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Milevskiy MJ, Coughlan HD, Kane SR, Johanson TM, Kordafshari S, Chan WF, Tsai M, Surgenor E, Wilcox S, Allan RS, Chen Y, Lindeman GJ, Smyth GK, Visvader JE. Three-dimensional genome architecture coordinates key regulators of lineage specification in mammary epithelial cells. CELL GENOMICS 2023; 3:100424. [PMID: 38020976 PMCID: PMC10667557 DOI: 10.1016/j.xgen.2023.100424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 06/20/2023] [Accepted: 09/20/2023] [Indexed: 12/01/2023]
Abstract
Although lineage-specific genes have been identified in the mammary gland, little is known about the contribution of the 3D genome organization to gene regulation in the epithelium. Here, we describe the chromatin landscape of the three major epithelial subsets through integration of long- and short-range chromatin interactions, accessibility, histone modifications, and gene expression. While basal genes display exquisite lineage specificity via distal enhancers, luminal-specific genes show widespread promoter priming in basal cells. Cell specificity in luminal progenitors is largely mediated through extensive chromatin interactions with super-enhancers in gene-body regions in addition to interactions with polycomb silencer elements. Moreover, lineage-specific transcription factors appear to be controlled through cell-specific chromatin interactivity. Finally, chromatin accessibility rather than interactivity emerged as a defining feature of the activation of quiescent basal stem cells. This work provides a comprehensive resource for understanding the role of higher-order chromatin interactions in cell-fate specification and differentiation in the adult mouse mammary gland.
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Affiliation(s)
- Michael J.G. Milevskiy
- ACRF Cancer Biology and Stem Cells Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Hannah D. Coughlan
- Department of Medical Biology, The University of Melbourne, Parkville, VIC 3010, Australia
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Serena R. Kane
- ACRF Cancer Biology and Stem Cells Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Timothy M. Johanson
- Department of Medical Biology, The University of Melbourne, Parkville, VIC 3010, Australia
- Immunology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Somayeh Kordafshari
- ACRF Cancer Biology and Stem Cells Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Wing Fuk Chan
- Department of Medical Biology, The University of Melbourne, Parkville, VIC 3010, Australia
- Immunology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Minhsuang Tsai
- ACRF Cancer Biology and Stem Cells Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Elliot Surgenor
- ACRF Cancer Biology and Stem Cells Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Stephen Wilcox
- Advanced Technology and Biology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Rhys S. Allan
- Department of Medical Biology, The University of Melbourne, Parkville, VIC 3010, Australia
- Immunology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Yunshun Chen
- ACRF Cancer Biology and Stem Cells Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC 3010, Australia
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Geoffrey J. Lindeman
- ACRF Cancer Biology and Stem Cells Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medicine, Royal Melbourne Hospital, The University of Melbourne, Parkville, VIC 3010, Australia
- Parkville Familial Cancer Centre and Department of Medical Oncology, The Royal Melbourne Hospital and Peter MacCallum Cancer Centre, Parkville, VIC 3050, Australia
| | - Gordon K. Smyth
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- School of Mathematics and Statistics, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Jane E. Visvader
- ACRF Cancer Biology and Stem Cells Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC 3010, Australia
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2
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Oubaddou Y, Ben Ali F, Oubaqui FE, Qmichou Z, Bakri Y, Rabii Ameziane RA. The Tumor Suppressor BRCA1/2, Cancer Susceptibility and Genome Instability in Gynecological and Mammary Cancers. Asian Pac J Cancer Prev 2023; 24:3139-3153. [PMID: 37774066 PMCID: PMC10762740 DOI: 10.31557/apjcp.2023.24.9.3139] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 09/10/2023] [Indexed: 10/01/2023] Open
Abstract
BRCA1 and BRCA2 germline alterations highly predispose women to breast and ovarian cancers. They are mostly found within the TNBC (Triple-Negative Breast Cancer) and the HGSOC (High-Grade Serous Ovarian Carcinoma) subsets, known by an aggressive phenotype, the lack of therapeutic targets and poor prognosis. Importantly, there is an increased risk for cervical cancer in BRCA1 and BRCA2 mutation carriers that raises questions about the link between the HPV-driven genome instability and BRCA1 and BRCA2 germline mutations. Clinical, preclinical, and in vitro studies explained the increased risk for breast and ovarian cancers by genome instability resulting from the lack or loss of many functions related to BRCA1 or BRCA2 proteins such as DNA damage repair, stalled forks and R-loops resolution, transcription regulation, cell cycle control, and oxidative stress. In this review, we decipher the relationship between BRCA1/2 alterations and genomic instability leading to gynecomammary cancers through results from patients, mice, and cell lines. Understanding the early events of BRCA1/2-driven genomic instability in gynecomammary cancers would help to find new biomarkers for early diagnosis, improve the sensitivity of emerging therapies such as PARP inhibitors, and reveal new potential therapeutic targets.
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Affiliation(s)
- Yassire Oubaddou
- Laboratory of Biology of Human Pathologies (BioPatH), Faculty of Sciences, Mohammed V University in Rabat, Rabat, Morocco.
| | - Fatima Ben Ali
- Laboratory of Biology of Human Pathologies (BioPatH), Faculty of Sciences, Mohammed V University in Rabat, Rabat, Morocco.
| | - Fatima Ezzahrae Oubaqui
- Laboratory of Biology of Human Pathologies (BioPatH), Faculty of Sciences, Mohammed V University in Rabat, Rabat, Morocco.
- Medical Biotechnology Center, Moroccan Foundation for Advanced Science, Innovation and Research (MAScIR), Rabat, Morocco.
| | - Zineb Qmichou
- Medical Biotechnology Center, Moroccan Foundation for Advanced Science, Innovation and Research (MAScIR), Rabat, Morocco.
| | - Youssef Bakri
- Laboratory of Biology of Human Pathologies (BioPatH), Faculty of Sciences, Mohammed V University in Rabat, Rabat, Morocco.
| | - Rabii Ameziane Rabii Ameziane
- Laboratory of Biology of Human Pathologies (BioPatH), Faculty of Sciences, Mohammed V University in Rabat, Rabat, Morocco.
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3
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Lin SH, Chien CH, Chang KP, Lu MF, Chen YT, Chu YW. SaBrcada: Survival Intervals Prediction for Breast Cancer Patients by Dimension Raising and Age Stratification. Cancers (Basel) 2023; 15:3690. [PMID: 37509351 PMCID: PMC10378351 DOI: 10.3390/cancers15143690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 07/03/2023] [Accepted: 07/18/2023] [Indexed: 07/30/2023] Open
Abstract
(1) Background: Breast cancer is the second leading cause of cancer death among women. The accurate prediction of survival intervals will help physicians make informed decisions about treatment strategies or the use of palliative care. (2) Methods: Gene expression is predictive and correlates to patient prognosis. To establish a reliable prediction tool, we collected a total of 1187 RNA-seq data points from breast cancer patients (median age 58 years) in Fragments Per Kilobase Million (FPKM) format from the TCGA database. Among them, we selected 144 patients with date of death information to establish the SaBrcada-AD dataset. We first normalized the SaBrcada-AD dataset to TPM to build the survival prediction model SaBrcada. After normalization and dimension raising, we used the differential gene expression data to test eight different deep learning architectures. Considering the effect of age on prognosis, we also performed a stratified random sampling test on all ages between the lower and upper quartiles of patient age, 48 and 69 years; (3) Results: Stratifying by age 61, the performance of SaBrcada built by GoogLeNet was improved to a highest accuracy of 0.798. We also built a free website tool to provide five predicted survival periods: within six months, six months to one year, one to three years, three to five years, or over five years, for clinician reference. (4) Conclusions: We built the prediction model, SaBrcada, and the website tool of the same name for breast cancer survival analysis. Through these models and tools, clinicians will be provided with survival interval information as a basis for formulating precision medicine.
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Affiliation(s)
- Shih-Huan Lin
- Ph.D. Program in Medical Biotechnology, National Chung Hsing University, Taichung 40227, Taiwan
| | - Ching-Hsuan Chien
- Ph.D. Program in Medical Biotechnology, National Chung Hsing University, Taichung 40227, Taiwan
| | - Kai-Po Chang
- Department of Pathology, China Medical University Hospital, Taichung 404327, Taiwan
| | - Min-Fang Lu
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung 40227, Taiwan
| | - Yu-Ting Chen
- Ph.D. Program in Medical Biotechnology, National Chung Hsing University, Taichung 40227, Taiwan
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung 40227, Taiwan
- Biotechnology Center, National Chung Hsing University, Taichung 40227, Taiwan
- Agricultural Biotechnology Center, National Chung Hsing University, Taichung 40227, Taiwan
| | - Yen-Wei Chu
- Ph.D. Program in Medical Biotechnology, National Chung Hsing University, Taichung 40227, Taiwan
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung 40227, Taiwan
- Biotechnology Center, National Chung Hsing University, Taichung 40227, Taiwan
- Agricultural Biotechnology Center, National Chung Hsing University, Taichung 40227, Taiwan
- Institute of Molecular Biology, National Chung Hsing University, Taichung 40227, Taiwan
- Smart Sustainable New Agriculture Research Center (SMARTer), Taichung 40227, Taiwan
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4
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Song Y, Fioramonti M, Bouvencourt G, Dubois C, Blanpain C, Van Keymeulen A. Cell type and stage specific transcriptional, chromatin and cell-cell communication landscapes in the mammary gland. Heliyon 2023; 9:e17842. [PMID: 37456014 PMCID: PMC10339025 DOI: 10.1016/j.heliyon.2023.e17842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 06/20/2023] [Accepted: 06/29/2023] [Indexed: 07/18/2023] Open
Abstract
The mammary gland (MG) is composed of three main epithelial lineages, the basal cells (BC), the estrogen receptor (ER) positive luminal cells (ER+ LC), and the ER negative LC (ER- LC). Defining the cell identity of each lineage and how it is modulated throughout the different stages of life is important to understand how these cells function and communicate throughout life. Here, we used transgenic mice specifically labelling ER+ LC combined to cell surface markers to isolate with high purity the 3 distinct cell lineages of the mammary gland and defined their expression profiles and chromatin landscapes by performing bulk RNAseq and ATACseq of these isolated populations in puberty, adulthood and mid-pregnancy. Our analysis identified conserved genes, ligands and transcription factor (TF) associated with a specific lineage throughout life as well as genes, ligands and TFs specific for a particular stage of the MG. In summary, our study identified genes and TF network associated with the identity, function and cell-cell communication of the different epithelial lineages of the MG at different stages of life.
