, Shenzhen, China.
| | - Xianxin Hua
- Department of Cancer Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania.
- Abramson Family Cancer Research Institute (AFCRI), Abramson Cancer Center, University of Pennsylvania, Philadelphia, Pennsylvania
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Crisman TJ, Zelaya I, Laks DR, Zhao Y, Kawaguchi R, Gao F, Kornblum HI, Coppola G. Identification of an Efficient Gene Expression Panel for Glioblastoma Classification. PLoS One 2016; 11:e0164649. [PMID: 27855170 PMCID: PMC5113897 DOI: 10.1371/journal.pone.0164649] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 09/28/2016] [Indexed: 11/21/2022] Open
Abstract
We present here a novel genetic algorithm-based random forest (GARF) modeling technique that enables a reduction in the complexity of large gene disease signatures to highly accurate, greatly simplified gene panels. When applied to 803 glioblastoma multiforme samples, this method allowed the 840-gene Verhaak et al. gene panel (the standard in the field) to be reduced to a 48-gene classifier, while retaining 90.91% classification accuracy, and outperforming the best available alternative methods. Additionally, using this approach we produced a 32-gene panel which allows for better consistency between RNA-seq and microarray-based classifications, improving cross-platform classification retention from 69.67% to 86.07%. A webpage producing these classifications is available at http://simplegbm.semel.ucla.edu.
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Affiliation(s)
- Thomas J. Crisman
- Semel Institute for Neuroscience & Human Behavior and Department of Psychiatry and Biobehavioral Sciences, University of California Los Angeles, Los Angeles, California 90095, United States of America
| | - Ivette Zelaya
- Semel Institute for Neuroscience & Human Behavior and Department of Psychiatry and Biobehavioral Sciences, University of California Los Angeles, Los Angeles, California 90095, United States of America
| | - Dan R. Laks
- Department of Biological Chemistry, University of California Los Angeles, Los Angeles, California 90095, United States of America
| | - Yining Zhao
- Semel Institute for Neuroscience & Human Behavior and Department of Psychiatry and Biobehavioral Sciences, University of California Los Angeles, Los Angeles, California 90095, United States of America
| | - Riki Kawaguchi
- Semel Institute for Neuroscience & Human Behavior and Department of Psychiatry and Biobehavioral Sciences, University of California Los Angeles, Los Angeles, California 90095, United States of America
| | - Fuying Gao
- Semel Institute for Neuroscience & Human Behavior and Department of Psychiatry and Biobehavioral Sciences, University of California Los Angeles, Los Angeles, California 90095, United States of America
| | - Harley I. Kornblum
- Semel Institute for Neuroscience & Human Behavior and Department of Psychiatry and Biobehavioral Sciences, University of California Los Angeles, Los Angeles, California 90095, United States of America
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California Los Angeles, Los Angeles, California 90095, United States of America
- Jonsson Comprehensive Cancer Center, University of California Los Angeles, Los Angeles, California 90095, United States of America
| | - Giovanni Coppola
- Semel Institute for Neuroscience & Human Behavior and Department of Psychiatry and Biobehavioral Sciences, University of California Los Angeles, Los Angeles, California 90095, United States of America
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Orillac C, Thomas C, Dastagirzada Y, Hidalgo ET, Golfinos JG, Zagzag D, Wisoff JH, Karajannis MA, Snuderl M. Pilocytic astrocytoma and glioneuronal tumor with histone H3 K27M mutation. Acta Neuropathol Commun 2016; 4:84. [PMID: 27519587 PMCID: PMC4983033 DOI: 10.1186/s40478-016-0361-0] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 08/01/2016] [Indexed: 11/25/2022] Open
Affiliation(s)
| | - Cheddhi Thomas
- NYU School of Medicine, New York, NY, 10016, USA
- Department of Pathology, NYU Langone Medical Center, 550 1st Ave, New York, NY, 10016, USA
| | | | - Eveline Teresa Hidalgo
- NYU School of Medicine, New York, NY, 10016, USA
- Department of Neurosurgery, NYU Langone Medical Center, 550 1st Ave, New York, NY, 10016, USA
| | - John G Golfinos
- NYU School of Medicine, New York, NY, 10016, USA
- Department of Neurosurgery, NYU Langone Medical Center, 550 1st Ave, New York, NY, 10016, USA
| | - David Zagzag
- NYU School of Medicine, New York, NY, 10016, USA
- Department of Pathology, NYU Langone Medical Center, 550 1st Ave, New York, NY, 10016, USA
| | - Jeffrey H Wisoff
- NYU School of Medicine, New York, NY, 10016, USA
- Department of Neurosurgery, NYU Langone Medical Center, 550 1st Ave, New York, NY, 10016, USA
| | - Matthias A Karajannis
- NYU School of Medicine, New York, NY, 10016, USA
- Division of Pediatric Hematology/Oncology, Departments of Pediatrics and Otolaryngology, NYU Langone Medical Center, 550 1st Ave, New York, NY, 10016, USA
| | - Matija Snuderl
- NYU School of Medicine, New York, NY, 10016, USA.
