1
|
Malta TM, Sabedot TS, Morosini NS, Datta I, Garofano L, Vallentgoed W, Varn FS, Aldape K, D'Angelo F, Bakas S, Barnholtz-Sloan JS, Gan HK, Hasanain M, Hau AC, Johnson KC, Cazacu S, deCarvalho AC, Khasraw M, Kocakavuk E, Kouwenhoven MC, Migliozzi S, Niclou SP, Niers JM, Ormond DR, Paek SH, Reifenberger G, Sillevis Smitt PA, Smits M, Stead LF, van den Bent MJ, Van Meir EG, Walenkamp A, Weiss T, Weller M, Westerman BA, Ylstra B, Wesseling P, Lasorella A, French PJ, Poisson LM, Verhaak RG, Iavarone A, Noushmehr H. The Epigenetic Evolution of Glioma Is Determined by the IDH1 Mutation Status and Treatment Regimen. Cancer Res 2024; 84:741-756. [PMID: 38117484 PMCID: PMC10911804 DOI: 10.1158/0008-5472.can-23-2093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 09/15/2023] [Accepted: 12/13/2023] [Indexed: 12/21/2023]
Abstract
Tumor adaptation or selection is thought to underlie therapy resistance in glioma. To investigate longitudinal epigenetic evolution of gliomas in response to therapeutic pressure, we performed an epigenomic analysis of 132 matched initial and recurrent tumors from patients with IDH-wildtype (IDHwt) and IDH-mutant (IDHmut) glioma. IDHwt gliomas showed a stable epigenome over time with relatively low levels of global methylation. The epigenome of IDHmut gliomas showed initial high levels of genome-wide DNA methylation that was progressively reduced to levels similar to those of IDHwt tumors. Integration of epigenomics, gene expression, and functional genomics identified HOXD13 as a master regulator of IDHmut astrocytoma evolution. Furthermore, relapse of IDHmut tumors was accompanied by histologic progression that was associated with survival, as validated in an independent cohort. Finally, the initial cell composition of the tumor microenvironment varied between IDHwt and IDHmut tumors and changed differentially following treatment, suggesting increased neoangiogenesis and T-cell infiltration upon treatment of IDHmut gliomas. This study provides one of the largest cohorts of paired longitudinal glioma samples with epigenomic, transcriptomic, and genomic profiling and suggests that treatment of IDHmut glioma is associated with epigenomic evolution toward an IDHwt-like phenotype. SIGNIFICANCE Standard treatments are related to loss of DNA methylation in IDHmut glioma, resulting in epigenetic activation of genes associated with tumor progression and alterations in the microenvironment that resemble treatment-naïve IDHwt glioma.
Collapse
Affiliation(s)
- Tathiane M. Malta
- School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Thais S. Sabedot
- Hermelin Brain Tumor Center, Henry Ford Health System, Detroit, Michigan
| | | | - Indrani Datta
- Hermelin Brain Tumor Center, Henry Ford Health System, Detroit, Michigan
| | - Luciano Garofano
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida
| | - Wies Vallentgoed
- Neurology Department, The Brain Tumour Center, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Frederick S. Varn
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut
| | | | - Fulvio D'Angelo
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida
- Department of Neurological Surgery, University of Miami Miller School of Medicine, Miami, Florida
| | - Spyridon Bakas
- Center for Biomedical Image Computing and Analytics, University of Pennsylvania, Philadelphia, Pennsylvania
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
- Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | | | - Hui K. Gan
- Olivia Newton-John Cancer Research Institute, Austin Health, Heidelberg, Melbourne, Australia
| | - Mohammad Hasanain
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida
| | | | - Kevin C. Johnson
- Department of Neurosurgery, Yale School of Medicine, New Haven, Connecticut
| | - Simona Cazacu
- Hermelin Brain Tumor Center, Henry Ford Health System, Detroit, Michigan
| | - Ana C. deCarvalho
- Hermelin Brain Tumor Center, Henry Ford Health System, Detroit, Michigan
| | | | - Emre Kocakavuk
- Department of Neurosurgery, Yale School of Medicine, New Haven, Connecticut
- Department of Hematology and Stem Cell Transplantation, West German Cancer Center (WTZ), National Center for Tumor Diseases (NCT) West, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Mathilde C.M. Kouwenhoven
- Department of Neurology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Simona Migliozzi
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida
| | | | - Johanna M. Niers
- Department of Neurology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - D. Ryan Ormond
- University of Colorado School of Medicine, Department of Neurosurgery, Aurora, Colorado
| | - Sun Ha Paek
- Department of Neurosurgery, Cancer Research Institute, Hypoxia Ischemia Disease Institute, Seoul National University, Seoul, Republic of Korea (South)
| | - Guido Reifenberger
- Institute of Neuropathology, Heinrich Heine University, Dusseldorf, Germany
| | - Peter A. Sillevis Smitt
- Department of Neurology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- The Brain Tumour Centre, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Marion Smits
- Department of Radiology and Nuclear Medicine, Erasmus MC, Rotterdam, the Netherlands
| | - Lucy F. Stead
- Leeds Institute of Medical Research, University of Leeds, Leeds, United Kingdom
| | - Martin J. van den Bent
- Department of Neurology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- The Brain Tumour Centre, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Erwin G. Van Meir
- Department of Neurosurgery and O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, Alabama
| | | | - Tobias Weiss
- Department of Neurology, University Hospital and University of Zurich, Zurich, Switzerland
| | - Michael Weller
- Department of Neurology, University Hospital and University of Zurich, Zurich, Switzerland
| | - Bart A. Westerman
- Department of Neurology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Bauke Ylstra
- Department of Pathology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Pieter Wesseling
- Department of Pathology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- Brain Tumor Center Amsterdam, Cancer Center Amsterdam, Amsterdam UMC, VU University Medical Center, Amsterdam, the Netherlands
- Laboratory for Childhood Cancer Pathology, Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Anna Lasorella
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, Florida
| | - Pim J. French
- Neurology Department, The Brain Tumour Center, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Laila M. Poisson
- Hermelin Brain Tumor Center, Henry Ford Health System, Detroit, Michigan
| | - Roel G.W. Verhaak
- Department of Neurosurgery, Yale School of Medicine, New Haven, Connecticut
- Department of Neurosurgery, Amsterdam University Medical Center, Amsterdam, the Netherlands
| | - Antonio Iavarone
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida
- Department of Neurological Surgery, University of Miami Miller School of Medicine, Miami, Florida
| | - Houtan Noushmehr
- Hermelin Brain Tumor Center, Henry Ford Health System, Detroit, Michigan
| |
Collapse
|
2
|
Yeo AT, Shah R, Aliazis K, Pal R, Xu T, Zhang P, Rawal S, Rose CM, Varn FS, Appleman VA, Yoon J, Varma H, Gygi SP, Verhaak RG, Boussiotis VA, Charest A. Driver Mutations Dictate the Immunologic Landscape and Response to Checkpoint Immunotherapy of Glioblastoma. Cancer Immunol Res 2023; 11:629-645. [PMID: 36881002 PMCID: PMC10155040 DOI: 10.1158/2326-6066.cir-22-0655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 12/20/2022] [Accepted: 03/03/2023] [Indexed: 03/08/2023]
Abstract
The composition of the tumor immune microenvironment (TIME) is considered a key determinant of patients' response to immunotherapy. The mechanisms underlying TIME formation and development over time are poorly understood. Glioblastoma (GBM) is a lethal primary brain cancer for which there are no curative treatments. GBMs are immunologically heterogeneous and impervious to checkpoint blockade immunotherapies. Utilizing clinically relevant genetic mouse models of GBM, we identified distinct immune landscapes associated with expression of EGFR wild-type and mutant EGFRvIII cancer driver mutations. Over time, accumulation of polymorphonuclear myeloid-derived suppressor cells (PMN-MDSC) was more pronounced in EGFRvIII-driven GBMs and was correlated with resistance to PD-1 and CTLA-4 combination checkpoint blockade immunotherapy. We determined that GBM-secreted CXCL1/2/3 and PMN-MDSC-expressed CXCR2 formed an axis regulating output of PMN-MDSCs from the bone marrow leading to systemic increase in these cells in the spleen and GBM tumor-draining lymph nodes. Pharmacologic targeting of this axis induced a systemic decrease in the numbers of PMN-MDSC, facilitated responses to PD-1 and CTLA-4 combination checkpoint blocking immunotherapy, and prolonged survival in mice bearing EGFRvIII-driven GBM. Our results uncover a relationship between cancer driver mutations, TIME composition, and sensitivity to checkpoint blockade in GBM and support the stratification of patients with GBM for checkpoint blockade therapy based on integrated genotypic and immunologic profiles.