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Affiliation(s)
- Yura Song
- Laboratory of Stem Cells and Cancer, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Marco Fioramonti
- Laboratory of Stem Cells and Cancer, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Gaëlle Bouvencourt
- Laboratory of Stem Cells and Cancer, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Christine Dubois
- Laboratory of Stem Cells and Cancer, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Cédric Blanpain
- Laboratory of Stem Cells and Cancer, Université Libre de Bruxelles (ULB), Brussels, Belgium
- WELBIO, Université Libre de Bruxelles (ULB), Brussels, Belgium
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5
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Islam R, Jenkins CE, Cao Q, Wong J, Bilenky M, Carles A, Moksa M, Weng AP, Hirst M. RUNX1 colludes with NOTCH1 to reprogram chromatin in T cell acute lymphoblastic leukemia. iScience 2023; 26:106795. [PMID: 37213235 PMCID: PMC10199266 DOI: 10.1016/j.isci.2023.106795] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 02/10/2023] [Accepted: 04/27/2023] [Indexed: 05/23/2023] Open
Abstract
Runt-related transcription factor 1 (RUNX1) is oncogenic in diverse types of leukemia and epithelial cancers where its expression is associated with poor prognosis. Current models suggest that RUNX1 cooperates with other oncogenic factors (e.g., NOTCH1, TAL1) to drive the expression of proto-oncogenes in T cell acute lymphoblastic leukemia (T-ALL) but the molecular mechanisms controlled by RUNX1 and its cooperation with other factors remain unclear. Integrative chromatin and transcriptional analysis following inhibition of RUNX1 and NOTCH1 revealed a surprisingly widespread role of RUNX1 in the establishment of global H3K27ac levels and that RUNX1 is required by NOTCH1 for cooperative transcription activation of key NOTCH1 target genes including MYC, DTX1, HES4, IL7R, and NOTCH3. Super-enhancers were preferentially sensitive to RUNX1 knockdown and RUNX1-dependent super-enhancers were disrupted following the treatment of a pan-BET inhibitor, I-BET151.
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Affiliation(s)
- Rashedul Islam
- Bioinformatics Graduate Program, University of British Columbia, Vancouver, BC V5Z 4S6, Canada
- Department of Microbiology and Immunology, Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | | | - Qi Cao
- Department of Microbiology and Immunology, Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Jasper Wong
- Genome Science and Technology Program, University of British Columbia, Vancouver, BC V6T 2B5, Canada
| | - Misha Bilenky
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | - Annaïck Carles
- Department of Microbiology and Immunology, Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Michelle Moksa
- Department of Microbiology and Immunology, Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Andrew P. Weng
- Terry Fox Laboratory, BC Cancer, Vancouver, BC V5Z 1L3, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 2B5, Canada
| | - Martin Hirst
- Bioinformatics Graduate Program, University of British Columbia, Vancouver, BC V5Z 4S6, Canada
- Department of Microbiology and Immunology, Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
- Genome Science and Technology Program, University of British Columbia, Vancouver, BC V6T 2B5, Canada
- Corresponding author
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6
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Rowton M, Perez-Cervantes C, Hur S, Jacobs-Li J, Lu E, Deng N, Guzzetta A, Hoffmann AD, Stocker M, Steimle JD, Lazarevic S, Oubaha S, Yang XH, Kim C, Yu S, Eckart H, Koska M, Hanson E, Chan SSK, Garry DJ, Kyba M, Basu A, Ikegami K, Pott S, Moskowitz IP. Hedgehog signaling activates a mammalian heterochronic gene regulatory network controlling differentiation timing across lineages. Dev Cell 2022; 57:2181-2203.e9. [PMID: 36108627 PMCID: PMC10506397 DOI: 10.1016/j.devcel.2022.08.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 06/24/2022] [Accepted: 08/22/2022] [Indexed: 11/18/2022]
Abstract
Many developmental signaling pathways have been implicated in lineage-specific differentiation; however, mechanisms that explicitly control differentiation timing remain poorly defined in mammals. We report that murine Hedgehog signaling is a heterochronic pathway that determines the timing of progenitor differentiation. Hedgehog activity was necessary to prevent premature differentiation of second heart field (SHF) cardiac progenitors in mouse embryos, and the Hedgehog transcription factor GLI1 was sufficient to delay differentiation of cardiac progenitors in vitro. GLI1 directly activated a de novo progenitor-specific network in vitro, akin to that of SHF progenitors in vivo, which prevented the onset of the cardiac differentiation program. A Hedgehog signaling-dependent active-to-repressive GLI transition functioned as a differentiation timer, restricting the progenitor network to the SHF. GLI1 expression was associated with progenitor status across germ layers, and it delayed the differentiation of neural progenitors in vitro, suggesting a broad role for Hedgehog signaling as a heterochronic pathway.
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Affiliation(s)
- Megan Rowton
- Departments of Pediatrics, Pathology, Human Genetics, and Genetic Medicine, The University of Chicago, Chicago, IL, USA
| | - Carlos Perez-Cervantes
- Departments of Pediatrics, Pathology, Human Genetics, and Genetic Medicine, The University of Chicago, Chicago, IL, USA
| | - Suzy Hur
- Departments of Pediatrics, Pathology, Human Genetics, and Genetic Medicine, The University of Chicago, Chicago, IL, USA
| | - Jessica Jacobs-Li
- Departments of Pediatrics, Pathology, Human Genetics, and Genetic Medicine, The University of Chicago, Chicago, IL, USA
| | - Emery Lu
- Departments of Pediatrics, Pathology, Human Genetics, and Genetic Medicine, The University of Chicago, Chicago, IL, USA
| | - Nikita Deng
- Departments of Pediatrics, Pathology, Human Genetics, and Genetic Medicine, The University of Chicago, Chicago, IL, USA
| | - Alexander Guzzetta
- Departments of Pediatrics, Pathology, Human Genetics, and Genetic Medicine, The University of Chicago, Chicago, IL, USA
| | - Andrew D Hoffmann
- Departments of Pediatrics, Pathology, Human Genetics, and Genetic Medicine, The University of Chicago, Chicago, IL, USA
| | - Matthew Stocker
- Departments of Pediatrics, Pathology, Human Genetics, and Genetic Medicine, The University of Chicago, Chicago, IL, USA
| | - Jeffrey D Steimle
- Departments of Pediatrics, Pathology, Human Genetics, and Genetic Medicine, The University of Chicago, Chicago, IL, USA
| | - Sonja Lazarevic
- Departments of Pediatrics, Pathology, Human Genetics, and Genetic Medicine, The University of Chicago, Chicago, IL, USA
| | - Sophie Oubaha
- Departments of Pediatrics, Pathology, Human Genetics, and Genetic Medicine, The University of Chicago, Chicago, IL, USA
| | - Xinan H Yang
- Departments of Pediatrics, Pathology, Human Genetics, and Genetic Medicine, The University of Chicago, Chicago, IL, USA
| | - Chul Kim
- Departments of Pediatrics, Pathology, Human Genetics, and Genetic Medicine, The University of Chicago, Chicago, IL, USA
| | - Shuhan Yu
- Departments of Pediatrics, Pathology, Human Genetics, and Genetic Medicine, The University of Chicago, Chicago, IL, USA
| | - Heather Eckart
- Departments of Pediatrics, Pathology, Human Genetics, and Genetic Medicine, The University of Chicago, Chicago, IL, USA
| | - Mervenaz Koska
- Departments of Pediatrics, Pathology, Human Genetics, and Genetic Medicine, The University of Chicago, Chicago, IL, USA
| | - Erika Hanson
- Departments of Pediatrics, Pathology, Human Genetics, and Genetic Medicine, The University of Chicago, Chicago, IL, USA
| | - Sunny S K Chan
- Lillehei Heart Institute, University of Minnesota, Minneapolis, MN 55455, USA; Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Daniel J Garry
- Lillehei Heart Institute, University of Minnesota, Minneapolis, MN 55455, USA; Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Michael Kyba
- Lillehei Heart Institute, University of Minnesota, Minneapolis, MN 55455, USA; Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Anindita Basu
- Departments of Pediatrics, Pathology, Human Genetics, and Genetic Medicine, The University of Chicago, Chicago, IL, USA
| | - Kohta Ikegami
- Departments of Pediatrics, Pathology, Human Genetics, and Genetic Medicine, The University of Chicago, Chicago, IL, USA
| | - Sebastian Pott
- Departments of Pediatrics, Pathology, Human Genetics, and Genetic Medicine, The University of Chicago, Chicago, IL, USA
| | - Ivan P Moskowitz
- Departments of Pediatrics, Pathology, Human Genetics, and Genetic Medicine, The University of Chicago, Chicago, IL, USA.