- Department of Pathology, NYU Langone Medical Center, 550 1st Ave, New York, NY, 10016, USA.
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Valle-García D, Qadeer ZA, McHugh DS, Ghiraldini FG, Chowdhury AH, Hasson D, Dyer MA, Recillas-Targa F, Bernstein E. ATRX binds to atypical chromatin domains at the 3' exons of zinc finger genes to preserve H3K9me3 enrichment. Epigenetics 2016; 11:398-414. [PMID: 27029610 PMCID: PMC4939920 DOI: 10.1080/15592294.2016.1169351] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 03/14/2016] [Accepted: 03/17/2016] [Indexed: 12/20/2022] Open
Abstract
ATRX is a SWI/SNF chromatin remodeler proposed to govern genomic stability through the regulation of repetitive sequences, such as rDNA, retrotransposons, and pericentromeric and telomeric repeats. However, few direct ATRX target genes have been identified and high-throughput genomic approaches are currently lacking for ATRX. Here we present a comprehensive ChIP-sequencing study of ATRX in multiple human cell lines, in which we identify the 3' exons of zinc finger genes (ZNFs) as a new class of ATRX targets. These 3' exonic regions encode the zinc finger motifs, which can range from 1-40 copies per ZNF gene and share large stretches of sequence similarity. These regions often contain an atypical chromatin signature: they are transcriptionally active, contain high levels of H3K36me3, and are paradoxically enriched in H3K9me3. We find that these ZNF 3' exons are co-occupied by SETDB1, TRIM28, and ZNF274, which form a complex with ATRX. CRISPR/Cas9-mediated loss-of-function studies demonstrate (i) a reduction of H3K9me3 at the ZNF 3' exons in the absence of ATRX and ZNF274 and, (ii) H3K9me3 levels at atypical chromatin regions are particularly sensitive to ATRX loss compared to other H3K9me3-occupied regions. As a consequence of ATRX or ZNF274 depletion, cells with reduced levels of H3K9me3 show increased levels of DNA damage, suggesting that ATRX binds to the 3' exons of ZNFs to maintain their genomic stability through preservation of H3K9me3.
