1
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El Ghamrasni S, Quevedo R, Hawley J, Mazrooei P, Hanna Y, Cirlan I, Zhu H, Bruce JP, Oldfield LE, Yang SYC, Guilhamon P, Reimand J, Cescon DW, Done SJ, Lupien M, Pugh TJ. Mutations in Noncoding Cis-Regulatory Elements Reveal Cancer Driver Cistromes in Luminal Breast Cancer. Mol Cancer Res 2022; 20:102-113. [PMID: 34556523 PMCID: PMC9398156 DOI: 10.1158/1541-7786.mcr-21-0471] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 07/31/2021] [Accepted: 09/17/2021] [Indexed: 01/07/2023]
Abstract
Whole-genome sequencing of primary breast tumors enabled the identification of cancer driver genes and noncoding cancer driver plexuses from somatic mutations. However, differentiating driver from passenger events among noncoding genetic variants remains a challenge. Herein, we reveal cancer-driver cis-regulatory elements linked to transcription factors previously shown to be involved in development of luminal breast cancers by defining a tumor-enriched catalogue of approximately 100,000 unique cis-regulatory elements from 26 primary luminal estrogen receptor (ER)+ progesterone receptor (PR)+ breast tumors. Integrating this catalog with somatic mutations from 350 publicly available breast tumor whole genomes, we uncovered cancer driver cistromes, defined as the sum of binding sites for a transcription factor, for ten transcription factors in luminal breast cancer such as FOXA1 and ER, nine of which are essential for growth in breast cancer with four exclusive to the luminal subtype. Collectively, we present a strategy to find cancer driver cistromes relying on quantifying the enrichment of noncoding mutations over cis-regulatory elements concatenated into a functional unit. IMPLICATIONS: Mapping the accessible chromatin of luminal breast cancer led to discovery of an accumulation of mutations within cistromes of transcription factors essential to luminal breast cancer. This demonstrates coopting of regulatory networks to drive cancer and provides a framework to derive insight into the noncoding space of cancer.
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Affiliation(s)
- Samah El Ghamrasni
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Rene Quevedo
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - James Hawley
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Parisa Mazrooei
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Genentech, South San Francisco, California
| | - Youstina Hanna
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Iulia Cirlan
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Helen Zhu
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Vector Institute, Toronto, Ontario, Canada
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Jeff P Bruce
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Leslie E Oldfield
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - S Y Cindy Yang
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Paul Guilhamon
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
- Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Jüri Reimand
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Dave W Cescon
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Susan J Done
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Department of Laboratory Medicine & Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Mathieu Lupien
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Trevor J Pugh
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
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2
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Sachamitr P, Ho JC, Ciamponi FE, Ba-Alawi W, Coutinho FJ, Guilhamon P, Kushida MM, Cavalli FMG, Lee L, Rastegar N, Vu V, Sánchez-Osuna M, Coulombe-Huntington J, Kanshin E, Whetstone H, Durand M, Thibault P, Hart K, Mangos M, Veyhl J, Chen W, Tran N, Duong BC, Aman AM, Che X, Lan X, Whitley O, Zaslaver O, Barsyte-Lovejoy D, Richards LM, Restall I, Caudy A, Röst HL, Bonday ZQ, Bernstein M, Das S, Cusimano MD, Spears J, Bader GD, Pugh TJ, Tyers M, Lupien M, Haibe-Kains B, Artee Luchman H, Weiss S, Massirer KB, Prinos P, Arrowsmith CH, Dirks PB. PRMT5 inhibition disrupts splicing and stemness in glioblastoma. Nat Commun 2021; 12:979. [PMID: 33579912 PMCID: PMC7881162 DOI: 10.1038/s41467-021-21204-5] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [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: 07/22/2019] [Accepted: 01/13/2021] [Indexed: 12/14/2022] Open
Abstract
Glioblastoma (GBM) is a deadly cancer in which cancer stem cells (CSCs) sustain tumor growth and contribute to therapeutic resistance. Protein arginine methyltransferase 5 (PRMT5) has recently emerged as a promising target in GBM. Using two orthogonal-acting inhibitors of PRMT5 (GSK591 or LLY-283), we show that pharmacological inhibition of PRMT5 suppresses the growth of a cohort of 46 patient-derived GBM stem cell cultures, with the proneural subtype showing greater sensitivity. We show that PRMT5 inhibition causes widespread disruption of splicing across the transcriptome, particularly affecting cell cycle gene products. We identify a GBM splicing signature that correlates with the degree of response to PRMT5 inhibition. Importantly, we demonstrate that LLY-283 is brain-penetrant and significantly prolongs the survival of mice with orthotopic patient-derived xenografts. Collectively, our findings provide a rationale for the clinical development of brain penetrant PRMT5 inhibitors as treatment for GBM.
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Affiliation(s)
- Patty Sachamitr
- Developmental and Stem Cell Biology Program and Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
- Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada
| | - Jolene C Ho
- Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada
| | - Felipe E Ciamponi
- Center for Molecular Biology and Genetic Engineering, University of Campinas (UNICAMP), Campinas, Brazil
- The Structural Genomics Consortium, University of Campinas (UNICAMP), Campinas, Brazil
| | - Wail Ba-Alawi
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Fiona J Coutinho
- Developmental and Stem Cell Biology Program and Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - Paul Guilhamon
- Developmental and Stem Cell Biology Program and Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Michelle M Kushida
- Developmental and Stem Cell Biology Program and Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - Florence M G Cavalli
- Developmental and Stem Cell Biology Program and Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - Lilian Lee
- Developmental and Stem Cell Biology Program and Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - Naghmeh Rastegar
- Developmental and Stem Cell Biology Program and Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - Victoria Vu
- Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - María Sánchez-Osuna
- Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, QC, Canada
| | | | - Evgeny Kanshin
- Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, QC, Canada
| | - Heather Whetstone
- Developmental and Stem Cell Biology Program and Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - Mathieu Durand
- RNomics Platform, Université de Sherbrooke, Sherbrooke, QC, Canada
| | | | - Kirsten Hart
- Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Maria Mangos
- Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada
| | - Joseph Veyhl
- Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada
| | - Wenjun Chen
- Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada
| | - Nhat Tran
- Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada
| | - Bang-Chi Duong
- Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada
| | - Ahmed M Aman
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Xinghui Che
- Developmental and Stem Cell Biology Program and Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - Xiaoyang Lan
- Developmental and Stem Cell Biology Program and Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - Owen Whitley
- The Donnelly Centre, University of Toronto, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Olga Zaslaver
- The Donnelly Centre, University of Toronto, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Dalia Barsyte-Lovejoy
- Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, Canada
| | - Laura M Richards
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Ian Restall
- Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Department of Cell Biology and Anatomy, University of Calgary, Calgary, AB, Canada
| | - Amy Caudy
- The Donnelly Centre, University of Toronto, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- Maple Flavored Solutions, LLC, Stony Brook, NY, USA
| | - Hannes L Röst
- The Donnelly Centre, University of Toronto, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | | | - Mark Bernstein
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, ON, Canada
- Division of Neurosurgery, Toronto Western Hospital, University Health Network, Toronto, ON, Canada
| | - Sunit Das
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, ON, Canada
- Division of Neurosurgery, Department of Surgery, St. Michael's Hospital, Toronto, ON, Canada
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - Michael D Cusimano
- Division of Neurosurgery, Department of Surgery, St. Michael's Hospital, Toronto, ON, Canada
| | - Julian Spears
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, ON, Canada
- Department of Medical Imaging, St. Michael's Hospital, University of Toronto, Toronto, ON, Canada
| | - Gary D Bader
- The Donnelly Centre, University of Toronto, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Trevor J Pugh
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Mike Tyers
- Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, QC, Canada
| | - Mathieu Lupien
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Benjamin Haibe-Kains
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Ontario Institute for Cancer Research, Toronto, ON, Canada
- Department of Computer Science, University of Toronto, Toronto, ON, Canada
- Vector Institute, Toronto, ON, Canada
| | - H Artee Luchman
- Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Department of Cell Biology and Anatomy, University of Calgary, Calgary, AB, Canada
- Clark H. Smith Brain Tumor Centre, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Samuel Weiss
- Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Department of Cell Biology and Anatomy, University of Calgary, Calgary, AB, Canada
- Clark H. Smith Brain Tumor Centre, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Katlin B Massirer
- Center for Molecular Biology and Genetic Engineering, University of Campinas (UNICAMP), Campinas, Brazil
- The Structural Genomics Consortium, University of Campinas (UNICAMP), Campinas, Brazil
| | - Panagiotis Prinos
- Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada.
| | - Cheryl H Arrowsmith
- Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada.
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.
| | - Peter B Dirks
- Developmental and Stem Cell Biology Program and Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, ON, Canada.
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, ON, Canada.
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada.
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada.
- Division of Neurosurgery, The Hospital for Sick Children, Toronto, ON, Canada.
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3
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Richards LM, Whitley OKN, MacLeod G, Cavalli FMG, Coutinho FJ, Jaramillo JE, Svergun N, Riverin M, Croucher DC, Kushida M, Yu K, Guilhamon P, Rastegar N, Ahmadi M, Bhatti JK, Bozek DA, Li N, Lee L, Che C, Luis E, Park NI, Xu Z, Ketela T, Moore RA, Marra MA, Spears J, Cusimano MD, Das S, Bernstein M, Haibe-Kains B, Lupien M, Luchman HA, Weiss S, Angers S, Dirks PB, Bader GD, Pugh TJ. Gradient of Developmental and Injury Response transcriptional states defines functional vulnerabilities underpinning glioblastoma heterogeneity. Nat Cancer 2021; 2:157-173. [PMID: 35122077 DOI: 10.1038/s43018-020-00154-9] [Citation(s) in RCA: 102] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 11/16/2020] [Indexed: 12/27/2022]
Abstract
Glioblastomas harbor diverse cell populations, including rare glioblastoma stem cells (GSCs) that drive tumorigenesis. To characterize functional diversity within this population, we performed single-cell RNA sequencing on >69,000 GSCs cultured from the tumors of 26 patients. We observed a high degree of inter- and intra-GSC transcriptional heterogeneity that could not be fully explained by DNA somatic alterations. Instead, we found that GSCs mapped along a transcriptional gradient spanning two cellular states reminiscent of normal neural development and inflammatory wound response. Genome-wide CRISPR-Cas9 dropout screens independently recapitulated this observation, with each state characterized by unique essential genes. Further single-cell RNA sequencing of >56,000 malignant cells from primary tumors found that the majority organize along an orthogonal astrocyte maturation gradient yet retain expression of founder GSC transcriptional programs. We propose that glioblastomas grow out of a fundamental GSC-based neural wound response transcriptional program, which is a promising target for new therapy development.
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Affiliation(s)
- Laura M Richards
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Owen K N Whitley
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Graham MacLeod
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada
| | - Florence M G Cavalli
- Developmental and Stem Cell Biology Program and Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Fiona J Coutinho
- Developmental and Stem Cell Biology Program and Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Julia E Jaramillo
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Developmental and Stem Cell Biology Program and Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Nataliia Svergun
- Developmental and Stem Cell Biology Program and Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Mazdak Riverin
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Danielle C Croucher
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Michelle Kushida
- Developmental and Stem Cell Biology Program and Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Kenny Yu
- Division of Neurosurgery, St. Michael's Hospital, Toronto, Ontario, Canada
| | - Paul Guilhamon
- Developmental and Stem Cell Biology Program and Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Naghmeh Rastegar
- Developmental and Stem Cell Biology Program and Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Moloud Ahmadi
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada
| | - Jasmine K Bhatti
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada
| | - Danielle A Bozek
- Department of Cell Biology and Anatomy, University of Calgary, Calgary, Alberta, Canada
- Arnie Charbonneau Cancer Institute and Hotchkiss Brain Institute, University of Calgary, Calgary, Alberta, Canada
| | - Naijin Li
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Developmental and Stem Cell Biology Program and Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Lilian Lee
- Developmental and Stem Cell Biology Program and Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Clare Che
- Developmental and Stem Cell Biology Program and Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Erika Luis
- Developmental and Stem Cell Biology Program and Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Nicole I Park
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Zhiyu Xu
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Troy Ketela
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Richard A Moore
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - Marco A Marra
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer, Vancouver, British Columbia, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Julian Spears
- Division of Neurosurgery, St. Michael's Hospital, Toronto, Ontario, Canada
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, Ontario, Canada
| | - Michael D Cusimano
- Division of Neurosurgery, St. Michael's Hospital, Toronto, Ontario, Canada
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, Ontario, Canada
| | - Sunit Das
- Developmental and Stem Cell Biology Program and Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
- Division of Neurosurgery, St. Michael's Hospital, Toronto, Ontario, Canada
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, Ontario, Canada
| | - Mark Bernstein
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, Ontario, Canada
- Division of Neurosurgery, Toronto Western Hospital, University Health Network, Toronto, Ontario, Canada
| | - Benjamin Haibe-Kains
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
- Vector Institute for Artificial Intelligence, Toronto, Ontario, Canada
| | - Mathieu Lupien
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - H Artee Luchman
- Department of Cell Biology and Anatomy, University of Calgary, Calgary, Alberta, Canada
- Arnie Charbonneau Cancer Institute and Hotchkiss Brain Institute, University of Calgary, Calgary, Alberta, Canada
| | - Samuel Weiss
- Department of Cell Biology and Anatomy, University of Calgary, Calgary, Alberta, Canada
- Arnie Charbonneau Cancer Institute and Hotchkiss Brain Institute, University of Calgary, Calgary, Alberta, Canada
| | - Stephane Angers
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Peter B Dirks
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.
- Developmental and Stem Cell Biology Program and Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada.
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, Ontario, Canada.
| | - Gary D Bader
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.
- The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada.
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada.
| | - Trevor J Pugh
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada.