Collapse
Affiliation(s)
- Alan T. Yeo
- Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, Massachusetts
- Sackler School of Graduate Studies, Tufts University School of Medicine, Boston, Massachusetts
| | - Rushil Shah
- Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - Konstantinos Aliazis
- Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - Rinku Pal
- Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - Tuoye Xu
- Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - Piyan Zhang
- Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - Shruti Rawal
- Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | | | - Frederick S. Varn
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut
| | - Vicky A. Appleman
- Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - Joon Yoon
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Hemant Varma
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
| | - Steven P. Gygi
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts
| | - Roel G.W. Verhaak
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut
| | - Vassiliki A. Boussiotis
- Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Al Charest
- Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| |
Collapse
|
3
|
Pecorino LT, Verhaak RG, Henssen A, Mischel PS. Extrachromosomal DNA (ecDNA): an origin of tumor heterogeneity, genomic remodeling, and drug resistance. Biochem Soc Trans 2022; 50:1911-1920. [PMID: 36355400 PMCID: PMC9788557 DOI: 10.1042/bst20221045] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 10/17/2022] [Accepted: 10/17/2022] [Indexed: 11/12/2022]
Abstract
The genome of cancer cells contains circular extrachromosomal DNA (ecDNA) elements not found in normal cells. Analysis of clinical samples reveal they are common in most cancers and their presence indicates poor prognosis. They often contain enhancers and driver oncogenes that are highly expressed. The circular ecDNA topology leads to an open chromatin conformation and generates new gene regulatory interactions, including with distal enhancers. The absence of centromeres leads to random distribution of ecDNAs during cell division and genes encoded on them are transmitted in a non-mendelian manner. ecDNA can integrate into and exit from chromosomal DNA. The numbers of specific ecDNAs can change in response to treatment. This dynamic ability to remodel the cancer genome challenges long-standing fundamentals, providing new insights into tumor heterogeneity, cancer genome remodeling, and drug resistance.
Collapse
Affiliation(s)
| | | | - Anton Henssen
- Department of Pediatric Hematology and Oncology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Paul S. Mischel
- Department of Pathology, Stanford University School of Medicine, Stanford University, Stanford, CA, U.S.A
- Sarafan ChEM-H, Standford, CA, U.S.A
| |
Collapse
|
4
|
Wu L, Wu W, Zhang J, Zhao Z, Li L, Zhu M, Wu M, Wu F, Zhou F, Du Y, Chai RC, Zhang W, Qiu X, Liu Q, Wang Z, Li J, Li K, Chen A, Jiang Y, Xiao X, Zou H, Srivastava R, Zhang T, Cai Y, Liang Y, Huang B, Zhang R, Lin F, Hu L, Wang X, Qian X, Lv S, Hu B, Zheng S, Hu Z, Shen H, You Y, Verhaak RG, Jiang T, Wang Q. Natural Coevolution of Tumor and Immunoenvironment in Glioblastoma. Cancer Discov 2022; 12:2820-2837. [PMID: 36122307 PMCID: PMC9716251 DOI: 10.1158/2159-8290.cd-22-0196] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 08/05/2022] [Accepted: 09/15/2022] [Indexed: 01/12/2023]
Abstract
Isocitrate dehydrogenase (IDH) wild-type glioblastoma (GBM) has a dismal prognosis. A better understanding of tumor evolution holds the key to developing more effective treatment. Here we study GBM's natural evolutionary trajectory by using rare multifocal samples. We sequenced 61,062 single cells from eight multifocal IDH wild-type primary GBMs and defined a natural evolution signature (NES) of the tumor. We show that the NES significantly associates with the activation of transcription factors that regulate brain development, including MYBL2 and FOSL2. Hypoxia is involved in inducing NES transition potentially via activation of the HIF1A-FOSL2 axis. High-NES tumor cells could recruit and polarize bone marrow-derived macrophages through activation of the FOSL2-ANXA1-FPR1/3 axis. These polarized macrophages can efficiently suppress T-cell activity and accelerate NES transition in tumor cells. Moreover, the polarized macrophages could upregulate CCL2 to induce tumor cell migration. SIGNIFICANCE GBM progression could be induced by hypoxia via the HIF1A-FOSL2 axis. Tumor-derived ANXA1 is associated with recruitment and polarization of bone marrow-derived macrophages to suppress the immunoenvironment. The polarized macrophages promote tumor cell NES transition and migration. This article is highlighted in the In This Issue feature, p. 2711.
Collapse
Affiliation(s)
- Lingxiang Wu
- The Affiliated Cancer Hospital of Nanjing Medical University, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing, China.,Department of Bioinformatics, Nanjing Medical University, Nanjing, China.,Institute for Brain Tumors, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
| | - Wei Wu
- The Affiliated Cancer Hospital of Nanjing Medical University, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing, China.,Department of Bioinformatics, Nanjing Medical University, Nanjing, China.,Institute for Brain Tumors, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
| | - Junxia Zhang
- Institute for Brain Tumors, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China.,Department of Neurosurgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Zheng Zhao
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Liangyu Li
- Department of Bioinformatics, Nanjing Medical University, Nanjing, China.,Institute for Brain Tumors, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
| | - Mengyan Zhu
- The Affiliated Cancer Hospital of Nanjing Medical University, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing, China.,Department of Bioinformatics, Nanjing Medical University, Nanjing, China.,Institute for Brain Tumors, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
| | - Min Wu
- The Affiliated Cancer Hospital of Nanjing Medical University, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing, China.,Department of Bioinformatics, Nanjing Medical University, Nanjing, China.,Institute for Brain Tumors, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
| | - Fan Wu
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Fengqi Zhou
- Department of Neurosurgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yuxin Du
- The Affiliated Cancer Hospital of Nanjing Medical University, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing, China
| | - Rui-Chao Chai
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Wei Zhang
- Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Xiaoguang Qiu
- Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Quanzhong Liu
- The Affiliated Cancer Hospital of Nanjing Medical University, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing, China.,Department of Bioinformatics, Nanjing Medical University, Nanjing, China.,Institute for Brain Tumors, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
| | - Ziyu Wang
- Department of Bioinformatics, Nanjing Medical University, Nanjing, China.,Institute for Brain Tumors, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
| | - Jie Li
- Department of Bioinformatics, Nanjing Medical University, Nanjing, China.,Institute for Brain Tumors, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
| | - Kening Li
- The Affiliated Cancer Hospital of Nanjing Medical University, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing, China.,Department of Bioinformatics, Nanjing Medical University, Nanjing, China.,Institute for Brain Tumors, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
| | - Apeng Chen
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China.,Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania.,John G. Rangos Sr. Research Center, University of Pittsburgh Medical Center (UPMC) Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania
| | - Yinan Jiang
- John G. Rangos Sr. Research Center, University of Pittsburgh Medical Center (UPMC) Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania.,Department of Pediatric Surgery, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Xiangwei Xiao
- John G. Rangos Sr. Research Center, University of Pittsburgh Medical Center (UPMC) Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania.,Department of Pediatric Surgery, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Han Zou
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania.,John G. Rangos Sr. Research Center, University of Pittsburgh Medical Center (UPMC) Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania
| | - Rashmi Srivastava
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania.,John G. Rangos Sr. Research Center, University of Pittsburgh Medical Center (UPMC) Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania
| | - Tingting Zhang
- Department of Bioinformatics, Nanjing Medical University, Nanjing, China.,Institute for Brain Tumors, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
| | - Yun Cai
- Department of Bioinformatics, Nanjing Medical University, Nanjing, China.,Institute for Brain Tumors, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
| | - Yuan Liang
- Department of Bioinformatics, Nanjing Medical University, Nanjing, China.,Institute for Brain Tumors, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
| | - Bin Huang
- Department of Bioinformatics, Nanjing Medical University, Nanjing, China.,Institute for Brain Tumors, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
| | - Ruohan Zhang
- Department of Bioinformatics, Nanjing Medical University, Nanjing, China
| | - Fan Lin
- Department of Cell Biology, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, China.,Institute for Brain Tumors and Key Laboratory of Rare Metabolic Diseases, Nanjing Medical University, Nanjing, China
| | - Lang Hu
- School of Basic Medical Sciences, Nanjing Medical University, Nanjing, China
| | - Xiuxing Wang
- School of Basic Medical Sciences, Nanjing Medical University, Nanjing, China
| | - Xu Qian
- Institute for Brain Tumors, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China.,Department of Nutrition and Food Hygiene, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Sali Lv
- Department of Bioinformatics, Nanjing Medical University, Nanjing, China.,Institute for Brain Tumors, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
| | - Baoli Hu