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Affiliation(s)
- David Valle-García
- a Departments of Oncological Sciences and Dermatology , Icahn School of Medicine at Mount Sinai , New York , NY , USA
- b Instituto de Fisiología Celular, Departamento de Genética Molecular, Universidad Nacional Autónoma de México , Ciudad de México , México
| | - Zulekha A Qadeer
- a Departments of Oncological Sciences and Dermatology , Icahn School of Medicine at Mount Sinai , New York , NY , USA
- c Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai , New York , NY , USA
| | - Domhnall S McHugh
- a Departments of Oncological Sciences and Dermatology , Icahn School of Medicine at Mount Sinai , New York , NY , USA
| | - Flávia G Ghiraldini
- a Departments of Oncological Sciences and Dermatology , Icahn School of Medicine at Mount Sinai , New York , NY , USA
| | - Asif H Chowdhury
- a Departments of Oncological Sciences and Dermatology , Icahn School of Medicine at Mount Sinai , New York , NY , USA
| | - Dan Hasson
- a Departments of Oncological Sciences and Dermatology , Icahn School of Medicine at Mount Sinai , New York , NY , USA
| | - Michael A Dyer
- d Department of Developmental Neurobiology , St Jude Children's Research Hospital , Memphis , Tennessee , USA
| | - Félix Recillas-Targa
- b Instituto de Fisiología Celular, Departamento de Genética Molecular, Universidad Nacional Autónoma de México , Ciudad de México , México
| | - Emily Bernstein
- a Departments of Oncological Sciences and Dermatology , Icahn School of Medicine at Mount Sinai , New York , NY , USA
- c Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai , New York , NY , USA
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Gocha ARS, Harris J, Groden J. Alternative mechanisms of telomere lengthening: permissive mutations, DNA repair proteins and tumorigenic progression. Mutat Res 2012; 743-744:142-150. [PMID: 23219603 DOI: 10.1016/j.mrfmmm.2012.11.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2012] [Revised: 11/22/2012] [Accepted: 11/24/2012] [Indexed: 01/05/2023]
Abstract
Telomeres protect chromosome termini to maintain genomic stability and regulate cellular lifespan. Maintenance of telomere length is required for neoplastic cells after the acquisition of mutations that deregulate cell cycle control and increase cellular proliferation, and can occur through expression of the enzyme telomerase or in a telomerase-independent manner termed alternative lengthening of telomeres (ALT). The precise mechanisms that govern the activation of ALT or telomerase in tumor cells are unknown, although cellular origin may favor one or the other mechanisms. ALT pathways are incompletely understood to date; however, recent publications have increasingly broadened our understanding of how ALT is activated, how it proceeds, and how it influences tumor growth. Specific mutational events influence ALT activation, as mutations in genes that suppress recombination and/or alterations in the regulation of telomerase expression are associated with ALT. Once engaged, ALT uses DNA repair proteins to maintain telomeres in the absence of telomerase; experiments that manipulate the expression of specific proteins in cells using ALT are illuminating some of its mechanisms. Furthermore, ALT may influence tumor growth, as experimental and clinical data suggest that telomerase expression may favor tumor progression. This review summarizes recent findings in mammalian cells and models, as well as clinical data, that identify the genetic mutations permissive to ALT, the DNA repair proteins involved in ALT mechanisms and the importance of telomere maintenance mechanisms for tumor progression. A comprehensive understanding of the mechanisms that permit tumor cell immortalization will be important for identifying novel therapeutic targets in cancer.
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Affiliation(s)
- April Renee Sandy Gocha
- Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State University College of Medicine, Columbus, OH 43210, United States
| | - Julia Harris
- Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State University College of Medicine, Columbus, OH 43210, United States
| | - Joanna Groden
- Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State University College of Medicine, Columbus, OH 43210, United States.
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Jiao Y, Killela PJ, Reitman ZJ, Rasheed BA, Heaphy CM, de Wilde RF, Rodriguez FJ, Rosemberg S, Oba-Shinjo SM, Marie SKN, Bettegowda C, Agrawal N, Lipp E, Pirozzi CJ, Lopez GY, He Y, Friedman HS, Friedman AH, Riggins GJ, Holdhoff M, Burger P, McLendon RE, Bigner DD, Vogelstein B, Meeker AK, Kinzler KW, Papadopoulos N, Diaz LA, Yan H. Frequent ATRX, CIC, FUBP1 and IDH1 mutations refine the classification of malignant gliomas. Oncotarget 2012; 3:709-22. [PMID: 22869205 PMCID: PMC3443254 DOI: 10.18632/oncotarget.588] [Citation(s) in RCA: 430] [Impact Index Per Article: 35.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Accepted: 08/02/2012] [Indexed: 11/25/2022] Open
Abstract
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.