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4
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Guilhamon P, Chesnelong C, Kushida MM, Nikolic A, Singhal D, MacLeod G, Madani Tonekaboni SA, Cavalli FM, Arlidge C, Rajakulendran N, Rastegar N, Hao X, Hassam R, Smith LJ, Whetstone H, Coutinho FJ, Nadorp B, Ellestad KI, Luchman HA, Chan JAW, Shoichet MS, Taylor MD, Haibe-Kains B, Weiss S, Angers S, Gallo M, Dirks PB, Lupien M. Single-cell chromatin accessibility profiling of glioblastoma identifies an invasive cancer stem cell population associated with lower survival. eLife 2021; 10:64090. [PMID: 33427645 PMCID: PMC7847307 DOI: 10.7554/elife.64090] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Accepted: 01/08/2021] [Indexed: 01/22/2023] Open
Abstract
Chromatin accessibility discriminates stem from mature cell populations, enabling the identification of primitive stem-like cells in primary tumors, such as glioblastoma (GBM) where self-renewing cells driving cancer progression and recurrence are prime targets for therapeutic intervention. We show, using single-cell chromatin accessibility, that primary human GBMs harbor a heterogeneous self-renewing population whose diversity is captured in patient-derived glioblastoma stem cells (GSCs). In-depth characterization of chromatin accessibility in GSCs identifies three GSC states: Reactive, Constructive, and Invasive, each governed by uniquely essential transcription factors and present within GBMs in varying proportions. Orthotopic xenografts reveal that GSC states associate with survival, and identify an invasive GSC signature predictive of low patient survival, in line with the higher invasive properties of Invasive state GSCs compared to Reactive and Constructive GSCs as shown by in vitro and in vivo assays. Our chromatin-driven characterization of GSC states improves prognostic precision and identifies dependencies to guide combination therapies.
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Affiliation(s)
- Paul Guilhamon
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada.,Developmental and Stem Cell Biology Program and Arthur and Sonia Labatt Brain tumor Research Centre, The Hospital for Sick Children, Toronto, Canada
| | - Charles Chesnelong
- Developmental and Stem Cell Biology Program and Arthur and Sonia Labatt Brain tumor Research Centre, The Hospital for Sick Children, Toronto, Canada
| | - Michelle M Kushida
- Developmental and Stem Cell Biology Program and Arthur and Sonia Labatt Brain tumor Research Centre, The Hospital for Sick Children, Toronto, Canada
| | - Ana Nikolic
- Clark Smith Brain Tumour Centre, Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, Canada.,Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Canada.,Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - Divya Singhal
- Clark Smith Brain Tumour Centre, Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, Canada.,Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Canada.,Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - Graham MacLeod
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Canada
| | - Seyed Ali Madani Tonekaboni
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Canada
| | - Florence Mg Cavalli
- Developmental and Stem Cell Biology Program and Arthur and Sonia Labatt Brain tumor Research Centre, The Hospital for Sick Children, Toronto, Canada
| | | | | | - Naghmeh Rastegar
- Developmental and Stem Cell Biology Program and Arthur and Sonia Labatt Brain tumor Research Centre, The Hospital for Sick Children, Toronto, Canada
| | - Xiaoguang Hao
- Clark Smith Brain Tumour Centre, Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, Canada.,Hotchkiss Brain Institute, University of Calgary, Calgary, Canada.,Department of Cell Biology & Anatomy, University of Calgary, Calgary, Canada
| | - Rozina Hassam
- Clark Smith Brain Tumour Centre, Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, Canada.,Hotchkiss Brain Institute, University of Calgary, Calgary, Canada.,Department of Cell Biology & Anatomy, University of Calgary, Calgary, Canada
| | - Laura J Smith
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Canada
| | - Heather Whetstone
- Developmental and Stem Cell Biology Program and Arthur and Sonia Labatt Brain tumor Research Centre, The Hospital for Sick Children, Toronto, Canada
| | - Fiona J Coutinho
- Developmental and Stem Cell Biology Program and Arthur and Sonia Labatt Brain tumor Research Centre, The Hospital for Sick Children, Toronto, Canada
| | - Bettina Nadorp
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Katrina I Ellestad
- Clark Smith Brain Tumour Centre, Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, Canada.,Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Canada
| | - H Artee Luchman
- Clark Smith Brain Tumour Centre, Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, Canada.,Hotchkiss Brain Institute, University of Calgary, Calgary, Canada.,Department of Cell Biology & Anatomy, University of Calgary, Calgary, Canada
| | - Jennifer Ai-Wen Chan
- Clark Smith Brain Tumour Centre, Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, Canada.,Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Canada.,Department of Pathology and Laboratory Medicine, University of Calgary, Calgary, Canada
| | - Molly S Shoichet
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Canada
| | - Michael D Taylor
- Developmental and Stem Cell Biology Program and Arthur and Sonia Labatt Brain tumor Research Centre, The Hospital for Sick Children, Toronto, Canada.,Division of Neurosurgery, University of Toronto, Toronto, Canada.,Departments of Molecular Genetics and Surgery, University of Toronto, Toronto, Canada
| | - Benjamin Haibe-Kains
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Canada.,Department of Computer Science, University of Toronto, Toronto, Canada.,Ontario Institute for Cancer Research, Toronto, Canada.,Vector Institute, Toronto, Canada
| | - Samuel Weiss
- Clark Smith Brain Tumour Centre, Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, Canada.,Hotchkiss Brain Institute, University of Calgary, Calgary, Canada.,Department of Cell Biology & Anatomy, University of Calgary, Calgary, Canada.,Department of Physiology & Pharmacology, University of Calgary, Calgary, Canada
| | - Stephane Angers
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Canada.,Department of Biochemistry, Faculty of Medicine, University of Toronto, Toronto, Canada
| | - Marco Gallo
- Clark Smith Brain Tumour Centre, Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, Canada.,Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Canada.,Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Canada.,Department of Physiology & Pharmacology, University of Calgary, Calgary, Canada
| | - Peter B Dirks
- Developmental and Stem Cell Biology Program and Arthur and Sonia Labatt Brain tumor Research Centre, The Hospital for Sick Children, Toronto, Canada.,Division of Neurosurgery, University of Toronto, Toronto, Canada.,Ontario Institute for Cancer Research, Toronto, Canada
| | - Mathieu Lupien
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Canada
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5
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Wu RS, Liedtke E, Mansouri S, Brazier S, Guilhamon P, Park NI, Chen E, Lupien M, De Carvalho DD, Dirks PG, Zadeh G, Wouters BG. Abstract 3438: Hypoxia inhibits BMP4-induced astrocytic differentiation in glioma stem cells. Cancer Res 2020. [DOI: 10.1158/1538-7445.am2020-3438] [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
The tumor microenvironment is an important contributor to malignancy in glioblastoma (GBM) by influencing stemness properties in glioma stem cells (GSCs) and their capacity for differentiation into various cell types. Tumor hypoxia is a common feature of the GBM microenvironment and can influence cell state through a variety of processes including the inhibition of oxygen-dependent lysine histone demethylases (KDMs) and subsequent epigenetic changes required for differentiation or maintenance of the stem cell state. However, the precise mechanisms underlying hypoxic restriction of differentiation to specific neural lineages is unclear. Here, we show that hypoxia suppresses astrocytic differentiation induced by bone morphogenetic protein 4 (BMP4) in patient-derived GSCs. In 8/10 patient derived GSC lines, BMP4 induced expression of astrocytic markers, such as glial fibrillary acidic protein, and this induction was repressed by hypoxia in 7/10 lines. Interestingly, significant anti-proliferative effects of BMP4 induced differentiation were only observed in 3/10 lines and was rescued in only one GSC line by hypoxia, suggesting that these processes are uncoupled. Although hypoxia may directly limit the activity of oxygen-dependent KDMs important in this process, levels of S-2-hydroxyglutarate (S-2HG), an endogenous KDM inhibitor, were also increased in 5/8 GSC lines under hypoxia. Exogenous treatment with S-2HG or a small molecule KDM6 family inhibitor, phenocopied the repressive effects of hypoxia on BMP4 induced differentiation. In patient tumors, hypoxic areas surrounding pseudopalisading necrosis showed high expression of hypoxia markers, and these hypoxia markers were anti-correlated with markers of astrocytic differentiation. Together, these results demonstrate that the hypoxic tumor microenvironment in GBM, through multiple mechanisms limiting oxygen-dependent KDM activity, promote maintenance of the malignant stemness state by inhibiting astrocytic differentiation. This study implicates tumour hypoxia as a key regulator of stemness and a therapeutic target to promote differentiation in GBM. Treatment strategies that target hypoxic cells are urgently needed to overcome these challenges.
Citation Format: Ronald S. Wu, Elisabeth Liedtke, Sheila Mansouri, Samantha Brazier, Paul Guilhamon, Nicole I. Park, Eric Chen, Mathieu Lupien, Daniel D. De Carvalho, Peter G. Dirks, Gelareh Zadeh, Bradley G. Wouters. Hypoxia inhibits BMP4-induced astrocytic differentiation in glioma stem cells [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 3438.
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Affiliation(s)
- Ronald S. Wu
- 1University of Toronto, Toronto, Ontario, Canada
| | | | - Sheila Mansouri
- 2Princess Margaret Cancer Research Centre, Toronto, Ontario, Canada
| | - Samantha Brazier
- 2Princess Margaret Cancer Research Centre, Toronto, Ontario, Canada
| | - Paul Guilhamon
- 3The Hospital for Sick Children, Toronto, Ontario, Canada
| | | | - Eric Chen
- 2Princess Margaret Cancer Research Centre, Toronto, Ontario, Canada
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6
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Whitley OK, Richards LM, Cavalli F, Guilhamon P, Coutinho F, Kushida M, Luchman HA, Weiss S, Lupien M, Dirks P, Pugh T, Bader G. Abstract 5724: Revelation of shared transcriptional gradients in glioblastoma tumors and cultured glioma stem cells. Cancer Res 2020. [DOI: 10.1158/1538-7445.am2020-5724] [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
The brain tumor Glioblastoma (GBM) is a virtual death sentence for anyone who is diagnosed, with a median survival time of 12-15 months with standard treatments1 and a 5 year survival rate of under 10% 2. There is a strong body of evidence supporting the existence of stem like cells, termed glioma stem cells (GSCs), that can repopulate the tumor after removal and therapy application3-6. Thus, GSCs present a tantalizing target for potential therapies against GBM. However, studies of GSCs have shown heterogeneity at the level of the transcriptome and drug response5,7, suggesting that there is significant biological variation that translates into differential sensitivity to various drugs. A full characterization of biological heterogeneity may aid in the search for targeted therapies.
Here, we profile the transcriptomes of 72 patient derived GSC cultures, and obtain scRNA-seq on 29 cultures from 26 patients (> 69,000 cells) plus 5 GBM tumors (> 14,000 cells). With this data, we find two anticorrelated transcriptional programs in the GSC cultures, one associated with immune or injury response related pathways and the other with neural developmental pathways. We then compare the GSC cultures to patient tumors in the scRNA-seq data, and find that a portion of GBM tumor cells are similar to GSC cultures. We find that a gradient between GSC and astrocyte programs separates cells with stemness properties from those that are not stem-like, and that within stem-like tumor cells and non stem-like tumor cells a gradient between the neural developmental and immune related programs exists as was seen for the cultured GSCs. In GSCs, we also find epigenetic variation in DNA methylation associated with the developmental and immune related programs. Overall these data suggest variation between two biological programs manifests at the level of gene expression and epigenetic regulation in GSCs in tumors.
1. Stupp, R. et al. Radiotherapy plus concomitant and adjuvant temozolomide for glioblastoma. N. Engl. J. Med. 352, 987-996 (2005).
2. Brennan, C. W. et al. The somatic genomic landscape of glioblastoma. Cell 155, 462-477 (2013).
3. Singh, S. K. et al. Identification of human brain tumour initiating cells. Nature 432, 396-401 (2004).
4. Chen, J. et al. A restricted cell population propagates glioblastoma growth after chemotherapy. Nature 488, 522-526 (2012).
5. Lan, X. et al. Fate mapping of human glioblastoma reveals an invariant stem cell hierarchy. Nature 549, 227-232 (2017).
6. Patel, A. P. et al. Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma. Science 344, 1396-1401 (2014).
7. Meyer, M. et al. Single cell-derived clonal analysis of human glioblastoma links functional and genomic heterogeneity. Proc. Natl. Acad. Sci. U. S. A. 112, 851-856 (2015).
Citation Format: Owen K. Whitley, Laura M. Richards, Florence Cavalli, Paul Guilhamon, Fiona Coutinho, Michelle Kushida, H. Artee Luchman, Samuel Weiss, Mathieu Lupien, Peter Dirks, Trevor Pugh, Gary Bader. Revelation of shared transcriptional gradients in glioblastoma tumors and cultured glioma stem cells [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5724.