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania.,John G. Rangos Sr. Research Center, University of Pittsburgh Medical Center (UPMC) Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania
| | - Siyuan Zheng
- Greehey Children's Cancer Research Institute, UT Health San Antonio, San Antonio, Texas.,Department of Population Health Sciences, UT Health San Antonio, San Antonio, Texas
| | - Zhibin Hu
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing, China.,Department of Epidemiology and Biostatistics, International Joint Research Center on Environment and Human Health, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Hongbing Shen
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing, China.,Department of Epidemiology and Biostatistics, International Joint Research Center on Environment and Human Health, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Yongping You
- Institute for Brain Tumors, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China.,Department of Neurosurgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,Corresponding Authors: Qianghu Wang, Nanjing Medical University, 211166 Nanjing, China. Phone: 8602-5868-69330; E-mail: ; Tao Jiang, Beijing Neurosurgical Institute, Beijing Tiantan Hospital, Capital Medical University, 100070 Beijing, China. Phone: 8601-0599-75624; E-mail: ; Roel G.W. Verhaak, The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032. Phone: 860-837-2140; E-mail: ; and Yongping You, Department of Neurosurgery, The First Affiliated Hospital of Nanjing Medical University, 210029 Nanjing, China. Phone: 8602-5681-36679; E-mail:
| | - Roel G.W. Verhaak
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut.,Corresponding Authors: Qianghu Wang, Nanjing Medical University, 211166 Nanjing, China. Phone: 8602-5868-69330; E-mail: ; Tao Jiang, Beijing Neurosurgical Institute, Beijing Tiantan Hospital, Capital Medical University, 100070 Beijing, China. Phone: 8601-0599-75624; E-mail: ; Roel G.W. Verhaak, The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032. Phone: 860-837-2140; E-mail: ; and Yongping You, Department of Neurosurgery, The First Affiliated Hospital of Nanjing Medical University, 210029 Nanjing, China. Phone: 8602-5681-36679; E-mail:
| | - Tao Jiang
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,Corresponding Authors: Qianghu Wang, Nanjing Medical University, 211166 Nanjing, China. Phone: 8602-5868-69330; E-mail: ; Tao Jiang, Beijing Neurosurgical Institute, Beijing Tiantan Hospital, Capital Medical University, 100070 Beijing, China. Phone: 8601-0599-75624; E-mail: ; Roel G.W. Verhaak, The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032. Phone: 860-837-2140; E-mail: ; and Yongping You, Department of Neurosurgery, The First Affiliated Hospital of Nanjing Medical University, 210029 Nanjing, China. Phone: 8602-5681-36679; E-mail:
| | - Qianghu Wang
- The Affiliated Cancer Hospital of Nanjing Medical University, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing, China.,Department of Bioinformatics, Nanjing Medical University, Nanjing, China.,Institute for Brain Tumors, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China.,Corresponding Authors: Qianghu Wang, Nanjing Medical University, 211166 Nanjing, China. Phone: 8602-5868-69330; E-mail: ; Tao Jiang, Beijing Neurosurgical Institute, Beijing Tiantan Hospital, Capital Medical University, 100070 Beijing, China. Phone: 8601-0599-75624; E-mail: ; Roel G.W. Verhaak, The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032. Phone: 860-837-2140; E-mail: ; and Yongping You, Department of Neurosurgery, The First Affiliated Hospital of Nanjing Medical University, 210029 Nanjing, China. Phone: 8602-5681-36679; E-mail:
| |
Collapse
|
5
|
Kocakavuk E, Anderson KJ, Varn FS, Johnson KC, Amin SB, Sulman EP, Lolkema M, Barthel FP, Verhaak RG. Abstract PO-019: Radiotherapy in cancer is associated with a deletion signature that contributes to poor patient outcomes. Clin Cancer Res 2021. [DOI: 10.1158/1557-3265.radsci21-po-019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Diffuse gliomas are highly aggressive brain tumors that invariably relapse despite treatment with chemo- and radiotherapy. Treatment with alkylating chemotherapy can drive tumors to develop a hypermutator phenotype. In contrast, the genomic effects of radiation therapy (RT) remain unknown. We analyzed the mutational spectra following treatment with ionizing radiation in sequencing data from 190 paired primary-recurrent gliomas from the Glioma Longitudinal Analysis (GLASS) dataset and 3693 post-treatment metastatic tumors from the Hartwig Medical Foundation (HMF). We identified a significant increase in the burden of small deletions following radiation therapy that was independent of other factors. These novel deletions demonstrated distinct characteristics when compared to pre-existing deletions present prior to RT-treatment and deletions in RT-untreated tumors. Radiation therapy-acquired deletions were characterized by a larger deletion size (GLASS and metastatic cohort, P=1.2e-02 and P=8e-11, respectively; Mann-Whitney U test), an increased distance to repetitive DNA elements (P<2.2e-16, Kolmogorov-Smirnov test) and a reduction in microhomology at breakpoints (P=3.2e-02, paired Wilcoxon signed-rank test). These observations suggested that canonical non-homologous end joining (c-NHEJ) was the preferred pathway for DNA double strand break repair of RT-induced DNA damage. Furthermore, radiotherapy resulted in frequent chromosomal deletions and significantly increased frequencies of CDKN2A homozygous deletions. Finally, a high burden of RT-associated deletions was associated with worse clinical outcomes (GLASS and metastatic cohort, P < 1e-04 and P = 2.6e-02, respectively; Wald test). Our results suggest that effective repair of RT-induced DNA damage is detrimental to patient survival and that inhibiting c-NHEJ may be a viable strategy for improving the cancer-killing effect of radiotherapy. Taken together, the identified genomic scars as a result of radiation therapy reflect a more aggressive tumor with increased levels of resistance to follow up treatments.
Citation Format: Emre Kocakavuk, Kevin J. Anderson, Frederick S. Varn, Kevin C. Johnson, Samirkumar B. Amin, Erik. P. Sulman, Martijn Lolkema, Floris P. Barthel, Roel G.W. Verhaak. Radiotherapy in cancer is associated with a deletion signature that contributes to poor patient outcomes [abstract]. In: Proceedings of the AACR Virtual Special Conference on Radiation Science and Medicine; 2021 Mar 2-3. Philadelphia (PA): AACR; Clin Cancer Res 2021;27(8_Suppl):Abstract nr PO-019.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Martijn Lolkema
- 3Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | | | | |
Collapse
|
6
|
Khasraw M, McDonald K, Yip S, Verhaak RG, Heimberger AB, Hall M, Barnes E, Hovey E, Ellingson BM, Lwin Z. P01.035 Nivolumab and Temozolomide (TMZ) vs TMZ alone in newly diagnosed elderly patients (pts) with Glioblastoma (GBM) (NUTMEG): Trial in progress. Neuro Oncol 2018. [DOI: 10.1093/neuonc/noy139.077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- M Khasraw
- Royal North Shore Hospital, St Leonards, Australia
- University of Sydney, Camperdown, Australia
| | - K McDonald
- University of New South Wales, Kensington, Australia
| | - S Yip
- Sydney Catalyst Translational Cancer Research Centre, Camperdown, Australia
| | - R G Verhaak
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, United States
| | - A B Heimberger
- The University of Texas M. D. Anderson Cancer Center, Houston, TX, United States
| | - M Hall
- NHMRC Clinical Trials Centre, The University of Sydney, Camperdown, Australia
| | - E Barnes
- NHMRC Clinical Trials Centre, The University of Sydney, Camperdown, Australia
| | - E Hovey
- Prince of Wales Hospital, Randwick, Australia
| | - B M Ellingson
- UCLA Brain Tumor Imaging Laboratory (BTIL), University of California, Los Angeles, CA, United States
| | - Z Lwin
- Royal Brisbane Hospital / University of Queensland, Brisbane, Australia
| |
Collapse
|
7
|
Johnson KC, Barthel FP, Tang M, Amin S, Wang Q, Sulman EP, Rai K, Verhaak RG. Abstract 4355: Identification and functional characterization of glioma structural variants. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-4355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Adult diffuse gliomas are a diverse class of brain tumors that ultimately result in fatal malignant progression. The highly variable disease progression intervals and poor treatment response observed in glioma have been explained, in part, by the extent of heterogeneity within and across gliomas. Somatic structural variants such as deletions, duplications, insertions, inversions, translocations, and extrachromosomal DNA contribute to glioma heterogeneity by generating genomic instability, a hallmark of cancer genomes. While comprehensive approaches such as whole genome sequencing have begun to catalog the glioma structural variant landscape, the molecular mechanisms by which they contribute to tumor progression remains poorly understood. Here, we identified genomic rearrangements in the whole genomes of 147 gliomas and glioma cell lines. Among the whole-genome sequencing samples were 62 glioblastomas (TCGA), 52 low-grade gliomas (TCGA), and our own set of 33 patient-derived glioma sphere-forming cells. On average, glioblastomas demonstrated a greater frequency of high-confidence structural variants (162 per tumor) than low-grade gliomas (130 per tumor, P=0.02) with two glioblastomas displaying evidence of chromothripsis. Across the World Heath Organization's molecular classifications, the IDH-mutant 1p/19q co-deleted tumors demonstrated the lowest structural variant burden when compared with both IDH-wildtype and IDH-mutant non-co-deleted tumors. Structural variant frequencies were found to be similar between patient tumors and an independent set of patient-derived cell lines. Across all samples, a majority of the structural variant breakpoints were found in intronic (42%) and intergenic regions (55%) suggesting that rearrangements predominantly impact distal regulatory regions. To investigate the functional consequences of structural variants in these regions we integrated these samples with available RNA-sequencing and epigenetic data to characterize deregulated transcriptional circuits. Analyses examining the association between genomic rearrangements and chromatin states to determine potential mechanisms of oncogene activation in select tumor and cell line samples are now underway. Together, our study demonstrates the importance of integrating structural variant calls from whole genome sequencing with expression and epigenetic data to define functional genomic rearrangements.