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Affiliation(s)
- Yuchen Jiao
- Ludwig Center for Cancer Genetics and Howard Hughes Medical Institutions, The Johns Hopkins Kimmel Cancer Center, the Department of Oncology, the Department of Pathology, the Department of Neurosurgery, the Johns Hopkins Medical Institutions, Baltimore, Maryland, USA
| | - Patrick J. Killela
- The Preston Robert Tisch Brain Tumor Center at Duke, The Pediatric Brain Tumor Foundation Institute, the Department of Pathology, the Department of Surgery, Duke University Medical Center, Durham, North Carolina, USA
| | - Zachary J. Reitman
- The Preston Robert Tisch Brain Tumor Center at Duke, The Pediatric Brain Tumor Foundation Institute, the Department of Pathology, the Department of Surgery, Duke University Medical Center, Durham, North Carolina, USA
| | - B. Ahmed Rasheed
- The Preston Robert Tisch Brain Tumor Center at Duke, The Pediatric Brain Tumor Foundation Institute, the Department of Pathology, the Department of Surgery, Duke University Medical Center, Durham, North Carolina, USA
| | - Christopher M. Heaphy
- Ludwig Center for Cancer Genetics and Howard Hughes Medical Institutions, The Johns Hopkins Kimmel Cancer Center, the Department of Oncology, the Department of Pathology, the Department of Neurosurgery, the Johns Hopkins Medical Institutions, Baltimore, Maryland, USA
| | - Roeland F. de Wilde
- Ludwig Center for Cancer Genetics and Howard Hughes Medical Institutions, The Johns Hopkins Kimmel Cancer Center, the Department of Oncology, the Department of Pathology, the Department of Neurosurgery, the Johns Hopkins Medical Institutions, Baltimore, Maryland, USA
| | - Fausto J. Rodriguez
- Ludwig Center for Cancer Genetics and Howard Hughes Medical Institutions, The Johns Hopkins Kimmel Cancer Center, the Department of Oncology, the Department of Pathology, the Department of Neurosurgery, the Johns Hopkins Medical Institutions, Baltimore, Maryland, USA
| | - Sergio Rosemberg
- The Department of Pathology, the Department of Neurology, School of Medicine, University of Sao Paulo, Sao Paulo, Sao Paulo, Brazil
| | - Sueli Mieko Oba-Shinjo
- The Department of Pathology, the Department of Neurology, School of Medicine, University of Sao Paulo, Sao Paulo, Sao Paulo, Brazil
| | - Suely Kazue Nagahashi Marie
- The Department of Pathology, the Department of Neurology, School of Medicine, University of Sao Paulo, Sao Paulo, Sao Paulo, Brazil
| | - Chetan Bettegowda
- Ludwig Center for Cancer Genetics and Howard Hughes Medical Institutions, The Johns Hopkins Kimmel Cancer Center, the Department of Oncology, the Department of Pathology, the Department of Neurosurgery, the Johns Hopkins Medical Institutions, Baltimore, Maryland, USA
| | - Nishant Agrawal
- Ludwig Center for Cancer Genetics and Howard Hughes Medical Institutions, The Johns Hopkins Kimmel Cancer Center, the Department of Oncology, the Department of Pathology, the Department of Neurosurgery, the Johns Hopkins Medical Institutions, Baltimore, Maryland, USA
| | - Eric Lipp
- The Preston Robert Tisch Brain Tumor Center at Duke, The Pediatric Brain Tumor Foundation Institute, the Department of Pathology, the Department of Surgery, Duke University Medical Center, Durham, North Carolina, USA
| | - Christopher J. Pirozzi
- The Preston Robert Tisch Brain Tumor Center at Duke, The Pediatric Brain Tumor Foundation Institute, the Department of Pathology, the Department of Surgery, Duke University Medical Center, Durham, North Carolina, USA
| | - Giselle Y. Lopez
- The Preston Robert Tisch Brain Tumor Center at Duke, The Pediatric Brain Tumor Foundation Institute, the Department of Pathology, the Department of Surgery, Duke University Medical Center, Durham, North Carolina, USA
| | - Yiping He
- The Preston Robert Tisch Brain Tumor Center at Duke, The Pediatric Brain Tumor Foundation Institute, the Department of Pathology, the Department of Surgery, Duke University Medical Center, Durham, North Carolina, USA