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Affiliation(s)
| | | | | | - Paul Guilhamon
- 2The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Fiona Coutinho
- 2The Hospital for Sick Children, Toronto, Ontario, Canada
| | | | | | - Samuel Weiss
- 3University of Calgary, Calgary, Alberta, Canada
| | - Mathieu Lupien
- 4Princess Margaret Cancer Centre, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Peter Dirks
- 2The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Trevor Pugh
- 1University of Toronto, Toronto, Ontario, Canada
| | - Gary Bader
- 1University of Toronto, Toronto, Ontario, Canada
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7
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Deblois G, Tonekaboni SAM, Grillo G, Martinez C, Kao YI, Tai F, Ettayebi I, Fortier AM, Savage P, Fedor AN, Liu X, Guilhamon P, Lima-Fernandes E, Murison A, Kuasne H, Ba-alawi W, Cescon DW, Arrowsmith CH, De Carvalho DD, Haibe-Kains B, Locasale JW, Park M, Lupien M. Epigenetic Switch–Induced Viral Mimicry Evasion in Chemotherapy-Resistant Breast Cancer. Cancer Discov 2020; 10:1312-1329. [DOI: 10.1158/2159-8290.cd-19-1493] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 04/20/2020] [Accepted: 06/09/2020] [Indexed: 11/16/2022]
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8
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Michealraj KA, Kumar SA, Kim LJY, Cavalli FMG, Przelicki D, Wojcik JB, Delaidelli A, Bajic A, Saulnier O, MacLeod G, Vellanki RN, Vladoiu MC, Guilhamon P, Ong W, Lee JJY, Jiang Y, Holgado BL, Rasnitsyn A, Malik AA, Tsai R, Richman CM, Juraschka K, Haapasalo J, Wang EY, De Antonellis P, Suzuki H, Farooq H, Balin P, Kharas K, Van Ommeren R, Sirbu O, Rastan A, Krumholtz SL, Ly M, Ahmadi M, Deblois G, Srikanthan D, Luu B, Loukides J, Wu X, Garzia L, Ramaswamy V, Kanshin E, Sánchez-Osuna M, El-Hamamy I, Coutinho FJ, Prinos P, Singh S, Donovan LK, Daniels C, Schramek D, Tyers M, Weiss S, Stein LD, Lupien M, Wouters BG, Garcia BA, Arrowsmith CH, Sorensen PH, Angers S, Jabado N, Dirks PB, Mack SC, Agnihotri S, Rich JN, Taylor MD. Metabolic Regulation of the Epigenome Drives Lethal Infantile Ependymoma. Cell 2020; 181:1329-1345.e24. [PMID: 32445698 PMCID: PMC10782558 DOI: 10.1016/j.cell.2020.04.047] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 03/16/2020] [Accepted: 04/24/2020] [Indexed: 01/24/2023]
Abstract
Posterior fossa A (PFA) ependymomas are lethal malignancies of the hindbrain in infants and toddlers. Lacking highly recurrent somatic mutations, PFA ependymomas are proposed to be epigenetically driven tumors for which model systems are lacking. Here we demonstrate that PFA ependymomas are maintained under hypoxia, associated with restricted availability of specific metabolites to diminish histone methylation, and increase histone demethylation and acetylation at histone 3 lysine 27 (H3K27). PFA ependymomas initiate from a cell lineage in the first trimester of human development that resides in restricted oxygen. Unlike other ependymomas, transient exposure of PFA cells to ambient oxygen induces irreversible cellular toxicity. PFA tumors exhibit a low basal level of H3K27me3, and, paradoxically, inhibition of H3K27 methylation specifically disrupts PFA tumor growth. Targeting metabolism and/or the epigenome presents a unique opportunity for rational therapy for infants with PFA ependymoma.
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Affiliation(s)
- Kulandaimanuvel Antony Michealraj
- The Arthur and Sonia Labatt Brain Tumor Research Center, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Sachin A Kumar
- The Arthur and Sonia Labatt Brain Tumor Research Center, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Leo J Y Kim
- Division of Regenerative Medicine, Department of Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Florence M G Cavalli
- The Arthur and Sonia Labatt Brain Tumor Research Center, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - David Przelicki
- The Arthur and Sonia Labatt Brain Tumor Research Center, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - John B Wojcik
- Department of Biochemistry and Biophysics and Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Alberto Delaidelli
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, BC V6T 1Z2, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 1Z2, Canada
| | - Andrea Bajic
- Department of Human Genetics, McGill University, Montreal, QC H3A 1B1, Canada
| | - Olivier Saulnier
- The Arthur and Sonia Labatt Brain Tumor Research Center, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Graham MacLeod
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON M5S 3M2, Canada
| | - Ravi N Vellanki
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Maria C Vladoiu
- The Arthur and Sonia Labatt Brain Tumor Research Center, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Paul Guilhamon
- The Arthur and Sonia Labatt Brain Tumor Research Center, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Winnie Ong
- The Arthur and Sonia Labatt Brain Tumor Research Center, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - John J Y Lee
- The Arthur and Sonia Labatt Brain Tumor Research Center, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Yanqing Jiang
- The Arthur and Sonia Labatt Brain Tumor Research Center, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Borja L Holgado
- The Arthur and Sonia Labatt Brain Tumor Research Center, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Alex Rasnitsyn
- The Arthur and Sonia Labatt Brain Tumor Research Center, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Ahmad A Malik
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Ricky Tsai
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
| | - Cory M Richman
- The Arthur and Sonia Labatt Brain Tumor Research Center, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Kyle Juraschka
- The Arthur and Sonia Labatt Brain Tumor Research Center, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Joonas Haapasalo
- The Arthur and Sonia Labatt Brain Tumor Research Center, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Evan Y Wang
- The Arthur and Sonia Labatt Brain Tumor Research Center, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Pasqualino De Antonellis
- The Arthur and Sonia Labatt Brain Tumor Research Center, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Hiromichi Suzuki
- The Arthur and Sonia Labatt Brain Tumor Research Center, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Hamza Farooq
- The Arthur and Sonia Labatt Brain Tumor Research Center, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Polina Balin
- The Arthur and Sonia Labatt Brain Tumor Research Center, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Kaitlin Kharas
- The Arthur and Sonia Labatt Brain Tumor Research Center, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Randy Van Ommeren
- The Arthur and Sonia Labatt Brain Tumor Research Center, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Olga Sirbu
- The Arthur and Sonia Labatt Brain Tumor Research Center, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Avesta Rastan
- The Arthur and Sonia Labatt Brain Tumor Research Center, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Stacey L Krumholtz
- The Arthur and Sonia Labatt Brain Tumor Research Center, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Michelle Ly
- The Arthur and Sonia Labatt Brain Tumor Research Center, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Moloud Ahmadi
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON M5S 3M2, Canada
| | - Geneviève Deblois
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Dilakshan Srikanthan
- The Arthur and Sonia Labatt Brain Tumor Research Center, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Betty Luu
- The Arthur and Sonia Labatt Brain Tumor Research Center, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - James Loukides
- The Arthur and Sonia Labatt Brain Tumor Research Center, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Xiaochong Wu
- The Arthur and Sonia Labatt Brain Tumor Research Center, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Livia Garzia
- Cancer Research Program, McGill University Health Centre Research Institute, Montreal, QC H4A 3J1, Canada
| | - Vijay Ramaswamy
- The Arthur and Sonia Labatt Brain Tumor Research Center, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Division of Haematology/Oncology, Department of Pediatrics, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Evgeny Kanshin
- Institute for Research in Immunology and Cancer (IRIC), Department of Medicine, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - María Sánchez-Osuna
- Institute for Research in Immunology and Cancer (IRIC), Department of Medicine, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Ibrahim El-Hamamy
- Computational Biology Program, Adaptive Oncology Theme, Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Fiona J Coutinho
- The Arthur and Sonia Labatt Brain Tumor Research Center, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Panagiotis Prinos
- Structural Genomics Consortium, University of Toronto, 101 College Street, MaRS Centre, South Tower, Toronto, ON M5G 1L7, Canada
| | - Sheila Singh
- Stem Cell and Cancer Research Institute, McMaster University, Hamilton, ON L8S 4K1, Canada; Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4K1, Canada; Department of Surgery, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Laura K Donovan
- The Arthur and Sonia Labatt Brain Tumor Research Center, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Craig Daniels
- The Arthur and Sonia Labatt Brain Tumor Research Center, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Daniel Schramek
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Mike Tyers
- Institute for Research in Immunology and Cancer (IRIC), Department of Medicine, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Samuel Weiss
- Hotchkiss Brain Institute, Department of Cell Biology and Anatomy, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Lincoln D Stein
- Computational Biology Program, Adaptive Oncology Theme, Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Mathieu Lupien
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Bradly G Wouters
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Benjamin A Garcia
- Department of Biochemistry and Biophysics and Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Cheryl H Arrowsmith
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada; Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Structural Genomics Consortium, University of Toronto, 101 College Street, MaRS Centre, South Tower, Toronto, ON M5G 1L7, Canada
| | - Poul H Sorensen
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, BC V6T 1Z2, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 1Z2, Canada
| | - Stephane Angers
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON M5S 3M2, Canada; Department of Biochemistry, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Nada Jabado
- Department of Human Genetics, McGill University, Montreal, QC H3A 1B1, Canada; Department of Pediatrics, McGill University, The Research Institute of the McGill University Health Center, Montreal, QC H4A 3J1, Canada
| | - Peter B Dirks
- The Arthur and Sonia Labatt Brain Tumor Research Center, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1L7, Canada; Division of Neurosurgery, The Hospital for Sick Children, Toronto, ON M5G 1L7, Canada
| | - Stephen C Mack
- Texas Children's Hospital Cancer Center, Department of Pediatrics, Baylor College of Medicine, Dan L. Duncan Cancer Center, Houston, TX 77030, USA.
| | - Sameer Agnihotri
- Department of Neurological Surgery, Children's Hospital of Pittsburgh, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA.
| | - Jeremy N Rich
- Division of Regenerative Medicine, Department of Medicine, University of California, San Diego, La Jolla, CA 92037, USA.
| | - Michael D Taylor
- The Arthur and Sonia Labatt Brain Tumor Research Center, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada; Division of Neurosurgery, The Hospital for Sick Children, Toronto, ON M5G 1L7, Canada.
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9
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Mazrooei P, Kron KJ, Zhu Y, Zhou S, Grillo G, Mehdi T, Ahmed M, Severson TM, Guilhamon P, Armstrong NS, Huang V, Yamaguchi TN, Fraser M, van der Kwast T, Boutros PC, He HH, Bergman AM, Bristow RG, Zwart W, Lupien M. Cistrome Partitioning Reveals Convergence of Somatic Mutations and Risk Variants on Master Transcription Regulators in Primary Prostate Tumors. Cancer Cell 2019; 36:674-689.e6. [PMID: 31735626 DOI: 10.1016/j.ccell.2019.10.005] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 08/02/2019] [Accepted: 10/17/2019] [Indexed: 12/26/2022]
Abstract
Thousands of noncoding somatic single-nucleotide variants (SNVs) of unknown function are reported in tumors. Partitioning the genome according to cistromes reveals the enrichment of somatic SNVs in prostate tumors as opposed to adjacent normal tissue cistromes of master transcription regulators, including AR, FOXA1, and HOXB13. This parallels enrichment of prostate cancer genetic predispositions over these transcription regulators' tumor cistromes, exemplified at the 8q24 locus harboring both risk variants and somatic SNVs in cis-regulatory elements upregulating MYC expression. However, Massively Parallel Reporter Assays reveal that few SNVs can alter the transactivation potential of individual cis-regulatory elements. Instead, similar to inherited risk variants, SNVs accumulate in cistromes of master transcription regulators required for prostate cancer development.
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Affiliation(s)
- Parisa Mazrooei
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Ken J Kron
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Yanyun Zhu
- Division of Oncogenomics, Oncode Institute, the Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Stanley Zhou
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Giacomo Grillo
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Tahmid Mehdi
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Musaddeque Ahmed
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Tesa M Severson
- Division of Oncogenomics, Oncode Institute, the Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Paul Guilhamon
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | | | - Vincent Huang
- Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada
| | | | - Michael Fraser
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada
| | - Theodorus van der Kwast
- Department of Pathology and Laboratory Medicine, Toronto General Hospital, University Health Network, Toronto, ON M5G 2C4, Canada
| | - Paul C Boutros
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada; Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada; Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Housheng Hansen He
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Andries M Bergman
- Division of Oncogenomics, Oncode Institute, the Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Robert G Bristow
- CRUK Manchester Institute and Manchester Cancer Research Centre, University of Manchester, Manchester M20 4GJ, UK
| | - Wilbert Zwart
- Division of Oncogenomics, Oncode Institute, the Netherlands Cancer Institute, Amsterdam, The Netherlands; Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, PO Box 513, 5600 MB Eindhoven, The Netherlands.
| | - Mathieu Lupien
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada; Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada.
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10
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Krug B, De Jay N, Harutyunyan AS, Deshmukh S, Marchione DM, Guilhamon P, Bertrand KC, Mikael LG, McConechy MK, Chen CC, Khazaei S, Koncar RF, Agnihotri S, Faury D, Ellezam B, Weil AG, Ursini-Siegel J, De Carvalho DD, Dirks PB, Lewis PW, Salomoni P, Lupien M, Arrowsmith C, Lasko PF, Garcia BA, Kleinman CL, Jabado N, Mack SC. Pervasive H3K27 Acetylation Leads to ERV Expression and a Therapeutic Vulnerability in H3K27M Gliomas. Cancer Cell 2019; 36:338-339. [PMID: 31526762 PMCID: PMC6949014 DOI: 10.1016/j.ccell.2019.08.012] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [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: 10/26/2022]
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11
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Sin-Chan P, Mumal I, Suwal T, Ho B, Fan X, Singh I, Du Y, Lu M, Patel N, Torchia J, Popovski D, Fouladi M, Guilhamon P, Hansford JR, Leary S, Hoffman LM, Mulcahy Levy JM, Lassaletta A, Solano-Paez P, Rivas E, Reddy A, Gillespie GY, Gupta N, Van Meter TE, Nakamura H, Wong TT, Ra YS, Kim SK, Massimi L, Grundy RG, Fangusaro J, Johnston D, Chan J, Lafay-Cousin L, Hwang EI, Wang Y, Catchpoole D, Michaud J, Ellezam B, Ramanujachar R, Lindsay H, Taylor MD, Hawkins CE, Bouffet E, Jabado N, Singh SK, Kleinman CL, Barsyte-Lovejoy D, Li XN, Dirks PB, Lin CY, Mack SC, Rich JN, Huang A. A C19MC-LIN28A-MYCN Oncogenic Circuit Driven by Hijacked Super-enhancers Is a Distinct Therapeutic Vulnerability in ETMRs: A Lethal Brain Tumor. Cancer Cell 2019; 36:51-67.e7. [PMID: 31287992 DOI: 10.1016/j.ccell.2019.06.002] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [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: 02/11/2019] [Revised: 04/26/2019] [Accepted: 06/03/2019] [Indexed: 12/26/2022]
Abstract
Embryonal tumors with multilayered rosettes (ETMRs) are highly lethal infant brain cancers with characteristic amplification of Chr19q13.41 miRNA cluster (C19MC) and enrichment of pluripotency factor LIN28A. Here we investigated C19MC oncogenic mechanisms and discovered a C19MC-LIN28A-MYCN circuit fueled by multiple complex regulatory loops including an MYCN core transcriptional network and super-enhancers resulting from long-range MYCN DNA interactions and C19MC gene fusions. Our data show that this powerful oncogenic circuit, which entraps an early neural lineage network, is potently abrogated by bromodomain inhibitor JQ1, leading to ETMR cell death.