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7
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Lorzadeh A, Hammond C, Wang F, Knapp DJHF, Wong JC, Zhu JYA, Cao Q, Heravi-Moussavi A, Carles A, Wong M, Sharafian Z, Steif J, Moksa M, Bilenky M, Lavoie PM, Eaves CJ, Hirst M. Polycomb contraction differentially regulates terminal human hematopoietic differentiation programs. BMC Biol 2022; 20:104. [PMID: 35550087 PMCID: PMC9102747 DOI: 10.1186/s12915-022-01315-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 04/28/2022] [Indexed: 12/05/2022] Open
Abstract
Background Lifelong production of the many types of mature blood cells from less differentiated progenitors is a hierarchically ordered process that spans multiple cell divisions. The nature and timing of the molecular events required to integrate the environmental signals, transcription factor activity, epigenetic modifications, and changes in gene expression involved are thus complex and still poorly understood. To address this gap, we generated comprehensive reference epigenomes of 8 phenotypically defined subsets of normal human cord blood. Results We describe a striking contraction of H3K27me3 density in differentiated myelo-erythroid cells that resembles a punctate pattern previously ascribed to pluripotent embryonic stem cells. Phenotypically distinct progenitor cell types display a nearly identical repressive H3K27me3 signature characterized by large organized chromatin K27-modification domains that are retained by mature lymphoid cells but lost in terminally differentiated monocytes and erythroblasts. We demonstrate that inhibition of polycomb group members predicted to control large organized chromatin K27-modification domains influences lymphoid and myeloid fate decisions of primary neonatal hematopoietic progenitors in vitro. We further show that a majority of active enhancers appear in early progenitors, a subset of which are DNA hypermethylated and become hypomethylated and induced during terminal differentiation. Conclusion Primitive human hematopoietic cells display a unique repressive H3K27me3 signature that is retained by mature lymphoid cells but is lost in monocytes and erythroblasts. Intervention data implicate that control of this chromatin state change is a requisite part of the process whereby normal human hematopoietic progenitor cells make lymphoid and myeloid fate decisions. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01315-1.
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Affiliation(s)
- A Lorzadeh
- Department of Microbiology and Immunology, Michael Smith Laboratories, UBC, Vancouver, Canada
| | - C Hammond
- Terry Fox Laboratory, BC Cancer, Vancouver, Canada.,Department of Medicine, UBC, Vancouver, Canada
| | - F Wang
- Terry Fox Laboratory, BC Cancer, Vancouver, Canada.,Department of Medical Genetics, UBC, Vancouver, Canada
| | - D J H F Knapp
- Terry Fox Laboratory, BC Cancer, Vancouver, Canada.,Department of Medicine, UBC, Vancouver, Canada
| | - J Ch Wong
- Department of Microbiology and Immunology, Michael Smith Laboratories, UBC, Vancouver, Canada
| | - J Y A Zhu
- Department of Microbiology and Immunology, Michael Smith Laboratories, UBC, Vancouver, Canada
| | - Q Cao
- Department of Microbiology and Immunology, Michael Smith Laboratories, UBC, Vancouver, Canada
| | - A Heravi-Moussavi
- Canada's Michael Smith Genome Science Centre, BC Cancer, Vancouver, Canada
| | - A Carles
- Department of Microbiology and Immunology, Michael Smith Laboratories, UBC, Vancouver, Canada
| | - M Wong
- Department of Microbiology and Immunology, Michael Smith Laboratories, UBC, Vancouver, Canada
| | - Z Sharafian
- BC Children's Hospital Research Institute, Department of Pediatrics, UBC, Vancouver, Canada
| | - J Steif
- Department of Microbiology and Immunology, Michael Smith Laboratories, UBC, Vancouver, Canada
| | - M Moksa
- Department of Microbiology and Immunology, Michael Smith Laboratories, UBC, Vancouver, Canada
| | - M Bilenky
- Canada's Michael Smith Genome Science Centre, BC Cancer, Vancouver, Canada
| | - P M Lavoie
- BC Children's Hospital Research Institute, Department of Pediatrics, UBC, Vancouver, Canada
| | - C J Eaves
- Terry Fox Laboratory, BC Cancer, Vancouver, Canada.,Department of Medicine, UBC, Vancouver, Canada.,Department of Medical Genetics, UBC, Vancouver, Canada
| | - M Hirst
- Department of Microbiology and Immunology, Michael Smith Laboratories, UBC, Vancouver, Canada. .,Canada's Michael Smith Genome Science Centre, BC Cancer, Vancouver, Canada.
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8
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Yu B, Dai W, Pang L, Sang Q, Li F, Yu J, Feng H, Li J, Hou J, Yan C, Su L, Zhu Z, Li YY, Liu B. The dynamic alteration of transcriptional regulation by crucial TFs during tumorigenesis of gastric cancer. Mol Med 2022; 28:41. [PMID: 35421923 PMCID: PMC9008954 DOI: 10.1186/s10020-022-00468-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Accepted: 04/04/2022] [Indexed: 11/26/2022] Open
Abstract
Background The mechanisms of Gastric cancer (GC) initiation and progression are complicated, at least partly owing to the dynamic changes of gene regulation during carcinogenesis. Thus, investigations on the changes in regulatory networks can improve the understanding of cancer development and provide novel insights into the molecular mechanisms of cancer. Methods Differential co-expression analysis (DCEA), differential gene regulation network (GRN) modeling and differential regulation analysis (DRA) were integrated to detect differential transcriptional regulation events between gastric normal mucosa and cancer samples based on GSE54129 dataset. Cytological experiments and IHC staining assays were used to validate the dynamic changes of CREB1 regulated targets in different stages. Results A total of 1955 differentially regulated genes (DRGs) were identified and prioritized in a quantitative way. Among the top 1% DRGs, 14 out of 19 genes have been reported to be GC relevant. The four transcription factors (TFs) among the top 1% DRGs, including CREB1, BPTF, GATA6 and CEBPA, were regarded as crucial TFs relevant to GC progression. The differentially regulated links (DRLs) around the four crucial TFs were then prioritized to generate testable hypotheses on the differential regulation mechanisms of gastric carcinogenesis. To validate the dynamic alterations of gene regulation patterns of crucial TFs during GC progression, we took CREB1 as an example to screen its differentially regulated targets by using cytological and IHC staining assays. Eventually, TCEAL2 and MBNL1 were proved to be differentially regulated by CREB1 during tumorigenesis of gastric cancer. Conclusions By combining differential networking information and molecular cell experiments verification, testable hypotheses on the regulation mechanisms of GC around the core TFs and their top ranked DRLs were generated. Since TCEAL2 and MBNL1 have been reported to be potential therapeutic targets in SCLC and breast cancer respectively, their translation values in GC are worthy of further investigation. Supplementary Information The online version contains supplementary material available at 10.1186/s10020-022-00468-7.
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9
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Functional annotation of breast cancer risk loci: current progress and future directions. Br J Cancer 2022; 126:981-993. [PMID: 34741135 PMCID: PMC8980003 DOI: 10.1038/s41416-021-01612-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 10/12/2021] [Accepted: 10/21/2021] [Indexed: 11/20/2022] Open
Abstract
Genome-wide association studies coupled with large-scale replication and fine-scale mapping studies have identified more than 150 genomic regions that are associated with breast cancer risk. Here, we review efforts to translate these findings into a greater understanding of disease mechanism. Our review comes in the context of a recently published fine-scale mapping analysis of these regions, which reported 352 independent signals and a total of 13,367 credible causal variants. The vast majority of credible causal variants map to noncoding DNA, implicating regulation of gene expression as the mechanism by which functional variants influence risk. Accordingly, we review methods for defining candidate-regulatory sequences, methods for identifying putative target genes and methods for linking candidate-regulatory sequences to putative target genes. We provide a summary of available data resources and identify gaps in these resources. We conclude that while much work has been done, there is still much to do. There are, however, grounds for optimism; combining statistical data from fine-scale mapping with functional data that are more representative of the normal "at risk" breast, generated using new technologies, should lead to a greater understanding of the mechanisms that influence an individual woman's risk of breast cancer.
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10
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Hsieh YP, Naler LB, Ma S, Lu C. Cell-type-specific epigenomic variations associated with BRCA1 mutation in pre-cancer human breast tissues. NAR Genom Bioinform 2022; 4:lqac006. [PMID: 35118379 PMCID: PMC8808540 DOI: 10.1093/nargab/lqac006] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 12/13/2021] [Accepted: 01/24/2022] [Indexed: 11/24/2022] Open
Abstract
BRCA1 germline mutation carriers are predisposed to breast cancers. Epigenomic regulations have been known to strongly interact with genetic variations and potentially mediate biochemical cascades involved in tumorigenesis. Due to the cell-type specificity of epigenomic features, profiling of individual cell types is critical for understanding the molecular events in various cellular compartments within complex breast tissue. Here, we produced cell-type-specific profiles of genome-wide histone modifications including H3K27ac and H3K4me3 in basal, luminal progenitor, mature luminal and stromal cells extracted from a small pilot cohort of pre-cancer BRCA1 mutation carriers (BRCA1mut/+) and non-carriers (BRCA1+/+), using a low-input ChIP-seq technology that we developed. We discovered that basal and stromal cells present the most extensive epigenomic differences between mutation carriers (BRCA1mut/+) and non-carriers (BRCA1+/+), while luminal progenitor and mature luminal cells are relatively unchanged with the mutation. Furthermore, the epigenomic changes in basal cells due to BRCA1 mutation appear to facilitate their transformation into luminal progenitor cells. Taken together, epigenomic regulation plays an important role in the case of BRCA1 mutation for shaping the molecular landscape that facilitates tumorigenesis.