Citation Format: Kevin C. Johnson, Floris P. Barthel, Ming Tang, Samirkumar Amin, Qianghu Wang, Erik P. Sulman, Kunal Rai, Roel G.W Verhaak. Identification and functional characterization of glioma structural variants [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4355.
Collapse
Affiliation(s)
| | | | - Ming Tang
- 2The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Samirkumar Amin
- 1The Jackson Laboratory for Genomic Medicine, Farmington, CT
| | - Qianghu Wang
- 2The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Erik P. Sulman
- 2The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Kunal Rai
- 2The University of Texas MD Anderson Cancer Center, Houston, TX
| | | |
Collapse
|
8
|
Wang Q, Hu B, Hu X, Kim H, Squatrito M, Scarpace L, deCarvalho AC, Lyu S, Li P, Li Y, Barthel F, Cho HJ, Lin YH, Satani N, Martinez-Ledesma E, Zheng S, Chang E, Sauvé CEG, Olar A, Lan ZD, Finocchiaro G, Phillips JJ, Berger MS, Gabrusiewicz KR, Wang G, Eskilsson E, Hu J, Mikkelsen T, DePinho RA, Muller F, Heimberger AB, Sulman EP, Nam DH, Verhaak RG. Tumor Evolution of Glioma-Intrinsic Gene Expression Subtypes Associates with Immunological Changes in the Microenvironment. Cancer Cell 2018; 33:152. [PMID: 29316430 PMCID: PMC5892424 DOI: 10.1016/j.ccell.2017.12.012] [Citation(s) in RCA: 132] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Do-Hyun Nam
- Correspondence:
(E.P.S.), (D.-H.N.),
(R.G.W.V.)
| | | |
Collapse
|
9
|
Park SY, Dong J, Martinez-Ledesma E, Piao Y, Verhaak RG, de Groot JF. CSIG-16. DEPLETION OF CLK2 SENSITIZES GLIOMA CELLS TO PI3K/mTOR AND FGFR INHIBITION. Neuro Oncol 2016. [DOI: 10.1093/neuonc/now212.177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
10
|
Cherba D, Poisson L, Winn M, Kim H, Verhaak RG, Mikkelsen T, deCarvalho AC. TMOD-36. GENE EXPRESSION ANALYSIS OF SHORT AND LONG SURVIVAL GROUPS OF GLIOBLASTOMA PATIENT-DERIVED ORTHOTOPIC XENOGRAFTS. Neuro Oncol 2016. [DOI: 10.1093/neuonc/now212.905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
11
|
Wang Q, Ezhilarasan R, Eskilsson E, Gumin J, Yang J, Jaffari M, Tang M, Aldape KD, Lang FF, Verhaak RG, Sulman EP. Abstract 1646: A glioblastoma methylation assay (GaMA) developedfrom genomic analysis of glioma spheroid cultures predicts response toradiation therapy in patients with glioblastoma. Cancer Res 2016. [DOI: 10.1158/1538-7445.am2016-1646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Radiation therapy (RT) remains one of the most effective treatments for patients with GBM and has been repeatedly demonstrated to improve survival; yet response to RT is variable. We explored the relationship between methylation status and radiation response to develop a predictor of RT response using the epigenetic data of glioma sphere-forming cells (GSCs). The DNA methylomes of 42 GSCs were profiled using Illumina Infinium 450K methylation bead arrays. 15 GSCs were irradiated with 2-, 4-, and 6-Gy RT and response determined using clonogenic assays. We discovered 168 CpG probes capable of distinguishing sensitive from resistant GSCs. To validate, we analyzed 362 TCGA GBM samples, 272 that received standard 60Gy RT and 90 treated with low or no RT. Using the glioblastoma methylation assay (GaMA) signature, we classified the samples as either RT sensitive or resistant. Survival was significantly different between the predicted sensitive vs resistant patients for those treated with standard RT (median 21.0m vs 14.7m, p<0.005). GaMA did not predict a survival difference among patients receiving no/low-dose RT, suggesting a predictive, but not prognostic, role for the signature. Using the ENCODE ChIP-Seq Significance Tool, we observed that the transcription factor EZH2 was significantly associated with the radiation resistant promoters in the GaMA signature. Among the hypermethylated genes with EZH2 binding sites, the NR2F2 promoter had the greatest number of hypermethylated CpG sites correlated to RT resistance. NR2F2 has previously been identified as negatively associated with activation of the wnt/β-catenin, a pathway associated with RT resistance of mammary progenitor cells. Expression of WNT1 in TCGA GBM cohort was negatively associated with NR2F2 expression. Our GSC RT response-based methylome analysis corroborates this association and provides a rationale for the methylation signature as a predictive biomarker of radiation response.
Citation Format: Qianghu Wang, Ravesanker Ezhilarasan, Eskil Eskilsson, Joy Gumin, Jie Yang, Mona Jaffari, Ming Tang, Kenneth D. Aldape, Frederick F. Lang, Roel G.W. Verhaak, Erik P. Sulman. A glioblastoma methylation assay (GaMA) developedfrom genomic analysis of glioma spheroid cultures predicts response toradiation therapy in patients with glioblastoma. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1646.