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MESH Headings
- Biomarkers, Tumor
- Brain Neoplasms/diagnosis
- Brain Neoplasms/etiology
- Brain Neoplasms/therapy
- Cell Cycle/genetics
- Cell Transformation, Neoplastic/drug effects
- Cell Transformation, Neoplastic/genetics
- Chromosomes, Human, Pair 19
- Chromosomes, Human, Pair 2
- DNA Copy Number Variations
- Enhancer Elements, Genetic
- Epigenesis, Genetic
- Gene Expression Regulation
- Gene Regulatory Networks
- Genetic Association Studies
- Genetic Predisposition to Disease
- Humans
- MicroRNAs/genetics
- Models, Biological
- Multigene Family
- N-Myc Proto-Oncogene Protein/genetics
- Neoplasms, Germ Cell and Embryonal/diagnosis
- Neoplasms, Germ Cell and Embryonal/etiology
- Neoplasms, Germ Cell and Embryonal/therapy
- Oncogenes
- RNA-Binding Proteins/genetics
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Affiliation(s)
- Patrick Sin-Chan
- Arthur and Sonia Labatt Brain Tumor Research Centre, Division of Haematology/Oncology, Hospital for Sick Children, Toronto, ON M5G0A4, Canada
| | - Iqra Mumal
- Arthur and Sonia Labatt Brain Tumor Research Centre, Division of Haematology/Oncology, Hospital for Sick Children, Toronto, ON M5G0A4, Canada; Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, ON M5S1A8, Canada
| | - Tannu Suwal
- Arthur and Sonia Labatt Brain Tumor Research Centre, Division of Haematology/Oncology, Hospital for Sick Children, Toronto, ON M5G0A4, Canada; Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, ON M5S1A8, Canada
| | - Ben Ho
- Arthur and Sonia Labatt Brain Tumor Research Centre, Division of Haematology/Oncology, Hospital for Sick Children, Toronto, ON M5G0A4, Canada
| | - Xiaolian Fan
- Arthur and Sonia Labatt Brain Tumor Research Centre, Division of Haematology/Oncology, Hospital for Sick Children, Toronto, ON M5G0A4, Canada
| | - Irtisha Singh
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yuchen Du
- Department of Pediatrics, Division of Hematology and Oncology, Baylor College of Medicine, Texas Children's Hospital, Houston, TX 77030, USA
| | - Mei Lu
- Arthur and Sonia Labatt Brain Tumor Research Centre, Division of Haematology/Oncology, Hospital for Sick Children, Toronto, ON M5G0A4, Canada
| | - Neilket Patel
- Arthur and Sonia Labatt Brain Tumor Research Centre, Division of Haematology/Oncology, Hospital for Sick Children, Toronto, ON M5G0A4, Canada
| | - Jonathon Torchia
- Princess Margaret Cancer Center-OICR Translational Genomics Laboratory, Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada
| | - Dean Popovski
- Arthur and Sonia Labatt Brain Tumor Research Centre, Division of Haematology/Oncology, Hospital for Sick Children, Toronto, ON M5G0A4, Canada
| | - Maryam Fouladi
- Division of Oncology, Department of Cancer and Blood Diseases, Cincinnati Children's Hospital, Cincinnati, OH 45229, USA
| | - Paul Guilhamon
- Developmental and Stem Cell Biology Program and Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, ON M5G0A4, Canada
| | - Jordan R Hansford
- Children's Cancer Centre, Royal Children's Hospital, Murdoch Children's Research Institute, Department of Pediatrics, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Sarah Leary
- Department of Hematology-Oncology, Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Lindsey M Hoffman
- Department of Pediatrics, University of Colorado Denver, Aurora, CO 80045, USA
| | - Jean M Mulcahy Levy
- Department of Pediatrics, University of Colorado Denver, Aurora, CO 80045, USA
| | - Alvaro Lassaletta
- Pediatric Hematology and Oncology Department, Hospital Infantil Universitario Niño Jesús, Madrid 28009, Spain
| | - Palma Solano-Paez
- Department of Pediatric Oncology, Hospital Infantil Virgen del Rocio, Seville 41013, Spain
| | - Eloy Rivas
- Department of Pathology, Neuropathology Division, Hospital Universitario Virgen del Rocio, Seville 41013, Spain
| | - Alyssa Reddy
- University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - G Yancey Gillespie
- Department of Neurosurgery, University of Alabama at Birmingham, Birmingham AL 35294, USA
| | - Nalin Gupta
- Department of Neurological Surgery, University of California, San Francisco, CA 94143-0112, USA
| | - Timothy E Van Meter
- Department of Pediatrics, Virginia Commonwealth University, Richmond, VA 23298-0631, USA
| | - Hideo Nakamura
- Department of Neurosurgery, Kurume University, Fukuoka 830-0011, Japan
| | - Tai-Tong Wong
- Pediatric Brain Tumor Program, Taipei Cancer Center, Taipei Medical University, Taipei 11031, Taiwan
| | - Young-Shin Ra
- Department of Neurosurgery, Asan Medical Center, Seoul 138-736, Korea
| | - Seung-Ki Kim
- Division of Pediatric Neurosurgery, Seoul National University Children's Hospital, Seoul 03080, Korea
| | - Luca Massimi
- Department of Neurosurgery, Fondazione Policlinico A. Gemelli IRCCS, Università Cattolica del Sacro Cuore, Rome 00168, Italy
| | - Richard G Grundy
- Children's Brain Tumor Research Centre, Queen's Medical Centre University of Nottingham, Nottingham NG72UH, UK
| | - Jason Fangusaro
- Department of Pediatric Hematology and Oncology at Children's Healthcare of Atlanta and the Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Donna Johnston
- Division of Hematology/Oncology, Children's Hospital of Eastern Ontario, Ottawa, ON K1H8L1, Canada
| | - Jennifer Chan
- Department of Pathology and Laboratory Medicine, University of Calgary, Calgary, AB T2N1N4, Canada
| | - Lucie Lafay-Cousin
- Department of Pediatric Oncology, Alberta Children's Hospital, Calgary, AB T3B6A8, Canada
| | - Eugene I Hwang
- Center for Cancer and Blood Disorders, Children's National Medical Center, Washington, DC 20010, USA
| | - Yin Wang
- Department of Neuropathology Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Daniel Catchpoole
- The Tumor Bank, Children's Cancer Research Unit, Kids Research, the Children's Hospital at Westmead, Westmead, NSW 2145, Australia
| | - Jean Michaud
- Department of Pathology and Laboratory Medicine, University of Ottawa, Ottawa, ON K1H8M5, Canada
| | - Benjamin Ellezam
- Department of Pathology, CHU Sainte-Justine Research Center, Université de Montréal, Montréal, QC H3T1C5, Canada
| | - Ramya Ramanujachar
- Paediatric Haematology and Oncology, Southampton Children's Hospital, Southampton SO166YD, UK
| | - Holly Lindsay
- Department of Pediatrics, Division of Hematology and Oncology, Baylor College of Medicine, Texas Children's Hospital, Houston, TX 77030, USA
| | - Michael D Taylor
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, ON M5S1A8, Canada; Arthur and Sonia Labatt Brain Tumor Research Centre, Division of Neurosurgery, Hospital for Sick Children, Toronto, ON M5G0A4, Canada
| | - Cynthia E Hawkins
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, ON M5S1A8, Canada; Department of Pathology, The Hospital for Sick Children, Toronto, ON M5G1X8, Canada
| | - Eric Bouffet
- Division of Hematology-Oncology, The Hospital for Sick Children, Department of Pediatrics, University of Toronto, Toronto, ON M5G0A4, Canada
| | - Nada Jabado
- Departments of Pediatrics and Human Genetics, McGill University, Montréal, QC H3A0C7, Canada
| | - Sheila K Singh
- McMaster Stem Cell and Cancer Research Institute, McMaster University, Hamilton, ON L8S4K1, Canada
| | - Claudia L Kleinman
- Departments of Pediatrics and Human Genetics, McGill University, Montréal, QC H3A0C7, Canada
| | | | - Xiao-Nan Li
- Department of Pediatrics, Division of Hematology and Oncology, Baylor College of Medicine, Texas Children's Hospital, Houston, TX 77030, USA; Department of Pediatrics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Peter B Dirks
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, ON M5S1A8, Canada; Arthur and Sonia Labatt Brain Tumor Research Centre, Division of Neurosurgery, Hospital for Sick Children, Toronto, ON M5G0A4, Canada
| | - Charles Y Lin
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Stephen C Mack
- Department of Pediatrics, Division of Hematology and Oncology, Baylor College of Medicine, Texas Children's Hospital, Houston, TX 77030, USA
| | - Jeremy N Rich
- Department of Medicine, Division of Regenerative Medicine, University of California, San Diego, CA 92093, USA
| | - Annie Huang
- Arthur and Sonia Labatt Brain Tumor Research Centre, Division of Haematology/Oncology, Hospital for Sick Children, Toronto, ON M5G0A4, Canada; Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, ON M5S1A8, Canada; Division of Hematology-Oncology, The Hospital for Sick Children, Department of Pediatrics, University of Toronto, Toronto, ON M5G0A4, Canada; Department of Medical Biophysics, Faculty of Medicine, University of Toronto, Toronto, ON M5G1L7, Canada.
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12
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Johnston MJ, Nikolic A, Ninkovic N, Guilhamon P, Cavalli FMG, Seaman S, Zemp FJ, Lee J, Abdelkareem A, Ellestad K, Murison A, Kushida MM, Coutinho FJ, Ma Y, Mungall AJ, Moore R, Marra MA, Taylor MD, Dirks PB, Pugh TJ, Morrissy S, St Croix B, Mahoney DJ, Lupien M, Gallo M. High-resolution structural genomics reveals new therapeutic vulnerabilities in glioblastoma. Genome Res 2019; 29:1211-1222. [PMID: 31249064 PMCID: PMC6673710 DOI: 10.1101/gr.246520.118] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [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: 11/16/2018] [Accepted: 06/26/2019] [Indexed: 12/20/2022]
Abstract
We investigated the role of 3D genome architecture in instructing functional properties of glioblastoma stem cells (GSCs) by generating sub-5-kb resolution 3D genome maps by in situ Hi-C. Contact maps at sub-5-kb resolution allow identification of individual DNA loops, domain organization, and large-scale genome compartmentalization. We observed differences in looping architectures among GSCs from different patients, suggesting that 3D genome architecture is a further layer of inter-patient heterogeneity for glioblastoma. Integration of DNA contact maps with chromatin and transcriptional profiles identified specific mechanisms of gene regulation, including the convergence of multiple super enhancers to individual stemness genes within individual cells. We show that the number of loops contacting a gene correlates with elevated transcription. These results indicate that stemness genes are hubs of interaction between multiple regulatory regions, likely to ensure their sustained expression. Regions of open chromatin common among the GSCs tested were poised for expression of immune-related genes, including CD276. We demonstrate that this gene is co-expressed with stemness genes in GSCs and that CD276 can be targeted with an antibody-drug conjugate to eliminate self-renewing cells. Our results demonstrate that integrated structural genomics data sets can be employed to rationally identify therapeutic vulnerabilities in self-renewing cells.