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Affiliation(s)
- Yuan-Pang Hsieh
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA 24061, USA
| | - Lynette B Naler
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA 24061, USA
| | - Sai Ma
- Department of Biomedical Engineering and Mechanics, Virginia Tech, Blacksburg, VA 24061, USA
| | - Chang Lu
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA 24061, USA
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11
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Shah JS, Milevskiy MJG, Petrova V, Au AYM, Wong JJL, Visvader JE, Schmitz U, Rasko JEJ. Towards resolution of the intron retention paradox in breast cancer. Breast Cancer Res 2022; 24:100. [PMID: 36581993 PMCID: PMC9798573 DOI: 10.1186/s13058-022-01593-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Accepted: 12/12/2022] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND After many years of neglect in the field of alternative splicing, the importance of intron retention (IR) in cancer has come into focus following landmark discoveries of aberrant IR patterns in cancer. Many solid and liquid tumours are associated with drastic increases in IR, and such patterns have been pursued as both biomarkers and therapeutic targets. Paradoxically, breast cancer (BrCa) is the only tumour type in which IR is reduced compared to adjacent normal breast tissue. METHODS In this study, we have conducted a pan-cancer analysis of IR with emphasis on BrCa and its subtypes. We explored mechanisms that could cause aberrant and pathological IR and clarified why normal breast tissue has unusually high IR. RESULTS Strikingly, we found that aberrantly decreasing IR in BrCa can be largely attributed to normal breast tissue having the highest occurrence of IR events compared to other healthy tissues. Our analyses suggest that low numbers of IR events in breast tumours are associated with poor prognosis, particularly in the luminal B subtype. Interestingly, we found that IR frequencies negatively correlate with cell proliferation in BrCa cells, i.e. rapidly dividing tumour cells have the lowest number of IR events. Aberrant RNA-binding protein expression and changes in tissue composition are among the causes of aberrantly decreasing IR in BrCa. CONCLUSIONS Our results suggest that IR should be considered for therapeutic manipulation in BrCa patients with aberrantly low IR levels and that further work is needed to understand the cause and impact of high IR in other tumour types.
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Affiliation(s)
- Jaynish S. Shah
- grid.1013.30000 0004 1936 834XComputational BioMedicine Laboratory Centenary Institute, The University of Sydney, Camperdown, Australia ,grid.1013.30000 0004 1936 834XGene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Locked Bag No. 6, Newtown, NSW 2042 Australia ,grid.1002.30000 0004 1936 7857Australian Centre for Blood Diseases, Central Clinical School, Monash University and Alfred Health, Melbourne, VIC Australia
| | - Michael J. G. Milevskiy
- grid.1042.70000 0004 0432 4889ACRF Cancer Biology and Stem Cells Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052 Australia ,grid.1008.90000 0001 2179 088XDepartment of Medical Biology, The University of Melbourne, Parkville, VIC 3010 Australia
| | - Veronika Petrova
- grid.1013.30000 0004 1936 834XComputational BioMedicine Laboratory Centenary Institute, The University of Sydney, Camperdown, Australia ,grid.1013.30000 0004 1936 834XGene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Locked Bag No. 6, Newtown, NSW 2042 Australia
| | - Amy Y. M. Au
- grid.1013.30000 0004 1936 834XGene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Locked Bag No. 6, Newtown, NSW 2042 Australia
| | - Justin J. L. Wong
- grid.1013.30000 0004 1936 834XEpigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown, 2050 Australia ,grid.1013.30000 0004 1936 834XFaculty of Medicine and Health, The University of Sydney, Camperdown, Australia
| | - Jane E. Visvader
- grid.1042.70000 0004 0432 4889ACRF Cancer Biology and Stem Cells Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052 Australia ,grid.1008.90000 0001 2179 088XDepartment of Medical Biology, The University of Melbourne, Parkville, VIC 3010 Australia
| | - Ulf Schmitz
- grid.1013.30000 0004 1936 834XComputational BioMedicine Laboratory Centenary Institute, The University of Sydney, Camperdown, Australia ,grid.1011.10000 0004 0474 1797Department of Molecular and Cell Biology, College of Public Health, Medical and Veterinary Sciences, James Cook University, 1 James Cook Drive, Townsville, QLD 4811 Australia ,grid.1011.10000 0004 0474 1797Centre for Tropical Bioinformatics and Molecular Biology, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, 4878 Australia
| | - John E. J. Rasko
- grid.1013.30000 0004 1936 834XGene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Locked Bag No. 6, Newtown, NSW 2042 Australia ,grid.1013.30000 0004 1936 834XFaculty of Medicine and Health, The University of Sydney, Camperdown, Australia ,grid.413249.90000 0004 0385 0051Cell and Molecular Therapies, Royal Prince Alfred Hospital, Camperdown, Australia
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12
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Sahin I, George A, Seyhan AA. Therapeutic Targeting of Alternative RNA Splicing in Gastrointestinal Malignancies and Other Cancers. Int J Mol Sci 2021; 22:11790. [PMID: 34769221 PMCID: PMC8583749 DOI: 10.3390/ijms222111790] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 10/27/2021] [Accepted: 10/28/2021] [Indexed: 12/22/2022] Open
Abstract
Recent comprehensive genomic studies including single-cell RNA sequencing and characterization have revealed multiple processes by which protein-coding and noncoding RNA processing are dysregulated in many cancers. More specifically, the abnormal regulation of mRNA and precursor mRNA (pre-mRNA) processing, which includes the removal of introns by splicing, is frequently altered in tumors, producing multiple different isoforms and diversifying protein expression. These alterations in RNA processing result in numerous cancer-specific mRNAs and pathogenically spliced events that generate altered levels of normal proteins or proteins with new functions, leading to the activation of oncogenes or the inactivation of tumor suppressor genes. Abnormally spliced pre-mRNAs are also associated with resistance to cancer treatment, and certain cancers are highly sensitive to the pharmacological inhibition of splicing. The discovery of these alterations in RNA processing has not only provided new insights into cancer pathogenesis but identified novel therapeutic vulnerabilities and therapeutic opportunities in targeting these aberrations in various ways (e.g., small molecules, splice-switching oligonucleotides (SSOs), and protein therapies) to modulate alternative RNA splicing or other RNA processing and modification mechanisms. Some of these strategies are currently progressing toward clinical development or are already in clinical trials. Additionally, tumor-specific neoantigens produced from these pathogenically spliced events and other abnormal RNA processes provide a potentially extensive source of tumor-specific therapeutic antigens (TAs) for targeted cancer immunotherapy. Moreover, a better understanding of the molecular mechanisms associated with aberrant RNA processes and the biological impact they play might provide insights into cancer initiation, progression, and metastasis. Our goal is to highlight key alternative RNA splicing and processing mechanisms and their roles in cancer pathophysiology as well as emerging therapeutic alternative splicing targets in cancer, particularly in gastrointestinal (GI) malignancies.
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Affiliation(s)
- Ilyas Sahin
- Division of Hematology Oncology, Department of Medicine, University of Florida Health Cancer Center, Gainesville, FL 32610, USA;
| | - Andrew George
- Department of Chemistry, Brown University, Providence, RI 02912, USA;
- Department of Molecular Biology, Cell Biology & Biochemistry, Division of Biology and Medicine, Brown University, Providence, RI 02912, USA
| | - Attila A. Seyhan
- Laboratory of Translational Oncology and Experimental Cancer Therapeutics, Warren Alpert Medical School, Brown University, Providence, RI 02912, USA
- The Joint Program in Cancer Biology, Brown University and Lifespan Health System, Providence, RI 02912, USA
- Cancer Center at Brown University, Warren Alpert Medical School, Brown University, Providence, RI 02912, USA
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, RI 02912, USA
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13
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Al-Kharashi LA, Bakheet T, AlHarbi WA, Al-Moghrabi N, Aboussekhra A. Eugenol modulates genomic methylation and inactivates breast cancer-associated fibroblasts through E2F1-dependent downregulation of DNMT1/DNMT3A. Mol Carcinog 2021; 60:784-795. [PMID: 34473867 DOI: 10.1002/mc.23344] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 08/16/2021] [Accepted: 08/17/2021] [Indexed: 11/09/2022]
Abstract
Active cancer-associated fibroblasts (CAFs) are major components of the tumor microenvironment, which promote carcinogenesis and modulate response to therapy. Therefore, targeting these cells or reducing their paracrine pro-carcinogenic effects could be of great therapeutic value. To this end, we sought to investigate the effect of eugenol, a natural phenolic molecule, on active breast CAFs. We have shown that decitabine (5-Aza-2'-deoxycytidine, DAC) and eugenol inhibit the expression of the DNA methyltransferase genes DNMT1 and DNMT3A at both the protein and mRNA levels in breast CAF cells. While the effect of eugenol was persistent, DAC had only a transient inhibitory effect on the mRNA level of both DNMT genes. Furthermore, eugenol and DAC suppressed the invasive/migratory and proliferative potential of CAF cells as well as their paracrine pro-carcinogenic effects both in vitro and in humanized orthotopic tumor xenografts. Interestingly, these inhibitory effects of decitabine and eugenol were mediated through E2F1 downregulation. Indeed, ectopic expression of E2F1 upregulated both genes and attenuated the effects of eugenol. Additionally, we provide clear evidence that eugenol, like DAC, strongly modulates the methylation pattern in active CAF cells, through methylating several oncogenes and demethylating various important tumor suppressor genes, which affected their mRNA expression levels. Importantly, the E2F1 promoter was also hypermethylated and the gene downregulated in response to eugenol. Together, these findings show that the active features of breast CAF cells can be normalized through eugenol-dependent targeting of DNMT1/DNMT3A and the consequent modulation in gene methylation.