| | - Henry S. Friedman
- The Preston Robert Tisch Brain Tumor Center at Duke, The Pediatric Brain Tumor Foundation Institute, the Department of Pathology, the Department of Surgery, Duke University Medical Center, Durham, North Carolina, USA
| | - Allan H. Friedman
- The Preston Robert Tisch Brain Tumor Center at Duke, The Pediatric Brain Tumor Foundation Institute, the Department of Pathology, the Department of Surgery, Duke University Medical Center, Durham, North Carolina, USA
| | - Gregory J. Riggins
- Ludwig Center for Cancer Genetics and Howard Hughes Medical Institutions, The Johns Hopkins Kimmel Cancer Center, the Department of Oncology, the Department of Pathology, the Department of Neurosurgery, the Johns Hopkins Medical Institutions, Baltimore, Maryland, USA
| | - Matthias Holdhoff
- Ludwig Center for Cancer Genetics and Howard Hughes Medical Institutions, The Johns Hopkins Kimmel Cancer Center, the Department of Oncology, the Department of Pathology, the Department of Neurosurgery, the Johns Hopkins Medical Institutions, Baltimore, Maryland, USA
- The Swim Across America Laboratory at Johns Hopkins, The Johns Hopkins Medical Institutions, Baltimore, Maryland, USA
| | - Peter Burger
- Ludwig Center for Cancer Genetics and Howard Hughes Medical Institutions, The Johns Hopkins Kimmel Cancer Center, the Department of Oncology, the Department of Pathology, the Department of Neurosurgery, the Johns Hopkins Medical Institutions, Baltimore, Maryland, USA
| | - Roger E. McLendon
- The Preston Robert Tisch Brain Tumor Center at Duke, The Pediatric Brain Tumor Foundation Institute, the Department of Pathology, the Department of Surgery, Duke University Medical Center, Durham, North Carolina, USA
| | - Darell D. Bigner
- The Preston Robert Tisch Brain Tumor Center at Duke, The Pediatric Brain Tumor Foundation Institute, the Department of Pathology, the Department of Surgery, Duke University Medical Center, Durham, North Carolina, USA
| | - Bert Vogelstein
- Ludwig Center for Cancer Genetics and Howard Hughes Medical Institutions, The Johns Hopkins Kimmel Cancer Center, the Department of Oncology, the Department of Pathology, the Department of Neurosurgery, the Johns Hopkins Medical Institutions, Baltimore, Maryland, USA
| | - Alan K. Meeker
- Ludwig Center for Cancer Genetics and Howard Hughes Medical Institutions, The Johns Hopkins Kimmel Cancer Center, the Department of Oncology, the Department of Pathology, the Department of Neurosurgery, the Johns Hopkins Medical Institutions, Baltimore, Maryland, USA
| | - Kenneth W. Kinzler
- Ludwig Center for Cancer Genetics and Howard Hughes Medical Institutions, The Johns Hopkins Kimmel Cancer Center, the Department of Oncology, the Department of Pathology, the Department of Neurosurgery, the Johns Hopkins Medical Institutions, Baltimore, Maryland, USA
| | - Nickolas Papadopoulos
- Ludwig Center for Cancer Genetics and Howard Hughes Medical Institutions, The Johns Hopkins Kimmel Cancer Center, the Department of Oncology, the Department of Pathology, the Department of Neurosurgery, the Johns Hopkins Medical Institutions, Baltimore, Maryland, USA
| | - Luis A. Diaz
- Ludwig Center for Cancer Genetics and Howard Hughes Medical Institutions, The Johns Hopkins Kimmel Cancer Center, the Department of Oncology, the Department of Pathology, the Department of Neurosurgery, the Johns Hopkins Medical Institutions, Baltimore, Maryland, USA
- The Swim Across America Laboratory at Johns Hopkins, The Johns Hopkins Medical Institutions, Baltimore, Maryland, USA
| | - Hai Yan
- The Preston Robert Tisch Brain Tumor Center at Duke, The Pediatric Brain Tumor Foundation Institute, the Department of Pathology, the Department of Surgery, Duke University Medical Center, Durham, North Carolina, USA
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