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Affiliation(s)
- Michael J Johnston
- Clark Smith Brain Tumour Centre, Charbonneau Cancer Institute, University of Calgary, Calgary, Alberta T2N 4N1, Canada.,Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | - Ana Nikolic
- Clark Smith Brain Tumour Centre, Charbonneau Cancer Institute, University of Calgary, Calgary, Alberta T2N 4N1, Canada.,Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta T2N 4N1, Canada.,Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | - Nicoletta Ninkovic
- Clark Smith Brain Tumour Centre, Charbonneau Cancer Institute, University of Calgary, Calgary, Alberta T2N 4N1, Canada.,Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta T2N 4N1, Canada.,Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | - Paul Guilhamon
- Princess Margaret Cancer Centre-University Health Network, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Florence M G Cavalli
- Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
| | - Steven Seaman
- Tumor Angiogenesis Unit, Mouse Cancer Genetics Program (MCGP), National Cancer Institute (NCI), NIH, Frederick, Maryland 21702, USA
| | - Franz J Zemp
- Clark Smith Brain Tumour Centre, Charbonneau Cancer Institute, University of Calgary, Calgary, Alberta T2N 4N1, Canada.,Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | - John Lee
- Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
| | - Aly Abdelkareem
- Clark Smith Brain Tumour Centre, Charbonneau Cancer Institute, University of Calgary, Calgary, Alberta T2N 4N1, Canada.,Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta T2N 4N1, Canada.,Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | - Katrina Ellestad
- Clark Smith Brain Tumour Centre, Charbonneau Cancer Institute, University of Calgary, Calgary, Alberta T2N 4N1, Canada.,Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | - Alex Murison
- Princess Margaret Cancer Centre-University Health Network, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Michelle M Kushida
- Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
| | - Fiona J Coutinho
- Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
| | - Yussanne Ma
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia VSZ 4S6, Canada
| | - Andrew J Mungall
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia VSZ 4S6, Canada
| | - Richard Moore
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia VSZ 4S6, Canada
| | - Marco A Marra
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia VSZ 4S6, Canada
| | - Michael D Taylor
- Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
| | - Peter B Dirks
- Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada.,Department of Molecular Genetics, University of Toronto, Ontario M5S 1A8, Canada
| | - Trevor J Pugh
- Princess Margaret Cancer Centre-University Health Network, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Sorana Morrissy
- Clark Smith Brain Tumour Centre, Charbonneau Cancer Institute, University of Calgary, Calgary, Alberta T2N 4N1, Canada.,Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta T2N 4N1, Canada.,Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | - Bradley St Croix
- Tumor Angiogenesis Unit, Mouse Cancer Genetics Program (MCGP), National Cancer Institute (NCI), NIH, Frederick, Maryland 21702, USA
| | - Douglas J Mahoney
- Clark Smith Brain Tumour Centre, Charbonneau Cancer Institute, University of Calgary, Calgary, Alberta T2N 4N1, Canada.,Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta T2N 4N1, Canada.,Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta T2N 4N1, Canada.,Department of Microbiology, Immunology and Infectious Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | - Mathieu Lupien
- Princess Margaret Cancer Centre-University Health Network, University of Toronto, Toronto, Ontario M5G 1L7, Canada.,Department of Medical Biophysics, University of Toronto, Ontario M5S 1A8, Canada.,Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3, Canada
| | - Marco Gallo
- Clark Smith Brain Tumour Centre, Charbonneau Cancer Institute, University of Calgary, Calgary, Alberta T2N 4N1, Canada.,Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta T2N 4N1, Canada.,Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta T2N 4N1, Canada.,Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, Alberta T2N 4N1, Canada
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13
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Krug B, De Jay N, Harutyunyan AS, Deshmukh S, Marchione DM, Guilhamon P, Bertrand KC, Mikael LG, McConechy MK, Chen CCL, Khazaei S, Koncar RF, Agnihotri S, Faury D, Ellezam B, Weil AG, Ursini-Siegel J, De Carvalho DD, Dirks PB, Lewis PW, Salomoni P, Lupien M, Arrowsmith C, Lasko PF, Garcia BA, Kleinman CL, Jabado N, Mack SC. Pervasive H3K27 Acetylation Leads to ERV Expression and a Therapeutic Vulnerability in H3K27M Gliomas. Cancer Cell 2019; 35:782-797.e8. [PMID: 31085178 PMCID: PMC6521975 DOI: 10.1016/j.ccell.2019.04.004] [Citation(s) in RCA: 103] [Impact Index Per Article: 20.6] [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: 09/25/2018] [Revised: 01/16/2019] [Accepted: 04/12/2019] [Indexed: 01/02/2023]
Abstract
High-grade gliomas defined by histone 3 K27M driver mutations exhibit global loss of H3K27 trimethylation and reciprocal gain of H3K27 acetylation, respectively shaping repressive and active chromatin landscapes. We generated tumor-derived isogenic models bearing this mutation and show that it leads to pervasive H3K27ac deposition across the genome. In turn, active enhancers and promoters are not created de novo and instead reflect the epigenomic landscape of the cell of origin. H3K27ac is enriched at repeat elements, resulting in their increased expression, which in turn can be further amplified by DNA demethylation and histone deacetylase inhibitors providing an exquisite therapeutic vulnerability. These agents may therefore modulate anti-tumor immune responses as a therapeutic modality for this untreatable disease.
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Affiliation(s)
- Brian Krug
- Department of Human Genetics, McGill University, Montreal, QC H3A 1B1, Canada
| | - Nicolas De Jay
- Department of Human Genetics, McGill University, Montreal, QC H3A 1B1, Canada; Lady Davis Research Institute, Jewish General Hospital, Montreal, QC H3T 1E2, Canada
| | - Ashot S Harutyunyan
- Department of Human Genetics, McGill University, Montreal, QC H3A 1B1, Canada
| | - Shriya Deshmukh
- Department of Human Genetics, McGill University, Montreal, QC H3A 1B1, Canada
| | - Dylan M Marchione
- Department of Biochemistry and Biophysics, and Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Paul Guilhamon
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5S 1A8, Canada; Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada
| | - Kelsey C Bertrand
- Department of Pediatrics, Division of Hematology and Oncology, Texas Children's Cancer and Hematology Centers, Dan L Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Leonie G Mikael
- Department of Pediatrics, McGill University, The Research Institute of the McGill University Health Center, Montreal, QC H4A 3J1, Canada
| | - Melissa K McConechy
- Department of Human Genetics, McGill University, Montreal, QC H3A 1B1, Canada
| | - Carol C L Chen
- Department of Human Genetics, McGill University, Montreal, QC H3A 1B1, Canada
| | - Sima Khazaei
- Department of Human Genetics, McGill University, Montreal, QC H3A 1B1, Canada
| | - Robert F Koncar
- Department of Neurological Surgery, Children's Hospital, University of Pittsburgh School of Medicine, Pittsburgh, PA 15232, USA
| | - Sameer Agnihotri
- Department of Neurological Surgery, Children's Hospital, University of Pittsburgh School of Medicine, Pittsburgh, PA 15232, USA
| | - Damien Faury
- Department of Pediatrics, McGill University, The Research Institute of the McGill University Health Center, Montreal, QC H4A 3J1, Canada
| | - Benjamin Ellezam
- Department of Pathology, Centre Hospitalier Universitaire Sainte-Justine, Université de Montréal, Montréal, QC H3T 1C5, Canada
| | - Alexander G Weil
- Department of Pediatric Neurosurgery, Centre Hospitalier Universitaire Sainte-Justine, Université de Montréal, Montréal, QC H3T 1C5, Canada
| | - Josie Ursini-Siegel
- Lady Davis Research Institute, Jewish General Hospital, Montreal, QC H3T 1E2, Canada
| | - Daniel D De Carvalho
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Peter B Dirks
- Department of Surgery and Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Peter W Lewis
- Department of Biomolecular Chemistry, School of Medicine and Public Health and Wisconsin Institute for Discovery, University of Wisconsin, Madison, WI 53715, USA
| | - Paolo Salomoni
- Nuclear Function in CNS Pathophysiology, German Center for Neurodegenerative Diseases, 53127 Bonn, Germany
| | - Mathieu Lupien
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5S 1A8, Canada; Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada
| | - Cheryl Arrowsmith
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Paul F Lasko
- Department of Biology, McGill University, Montreal, QC H3A 1B1, Canada
| | - Benjamin A Garcia
- Department of Biochemistry and Biophysics, and Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Claudia L Kleinman
- Department of Human Genetics, McGill University, Montreal, QC H3A 1B1, Canada; Lady Davis Research Institute, Jewish General Hospital, Montreal, QC H3T 1E2, Canada.
| | - Nada Jabado
- Department of Human Genetics, McGill University, Montreal, QC H3A 1B1, Canada; Department of Pediatrics, McGill University, The Research Institute of the McGill University Health Center, Montreal, QC H4A 3J1, Canada.
| | - Stephen C Mack
- Department of Pediatrics, Division of Hematology and Oncology, Texas Children's Cancer and Hematology Centers, Dan L Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA.
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14
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Abstract
BACKGROUND Single Nucleotide Variants (SNVs), including somatic point mutations and Single Nucleotide Polymorphisms (SNPs), in noncoding cis-regulatory elements (CREs) can affect gene regulation and lead to disease development. Several approaches have been developed to identify highly mutated regions, but these do not take into account the specific genomic context, and thus likelihood of mutation, of CREs. RESULTS Here, we present SMuRF (Significantly Mutated Region Finder), a user-friendly command-line tool to identify these significantly mutated regions from user-defined genomic intervals and SNVs. We demonstrate this using publicly available datasets in which SMuRF identifies 72 significantly mutated CREs in liver cancer, including known mutated gene promoters as well as previously unreported regions. CONCLUSIONS SMuRF is a helpful tool to allow the simple identification of significantly mutated regulatory elements. It is open-source and freely available on GitHub ( https://github.com/LupienLab/SMURF ).
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Affiliation(s)
- Paul Guilhamon
- Princess Margaret Cancer Centre, The MaRS Center, University Health Network, 101 College Street, Toronto, ON M5G 1L7 Canada
| | - Mathieu Lupien
- Princess Margaret Cancer Centre, The MaRS Center, University Health Network, 101 College Street, Toronto, ON M5G 1L7 Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON Canada
- Ontario Institute for Cancer Research, Toronto, ON Canada
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15
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Mehdi T, Bailey SD, Guilhamon P, Lupien M. C3D: a tool to predict 3D genomic interactions between cis-regulatory elements. Bioinformatics 2018; 35:877-879. [DOI: 10.1093/bioinformatics/bty717] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Revised: 06/15/2018] [Accepted: 08/20/2018] [Indexed: 12/17/2022] Open
Affiliation(s)
- Tahmid Mehdi
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Statistics and Actuarial Science, University of Waterloo, Waterloo, ON, Canada
| | - Swneke D Bailey
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Paul Guilhamon
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Mathieu Lupien
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Ontario Institute for Cancer Research, Toronto, ON, Canada
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16
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Badodi S, Dubuc A, Zhang X, Rosser G, Da Cunha Jaeger M, Kameda-Smith MM, Morrissy AS, Guilhamon P, Suetterlin P, Li XN, Guglielmi L, Merve A, Farooq H, Lupien M, Singh SK, Basson MA, Taylor MD, Marino S. Convergence of BMI1 and CHD7 on ERK Signaling in Medulloblastoma. Cell Rep 2017; 21:2772-2784. [PMID: 29212025 PMCID: PMC5732319 DOI: 10.1016/j.celrep.2017.11.021] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 10/09/2017] [Accepted: 11/03/2017] [Indexed: 02/08/2023] Open
Abstract
We describe molecular convergence between BMI1 and CHD7 in the initiation of medulloblastoma. Identified in a functional genomic screen in mouse models, a BMI1High;CHD7Low expression signature within medulloblastoma characterizes patients with poor overall survival. We show that BMI1-mediated repression of the ERK1/2 pathway leads to increased proliferation and tumor burden in primary human MB cells and in a xenograft model, respectively. We provide evidence that repression of the ERK inhibitor DUSP4 by BMI1 is dependent on a more accessible chromatin configuration in G4 MB cells with low CHD7 expression. These findings extend current knowledge of the role of BMI1 and CHD7 in medulloblastoma pathogenesis, and they raise the possibility that pharmacological targeting of BMI1 or ERK may be particularly indicated in a subgroup of MB with low expression levels of CHD7.
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Affiliation(s)
- Sara Badodi
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, 4 Newark Street, London E1 2AT, UK
| | - Adrian Dubuc
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, 101 College Street, TMDT-11-401M, Toronto, ON M5G 1L7, Canada
| | - Xinyu Zhang
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, 4 Newark Street, London E1 2AT, UK
| | - Gabriel Rosser
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, 4 Newark Street, London E1 2AT, UK
| | - Mariane Da Cunha Jaeger
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, 4 Newark Street, London E1 2AT, UK
| | - Michelle M Kameda-Smith
- Pediatric Neurosurgery, Department of Surgery, McMaster Children's Hospital and McMaster Stem Cell & Cancer Research Institute, MDCL 5027, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada
| | - Anca Sorana Morrissy
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, 101 College Street, TMDT-11-401M, Toronto, ON M5G 1L7, Canada
| | - Paul Guilhamon
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada; Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Philipp Suetterlin
- Department of Craniofacial Development and Stem Cell Biology, King's College London, Floor 27, Guy's Hospital Tower Wing, London SE1 9RT, UK
| | - Xiao-Nan Li
- Texas Children's Cancer Centre, Texas Children's Hospital, Baylor College of Medicine, 6621 Fannin Street, MC-3-3320, Houston, TX 77479, USA
| | - Loredana Guglielmi
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, 4 Newark Street, London E1 2AT, UK
| | - Ashirwad Merve
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, 4 Newark Street, London E1 2AT, UK
| | - Hamza Farooq
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, 101 College Street, TMDT-11-401M, Toronto, ON M5G 1L7, Canada
| | - Mathieu Lupien
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada; Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Sheila K Singh
- Pediatric Neurosurgery, Department of Surgery, McMaster Children's Hospital and McMaster Stem Cell & Cancer Research Institute, MDCL 5027, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada
| | - M Albert Basson
- Department of Craniofacial Development and Stem Cell Biology, King's College London, Floor 27, Guy's Hospital Tower Wing, London SE1 9RT, UK
| | - Michael D Taylor
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, 101 College Street, TMDT-11-401M, Toronto, ON M5G 1L7, Canada
| | - Silvia Marino
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, 4 Newark Street, London E1 2AT, UK.