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Affiliation(s)
- Layla A Al-Kharashi
- Department of Molecular Oncology, King Faisal Specialist Hospital and Research Center, Riyadh, Kingdom of Saudi Arabia.,Department of Pharmacology and Toxicology, Faculty of Pharmacy, King Saud University, Riyadh, Kingdom of Saudi Arabia
| | - Tala Bakheet
- Department of Molecular BioMedicine, Research Centre, King Faisal Specialist Hospital and Research Centre, Riyadh, Kingdom of Saudi Arabia
| | - Wejdan A AlHarbi
- Department of Molecular Oncology, King Faisal Specialist Hospital and Research Center, Riyadh, Kingdom of Saudi Arabia
| | - Nisreen Al-Moghrabi
- Department of Molecular Oncology, King Faisal Specialist Hospital and Research Center, Riyadh, Kingdom of Saudi Arabia
| | - Abdelilah Aboussekhra
- Department of Molecular Oncology, King Faisal Specialist Hospital and Research Center, Riyadh, Kingdom of Saudi Arabia
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14
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Schmitz U, Monteuuis G, Petrova V, Shah JS, Rasko JE. Computational Methods for Intron Retention Identification and Quantification. SYSTEMS MEDICINE 2021. [DOI: 10.1016/b978-0-12-801238-3.11567-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
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15
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Li L, Maire CL, Bilenky M, Carles A, Heravi-Moussavi A, Hong C, Tam A, Kamoh B, Cho S, Cheung D, Li I, Wong T, Nagarajan RP, Mungall AJ, Moore R, Wang T, Kleinman CL, Jabado N, Jones SJM, Marra MA, Ligon KL, Costello JF, Hirst M. Epigenomic programming in early fetal brain development. Epigenomics 2020; 12:1053-1070. [PMID: 32677466 PMCID: PMC7857341 DOI: 10.2217/epi-2019-0319] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 03/19/2020] [Indexed: 12/21/2022] Open
Abstract
Aim: To provide a comprehensive understanding of gene regulatory networks in the developing human brain and a foundation for interpreting pathogenic deregulation. Materials & methods: We generated reference epigenomes and transcriptomes of dissected brain regions and primary neural progenitor cells (NPCs) derived from cortical and ganglionic eminence tissues of four normal human fetuses. Results: Integration of these data across developmental stages revealed a directional increase in active regulatory states, transcription factor activities and gene transcription with developmental stage. Consistent with differences in their biology, NPCs derived from cortical and ganglionic eminence regions contained common, region specific, and gestational week specific regulatory states. Conclusion: We provide a high-resolution regulatory network for NPCs from different brain regions as a comprehensive reference for future studies.
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Affiliation(s)
- Luolan Li
- Department of Microbiology & Immunology, Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Cecile L Maire
- Department of Medical Oncology, Center for Molecular Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Misha Bilenky
- Canada's Michael Smith Genome Science Center, BC Cancer, Vancouver, BC, V5Z 4S6, Canada
| | - Annaïck Carles
- Department of Microbiology & Immunology, Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | | | - Chibo Hong
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA 94158, USA
| | - Angela Tam
- Canada's Michael Smith Genome Science Center, BC Cancer, Vancouver, BC, V5Z 4S6, Canada
| | - Baljit Kamoh
- Canada's Michael Smith Genome Science Center, BC Cancer, Vancouver, BC, V5Z 4S6, Canada
| | - Stephanie Cho
- Canada's Michael Smith Genome Science Center, BC Cancer, Vancouver, BC, V5Z 4S6, Canada
| | - Dorothy Cheung
- Canada's Michael Smith Genome Science Center, BC Cancer, Vancouver, BC, V5Z 4S6, Canada
| | - Irene Li
- Canada's Michael Smith Genome Science Center, BC Cancer, Vancouver, BC, V5Z 4S6, Canada
| | - Tina Wong
- Canada's Michael Smith Genome Science Center, BC Cancer, Vancouver, BC, V5Z 4S6, Canada
| | - Raman P Nagarajan
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA 94158, USA
| | - Andrew J Mungall
- Canada's Michael Smith Genome Science Center, BC Cancer, Vancouver, BC, V5Z 4S6, Canada
| | - Richard Moore
- Canada's Michael Smith Genome Science Center, BC Cancer, Vancouver, BC, V5Z 4S6, Canada
| | - Ting Wang
- Department of Genetics, Washington University, St Louis, MO 63108, USA
| | - Claudia L Kleinman
- Department of Human Genetics, McGill University, Montreal, QC, H3T 1E2, Canada
| | - Nada Jabado
- Department of Human Genetics, McGill University, Montreal, QC, H3T 1E2, Canada
| | - Steven JM Jones
- Canada's Michael Smith Genome Science Center, BC Cancer, Vancouver, BC, V5Z 4S6, Canada
| | - Marco A Marra
- Canada's Michael Smith Genome Science Center, BC Cancer, Vancouver, BC, V5Z 4S6, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6H 3N1, Canada
| | - Keith L Ligon
- Department of Medical Oncology, Center for Molecular Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Joseph F Costello
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA 94158, USA
| | - Martin Hirst
- Department of Microbiology & Immunology, Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
- Canada's Michael Smith Genome Science Center, BC Cancer, Vancouver, BC, V5Z 4S6, Canada
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16
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Monteuuis G, Wong JJL, Bailey CG, Schmitz U, Rasko JEJ. The changing paradigm of intron retention: regulation, ramifications and recipes. Nucleic Acids Res 2020; 47:11497-11513. [PMID: 31724706 PMCID: PMC7145568 DOI: 10.1093/nar/gkz1068] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 10/04/2019] [Accepted: 10/30/2019] [Indexed: 12/13/2022] Open
Abstract
Intron retention (IR) is a form of alternative splicing that has long been neglected in mammalian systems although it has been studied for decades in non-mammalian species such as plants, fungi, insects and viruses. It was generally assumed that mis-splicing, leading to the retention of introns, would have no physiological consequence other than reducing gene expression by nonsense-mediated decay. Relatively recent landmark discoveries have highlighted the pivotal role that IR serves in normal and disease-related human biology. Significant technical hurdles have been overcome, thereby enabling the robust detection and quantification of IR. Still, relatively little is known about the cis- and trans-acting modulators controlling this phenomenon. The fate of an intron to be, or not to be, retained in the mature transcript is the direct result of the influence exerted by numerous intrinsic and extrinsic factors at multiple levels of regulation. These factors have altered current biological paradigms and provided unexpected insights into the transcriptional landscape. In this review, we discuss the regulators of IR and methods to identify them. Our focus is primarily on mammals, however, we broaden the scope to non-mammalian organisms in which IR has been shown to be biologically relevant.
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Affiliation(s)
- Geoffray Monteuuis
- Gene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, Australia
| | - Justin J L Wong
- Faculty of Medicine and Health, The University of Sydney, NSW 2006, Australia.,Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown, Australia
| | - Charles G Bailey
- Gene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, Australia.,Faculty of Medicine and Health, The University of Sydney, NSW 2006, Australia
| | - Ulf Schmitz
- Gene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, Australia.,Faculty of Medicine and Health, The University of Sydney, NSW 2006, Australia.,Computational Biomedicine Laboratory Centenary Institute, The University of Sydney, Camperdown, Australia
| | - John E J Rasko
- Gene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, Australia.,Faculty of Medicine and Health, The University of Sydney, NSW 2006, Australia.,Cell and Molecular Therapies, Royal Prince Alfred Hospital, Camperdown, Australia
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17
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Epigenetics in Inflammatory Breast Cancer: Biological Features and Therapeutic Perspectives. Cells 2020; 9:cells9051164. [PMID: 32397183 PMCID: PMC7291154 DOI: 10.3390/cells9051164] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 04/25/2020] [Accepted: 04/30/2020] [Indexed: 12/12/2022] Open
Abstract
Evidence has emerged implicating epigenetic alterations in inflammatory breast cancer (IBC) origin and progression. IBC is a rare and rapidly progressing disease, considered the most aggressive type of breast cancer (BC). At clinical presentation, IBC is characterized by diffuse erythema, skin ridging, dermal lymphatic invasion, and peau d'orange aspect. The widespread distribution of the tumor as emboli throughout the breast and intra- and intertumor heterogeneity is associated with its poor prognosis. In this review, we highlighted studies documenting the essential roles of epigenetic mechanisms in remodeling chromatin and modulating gene expression during mammary gland differentiation and the development of IBC. Compiling evidence has emerged implicating epigenetic changes as a common denominator linking the main risk factors (socioeconomic status, environmental exposure to endocrine disruptors, racial disparities, and obesity) with IBC development. DNA methylation changes and their impact on the diagnosis, prognosis, and treatment of IBC are also described. Recent studies are focusing on the use of histone deacetylase inhibitors as promising epigenetic drugs for treating IBC. All efforts must be undertaken to unravel the epigenetic marks that drive this disease and how this knowledge could impact strategies to reduce the risk of IBC development and progression.
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18
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Xuan P, Jia L, Zhang T, Sheng N, Li X, Li J. LDAPred: A Method Based on Information Flow Propagation and a Convolutional Neural Network for the Prediction of Disease-Associated lncRNAs. Int J Mol Sci 2019; 20:E4458. [PMID: 31510011 PMCID: PMC6771133 DOI: 10.3390/ijms20184458] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Revised: 09/05/2019] [Accepted: 09/06/2019] [Indexed: 12/26/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) play a crucial role in the pathogenesis and development of complex diseases. Predicting potential lncRNA-disease associations can improve our understanding of the molecular mechanisms of human diseases and help identify biomarkers for disease diagnosis, treatment, and prevention. Previous research methods have mostly integrated the similarity and association information of lncRNAs and diseases, without considering the topological structure information among these nodes, which is important for predicting lncRNA-disease associations. We propose a method based on information flow propagation and convolutional neural networks, called LDAPred, to predict disease-related lncRNAs. LDAPred not only integrates the similarities, associations, and interactions among lncRNAs, diseases, and miRNAs, but also exploits the topological structures formed by them. In this study, we construct a dual convolutional neural network-based framework that comprises the left and right sides. The embedding layer on the left side is established by utilizing lncRNA, miRNA, and disease-related biological premises. On the right side of the frame, multiple types of similarity, association, and interaction relationships among lncRNAs, diseases, and miRNAs are calculated based on information flow propagation on the bi-layer networks, such as the lncRNA-disease network. They contain the network topological structure and they are learned by the right side of the framework. The experimental results based on five-fold cross-validation indicate that LDAPred performs better than several state-of-the-art methods. Case studies on breast cancer, colon cancer, and osteosarcoma further demonstrate LDAPred's ability to discover potential lncRNA-disease associations.