Collapse
Affiliation(s)
- Qianghu Wang
- 1The University of Texas, MD Anderson Cancer Center, Houston, TX
| | | | - Eskil Eskilsson
- 1The University of Texas, MD Anderson Cancer Center, Houston, TX
| | - Joy Gumin
- 1The University of Texas, MD Anderson Cancer Center, Houston, TX
| | - Jie Yang
- 1The University of Texas, MD Anderson Cancer Center, Houston, TX
| | - Mona Jaffari
- 1The University of Texas, MD Anderson Cancer Center, Houston, TX
| | - Ming Tang
- 1The University of Texas, MD Anderson Cancer Center, Houston, TX
| | | | | | | | - Erik P. Sulman
- 1The University of Texas, MD Anderson Cancer Center, Houston, TX
| |
Collapse
|
12
|
Barthel FP, Ceccarelli M, Malta TM, Sabedot TS, Salama SR, Pagnotta SM, Murray BA, Morozova O, Newton Y, Brat DJ, Cherniack AD, Zhang H, Poisson L, Cooper L, Rabadan R, Laird PW, Gutmann DH, Noushmehr H, Iavarone A, Verhaak RG. GENO-06A PAN-GLIOMA CHARACTERIZATION OF GENOMIC, EPIGENOMIC AND TRANSCRIPTOMIC ACTIVITIES REVEALS NOVEL RELATIONSHIPS BETWEEN HISTOLOGICAL SUBTYPES AND MOLECULAR SIGNATURES. Neuro Oncol 2015. [DOI: 10.1093/neuonc/nov215.06] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
|
13
|
Wang Q, Hu X, Muller F, Kim H, Mikkelsen T, Scarpace L, Lin YH, Satani N, Chang E, Olar A, Decarvalho A, Eskilsson E, Rabadan R, Iavarone A, Finocchiaro G, Nam DH, Zheng S, Sulman E, Verhaak RG. MTR-19A MACROPHAGE-/MICROGLIAL-RICH TUMOR MICROENVIRONMENT MIMICS PRONEURAL TO MESENCHYMAL TRANSITION IN GLIOBLASTOMA. Neuro Oncol 2015. [DOI: 10.1093/neuonc/nov219.19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
|
14
|
Wang Q, Ezhilarasan R, Goodman LD, Gumin J, Zheng S, Yoshihara K, Sun P, Yang J, Heffernan T, Draetta G, Aldape KD, Lang FF, Verhaak RG, Sulman EP. Abstract 4795: A novel gene fusion in glioblastoma and a radiation response methylation signature identified by genomic characterization of glioma sphere-forming cells. Cancer Res 2015. [DOI: 10.1158/1538-7445.am2015-4795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Purpose: High fidelity models of the lethal primary brain tumor glioblastoma (GBM) are essential to develop new therapies. Glioma sphere-forming cells (GSCs) are derived from surgical specimens and are thought to play important roles in tumor maintenance and treatment resistance. We performed genomic characterization of the largest reported panel of GSCs. We hypothesized that GSCs would recapitulate the genomic alterations of their GBMs of origin while identifying novel changes identifiable only in a pure tumor cell population.
Methods: All GSCs were obtained at the time of surgical resection and all analyses were conducted at early passage. We performed exome and transcriptome sequencing, DNA methylation profiling (Illumina Infinium 450K Bead Arrays) and DNA copy number determination (Affymetrix OncoScan). Radiation (RT) sensitivity was determined by clonogenic survival and in vivo survival by orthotopic xenograft.
Results: We analyzed 43 GSCs, 40 of which had tissue available from their tumors of origin. Somatically mutated genes previously described in GBM, such as TP53, EGFR, PTEN, NF1, PIK3CA and RB1, were found at similar mutation frequencies. Likewise, DNA copy number variations were similar to their matched tumor and those reported by the TCGA, with novel or more pronounced alterations, such as MYC application and QKI deletion, identified in the GSCs. GSCs were classified into TCGA GBM subtypes by expression signatures, identifying a subset of GSCs with a subtype differing from their matched tumors that correlated to decreased stromal enrichment. GSCs exhibited upregulation of self-renewal pathways, such as MYC, WNT, and NOTCH, and of stem-cell factors, such as MSI1, NESTIN, OLIG2, and SOX2, consistent with the stem-like phenotype attributed to GSCs. Transcript analyses identified the previously reported FGFR3-TACC3 and EGFR-SEPT14 gene fusions as well as a novel KIF1B-KMT2A (MLL) fusion, which was found to have been retained in the matching recurrent GBM as well as the GSC derived from the recurrence. A signature derived by the differential methylation pattern of RT sensitive vs. resistant GSCs was applied to the subset of TCGA cases that received upfront RT. Survival by methylation class in this subset was significantly different (median survival 84 vs. 61 weeks; HR 1.64 adjusting for patient age, p-value<0.008), suggesting this signature is predictive of clinical RT response.
Conclusions: Based on genomic analyses, GSCs are robust models of GBM which can be used for therapeutic development. We have identified a novel gene fusion involving MLL with a predicted driving role suggesting a new mode of gliomagenesis. A methylation signature predictive of RT response may have potential for personalizing RT treatment of GBM patients and provides insights into RT sensitivity phenotypes.
Citation Format: Qianghu Wang, Ravesanker Ezhilarasan, Lindsey D. Goodman, Joy Gumin, Siyuan Zheng, Kosuke Yoshihara, Peng Sun, Jie Yang, Tim Heffernan, Giulio Draetta, Kenneth D. Aldape, Frederick F. Lang, Roel G.W. Verhaak, Erik P. Sulman. A novel gene fusion in glioblastoma and a radiation response methylation signature identified by genomic characterization of glioma sphere-forming cells. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4795. doi:10.1158/1538-7445.AM2015-4795
Collapse
Affiliation(s)
- Qianghu Wang
- 1The University of Texas, MD Anderson Cancer Center, Houston, TX
| | | | | | - Joy Gumin
- 1The University of Texas, MD Anderson Cancer Center, Houston, TX
| | - Siyuan Zheng
- 1The University of Texas, MD Anderson Cancer Center, Houston, TX
| | - Kosuke Yoshihara
- 1The University of Texas, MD Anderson Cancer Center, Houston, TX
| | - Peng Sun
- 1The University of Texas, MD Anderson Cancer Center, Houston, TX
| | - Jie Yang
- 1The University of Texas, MD Anderson Cancer Center, Houston, TX
| | - Tim Heffernan
- 1The University of Texas, MD Anderson Cancer Center, Houston, TX
| | - Giulio Draetta
- 1The University of Texas, MD Anderson Cancer Center, Houston, TX
| | | | | | | | - Erik P. Sulman
- 1The University of Texas, MD Anderson Cancer Center, Houston, TX
| |
Collapse
|
15
|
Verhaak RG, Chang K, Kim H, Carter SL, Schultz N, Zhao F, Shen H, Laird P, Sinah R, Muzny D, Reid J, Nu J, Drummond J, Getz G, Levine DA, Wheeler DA. Abstract 4922: Patterns of tumor evolution in high grade serous ovarian carcinoma. Cancer Res 2012. [DOI: 10.1158/1538-7445.am2012-4922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
BACKGROUND High grade serous ovarian cancer (HGS-OvCa) is the fifth leading cause of cancer death amongst women in the United States and is characterized by a 25% rate of recurrence within six months after the end of treatment. To gain insight into the mechanisms used by tumor cells to evade the toxic effects of DNA damaging therapy, we genomically characterized sixteen triplets of tumor primary, tumor recurrence and normal samples using whole exome sequencing, DNA copy number arrays, methylation arrays and gene expression arrays. RESULTS Fifteen out of sixteen recurrent samples acquired both somatic mutations as well as DNA copy number alterations, and the number of novel abnormalities acquired was correlated with the time elapsed between primary and recurrence. Interestingly, nine of sixteen recurrence samples harbored only a subset of the mutations identified in the primary tumor. Similarly, these cases appeared to have lost a subset of the copy number alterations with which the primary sample originally presented, suggesting that primary and recurrent tumors were derived from an ancestral clone rather than to have evolved from the dominant clone present at diagnosis. The remaining seven recurrent samples contained all abnormalities found at time of diagnosis and are thus likely to have evolved from the dominant diagnostic clone. The time to recurrence was shorter for ‘diagnostic clone’ patients than for ‘ancestral clone’ patients, with borderline significance (likelihoodratio test p-value 0.08). Analysis of mutation allele fractions suggested a higher degree of tumor heterogeneity in primary tumor samples than in recurrent tumor samples. Recurrence was not associated with a specific mutation or copy number alteration. Tumors from patients whose interval between end of platinum therapy and recurrence was less than six months were not characterized by specific patterns of abnormalities. DISCUSSION Analysis of genomic alterations in primary and recurrent ovarian cancer tumor samples suggests that recurrences can be classified into two dominant groups: recurrences derived from an ancestral clone and recurrences originating from the same dominant clone present at time of diagnosis. Analysis of mutation allele fractions provided further insights into the clonality of primary and recurrent tumor samples. These findings shed light on the mechanism by which tumors overcome the effects of DNA damaging agents and may lead to development of therapies that specifically address the clonal origin properties of recurrent tumors.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 4922. doi:1538-7445.AM2012-4922
Collapse
Affiliation(s)
| | - Kyle Chang
- 2Baylor College of Medicine, Houston, TX
| | - Hoon Kim
- 1MD Anderson Cancer Center, Houston, TX
| | | | | | | | - Hui Shen
- 5University of South California, Los Angeles, CA
| | - Peter Laird
- 5University of South California, Los Angeles, CA
| | - Rileen Sinah
- 4Memorial Sloan-Kettering Cancer Center, New York, NY
| | | | - Jeff Reid
- 2Baylor College of Medicine, Houston, TX
| | | | | | - Gad Getz
- 3Broad Institute of Harvard and MIT, Cambridge, MA
| | | | | |
Collapse
|
16
|
Liu C, Sage JC, Miller MR, Verhaak RG, Hippenmeyer S, Vogel H, Foreman O, Bronson RT, Nishiyama A, Luo L, Zong H. Mosaic analysis with double markers reveals tumor cell of origin in glioma. Cell 2011; 146:209-21. [PMID: 21737130 PMCID: PMC3143261 DOI: 10.1016/j.cell.2011.06.014] [Citation(s) in RCA: 487] [Impact Index Per Article: 37.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2011] [Revised: 05/03/2011] [Accepted: 06/03/2011] [Indexed: 12/26/2022]
Abstract
Cancer cell of origin is difficult to identify by analyzing cells within terminal stage tumors, whose identity could be concealed by the acquired plasticity. Thus, an ideal approach to identify the cell of origin is to analyze proliferative abnormalities in distinct lineages prior to malignancy. Here, we use mosaic analysis with double markers (MADM) in mice to model gliomagenesis by initiating concurrent p53/Nf1 mutations sporadically in neural stem cells (NSCs). Surprisingly, MADM-based lineage tracing revealed significant aberrant growth prior to malignancy only in oligodendrocyte precursor cells (OPCs), but not in any other NSC-derived lineages or NSCs themselves. Upon tumor formation, phenotypic and transcriptome analyses of tumor cells revealed salient OPC features. Finally, introducing the same p53/Nf1 mutations directly into OPCs consistently led to gliomagenesis. Our findings suggest OPCs as the cell of origin in this model, even when initial mutations occur in NSCs, and highlight the importance of analyzing premalignant stages to identify the cancer cell of origin.