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17
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Park NI, Guilhamon P, Desai K, McAdam RF, Langille E, O'Connor M, Lan X, Whetstone H, Coutinho FJ, Vanner RJ, Ling E, Prinos P, Lee L, Selvadurai H, Atwal G, Kushida M, Clarke ID, Voisin V, Cusimano MD, Bernstein M, Das S, Bader G, Arrowsmith CH, Angers S, Huang X, Lupien M, Dirks PB. ASCL1 Reorganizes Chromatin to Direct Neuronal Fate and Suppress Tumorigenicity of Glioblastoma Stem Cells. Cell Stem Cell 2017; 21:411. [PMID: 28886368 DOI: 10.1016/j.stem.2017.08.008] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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18
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Park NI, Guilhamon P, Desai K, McAdam RF, Langille E, O'Connor M, Lan X, Whetstone H, Coutinho FJ, Vanner RJ, Ling E, Prinos P, Lee L, Selvadurai H, Atwal G, Kushida M, Clarke ID, Voisin V, Cusimano MD, Bernstein M, Das S, Bader G, Arrowsmith CH, Angers S, Huang X, Lupien M, Dirks PB. ASCL1 Reorganizes Chromatin to Direct Neuronal Fate and Suppress Tumorigenicity of Glioblastoma Stem Cells. Cell Stem Cell 2017; 21:209-224.e7. [PMID: 28712938 DOI: 10.1016/j.stem.2017.06.004] [Citation(s) in RCA: 106] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Revised: 05/10/2017] [Accepted: 06/15/2017] [Indexed: 12/17/2022]
Abstract
Glioblastomas exhibit a hierarchical cellular organization, suggesting that they are driven by neoplastic stem cells that retain partial yet abnormal differentiation potential. Here, we show that a large subset of patient-derived glioblastoma stem cells (GSCs) express high levels of Achaete-scute homolog 1 (ASCL1), a proneural transcription factor involved in normal neurogenesis. ASCL1hi GSCs exhibit a latent capacity for terminal neuronal differentiation in response to inhibition of Notch signaling, whereas ASCL1lo GSCs do not. Increasing ASCL1 levels in ASCL1lo GSCs restores neuronal lineage potential, promotes terminal differentiation, and attenuates tumorigenicity. ASCL1 mediates these effects by functioning as a pioneer factor at closed chromatin, opening new sites to activate a neurogenic gene expression program. Directing GSCs toward terminal differentiation may provide therapeutic applications for a subset of GBM patients and strongly supports efforts to restore differentiation potential in GBM and other cancers.
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Affiliation(s)
- Nicole I Park
- Developmental and Stem Cell Biology Program and Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Paul Guilhamon
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Kinjal Desai
- Developmental and Stem Cell Biology Program and Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Rochelle F McAdam
- Developmental and Stem Cell Biology Program and Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Ellen Langille
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Madlen O'Connor
- Developmental and Stem Cell Biology Program and Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Xiaoyang Lan
- Developmental and Stem Cell Biology Program and Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Heather Whetstone
- Developmental and Stem Cell Biology Program and Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Fiona J Coutinho
- Developmental and Stem Cell Biology Program and Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Robert J Vanner
- Developmental and Stem Cell Biology Program and Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Erick Ling
- Developmental and Stem Cell Biology Program and Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Panagiotis Prinos
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Lilian Lee
- Developmental and Stem Cell Biology Program and Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Hayden Selvadurai
- Developmental and Stem Cell Biology Program and Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Gurnit Atwal
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Michelle Kushida
- Developmental and Stem Cell Biology Program and Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Ian D Clarke
- Developmental and Stem Cell Biology Program and Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; OCAD University, Toronto, ON M5T 1W1, Canada
| | - Veronique Voisin
- The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Michael D Cusimano
- Division of Neurosurgery, University of Toronto, Toronto, ON M5S 1A8, Canada; St. Michael's Hospital, Toronto, ON M5B 1W8, Canada
| | - Mark Bernstein
- Division of Neurosurgery, University of Toronto, Toronto, ON M5S 1A8, Canada; Toronto Western Hospital, Toronto, ON M5T 2S8, Canada
| | - Sunit Das
- Division of Neurosurgery, University of Toronto, Toronto, ON M5S 1A8, Canada; St. Michael's Hospital, Toronto, ON M5B 1W8, Canada
| | - Gary Bader
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Cheryl H Arrowsmith
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Stephane Angers
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON M5S 3M2, Canada
| | - Xi Huang
- Developmental and Stem Cell Biology Program and Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Mathieu Lupien
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5S 1A8, Canada; Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada
| | - Peter B Dirks
- Developmental and Stem Cell Biology Program and Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada; Division of Neurosurgery, University of Toronto, Toronto, ON M5S 1A8, Canada.
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19
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Ghamrasni SE, Guilhamon P, Quevedo R, Yang C, Lupien M, Pugh T. Abstract 2410: Toward mutation analysis of regulatory elements: Epigenetic profiling of primary breast tumors. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-2410] [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
Non-coding mutations found in regulatory elements can function as driver mutations in breast cancer by changing the binding affinity of transcription factors for DNA, thereby resulting in direct change of expression of genes that promote cancer development. Identifying such additional driver mutations can reveal the molecular mechanisms favorable to breast cancer development and progression, as well as reveal new biomarkers to better tailor personalized/precision cancer medicine. In this study we have collected 20 primary luminal breast tumors and optimized experimental workflow to dissociate solid tumors and map open chromatin using ATAC-seq. In our initial experiments using ATAC-seq profiling of bulk tumor tissues, we were able to call an average of 15x103 peaks. Subsequently, flow cytometry analysis showed the presence of 15-25% of immune cells in our primary tumors. Therefore, we have optimized a workflow to eliminate immune cells and focus mainly on epithelial tumor cells. Primary breast tumors were digested using collagenase and further dissociated with dispase. Cells were sorted into two populations (mammary epithelial and immune cells) using anti-CD45, anti-CD49f and anti-EpCAM antibodies. Sorted mammary epithelial cells were then used for ATAC- and RNA-seq library preparation as well as for generation of patient derived organoids. Our new workflow resulted in an increased number of called peaks (40x103 vs 15x103), as well as a significant increase in the percentage of unique peaks compared to bulk sequencing (45% vs 15%). By refining our workflow to enrich for tumour content, we will continue our ongoing effort to profile these open chromatin regions and contextualize the mutations within in a large cohort of luminal breast cancers using targeted sequencing. These data will be compared with large-scale whole genome data generated by our group and made publicly available by others.
Citation Format: Samah El Ghamrasni, Paul Guilhamon, Rene Quevedo, Cindy Yang, Mathieu Lupien, Trevor Pugh. Toward mutation analysis of regulatory elements: Epigenetic profiling of primary breast tumors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2410. doi:10.1158/1538-7445.AM2017-2410
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Affiliation(s)
- Samah El Ghamrasni
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Paul Guilhamon
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Rene Quevedo
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Cindy Yang
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Mathieu Lupien
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Trevor Pugh
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
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20
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Torchia J, Golbourn B, Feng S, Ho KC, Sin-Chan P, Vasiljevic A, Norman JD, Guilhamon P, Garzia L, Agamez NR, Lu M, Chan TS, Picard D, de Antonellis P, Khuong-Quang DA, Planello AC, Zeller C, Barsyte-Lovejoy D, Lafay-Cousin L, Letourneau L, Bourgey M, Yu M, Gendoo DMA, Dzamba M, Barszczyk M, Medina T, Riemenschneider AN, Morrissy AS, Ra YS, Ramaswamy V, Remke M, Dunham CP, Yip S, Ng HK, Lu JQ, Mehta V, Albrecht S, Pimentel J, Chan JA, Somers GR, Faria CC, Roque L, Fouladi M, Hoffman LM, Moore AS, Wang Y, Choi SA, Hansford JR, Catchpoole D, Birks DK, Foreman NK, Strother D, Klekner A, Bognár L, Garami M, Hauser P, Hortobágyi T, Wilson B, Hukin J, Carret AS, Van Meter TE, Hwang EI, Gajjar A, Chiou SH, Nakamura H, Toledano H, Fried I, Fults D, Wataya T, Fryer C, Eisenstat DD, Scheinemann K, Fleming AJ, Johnston DL, Michaud J, Zelcer S, Hammond R, Afzal S, Ramsay DA, Sirachainan N, Hongeng S, Larbcharoensub N, Grundy RG, Lulla RR, Fangusaro JR, Druker H, Bartels U, Grant R, Malkin D, McGlade CJ, Nicolaides T, Tihan T, Phillips J, Majewski J, Montpetit A, Bourque G, Bader GD, Reddy AT, Gillespie GY, Warmuth-Metz M, Rutkowski S, Tabori U, Lupien M, Brudno M, Schüller U, Pietsch T, Judkins AR, Hawkins CE, Bouffet E, Kim SK, Dirks PB, Taylor MD, Erdreich-Epstein A, Arrowsmith CH, De Carvalho DD, Rutka JT, Jabado N, Huang A. Integrated (epi)-Genomic Analyses Identify Subgroup-Specific Therapeutic Targets in CNS Rhabdoid Tumors. Cancer Cell 2016; 30:891-908. [PMID: 27960086 PMCID: PMC5500911 DOI: 10.1016/j.ccell.2016.11.003] [Citation(s) in RCA: 164] [Impact Index Per Article: 20.5] [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: 01/06/2016] [Revised: 09/19/2016] [Accepted: 10/31/2016] [Indexed: 02/07/2023]
Abstract
We recently reported that atypical teratoid rhabdoid tumors (ATRTs) comprise at least two transcriptional subtypes with different clinical outcomes; however, the mechanisms underlying therapeutic heterogeneity remained unclear. In this study, we analyzed 191 primary ATRTs and 10 ATRT cell lines to define the genomic and epigenomic landscape of ATRTs and identify subgroup-specific therapeutic targets. We found ATRTs segregated into three epigenetic subgroups with distinct genomic profiles, SMARCB1 genotypes, and chromatin landscape that correlated with differential cellular responses to a panel of signaling and epigenetic inhibitors. Significantly, we discovered that differential methylation of a PDGFRB-associated enhancer confers specific sensitivity of group 2 ATRT cells to dasatinib and nilotinib, and suggest that these are promising therapies for this highly lethal ATRT subtype.
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Affiliation(s)
- Jonathon Torchia
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5G0A4, Canada; Department of Paediatrics, University of Toronto, Toronto, ON M5G0A4, Canada; Division of Hematology/Oncology, Hospital for Sick Children, Toronto, ON M5G1X8, Canada; Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, ON M5G1X8, Canada
| | - Brian Golbourn
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5G0A4, Canada; Division of Neurosurgery, Hospital for Sick Children, Toronto, ON M5G1X8, Canada; Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, ON M5G1X8, Canada
| | - Shengrui Feng
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G0A4, Canada; Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G1L7, Canada
| | - King Ching Ho
- Division of Hematology/Oncology, Hospital for Sick Children, Toronto, ON M5G1X8, Canada; Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, ON M5G1X8, Canada
| | - Patrick Sin-Chan
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5G0A4, Canada; Department of Paediatrics, University of Toronto, Toronto, ON M5G0A4, Canada; Division of Hematology/Oncology, Hospital for Sick Children, Toronto, ON M5G1X8, Canada; Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, ON M5G1X8, Canada
| | - Alexandre Vasiljevic
- Department of Pathology, Groupement Hospitalier Est, CHU de Lyon, Lyon-Bron 69677, France
| | - Joseph D Norman
- Division of Hematology/Oncology, Hospital for Sick Children, Toronto, ON M5G1X8, Canada; Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, ON M5G1X8, Canada
| | - Paul Guilhamon
- Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G1L7, Canada
| | - Livia Garzia
- Program in Developmental & Stem Cell Biology, Hospital for Sick Children, Toronto, ON M5G1X8, Canada; Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, ON M5G1X8, Canada
| | - Natalia R Agamez
- Division of Hematology/Oncology, Hospital for Sick Children, Toronto, ON M5G1X8, Canada; Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, ON M5G1X8, Canada
| | - Mei Lu
- Division of Hematology/Oncology, Hospital for Sick Children, Toronto, ON M5G1X8, Canada; Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, ON M5G1X8, Canada
| | - Tiffany S Chan
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5G0A4, Canada; Department of Paediatrics, University of Toronto, Toronto, ON M5G0A4, Canada; Division of Hematology/Oncology, Hospital for Sick Children, Toronto, ON M5G1X8, Canada; Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, ON M5G1X8, Canada
| | - Daniel Picard
- Division of Hematology/Oncology, Hospital for Sick Children, Toronto, ON M5G1X8, Canada; Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, ON M5G1X8, Canada
| | - Pasqualino de Antonellis
- Program in Developmental & Stem Cell Biology, Hospital for Sick Children, Toronto, ON M5G1X8, Canada; Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, ON M5G1X8, Canada
| | - Dong-Anh Khuong-Quang
- Department of Pediatrics, McGill University, Montreal, QC H3Z2Z3, Canada; Department of Human Genetics, McGill University, Montreal, QC H3Z2Z3, Canada
| | - Aline C Planello
- Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G1L7, Canada
| | - Constanze Zeller
- Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G1L7, Canada
| | - Dalia Barsyte-Lovejoy
- Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G1L7, Canada
| | - Lucie Lafay-Cousin
- Division of Pediatric Hematology/Oncology, Alberta Children's Hospital, AB T3B6A8, Canada
| | - Louis Letourneau
- Genome Quebec Innovation Centre, McGill University, Montreal, QC H3A1A4, Canada
| | - Mathieu Bourgey
- Genome Quebec Innovation Centre, McGill University, Montreal, QC H3A1A4, Canada
| | - Man Yu
- Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, ON M5G1X8, Canada
| | - Deena M A Gendoo
- Division of Hematology/Oncology, Hospital for Sick Children, Toronto, ON M5G1X8, Canada; Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, ON M5G1X8, Canada
| | - Misko Dzamba