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Affiliation(s)
- Ping Xuan
- School of Computer Science and Technology, Heilongjiang University, Harbin 150080, China.
- Postdoctoral Program of Heilongjiang Hengxun Technology Co., Ltd., Harbin 150090, China.
| | - Lan Jia
- School of Computer Science and Technology, Heilongjiang University, Harbin 150080, China.
| | - Tiangang Zhang
- School of Mathematical Science, Heilongjiang University, Harbin 150080, China.
| | - Nan Sheng
- School of Computer Science and Technology, Heilongjiang University, Harbin 150080, China.
| | - Xiaokun Li
- Postdoctoral Program of Heilongjiang Hengxun Technology Co., Ltd., Harbin 150090, China.
| | - Jinbao Li
- School of Computer Science and Technology, Heilongjiang University, Harbin 150080, China.
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19
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Tharmapalan P, Mahendralingam M, Berman HK, Khokha R. Mammary stem cells and progenitors: targeting the roots of breast cancer for prevention. EMBO J 2019; 38:e100852. [PMID: 31267556 PMCID: PMC6627238 DOI: 10.15252/embj.2018100852] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 03/11/2019] [Accepted: 04/11/2019] [Indexed: 12/24/2022] Open
Abstract
Breast cancer prevention is daunting, yet not an unsurmountable goal. Mammary stem and progenitors have been proposed as the cells-of-origin in breast cancer. Here, we present the concept of limiting these breast cancer precursors as a risk reduction approach in high-risk women. A wealth of information now exists for phenotypic and functional characterization of mammary stem and progenitor cells in mouse and human. Recent work has also revealed the hormonal regulation of stem/progenitor dynamics as well as intrinsic lineage distinctions between mammary epithelial populations. Leveraging these insights, molecular marker-guided chemoprevention is an achievable reality.
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Affiliation(s)
| | - Mathepan Mahendralingam
- Princess Margaret Cancer CentreUniversity Health NetworkUniversity of TorontoTorontoONCanada
| | - Hal K Berman
- Princess Margaret Cancer CentreUniversity Health NetworkUniversity of TorontoTorontoONCanada
| | - Rama Khokha
- Princess Margaret Cancer CentreUniversity Health NetworkUniversity of TorontoTorontoONCanada
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20
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Pellacani D, Tan S, Lefort S, Eaves CJ. Transcriptional regulation of normal human mammary cell heterogeneity and its perturbation in breast cancer. EMBO J 2019; 38:e100330. [PMID: 31304632 PMCID: PMC6627240 DOI: 10.15252/embj.2018100330] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 10/22/2018] [Accepted: 11/08/2018] [Indexed: 12/18/2022] Open
Abstract
The mammary gland in adult women consists of biologically distinct cell types that differ in their surface phenotypes. Isolation and molecular characterization of these subpopulations of mammary cells have provided extensive insights into their different transcriptional programs and regulation. This information is now serving as a baseline for interpreting the heterogeneous features of human breast cancers. Examination of breast cancer mutational profiles further indicates that most have undergone a complex evolutionary process even before being detected. The consequent intra-tumoral as well as inter-tumoral heterogeneity of these cancers thus poses major challenges to deriving information from early and hence likely pervasive changes in potential therapeutic interest. Recently described reproducible and efficient methods for generating human breast cancers de novo in immunodeficient mice transplanted with genetically altered primary cells now offer a promising alternative to investigate initial stages of human breast cancer development. In this review, we summarize current knowledge about key transcriptional regulatory processes operative in these partially characterized subpopulations of normal human mammary cells and effects of disrupting these processes in experimentally produced human breast cancers.
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Affiliation(s)
- Davide Pellacani
- Terry Fox LaboratoryBritish Columbia Cancer AgencyVancouverBCCanada
| | - Susanna Tan
- Terry Fox LaboratoryBritish Columbia Cancer AgencyVancouverBCCanada
| | - Sylvain Lefort
- Terry Fox LaboratoryBritish Columbia Cancer AgencyVancouverBCCanada
| | - Connie J Eaves
- Terry Fox LaboratoryBritish Columbia Cancer AgencyVancouverBCCanada
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21
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Gao Z, Moorjani P, Sasani TA, Pedersen BS, Quinlan AR, Jorde LB, Amster G, Przeworski M. Overlooked roles of DNA damage and maternal age in generating human germline mutations. Proc Natl Acad Sci U S A 2019; 116:9491-9500. [PMID: 31019089 PMCID: PMC6511033 DOI: 10.1073/pnas.1901259116] [Citation(s) in RCA: 104] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The textbook view that most germline mutations in mammals arise from replication errors is indirectly supported by the fact that there are both more mutations and more cell divisions in the male than in the female germline. When analyzing large de novo mutation datasets in humans, we find multiple lines of evidence that call that view into question. Notably, despite the drastic increase in the ratio of male to female germ cell divisions after the onset of spermatogenesis, even young fathers contribute three times more mutations than young mothers, and this ratio barely increases with parental age. This surprising finding points to a substantial contribution of damage-induced mutations. Indeed, C-to-G transversions and CpG transitions, which together constitute over one-fourth of all base substitution mutations, show genomic distributions and sex-specific age dependencies indicative of double-strand break repair and methylation-associated damage, respectively. Moreover, we find evidence that maternal age at conception influences the mutation rate both because of the accumulation of damage in oocytes and potentially through an influence on the number of postzygotic mutations in the embryo. These findings reveal underappreciated roles of DNA damage and maternal age in the genesis of human germline mutations.
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Affiliation(s)
- Ziyue Gao
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305;
- Department of Genetics, Stanford University, Stanford, CA 94305
| | - Priya Moorjani
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
- Center for Computational Biology, University of California, Berkeley, CA 94720
| | - Thomas A Sasani
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112
| | - Brent S Pedersen
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112
| | - Aaron R Quinlan
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112
- Department of Biomedical Informatics, University of Utah School of Medicine, Salt Lake City, UT 84108
| | - Lynn B Jorde
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112
| | - Guy Amster
- Department of Biological Sciences, Columbia University, New York, NY 10027
| | - Molly Przeworski
- Department of Biological Sciences, Columbia University, New York, NY 10027;
- Department of Systems Biology, Columbia University, New York, NY 10027
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22
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Zendehbad Z, Izadi P, Daraei A, Yekaninejad MS, Nafissi N, Younosi N, Khorasani G, Tavakkoly Bazzaz J. Early Parity Epigenetic Footprint of FOXA1 Gene Body in Normal Breast Tissue of Iranian Women. IRANIAN BIOMEDICAL JOURNAL 2019; 23. [PMID: 30054444 PMCID: PMC6707108 DOI: 10.29252/.23.2.99] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
BACKGROUND Young age at first full-term pregnancy (FFTP) is an important factor in breast cancer risk reduction. It is postulated that this protective effect is the result of stable molecular signatures imprinted by physiological process of pregnancy, but the molecular mechanism of this protective role is unclear. The aim of the current study was to identify the effect of early FFTP on methylation status of FOXA1 gene body. FOXA1 is an essential transcription factor for mammary gland development and estrogen responsiveness of breast tissue. METHODS Fresh frozen normal breast tissues (n = 51) were collected from Iranian women who underwent cosmetic mammoplasty (27 nulliparous women and 24 parous women who have experienced first pregnancy before the age of 25). DNA was extracted and then methylated DNA immunoprecipitation (MeDIP) real-time PCR was used to assess FOXA1 gene body methylation. RESULTS Our results revealed that FOXA1 methylation level is significantly higher in early parous compared with nulliparous group (p = 0.041). CONCLUSION Our study provides new hint about the association between early FFTP and epigenetic modifications within gene body of FOXA1 in normal breast tissue. More investigation is required for clarifying molecular mechanisms underlying this association in order to develop breast cancer prevention strategies.
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Affiliation(s)
- Zahra Zendehbad
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Pantea Izadi
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran;,Corresponding Author: Pantea Izadi, Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran; Tel.: (+98-21) 64053278; Fax: (+98-21) 88953005; E-mail:
| | - Abdolreza Daraei
- Genetic Department, Faculty of Medicine, Babol University of Medical Sciences, Babol, Iran
| | - Mir Saeed Yekaninejad
- Department of Epidemiology and Biostatistics, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Nahid Nafissi
- Surgical Department, School of Medicine, Iran University of Medical Science, Tehran, Iran
| | - Nasim Younosi
- Surgical Department, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Ghasemali Khorasani
- Division of Plastic and Reconstructive Surgery, Imam Khomeini Hospital Complex, Tehran University of Medical Sciences, Tehran, Iran
| | - Javad Tavakkoly Bazzaz
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
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23
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Milevskiy MJG, Gujral U, Del Lama Marques C, Stone A, Northwood K, Burke LJ, Gee JMW, Nephew K, Clark S, Brown MA. MicroRNA-196a is regulated by ER and is a prognostic biomarker in ER+ breast cancer. Br J Cancer 2019; 120:621-632. [PMID: 30783203 PMCID: PMC6461839 DOI: 10.1038/s41416-019-0395-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 12/16/2018] [Accepted: 01/15/2019] [Indexed: 12/18/2022] Open
Abstract
Background MicroRNAs are potent post-transcriptional regulators involved in all hallmarks of cancer. Mir-196a is transcribed from two loci and has been implicated in a wide range of developmental and pathogenic processes, with targets including Hox, Fox, Cdk inhibitors and annexins. Genetic variants and altered expression of MIR196A are associated with risk and progression of multiple cancers including breast cancer, however little is known about the regulation of the genes encoding this miRNA, nor the impact of variants therein. Methods Genomic data and chromatin interaction analysis were used to discover functional promoter and enhancer elements for MIR196A. Expression data were used to associate MIR196A with mechanisms of resistance, breast cancer subtypes and prognosis. Results Here we demonstrate that MIR196A displays complex and dynamic expression patterns, in part controlled by long-range transcriptional regulation between promoter and enhancer elements bound by ERα. Expression of this miRNA is significantly increased in drug-resistant models of hormone-receptor positive disease. The expression of MIR196A also proves to be a robust prognostic factor for patients with advanced and post-menopausal ER+ disease. Conclusion This work sheds light on the normal and abnormal regulation of MIR196A and provides a novel stratification method for therapeutically resistant breast cancer.