Collapse
Affiliation(s)
- Chong Liu
- Institute of Molecular Biology, University of Oregon, Eugene, OR97403
| | - Jonathan C. Sage
- Institute of Molecular Biology, University of Oregon, Eugene, OR97403
| | - Michael R. Miller
- Institute of Molecular Biology, University of Oregon, Eugene, OR97403
| | - Roel G.W. Verhaak
- Department of Bioinformatics and Computational Biology, MD Anderson Cancer Center, Houston, TX 77030
| | - Simon Hippenmeyer
- HHMI and Department of Biology, Stanford University, Stanford, CA94305
| | - Hannes Vogel
- Neuropathology, Stanford University School of Medicine, Stanford, CA94305
| | | | - Roderick T. Bronson
- Department of Biomedical Sciences, Tufts Cummings School of Veterinary Medicine, North Grafton, MA01536
| | - Akiko Nishiyama
- Department of Physiology and Neurobiology, University of Connecticut, Storrs, CT06269
| | - Liqun Luo
- HHMI and Department of Biology, Stanford University, Stanford, CA94305
| | - Hui Zong
- Institute of Molecular Biology, University of Oregon, Eugene, OR97403
| |
Collapse
|
17
|
Noushmehr H, Weisenberger DJ, Diefes K, Phillips HS, Pujara K, Berman BP, Pan F, Pelloski CE, Sulman EP, Bhat KP, Verhaak RG, Hoadley KA, Hayes DN, Perou CM, Schmidt HK, Ding L, Wilson RK, Van Den Berg D, Shen H, Bengtsson H, Neuvial P, Cope LM, Buckley J, Herman JG, Baylin SB, Laird PW, Aldape K. Identification of a CpG island methylator phenotype that defines a distinct subgroup of glioma. Cancer Cell 2010; 17:510-22. [PMID: 20399149 PMCID: PMC2872684 DOI: 10.1016/j.ccr.2010.03.017] [Citation(s) in RCA: 1749] [Impact Index Per Article: 124.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/08/2009] [Revised: 02/18/2010] [Accepted: 03/30/2010] [Indexed: 12/14/2022]
Abstract
We have profiled promoter DNA methylation alterations in 272 glioblastoma tumors in the context of The Cancer Genome Atlas (TCGA). We found that a distinct subset of samples displays concerted hypermethylation at a large number of loci, indicating the existence of a glioma-CpG island methylator phenotype (G-CIMP). We validated G-CIMP in a set of non-TCGA glioblastomas and low-grade gliomas. G-CIMP tumors belong to the proneural subgroup, are more prevalent among lower-grade gliomas, display distinct copy-number alterations, and are tightly associated with IDH1 somatic mutations. Patients with G-CIMP tumors are younger at the time of diagnosis and experience significantly improved outcome. These findings identify G-CIMP as a distinct subset of human gliomas on molecular and clinical grounds.
Collapse
Affiliation(s)
- Houtan Noushmehr
- USC Epigenome Center, University of Southern California, Los Angeles, CA, 90033 USA
| | | | - Kristin Diefes
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Heidi S. Phillips
- Department of Tumor Biology and Angiogenesis, Genentech, Inc., South San Francisco, California 94080, USA
| | - Kanan Pujara
- Department of Tumor Biology and Angiogenesis, Genentech, Inc., South San Francisco, California 94080, USA
| | - Benjamin P. Berman
- USC Epigenome Center, University of Southern California, Los Angeles, CA, 90033 USA
| | - Fei Pan
- USC Epigenome Center, University of Southern California, Los Angeles, CA, 90033 USA
| | - Christopher E. Pelloski
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Erik P. Sulman
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Krishna P. Bhat
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Roel G.W. Verhaak
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts 02142, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA
| | - Katherine A. Hoadley
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - D. Neil Hayes
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Charles M. Perou
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Heather K. Schmidt
- The Genome Center at Washington University, Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| | - Li Ding
- The Genome Center at Washington University, Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| | - Richard K. Wilson
- The Genome Center at Washington University, Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| | - David Van Den Berg
- USC Epigenome Center, University of Southern California, Los Angeles, CA, 90033 USA
| | - Hui Shen
- USC Epigenome Center, University of Southern California, Los Angeles, CA, 90033 USA
| | - Henrik Bengtsson
- Department of Statistics, University of California, Berkeley, California, USA
| | - Pierre Neuvial
- Department of Statistics, University of California, Berkeley, California, USA
| | - Leslie M. Cope
- Department on Oncology, Johns Hopkins School of Medicine, Baltimore, MD, 21231, USA
| | - Jonathan Buckley
- USC Epigenome Center, University of Southern California, Los Angeles, CA, 90033 USA
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - James G. Herman
- Department on Oncology, Johns Hopkins School of Medicine, Baltimore, MD, 21231, USA
| | - Stephen B. Baylin
- Department on Oncology, Johns Hopkins School of Medicine, Baltimore, MD, 21231, USA
| | - Peter W. Laird
- USC Epigenome Center, University of Southern California, Los Angeles, CA, 90033 USA
- To whom correspondence should be addressed. , FAX: (323) 442-7880
| | - Kenneth Aldape
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | | |
Collapse
|
18
|
Steidl U, Steidl C, Ebralidze A, Chapuy B, Han HJ, Will B, Rosenbauer F, Becker A, Wagner K, Koschmieder S, Kobayashi S, Costa DB, Schulz T, O’Brien KB, Verhaak RG, Delwel R, Haase D, Trümper L, Krauter J, Kohwi-Shigematsu T, Griesinger F, Tenen DG. A distal single nucleotide polymorphism alters long-range regulation of the PU.1 gene in acute myeloid leukemia. J Clin Invest 2007; 117:2611-20. [PMID: 17694175 PMCID: PMC1937499 DOI: 10.1172/jci30525] [Citation(s) in RCA: 97] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2006] [Accepted: 05/14/2007] [Indexed: 01/20/2023] Open
Abstract
Targeted disruption of a highly conserved distal enhancer reduces expression of the PU.1 transcription factor by 80% and leads to acute myeloid leukemia (AML) with frequent cytogenetic aberrations in mice. Here we identify a SNP within this element in humans that is more frequent in AML with a complex karyotype, leads to decreased enhancer activity, and reduces PU.1 expression in myeloid progenitors in a development-dependent manner. This SNP inhibits binding of the chromatin-remodeling transcriptional regulator special AT-rich sequence binding protein 1 (SATB1). Overexpression of SATB1 increased PU.1 expression, and siRNA inhibition of SATB1 downregulated PU.1 expression. Targeted disruption of the distal enhancer led to a loss of regulation of PU.1 by SATB1. Interestingly, disruption of SATB1 in mice led to a selective decrease of PU.1 RNA in specific progenitor types (granulocyte-macrophage and megakaryocyte-erythrocyte progenitors) and a similar effect was observed in AML samples harboring this SNP. Thus we have identified a SNP within a distal enhancer that is associated with a subtype of leukemia and exerts a deleterious effect through remote transcriptional dysregulation in specific progenitor subtypes.