- Department of Computer Science, University of Toronto, Toronto, ON M5G0A4, Canada
| | - Mark Barszczyk
- Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, ON M5G1X8, Canada
| | - Tiago Medina
- Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G1L7, Canada
| | - Alexandra N Riemenschneider
- Division of Neurosurgery, Hospital for Sick Children, Toronto, ON M5G1X8, Canada; Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, ON M5G1X8, Canada
| | - A Sorana Morrissy
- Program in Developmental & Stem Cell Biology, Hospital for Sick Children, Toronto, ON M5G1X8, Canada; Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, ON M5G1X8, Canada
| | - Young-Shin Ra
- Department of Neurosurgery, Asan Medical Center, Seoul 138-736, Korea
| | - Vijay Ramaswamy
- Division of Hematology/Oncology, Hospital for Sick Children, Toronto, ON M5G1X8, Canada; Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, ON M5G1X8, Canada
| | - Marc Remke
- Division of Hematology/Oncology, Hospital for Sick Children, Toronto, ON M5G1X8, Canada; Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, ON M5G1X8, Canada
| | - Christopher P Dunham
- Division of Anatomic Pathology, Children's and Women's Health Centre of B.C, University of British Columbia, Vancouver, BC V6H3N1, Canada
| | - Stephen Yip
- Department of Pathology & Laboratory Medicine, University of British Columbia, V6T1Z3, Canada
| | - Ho-Keung Ng
- Department of Anatomical and Cellular Pathology, Chinese University of Hong Kong, Hong Kong, China
| | - Jian-Qiang Lu
- Laboratory Medicine and Pathology, Stollery Children's Hospital, University of Alberta, Edmonton, AB T2W3N2, Canada
| | - Vivek Mehta
- Division of Neurosurgery, Stollery Children's Hospital, University of Alberta, Edmonton, AB T2W3N2, Canada
| | - Steffen Albrecht
- Department of Pathology, McGill University, Montreal, QC H3Z2Z3, Canada
| | - Jose Pimentel
- Divison of Pathology, Hospital de Santa Maria, Centro Hospitalar Lisboa Norte, Lisbon 1649-035, Portugal
| | - Jennifer A Chan
- Department of Pathology and Laboratory Medicine, University of Calgary, Calgary, AB T2N1N4, Canada
| | - Gino R Somers
- Department of Paediatric Laboratory Medicine, Hospital for Sick Children, Toronto, ON M5G1X8, Canada
| | - Claudia C Faria
- Department of Neurosurgery, Hospital de Santa Maria, Centro Hospitalar Lisboa Norte, Lisbon 1649-035, Portugal
| | - Lucia Roque
- Cytometry and Cytogenetic Laboratory, CIPM, Portuguese Cancer Institute, Lisbon 1099-023, Portugal
| | - Maryam Fouladi
- Division of Oncology, Department of Cancer and Blood Diseases, Cincinnati Children's Hospital, Cincinnati, OH 45229, USA
| | - Lindsey M Hoffman
- Department of Pediatrics, University of Colorado, Denver, CO 80045, USA
| | - Andrew S Moore
- Oncology Service, Children's Health Queensland Hospital; University of Queensland Diamantina Institute, Brisbane, QLD 4102, Australia
| | - Yin Wang
- Research Institute of Health Development Strategies, Fudan University, Shanghai 200032, China
| | - Seung Ah Choi
- Division of Pediatric Neurosurgery, Seoul National University Children's Hospital, Seoul 03080, Korea
| | - Jordan R Hansford
- Royal Children's Hospital, Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia
| | - Daniel Catchpoole
- Children's Cancer Research Unit, Children's Hospital at Westmead, Westmead, NSW 2145, Australia
| | - Diane K Birks
- Department of Pediatrics, University of Colorado, Denver, CO 80045, USA
| | | | - Doug Strother
- Division of Pediatric Hematology/Oncology, Stollery Children's Hospital, University of Alberta, Edmonton, AB T2W3N2, Canada
| | - Almos Klekner
- Department of Neurosurgery, University of Debrecen, Debrecen 4032, Hungary
| | - Laszló Bognár
- Department of Neurosurgery, University of Debrecen, Debrecen 4032, Hungary
| | - Miklós Garami
- Second Department of Pediatrics, Semmelweis University, Budapest 1094, Hungary
| | - Péter Hauser
- Second Department of Pediatrics, Semmelweis University, Budapest 1094, Hungary
| | - Tibor Hortobágyi
- Department of Histopathology, University of Szeged, Szeged 6720, Hungary
| | - Beverly Wilson
- Division of Pediatric Hematology/Oncology, Stollery Children's Hospital, University of Alberta, Edmonton, AB T2W3N2, Canada
| | - Juliette Hukin
- Division of Hematology and Oncology, Children's and Women's Health Centre of B.C, University of British Columbia, Vancouver, BC V6H3N1, Canada
| | - Anne-Sophie Carret
- Department of Pediatrics, Division of Hematology-Oncology, Université de Montréal/CHU Sainte-Justine, Montreal, QC H3T1C5, Canada
| | - Timothy E Van Meter
- Department of Neurosurgery, Virginia Commonwealth University, Richmond, VA 23298-0631, USA
| | - Eugene I Hwang
- Department of Oncology, Children's National Medical Center, Washington, DC 20010, USA
| | - Amar Gajjar
- Division of Neuro-Oncology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Shih-Hwa Chiou
- Department of Medical Research, Taipei Veterans General Hospital and National Yang-Ming University, Taipei 112, Taiwan
| | - Hideo Nakamura
- Department of Neurosurgery, Kumamoto University, Kumamoto 860-8556, Japan
| | - Helen Toledano
- Department of Pediatric Hematology Oncology, Children's Medical Center of Israel, Petach Tikva 49202, Isreal
| | - Iris Fried
- Department of Pediatric Hematology-Oncology, Hadassah Hebrew University Medical Center, Jerusalem 91120, Israel
| | - Daniel Fults
- Department of Neurosurgery, University of Utah, School of Medicine, Salt Lake City, UT 84132, USA
| | - Takafumi Wataya
- Department of Neurosurgery, Shizuoka Children's Hospital, Shizuoka 420-8660, Japan
| | - Chris Fryer
- Division of Hematology and Oncology, Children's and Women's Health Centre of B.C, University of British Columbia, Vancouver, BC V6H3N1, Canada
| | - David D Eisenstat
- Division of Pediatric Hematology/Oncology, Stollery Children's Hospital, University of Alberta, Edmonton, AB T2W3N2, Canada
| | - Katrin Scheinemann
- Department of Pediatrics, McMaster University, Hamilton, ON L8S4K1, Canada
| | - Adam J Fleming
- Department of Pediatrics, McMaster University, Hamilton, ON L8S4K1, Canada
| | - Donna L Johnston
- Department of Pediatrics, Children's Hospital of Eastern Ontario, University of Ottawa, Ottawa, ON K1H8L1, Canada
| | - Jean Michaud
- Pathology and Laboratory Medicine, Children's Hospital of Eastern Ontario, University of Ottawa, Ottawa, ON K1H8L1, Canada
| | - Shayna Zelcer
- Division of Pediatric Hematology/Oncology, Children's Hospital, London Health Sciences Center, London, ON N6A5A5, Canada
| | - Robert Hammond
- Department of Pathology and Laboratory Medicine, Children's Hospital of Western Ontario, University of Western Ontario, London, ON N6A5W9, Canada
| | - Samina Afzal
- Department of Pediatrics, Dalhousie University, Halifax, NS B3H4R2, Canada
| | - David A Ramsay
- Department of Pathology and Laboratory Medicine, Children's Hospital of Western Ontario, University of Western Ontario, London, ON N6A5W9, Canada
| | - Nongnuch Sirachainan
- Department of Pediatrics, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok 10300, Thailand
| | - Suradej Hongeng
- Department of Pediatrics, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok 10300, Thailand
| | - Noppadol Larbcharoensub
- Department of Pathology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand
| | - Richard G Grundy
- Children's Brain Tumour Research Centre, University of Nottingham, Nottingham NG72RD, England
| | - Rishi R Lulla
- Division of Pediatric Hematology-Oncology and Stem Cell Transplantation, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, IL 60611, USA
| | - Jason R Fangusaro
- Division of Pediatric Hematology-Oncology and Stem Cell Transplantation, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, IL 60611, USA
| | - Harriet Druker
- Division of Hematology/Oncology, Hospital for Sick Children, Toronto, ON M5G1X8, Canada
| | - Ute Bartels
- Division of Hematology/Oncology, Hospital for Sick Children, Toronto, ON M5G1X8, Canada
| | - Ronald Grant
- Division of Hematology/Oncology, Hospital for Sick Children, Toronto, ON M5G1X8, Canada
| | - David Malkin
- Department of Paediatrics, University of Toronto, Toronto, ON M5G0A4, Canada; Division of Hematology/Oncology, Hospital for Sick Children, Toronto, ON M5G1X8, Canada; Program in Genetics & Genome Biology, Hospital for Sick Children, Toronto, ON M5G1X8, Canada
| | - C Jane McGlade
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G0A4, Canada; Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, ON M5G1X8, Canada
| | - Theodore Nicolaides
- Department of Pediatrics (Hematology/Oncology), University of California, San Francisco, San Francisco, CA 94143-0112, USA
| | - Tarik Tihan
- Department of Neurosurgery, University of California, San Francisco, San Francisco, CA 94143-0112, USA
| | - Joanna Phillips
- Department of Neurosurgery, University of California, San Francisco, San Francisco, CA 94143-0112, USA
| | - Jacek Majewski
- Department of Human Genetics, McGill University, Montreal, QC H3Z2Z3, Canada; Genome Quebec Innovation Centre, McGill University, Montreal, QC H3A1A4, Canada
| | - Alexandre Montpetit
- Genome Quebec Innovation Centre, McGill University, Montreal, QC H3A1A4, Canada
| | - Guillaume Bourque
- Department of Human Genetics, McGill University, Montreal, QC H3Z2Z3, Canada; Genome Quebec Innovation Centre, McGill University, Montreal, QC H3A1A4, Canada
| | - Gary D Bader
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5G0A4, Canada
| | - Alyssa T Reddy
- Department of Pediatric Hematology and Oncology, University of Alabama, Birmingham, AL 35233, USA
| | - G Yancey Gillespie
- Department of Neurosurgery, University of Alabama, Birmingham, AL 35233, USA
| | - Monika Warmuth-Metz
- Department of Neuroradiology, University of Würzburg, Würzburg 97070, Germany
| | - Stefan Rutkowski
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg 20246, Germany
| | - Uri Tabori
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5G0A4, Canada; Division of Hematology/Oncology, Hospital for Sick Children, Toronto, ON M5G1X8, Canada; Program in Genetics & Genome Biology, Hospital for Sick Children, Toronto, ON M5G1X8, Canada; Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, ON M5G1X8, Canada
| | - Mathieu Lupien
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G0A4, Canada; Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G1L7, Canada
| | - Michael Brudno
- Department of Computer Science, University of Toronto, Toronto, ON M5G0A4, Canada; Program in Genetics & Genome Biology, Hospital for Sick Children, Toronto, ON M5G1X8, Canada
| | - Ulrich Schüller
- Department of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg 20246, Germany
| | - Torsten Pietsch
- Institute for Neuropathology, University of Bonn Medical Center, Bonn 53105, Germany
| | - Alexander R Judkins
- Department of Pathology & Laboratory Medicine, Children's Hospital of Los Angeles, Los Angeles, CA 90027, USA
| | - Cynthia E Hawkins
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5G0A4, Canada; Division of Pathology, Hospital for Sick Children, Toronto, ON M5G1X8, Canada; Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, ON M5G1X8, Canada
| | - Eric Bouffet
- Division of Hematology/Oncology, Hospital for Sick Children, Toronto, ON M5G1X8, Canada; Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, ON M5G1X8, Canada
| | - Seung-Ki Kim
- Division of Pediatric Neurosurgery, Seoul National University Children's Hospital, Seoul 03080, Korea
| | - Peter B Dirks
- Division of Neurosurgery, Hospital for Sick Children, Toronto, ON M5G1X8, Canada; Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, ON M5G1X8, Canada
| | - Michael D Taylor
- Division of Neurosurgery, Hospital for Sick Children, Toronto, ON M5G1X8, Canada; Program in Developmental & Stem Cell Biology, Hospital for Sick Children, Toronto, ON M5G1X8, Canada; Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, ON M5G1X8, Canada
| | - Anat Erdreich-Epstein
- Department of Pediatrics, Children's Hospital Los Angeles, Keck School of Medicine, University of Southern California, Los Angeles, CA 90027, USA
| | - Cheryl H Arrowsmith
- Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G1L7, Canada
| | - Daniel D De Carvalho
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G0A4, Canada; Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G1L7, Canada.
| | - James T Rutka
- Department of Surgery, University of Toronto, Toronto, ON M5G0A4, Canada; Division of Neurosurgery, Hospital for Sick Children, Toronto, ON M5G1X8, Canada; Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, ON M5G1X8, Canada.
| | - Nada Jabado
- Department of Pediatrics, McGill University, Montreal, QC H3Z2Z3, Canada; Department of Human Genetics, McGill University, Montreal, QC H3Z2Z3, Canada.
| | - Annie Huang
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5G0A4, Canada; Department of Paediatrics, University of Toronto, Toronto, ON M5G0A4, Canada; Division of Hematology/Oncology, Hospital for Sick Children, Toronto, ON M5G1X8, Canada; Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, ON M5G1X8, Canada.
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21
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Charlton J, Williams RD, Sebire NJ, Popov S, Vujanic G, Chagtai T, Alcaide-German M, Morris T, Butcher LM, Guilhamon P, Beck S, Pritchard-Jones K. Comparative methylome analysis identifies new tumour subtypes and biomarkers for transformation of nephrogenic rests into Wilms tumour. Genome Med 2015; 7:11. [PMID: 25763109 PMCID: PMC4354990 DOI: 10.1186/s13073-015-0136-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 01/21/2015] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Wilms tumours (WTs) are characterised by several hallmarks that suggest epimutations such as aberrant DNA methylation are involved in tumour progression: loss of imprinting at 11p15, lack of recurrent mutations and formation of nephrogenic rests (NRs), which are lesions of retained undifferentiated embryonic tissue that can give rise to WTs. METHODS To identify such epimutations, we performed a comprehensive methylome analysis on 20 matched trios of micro-dissected WTs, NRs and surrounding normal kidneys (NKs) using Illumina Infinium HumanMethylation450 Bead Chips and functionally validated findings using RNA sequencing. RESULTS Comparison of NRs with NK revealed prominent tissue biomarkers: 629 differentially methylated regions, of which 55% were hypermethylated and enriched for domains that are bivalent in embryonic stem cells and for genes expressed during development (P = 2.49 × 10(-5)). Comparison of WTs with NRs revealed two WT subgroups; group-2 WTs and NRs were epigenetically indistinguishable whereas group-1 WTs showed an increase in methylation variability, hypomethylation of renal development genes, hypermethylation and relative loss of expression of cell adhesion genes and known and potential new WT tumour suppressor genes (CASP8, H19, MIR195, RB1 and TSPAN32) and was strongly associated with bilateral disease (P = 0.032). Comparison of WTs and NRs to embryonic kidney highlighted the significance of polycomb target methylation in Wilms tumourigenesis. CONCLUSIONS Methylation levels vary during cancer evolution. We have described biomarkers related to WT evolution from its precursor NRs which may be useful to differentiate between these tissues for patients with bilateral disease.