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Affiliation(s)
- Michael J G Milevskiy
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, Australia. .,ACRF Stem Cells and Cancer, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.
| | - Udai Gujral
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, Australia
| | | | - Andrew Stone
- Division of Genomics and Epigenetics, Epigenetics Research Laboratory, Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Korinne Northwood
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, Australia.,UQ Centre for Clinical Research, The University of Queensland, Herston, QLD, Australia
| | - Lez J Burke
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, Australia
| | - Julia M W Gee
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University, Cardiff, UK
| | - Kenneth Nephew
- School of Medicine, Indiana University, Bloomington, IN, USA
| | - Susan Clark
- Division of Genomics and Epigenetics, Epigenetics Research Laboratory, Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Melissa A Brown
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, Australia
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24
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Gao D, Pinello N, Nguyen TV, Thoeng A, Nagarajah R, Holst J, Rasko JEJ, Wong JJL. DNA methylation/hydroxymethylation regulate gene expression and alternative splicing during terminal granulopoiesis. Epigenomics 2019; 11:95-109. [DOI: 10.2217/epi-2018-0050] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Aim: To determine whether epigenetic modifications of DNA regulate gene expression and alternative splicing during terminal granulopoiesis. Materials & methods: Using whole genome bisulfite sequencing, reduced representation hydroxymethylation profiling and mRNA sequencing, we compare changes in DNA methylation, DNA hydroxymethylation, gene expression and alternative splicing in mouse promyelocytes and granulocytes. Results & conclusion: We show reduced DNA methylation at the promoters and enhancers of key granulopoiesis genes, indicating a regulatory role in the activation of lineage-specific genes during differentiation. Notably, increased DNA hydroxymethylation in exons is associated with preferential inclusion of specific exons in granulocytes. Overall, DNA methylation and hydroxymethylation changes at particular genomic loci may play specific roles in gene regulation or alternative splicing during terminal granulopoiesis. Data deposition: Whole genome bisulfite sequencing of mouse promyelocytes and granulocytes: Gene Expression Omnibus (GSE85517); mRNA sequencing of mouse promyelocytes and granulocytes: Gene Expression Omnibus (GSE48307); reduced representation 5-hydroxymethylation profiling of mouse promyelocytes and granulocytes: Bioproject (PRJNA495696).
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Affiliation(s)
- Dadi Gao
- Gene & Stem Cell Therapy Program Centenary Institute, University of Sydney, Camperdown 2050, Australia
- Bioinformatics Laboratory Centenary Institute, University of Sydney, Camperdown 2050, Australia
- Sydney Medical School, University of Sydney, NSW 2006, Australia
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Neurology, Harvard Medical School, Boston, MA 02115, USA
| | - Natalia Pinello
- Gene & Stem Cell Therapy Program Centenary Institute, University of Sydney, Camperdown 2050, Australia
- Sydney Medical School, University of Sydney, NSW 2006, Australia
- Gene Regulation in Cancer Laboratory Centenary Institute, University of Sydney, Camperdown 2050, Australia
| | - Trung V Nguyen
- Gene & Stem Cell Therapy Program Centenary Institute, University of Sydney, Camperdown 2050, Australia
- Sydney Medical School, University of Sydney, NSW 2006, Australia
- Gene Regulation in Cancer Laboratory Centenary Institute, University of Sydney, Camperdown 2050, Australia
| | - Annora Thoeng
- Gene & Stem Cell Therapy Program Centenary Institute, University of Sydney, Camperdown 2050, Australia
- Sydney Medical School, University of Sydney, NSW 2006, Australia
| | - Rajini Nagarajah
- Gene & Stem Cell Therapy Program Centenary Institute, University of Sydney, Camperdown 2050, Australia
- Sydney Medical School, University of Sydney, NSW 2006, Australia
| | - Jeff Holst
- Sydney Medical School, University of Sydney, NSW 2006, Australia
- Origins of Cancer Program Centenary Institute, University of Sydney, Camperdown 2050, Australia
| | - John EJ Rasko
- Gene & Stem Cell Therapy Program Centenary Institute, University of Sydney, Camperdown 2050, Australia
- Sydney Medical School, University of Sydney, NSW 2006, Australia
- Cell & Molecular Therapies, Royal Prince Alfred Hospital, Camperdown 2050, Australia
| | - Justin J-L Wong
- Gene & Stem Cell Therapy Program Centenary Institute, University of Sydney, Camperdown 2050, Australia
- Sydney Medical School, University of Sydney, NSW 2006, Australia
- Gene Regulation in Cancer Laboratory Centenary Institute, University of Sydney, Camperdown 2050, Australia
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25
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Zhang X, Li R. BRCA1-Dependent Transcriptional Regulation: Implication in Tissue-Specific Tumor Suppression. Cancers (Basel) 2018; 10:cancers10120513. [PMID: 30558184 PMCID: PMC6316118 DOI: 10.3390/cancers10120513] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Revised: 11/24/2018] [Accepted: 12/11/2018] [Indexed: 12/11/2022] Open
Abstract
Germ-line mutations in breast cancer susceptibility gene 1 (BRCA1) predominantly predispose women to breast and ovarian cancers. BRCA1 is best known for its functions in maintenance of genomic integrity including repairing DNA double-strand breaks through homologous recombination and suppressing DNA replication stress. However, whether these universally important BRCA1 functions in maintenance of genomic stability are sufficient to account for its tissue-specific tumor-suppressing function remains unclear. Accumulating evidence indicates that there are previously underappreciated roles of BRCA1 in transcriptional regulation and chromatin remodeling. In this review, we discuss the functional significance of interactions between BRCA1 and various transcription factors, its role in epigenetic regulation and chromatin dynamics, and BRCA1-dependent crosstalk between the machineries of transcription and genome integrity. Furthermore, we propose a model of how transcriptional regulation could contribute to tissue-dependent tumor-suppressing function of BRCA1.
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Affiliation(s)
- Xiaowen Zhang
- Department of Biochemistry & Molecular Medicine, School of Medicine & Health Sciences, The George Washington University, Washington, DC 20037, USA.
| | - Rong Li
- Department of Biochemistry & Molecular Medicine, School of Medicine & Health Sciences, The George Washington University, Washington, DC 20037, USA.
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26
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Yu D, Wang J, Zou H, Feng T, Chen L, Li J, Qi X, Li Z, Duan X, Xu C, Zhang L, Long X, Lan J, Chen C, Wang C, Xu X, Ren J, Zhao Y, Hu X, Lian Z, Men H, Pan D, Li N, Capecchi MR, Du X, Zhao Y, Wu S. Silencing of retrotransposon-derived imprinted gene RTL1 is the main cause for postimplantational failures in mammalian cloning. Proc Natl Acad Sci U S A 2018; 115:E11071-E11080. [PMID: 30381455 PMCID: PMC6255163 DOI: 10.1073/pnas.1814514115] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Substantial rates of fetal loss plague all in vitro procedures involving embryo manipulations, including human-assisted reproduction, and are especially problematic for mammalian cloning where over 90% of reconstructed nuclear transfer embryos are typically lost during pregnancy. However, the epigenetic mechanism of these pregnancy failures has not been well described. Here we performed methylome and transcriptome analyses of pig induced pluripotent stem cells and associated cloned embryos, and revealed that aberrant silencing of imprinted genes, in particular the retrotransposon-derived RTL1 gene, is the principal epigenetic cause of pregnancy failure. Remarkably, restoration of RTL1 expression in pig induced pluripotent stem cells rescued fetal loss. Furthermore, in other mammals, including humans, low RTL1 levels appear to be the main epigenetic cause of pregnancy failure.