Collapse
MESH Headings
- Animals
- Base Sequence
- Cell Adhesion Molecules, Neuronal/genetics
- Cell Adhesion Molecules, Neuronal/metabolism
- Cell Line, Tumor
- Down-Regulation
- Gene Expression Regulation, Neoplastic
- Genome, Human/genetics
- Humans
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/metabolism
- Mice
- Mice, Knockout
- Molecular Sequence Data
- Polymorphism, Single Nucleotide/genetics
- Proto-Oncogene Proteins/deficiency
- Proto-Oncogene Proteins/genetics
- Proto-Oncogene Proteins/metabolism
- Receptors, Lymphocyte Homing/genetics
- Receptors, Lymphocyte Homing/metabolism
- Stem Cells/metabolism
- Trans-Activators/deficiency
- Trans-Activators/genetics
- Trans-Activators/metabolism
Collapse
Affiliation(s)
- Ulrich Steidl
- Harvard Institutes of Medicine, Harvard Medical School, and Harvard Stem Cell Institute, Boston, Massachusetts, USA.
Department of Hematology and Oncology, Georg-August University of Göttingen, Goettingen, Germany.
Department of Pathology, British Columbia Cancer Agency, Vancouver, British Columbia, Canada.
Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
Department of Cell Biology, University of Freiburg, Freiburg, Germany.
Max Delbrück Center for Molecular Medicine, Berlin, Germany.
Department of Hematology, Hemostasis and Oncology, Hannover Medical School, Hannover, Germany.
Department of Medicine, Hematology and Oncology, University Hospital Münster, Muenster, Germany.
Department of Hematology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Christian Steidl
- Harvard Institutes of Medicine, Harvard Medical School, and Harvard Stem Cell Institute, Boston, Massachusetts, USA.
Department of Hematology and Oncology, Georg-August University of Göttingen, Goettingen, Germany.
Department of Pathology, British Columbia Cancer Agency, Vancouver, British Columbia, Canada.
Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
Department of Cell Biology, University of Freiburg, Freiburg, Germany.
Max Delbrück Center for Molecular Medicine, Berlin, Germany.
Department of Hematology, Hemostasis and Oncology, Hannover Medical School, Hannover, Germany.
Department of Medicine, Hematology and Oncology, University Hospital Münster, Muenster, Germany.
Department of Hematology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Alexander Ebralidze
- Harvard Institutes of Medicine, Harvard Medical School, and Harvard Stem Cell Institute, Boston, Massachusetts, USA.
Department of Hematology and Oncology, Georg-August University of Göttingen, Goettingen, Germany.
Department of Pathology, British Columbia Cancer Agency, Vancouver, British Columbia, Canada.
Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
Department of Cell Biology, University of Freiburg, Freiburg, Germany.
Max Delbrück Center for Molecular Medicine, Berlin, Germany.
Department of Hematology, Hemostasis and Oncology, Hannover Medical School, Hannover, Germany.
Department of Medicine, Hematology and Oncology, University Hospital Münster, Muenster, Germany.
Department of Hematology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Björn Chapuy
- Harvard Institutes of Medicine, Harvard Medical School, and Harvard Stem Cell Institute, Boston, Massachusetts, USA.
Department of Hematology and Oncology, Georg-August University of Göttingen, Goettingen, Germany.
Department of Pathology, British Columbia Cancer Agency, Vancouver, British Columbia, Canada.
Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
Department of Cell Biology, University of Freiburg, Freiburg, Germany.
Max Delbrück Center for Molecular Medicine, Berlin, Germany.
Department of Hematology, Hemostasis and Oncology, Hannover Medical School, Hannover, Germany.
Department of Medicine, Hematology and Oncology, University Hospital Münster, Muenster, Germany.
Department of Hematology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Hye-Jung Han
- Harvard Institutes of Medicine, Harvard Medical School, and Harvard Stem Cell Institute, Boston, Massachusetts, USA.
Department of Hematology and Oncology, Georg-August University of Göttingen, Goettingen, Germany.
Department of Pathology, British Columbia Cancer Agency, Vancouver, British Columbia, Canada.
Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
Department of Cell Biology, University of Freiburg, Freiburg, Germany.
Max Delbrück Center for Molecular Medicine, Berlin, Germany.
Department of Hematology, Hemostasis and Oncology, Hannover Medical School, Hannover, Germany.
Department of Medicine, Hematology and Oncology, University Hospital Münster, Muenster, Germany.
Department of Hematology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Britta Will
- Harvard Institutes of Medicine, Harvard Medical School, and Harvard Stem Cell Institute, Boston, Massachusetts, USA.
Department of Hematology and Oncology, Georg-August University of Göttingen, Goettingen, Germany.
Department of Pathology, British Columbia Cancer Agency, Vancouver, British Columbia, Canada.
Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
Department of Cell Biology, University of Freiburg, Freiburg, Germany.
Max Delbrück Center for Molecular Medicine, Berlin, Germany.
Department of Hematology, Hemostasis and Oncology, Hannover Medical School, Hannover, Germany.
Department of Medicine, Hematology and Oncology, University Hospital Münster, Muenster, Germany.
Department of Hematology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Frank Rosenbauer
- Harvard Institutes of Medicine, Harvard Medical School, and Harvard Stem Cell Institute, Boston, Massachusetts, USA.
Department of Hematology and Oncology, Georg-August University of Göttingen, Goettingen, Germany.
Department of Pathology, British Columbia Cancer Agency, Vancouver, British Columbia, Canada.
Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
Department of Cell Biology, University of Freiburg, Freiburg, Germany.
Max Delbrück Center for Molecular Medicine, Berlin, Germany.
Department of Hematology, Hemostasis and Oncology, Hannover Medical School, Hannover, Germany.
Department of Medicine, Hematology and Oncology, University Hospital Münster, Muenster, Germany.
Department of Hematology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Annegret Becker
- Harvard Institutes of Medicine, Harvard Medical School, and Harvard Stem Cell Institute, Boston, Massachusetts, USA.
Department of Hematology and Oncology, Georg-August University of Göttingen, Goettingen, Germany.
Department of Pathology, British Columbia Cancer Agency, Vancouver, British Columbia, Canada.
Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
Department of Cell Biology, University of Freiburg, Freiburg, Germany.
Max Delbrück Center for Molecular Medicine, Berlin, Germany.
Department of Hematology, Hemostasis and Oncology, Hannover Medical School, Hannover, Germany.
Department of Medicine, Hematology and Oncology, University Hospital Münster, Muenster, Germany.
Department of Hematology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Katharina Wagner
- Harvard Institutes of Medicine, Harvard Medical School, and Harvard Stem Cell Institute, Boston, Massachusetts, USA.
Department of Hematology and Oncology, Georg-August University of Göttingen, Goettingen, Germany.
Department of Pathology, British Columbia Cancer Agency, Vancouver, British Columbia, Canada.
Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
Department of Cell Biology, University of Freiburg, Freiburg, Germany.
Max Delbrück Center for Molecular Medicine, Berlin, Germany.
Department of Hematology, Hemostasis and Oncology, Hannover Medical School, Hannover, Germany.
Department of Medicine, Hematology and Oncology, University Hospital Münster, Muenster, Germany.
Department of Hematology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Steffen Koschmieder
- Harvard Institutes of Medicine, Harvard Medical School, and Harvard Stem Cell Institute, Boston, Massachusetts, USA.
Department of Hematology and Oncology, Georg-August University of Göttingen, Goettingen, Germany.
Department of Pathology, British Columbia Cancer Agency, Vancouver, British Columbia, Canada.
Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
Department of Cell Biology, University of Freiburg, Freiburg, Germany.
Max Delbrück Center for Molecular Medicine, Berlin, Germany.
Department of Hematology, Hemostasis and Oncology, Hannover Medical School, Hannover, Germany.
Department of Medicine, Hematology and Oncology, University Hospital Münster, Muenster, Germany.
Department of Hematology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Susumu Kobayashi
- Harvard Institutes of Medicine, Harvard Medical School, and Harvard Stem Cell Institute, Boston, Massachusetts, USA.