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Affiliation(s)
- Jocelyn Charlton
- />UCL Institute of Child Health, University College London, 30 Guilford Street, London, WC1N 1EH UK
| | - Richard D Williams
- />UCL Institute of Child Health, University College London, 30 Guilford Street, London, WC1N 1EH UK
| | - Neil J Sebire
- />UCL Institute of Child Health, University College London, 30 Guilford Street, London, WC1N 1EH UK
| | - Sergey Popov
- />The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG UK
| | - Gordan Vujanic
- />Department of Pathology, Cardiff University School of Medicine, Heath Park, Cardiff, CF14 4XN UK
| | - Tasnim Chagtai
- />UCL Institute of Child Health, University College London, 30 Guilford Street, London, WC1N 1EH UK
| | - Marisa Alcaide-German
- />UCL Institute of Child Health, University College London, 30 Guilford Street, London, WC1N 1EH UK
| | - Tiffany Morris
- />UCL Cancer Institute, University College London, 72 Huntley Street, London, WC1E 6BT UK
| | - Lee M Butcher
- />UCL Cancer Institute, University College London, 72 Huntley Street, London, WC1E 6BT UK
| | - Paul Guilhamon
- />UCL Cancer Institute, University College London, 72 Huntley Street, London, WC1E 6BT UK
| | - Stephan Beck
- />UCL Cancer Institute, University College London, 72 Huntley Street, London, WC1E 6BT UK
| | - Kathy Pritchard-Jones
- />UCL Institute of Child Health, University College London, 30 Guilford Street, London, WC1N 1EH UK
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22
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Stewart SK, Morris TJ, Guilhamon P, Bulstrode H, Bachman M, Balasubramanian S, Beck S. oxBS-450K: a method for analysing hydroxymethylation using 450K BeadChips. Methods 2015; 72:9-15. [PMID: 25175075 PMCID: PMC4304834 DOI: 10.1016/j.ymeth.2014.08.009] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Revised: 08/07/2014] [Accepted: 08/15/2014] [Indexed: 12/14/2022] Open
Abstract
DNA methylation analysis has become an integral part of biomedical research. For high-throughput applications such as epigenome-wide association studies, the Infinium HumanMethylation450 (450K) BeadChip is currently the platform of choice. However, BeadChip processing relies on traditional bisulfite (BS) based protocols which cannot discriminate between 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC). Here, we report the adaptation of the recently developed oxidative bisulfite (oxBS) chemistry to specifically detect both 5mC and 5hmC in a single workflow using 450K BeadChips, termed oxBS-450K. Supported by validation using mass spectrometry and pyrosequencing, we demonstrate reproducible (R(2)>0.99) detection of 5hmC in human brain tissue using the optimised oxBS-450K protocol described here.
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Affiliation(s)
- Sabrina K Stewart
- Department of Cancer Biology, UCL Cancer Institute, University College London, London WC1E 6BT, UK
| | - Tiffany J Morris
- Department of Cancer Biology, UCL Cancer Institute, University College London, London WC1E 6BT, UK
| | - Paul Guilhamon
- Department of Cancer Biology, UCL Cancer Institute, University College London, London WC1E 6BT, UK
| | - Harry Bulstrode
- Scottish Centre for Regenerative Medicine, Edinburgh EH16 4UU, UK
| | - Martin Bachman
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | | | - Stephan Beck
- Department of Cancer Biology, UCL Cancer Institute, University College London, London WC1E 6BT, UK.
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23
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Guilhamon P, Butcher LM, Presneau N, Wilson GA, Feber A, Paul DS, Schütte M, Haybaeck J, Keilholz U, Hoffman J, Ross MT, Flanagan AM, Beck S. Assessment of patient-derived tumour xenografts (PDXs) as a discovery tool for cancer epigenomics. Genome Med 2014; 6:116. [PMID: 25587359 PMCID: PMC4292812 DOI: 10.1186/s13073-014-0116-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [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: 07/16/2014] [Accepted: 11/25/2014] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND The use of tumour xenografts is a well-established research tool in cancer genomics but has not yet been comprehensively evaluated for cancer epigenomics. METHODS In this study, we assessed the suitability of patient-derived tumour xenografts (PDXs) for methylome analysis using Infinium 450 K Beadchips and MeDIP-seq. RESULTS Controlled for confounding host (mouse) sequences, comparison of primary PDXs and matching patient tumours in a rare (osteosarcoma) and common (colon) cancer revealed that an average 2.7% of the assayed CpG sites undergo major (Δβ ≥ 0.51) methylation changes in a cancer-specific manner as a result of the xenografting procedure. No significant subsequent methylation changes were observed after a second round of xenografting between primary and secondary PDXs. Based on computational simulation using publically available methylation data, we additionally show that future studies comparing two groups of PDXs should use 15 or more samples in each group to minimise the impact of xenografting-associated changes in methylation on comparison results. CONCLUSIONS Our results from rare and common cancers indicate that PDXs are a suitable discovery tool for cancer epigenomics and we provide guidance on how to overcome the observed limitations.
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Affiliation(s)
- Paul Guilhamon
- Medical Genomics, UCL Cancer Institute, University College London, London, WC1E 6DD UK
| | - Lee M Butcher
- Medical Genomics, UCL Cancer Institute, University College London, London, WC1E 6DD UK
| | - Nadege Presneau
- Genetics and Cell Biology of Sarcoma, UCL Cancer Institute, University College London, London, WC1E 6DD UK ; Department of Biomedical Sciences, University of Westminster, London, W1W 6UW UK
| | - Gareth A Wilson
- Medical Genomics, UCL Cancer Institute, University College London, London, WC1E 6DD UK ; Translational Cancer Therapeutics Laboratory, CR-UK London Research Institute, London, WC2A 3LY UK
| | - Andrew Feber
- Medical Genomics, UCL Cancer Institute, University College London, London, WC1E 6DD UK
| | - Dirk S Paul
- Medical Genomics, UCL Cancer Institute, University College London, London, WC1E 6DD UK
| | | | - Johannes Haybaeck
- Institute of Pathology, Medical University of Graz, 8036 Graz, Austria
| | - Ulrich Keilholz
- Department of Hematology and Medical Oncology, Charité Comprehensive Cancer Center, D-10117 Berlin, Germany
| | | | - Mark T Ross
- Illumina Cambridge Ltd, Chesterford Research Park, Little Chesterford, CB10 1XL UK
| | - Adrienne M Flanagan
- Genetics and Cell Biology of Sarcoma, UCL Cancer Institute, University College London, London, WC1E 6DD UK ; Department of Histopathology, Royal National Orthopaedic Hospital NHS Trust, Stanmore, Middlesex, London, HA7 4LP UK
| | - Stephan Beck
- Medical Genomics, UCL Cancer Institute, University College London, London, WC1E 6DD UK
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24
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Paul DS, Guilhamon P, Karpathakis A, Butcher LM, Thirlwell C, Feber A, Beck S. Assessment of RainDrop BS-seq as a method for large-scale, targeted bisulfite sequencing. Epigenetics 2014; 9:678-84. [PMID: 24518816 PMCID: PMC4063826 DOI: 10.4161/epi.28041] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
We present a systematic assessment of RainDrop BS-seq, a novel method for large-scale, targeted bisulfite sequencing using microdroplet-based PCR amplification coupled with next-generation sequencing. We compared DNA methylation levels at 498 target loci (1001 PCR amplicons) in human whole blood, osteosarcoma cells and an archived tumor tissue sample. We assessed the ability of RainDrop BS-seq to accurately measure DNA methylation over a range of DNA quantities (from 10 to 1500 ng), both with and without whole-genome amplification (WGA) following bisulfite conversion. DNA methylation profiles generated using at least 100 ng correlated well (median R = 0.92) with those generated on Illumina Infinium HumanMethylation450 BeadChips, currently the platform of choice for epigenome-wide association studies (EWAS). WGA allowed for testing of samples with a starting DNA amount of 10 and 50 ng, although a reduced correlation was observed (median R = 0.79). We conclude that RainDrop BS-seq is suitable for measuring DNA methylation levels using nanogram quantities of DNA, and can be used to study candidate epigenetic biomarker loci in an accurate and high-throughput manner, paving the way for its application to routine clinical diagnostics.
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Affiliation(s)
- Dirk S Paul
- UCL Cancer Institute; University College London; London, United Kingdom
| | - Paul Guilhamon
- UCL Cancer Institute; University College London; London, United Kingdom
| | - Anna Karpathakis
- UCL Cancer Institute; University College London; London, United Kingdom
| | - Lee M Butcher
- UCL Cancer Institute; University College London; London, United Kingdom
| | | | - Andrew Feber
- UCL Cancer Institute; University College London; London, United Kingdom
| | - Stephan Beck
- UCL Cancer Institute; University College London; London, United Kingdom
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25
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Feber A, Guilhamon P, Lechner M, Fenton T, Wilson GA, Thirlwell C, Morris TJ, Flanagan AM, Teschendorff AE, Kelly JD, Beck S. Using high-density DNA methylation arrays to profile copy number alterations. Genome Biol 2014; 15:R30. [PMID: 24490765 PMCID: PMC4054098 DOI: 10.1186/gb-2014-15-2-r30] [Citation(s) in RCA: 97] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Accepted: 02/03/2014] [Indexed: 12/17/2022] Open
Abstract
The integration of genomic and epigenomic data is an increasingly popular approach for studying the complex mechanisms driving cancer development. We have developed a method for evaluating both methylation and copy number from high-density DNA methylation arrays. Comparing copy number data from Infinium HumanMethylation450 BeadChips and SNP arrays, we demonstrate that Infinium arrays detect copy number alterations with the sensitivity of SNP platforms. These results show that high-density methylation arrays provide a robust and economic platform for detecting copy number and methylation changes in a single experiment. Our method is available in the ChAMP Bioconductor package: http://www.bioconductor.org/packages/2.13/bioc/html/ChAMP.html.
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Affiliation(s)
- Andrew Feber
- UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6BT, UK
| | - Paul Guilhamon
- UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6BT, UK
| | - Matthias Lechner
- UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6BT, UK
| | - Tim Fenton
- UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6BT, UK
| | - Gareth A Wilson
- UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6BT, UK
| | - Christina Thirlwell
- UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6BT, UK
| | - Tiffany J Morris
- UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6BT, UK
| | - Adrienne M Flanagan
- UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6BT, UK
- Royal National Orthopaedic Hospital, Stanmore, Brockly Hill, Middlesex HA7 4LP, UK
| | - Andrew E Teschendorff
- UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6BT, UK
| | - John D Kelly
- UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6BT, UK
- Division of Surgery and Interventional Science, UCL Medical School, University College London, London WC1E 6BT, UK
| | - Stephan Beck
- UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6BT, UK
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Guilhamon P, Eskandarpour M, Halai D, Wilson GA, Feber A, Teschendorff AE, Gomez V, Hergovich A, Tirabosco R, Fernanda Amary M, Baumhoer D, Jundt G, Ross MT, Flanagan AM, Beck S. Meta-analysis of IDH-mutant cancers identifies EBF1 as an interaction partner for TET2. Nat Commun 2014; 4:2166. [PMID: 23863747 PMCID: PMC3759038 DOI: 10.1038/ncomms3166] [Citation(s) in RCA: 140] [Impact Index Per Article: 14.0] [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: 02/14/2013] [Accepted: 06/18/2013] [Indexed: 12/22/2022] Open
Abstract
Isocitrate dehydrogenase (IDH) genes 1 and 2 are frequently mutated in acute myeloid leukaemia (AML), low-grade glioma, cholangiocarcinoma (CC) and chondrosarcoma (CS). For AML, low-grade glioma and CC, mutant IDH status is associated with a DNA hypermethylation phenotype, implicating altered epigenome dynamics in the aetiology of these cancers. Here we show that the IDH variants in CS are also associated with a hypermethylation phenotype and display increased production of the oncometabolite 2-hydroxyglutarate, supporting the role of mutant IDH-produced 2-hydroxyglutarate as an inhibitor of TET-mediated DNA demethylation. Meta-analysis of the acute myeloid leukaemia, low-grade glioma, cholangiocarcinoma and CS methylation data identifies cancer-specific effectors within the retinoic acid receptor activation pathway among the hypermethylated targets. By analysing sequence motifs surrounding hypermethylated sites across the four cancer types, and using chromatin immunoprecipitation and western blotting, we identify the transcription factor EBF1 (early B-cell factor 1) as an interaction partner for TET2, suggesting a sequence-specific mechanism for regulating DNA methylation. Cancer-associated mutations in isocitrate dehydrogenase are proposed to impair TET2-dependent DNA demethylation. By comparing the methylomes of IDH-mutant cancers, the authors identify the transcription factor EBF1 as a partner of TET2, suggesting a possible means for targeting TET2 to specific DNA sequences.
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Affiliation(s)
- Paul Guilhamon
- Medical Genomics, UCL Cancer Institute, University College London, London, UK
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