Department of Hematology and Oncology, Georg-August University of Göttingen, Goettingen, Germany.
Department of Pathology, British Columbia Cancer Agency, Vancouver, British Columbia, Canada.
Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
Department of Cell Biology, University of Freiburg, Freiburg, Germany.
Max Delbrück Center for Molecular Medicine, Berlin, Germany.
Department of Hematology, Hemostasis and Oncology, Hannover Medical School, Hannover, Germany.
Department of Medicine, Hematology and Oncology, University Hospital Münster, Muenster, Germany.
Department of Hematology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Daniel B. Costa
- Harvard Institutes of Medicine, Harvard Medical School, and Harvard Stem Cell Institute, Boston, Massachusetts, USA.
Department of Hematology and Oncology, Georg-August University of Göttingen, Goettingen, Germany.
Department of Pathology, British Columbia Cancer Agency, Vancouver, British Columbia, Canada.
Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
Department of Cell Biology, University of Freiburg, Freiburg, Germany.
Max Delbrück Center for Molecular Medicine, Berlin, Germany.
Department of Hematology, Hemostasis and Oncology, Hannover Medical School, Hannover, Germany.
Department of Medicine, Hematology and Oncology, University Hospital Münster, Muenster, Germany.
Department of Hematology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Thomas Schulz
- Harvard Institutes of Medicine, Harvard Medical School, and Harvard Stem Cell Institute, Boston, Massachusetts, USA.
Department of Hematology and Oncology, Georg-August University of Göttingen, Goettingen, Germany.
Department of Pathology, British Columbia Cancer Agency, Vancouver, British Columbia, Canada.
Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
Department of Cell Biology, University of Freiburg, Freiburg, Germany.
Max Delbrück Center for Molecular Medicine, Berlin, Germany.
Department of Hematology, Hemostasis and Oncology, Hannover Medical School, Hannover, Germany.
Department of Medicine, Hematology and Oncology, University Hospital Münster, Muenster, Germany.
Department of Hematology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Karen B. O’Brien
- Harvard Institutes of Medicine, Harvard Medical School, and Harvard Stem Cell Institute, Boston, Massachusetts, USA.
Department of Hematology and Oncology, Georg-August University of Göttingen, Goettingen, Germany.
Department of Pathology, British Columbia Cancer Agency, Vancouver, British Columbia, Canada.
Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
Department of Cell Biology, University of Freiburg, Freiburg, Germany.
Max Delbrück Center for Molecular Medicine, Berlin, Germany.
Department of Hematology, Hemostasis and Oncology, Hannover Medical School, Hannover, Germany.
Department of Medicine, Hematology and Oncology, University Hospital Münster, Muenster, Germany.
Department of Hematology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Roel G.W. Verhaak
- Harvard Institutes of Medicine, Harvard Medical School, and Harvard Stem Cell Institute, Boston, Massachusetts, USA.
Department of Hematology and Oncology, Georg-August University of Göttingen, Goettingen, Germany.
Department of Pathology, British Columbia Cancer Agency, Vancouver, British Columbia, Canada.
Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
Department of Cell Biology, University of Freiburg, Freiburg, Germany.
Max Delbrück Center for Molecular Medicine, Berlin, Germany.
Department of Hematology, Hemostasis and Oncology, Hannover Medical School, Hannover, Germany.
Department of Medicine, Hematology and Oncology, University Hospital Münster, Muenster, Germany.
Department of Hematology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Ruud Delwel
- Harvard Institutes of Medicine, Harvard Medical School, and Harvard Stem Cell Institute, Boston, Massachusetts, USA.
Department of Hematology and Oncology, Georg-August University of Göttingen, Goettingen, Germany.
Department of Pathology, British Columbia Cancer Agency, Vancouver, British Columbia, Canada.
Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
Department of Cell Biology, University of Freiburg, Freiburg, Germany.
Max Delbrück Center for Molecular Medicine, Berlin, Germany.
Department of Hematology, Hemostasis and Oncology, Hannover Medical School, Hannover, Germany.
Department of Medicine, Hematology and Oncology, University Hospital Münster, Muenster, Germany.
Department of Hematology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Detlef Haase
- Harvard Institutes of Medicine, Harvard Medical School, and Harvard Stem Cell Institute, Boston, Massachusetts, USA.
Department of Hematology and Oncology, Georg-August University of Göttingen, Goettingen, Germany.
Department of Pathology, British Columbia Cancer Agency, Vancouver, British Columbia, Canada.
Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
Department of Cell Biology, University of Freiburg, Freiburg, Germany.
Max Delbrück Center for Molecular Medicine, Berlin, Germany.
Department of Hematology, Hemostasis and Oncology, Hannover Medical School, Hannover, Germany.
Department of Medicine, Hematology and Oncology, University Hospital Münster, Muenster, Germany.
Department of Hematology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Lorenz Trümper
- Harvard Institutes of Medicine, Harvard Medical School, and Harvard Stem Cell Institute, Boston, Massachusetts, USA.
Department of Hematology and Oncology, Georg-August University of Göttingen, Goettingen, Germany.
Department of Pathology, British Columbia Cancer Agency, Vancouver, British Columbia, Canada.
Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
Department of Cell Biology, University of Freiburg, Freiburg, Germany.
Max Delbrück Center for Molecular Medicine, Berlin, Germany.
Department of Hematology, Hemostasis and Oncology, Hannover Medical School, Hannover, Germany.
Department of Medicine, Hematology and Oncology, University Hospital Münster, Muenster, Germany.
Department of Hematology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Jürgen Krauter
- Harvard Institutes of Medicine, Harvard Medical School, and Harvard Stem Cell Institute, Boston, Massachusetts, USA.
Department of Hematology and Oncology, Georg-August University of Göttingen, Goettingen, Germany.
Department of Pathology, British Columbia Cancer Agency, Vancouver, British Columbia, Canada.
Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
Department of Cell Biology, University of Freiburg, Freiburg, Germany.
Max Delbrück Center for Molecular Medicine, Berlin, Germany.
Department of Hematology, Hemostasis and Oncology, Hannover Medical School, Hannover, Germany.
Department of Medicine, Hematology and Oncology, University Hospital Münster, Muenster, Germany.
Department of Hematology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Terumi Kohwi-Shigematsu
- Harvard Institutes of Medicine, Harvard Medical School, and Harvard Stem Cell Institute, Boston, Massachusetts, USA.
Department of Hematology and Oncology, Georg-August University of Göttingen, Goettingen, Germany.
Department of Pathology, British Columbia Cancer Agency, Vancouver, British Columbia, Canada.
Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
Department of Cell Biology, University of Freiburg, Freiburg, Germany.
Max Delbrück Center for Molecular Medicine, Berlin, Germany.
Department of Hematology, Hemostasis and Oncology, Hannover Medical School, Hannover, Germany.
Department of Medicine, Hematology and Oncology, University Hospital Münster, Muenster, Germany.
Department of Hematology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Frank Griesinger
- Harvard Institutes of Medicine, Harvard Medical School, and Harvard Stem Cell Institute, Boston, Massachusetts, USA.
Department of Hematology and Oncology, Georg-August University of Göttingen, Goettingen, Germany.
Department of Pathology, British Columbia Cancer Agency, Vancouver, British Columbia, Canada.
Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
Department of Cell Biology, University of Freiburg, Freiburg, Germany.
Max Delbrück Center for Molecular Medicine, Berlin, Germany.
Department of Hematology, Hemostasis and Oncology, Hannover Medical School, Hannover, Germany.
Department of Medicine, Hematology and Oncology, University Hospital Münster, Muenster, Germany.
Department of Hematology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Daniel G. Tenen
- Harvard Institutes of Medicine, Harvard Medical School, and Harvard Stem Cell Institute, Boston, Massachusetts, USA.
Department of Hematology and Oncology, Georg-August University of Göttingen, Goettingen, Germany.
Department of Pathology, British Columbia Cancer Agency, Vancouver, British Columbia, Canada.
Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
Department of Cell Biology, University of Freiburg, Freiburg, Germany.
Max Delbrück Center for Molecular Medicine, Berlin, Germany.
Department of Hematology, Hemostasis and Oncology, Hannover Medical School, Hannover, Germany.
Department of Medicine, Hematology and Oncology, University Hospital Münster, Muenster, Germany.
Department of Hematology, Erasmus University Medical Center, Rotterdam, The Netherlands
| |
Collapse
|