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Affiliation(s)
- Dawei Yu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, 100193 Beijing, China
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China
| | - Jing Wang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, 100193 Beijing, China
| | - Huiying Zou
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, 100193 Beijing, China
- Embryo Biotechnology and Reproduction Laboratory, Institute of Animal Science, Chinese Academy of Agricultural Sciences, 100193 Beijing, China
| | - Tao Feng
- College of Veterinary Medicine, China Agricultural University, 100193 Beijing, China
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, China Agricultural University, 100193 Beijing, China
| | - Lei Chen
- Chongqing Academy of Animal Science, 402460 Chongqing, China
| | - Jia Li
- Center for Epigenetics & Disease Prevention, Institute of Biosciences and Technology, College of Medicine, Texas A&M University, Houston, TX 77030
| | - Xiaolan Qi
- College of Veterinary Medicine, China Agricultural University, 100193 Beijing, China
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, China Agricultural University, 100193 Beijing, China
| | - Zhifang Li
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, 100193 Beijing, China
| | - Xiaoyue Duan
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, 100193 Beijing, China
| | - Chunlong Xu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, 100193 Beijing, China
| | - Liang Zhang
- Chongqing Academy of Animal Science, 402460 Chongqing, China
| | - Xi Long
- Chongqing Academy of Animal Science, 402460 Chongqing, China
| | - Jing Lan
- Chongqing Academy of Animal Science, 402460 Chongqing, China
| | - Chao Chen
- Tang Tang Biomedical Technology (Beijing) Co., 100101 Beijing, China
| | - Chao Wang
- Department of Computer and Technology, Tsinghua University, 100101 Beijing, China
| | - Xinyu Xu
- School of Life Sciences, Tsinghua University, 100101 Beijing, China
| | - Jilong Ren
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China
| | - Yiqiang Zhao
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, 100193 Beijing, China
| | - Xiaoxiang Hu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, 100193 Beijing, China
| | - Zhengxing Lian
- College of Animal Science and Technology, China Agriculture University, 100193 Beijing, China
| | - Hongsheng Men
- Rat Resource and Research Center, University of Missouri, Columbia, MO 65201
- Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, MO 65201
| | - Dengke Pan
- Embryo Biotechnology and Reproduction Laboratory, Institute of Animal Science, Chinese Academy of Agricultural Sciences, 100193 Beijing, China
| | - Ning Li
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, 100193 Beijing, China
| | - Mario R Capecchi
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112
| | - Xuguang Du
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, 100193 Beijing, China;
- College of Animal Science and Technology, China Agriculture University, 100193 Beijing, China
| | - Yaofeng Zhao
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, 100193 Beijing, China;
| | - Sen Wu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, 100193 Beijing, China;
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27
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Differentiation-state plasticity is a targetable resistance mechanism in basal-like breast cancer. Nat Commun 2018; 9:3815. [PMID: 30232459 PMCID: PMC6145927 DOI: 10.1038/s41467-018-05729-w] [Citation(s) in RCA: 120] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 07/24/2018] [Indexed: 01/03/2023] Open
Abstract
Intratumoral heterogeneity in cancers arises from genomic instability and epigenomic plasticity and is associated with resistance to cytotoxic and targeted therapies. We show here that cell-state heterogeneity, defined by differentiation-state marker expression, is high in triple-negative and basal-like breast cancer subtypes, and that drug tolerant persister (DTP) cell populations with altered marker expression emerge during treatment with a wide range of pathway-targeted therapeutic compounds. We show that MEK and PI3K/mTOR inhibitor-driven DTP states arise through distinct cell-state transitions rather than by Darwinian selection of preexisting subpopulations, and that these transitions involve dynamic remodeling of open chromatin architecture. Increased activity of many chromatin modifier enzymes, including BRD4, is observed in DTP cells. Co-treatment with the PI3K/mTOR inhibitor BEZ235 and the BET inhibitor JQ1 prevents changes to the open chromatin architecture, inhibits the acquisition of a DTP state, and results in robust cell death in vitro and xenograft regression in vivo. Resistance to therapy can be driven by intratumoral heterogeneity. Here, the authors show that drug tolerant persistent cell populations emerge during treatment, and these emergent populations arise through epigenetically mediated cell state transitions rather than sub population selection.
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28
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Identification of protein kinase inhibitors to reprogram breast cancer cells. Cell Death Dis 2018; 9:915. [PMID: 30206213 PMCID: PMC6133942 DOI: 10.1038/s41419-018-1002-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 05/09/2018] [Accepted: 05/11/2018] [Indexed: 12/22/2022]
Abstract
Direct reversion of cancers into normal-like tissues is an ideal strategy for cancer treatment. Recent reports have showed that defined transcription factors can induce reprogramming of cancer cells into pluripotent stem cells, supporting this notion. Here, we have developed a reprogramming method that uses a conceptually unique strategy for breast cancer cell treatment. We have screened a kinase inhibitor library and found that Rho-associated protein kinase (ROCK) and mammalian target of rapamycin (mTOR) kinase inhibitors can substitute for all transcription factors to be sufficient to reprogram breast cancer cells into progenitor cells. Furthermore, ROCK–mTOR inhibitors could reprogram breast cancer cells to another terminal lineage-adipogenic cells. Genome-wide transcriptional analysis shows that the induced fat-like cells have a profile different from breast cancer cells and similar to that of normal adipocytes. In vitro and in vivo tumorigenesis assays have shown that induced fat-like cells lose proliferation and tumorigenicity. Moreover, reprogramming treatment with ROCK–mTOR inhibitors prevents breast cancer local recurrence in mice. Currently, ROCK–mTOR inhibitors are already used as antitumor drugs in patients, thus, this reprogramming strategy has significant potential to move rapidly toward clinical trials for breast cancer treatment.
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29
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MiR-29b-1-5p is altered in BRCA1 mutant tumours and is a biomarker in basal-like breast cancer. Oncotarget 2018; 9:33577-33588. [PMID: 30323900 PMCID: PMC6173367 DOI: 10.18632/oncotarget.26094] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2018] [Accepted: 08/27/2018] [Indexed: 12/19/2022] Open
Abstract
Depletion of BRCA1 protein in mouse mammary glands results in defects in lactational development and increased susceptibility to mammary cancer. Extensive work has focussed on the role of BRCA1 in the normal breast and in the development of breast cancer, the cell of origin for BRCA1 tumours and the protein-coding genes altered in BRCA1 deficient cells. However, the role of non-coding RNAs in BRCA1-deficient cells is poorly understood. To evaluate miRNA expression in BRCA1 deficient mammary cells, RNA sequencing was performed on the mammary glands of Brca1 knockout mice. We identified 140 differentially expressed miRNAs, 9 of which were also differentially expressed in human BRCA1 breast tumours or familial non-BRCA1 patients and during normal gland development. We show that BRCA1 binds to putative cis-elements in promoter regions of the miRNAs with the potential to regulate their expression, and that four miRNAs (miR-29b-1-5p, miR-664, miR-16-2 and miR-744) significantly stratified the overall survival of basal-like tumours. Importantly the prognostic value of miR-29b-1-5p was higher in significance than several commonly used clinical biomarkers. These results emphasise the role of Brca1 in modulating expression of miRNAs and highlights the potential for BRCA1 regulated miRNAs to be informative biomarkers associated with BRCA1 loss and survival in breast cancer.
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30
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Abstract
Differentiation of stem cells into highly specialised cells requires gene expression changes brought about by remodelling of the chromatin architecture. During this lineage-commitment process, the majority of DNA needs to be packaged into inactive heterochromatin, allowing only a subset of regulatory elements to remain open and functionally required genes to be expressed. Epigenetic mechanisms such as DNA methylation, post-translational modifications to histone tails, and nucleosome positioning all potentially contribute to the changes in higher order chromatin structure during differentiation. The mammary gland is a particularly useful model to study these complex epigenetic processes since the majority of its development is postnatal, the gland is easily accessible, and development occurs in a highly reproducible manner. Inappropriate epigenetic remodelling can also drive tumourigenesis; thus, insights into epigenetic remodelling during mammary gland development advance our understanding of breast cancer aetiology. We review the current literature surrounding DNA methylation and histone modifications in the developing mammary gland and its implications for breast cancer.
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Affiliation(s)
- Holly Holliday
- The Kinghorn Cancer Centre, Cancer Research Division, Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia.,St Vincent's Clinical School, Faculty of Medicine, UNSW, Darlinghurst, NSW, 2010, Australia
| | - Laura A Baker
- The Kinghorn Cancer Centre, Cancer Research Division, Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia.,St Vincent's Clinical School, Faculty of Medicine, UNSW, Darlinghurst, NSW, 2010, Australia
| | - Simon R Junankar
- The Kinghorn Cancer Centre, Cancer Research Division, Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia.,St Vincent's Clinical School, Faculty of Medicine, UNSW, Darlinghurst, NSW, 2010, Australia
| | - Susan J Clark
- St Vincent's Clinical School, Faculty of Medicine, UNSW, Darlinghurst, NSW, 2010, Australia.,Epigenetics Research Program, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia
| | - Alexander Swarbrick
- The Kinghorn Cancer Centre, Cancer Research Division, Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia. .,St Vincent's Clinical School, Faculty of Medicine, UNSW, Darlinghurst, NSW, 2010, Australia.
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31
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Hui T, Cao Q, Wegrzyn-Woltosz J, O'Neill K, Hammond CA, Knapp DJHF, Laks E, Moksa M, Aparicio S, Eaves CJ, Karsan A, Hirst M. High-Resolution Single-Cell DNA Methylation Measurements Reveal Epigenetically Distinct Hematopoietic Stem Cell Subpopulations. Stem Cell Reports 2018; 11:578-592. [PMID: 30078558 PMCID: PMC6093082 DOI: 10.1016/j.stemcr.2018.07.003] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 07/08/2018] [Accepted: 07/09/2018] [Indexed: 02/06/2023] Open
Abstract
Increasing evidence of functional and transcriptional heterogeneity in phenotypically similar cells examined individually has prompted interest in obtaining parallel methylome data. We describe the development and application of such a protocol to index-sorted murine and human hematopoietic cells that are highly enriched in their content of functionally defined stem cells. Utilizing an optimized single-cell bisulfite sequencing protocol, we obtained quantitative DNA methylation measurements of up to 5.7 million CpGs in single hematopoietic cells. In parallel, we developed an analytical strategy (PDclust) to define single-cell DNA methylation states through pairwise comparisons of single-CpG methylation measurements. PDclust revealed that a single-cell epigenetic state can be described by a small (<1%) stochastically sampled fraction of CpGs and that these states are reflective of cell identity and state. Using relationships revealed by PDclust, we derive near complete methylomes for epigenetically distinct subpopulations of hematopoietic cells enriched for functional stem cell content.
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Affiliation(s)
- Tony Hui
- Department of Microbiology and Immunology and Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 1L3, Canada
| | - Qi Cao
- Department of Microbiology and Immunology and Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Joanna Wegrzyn-Woltosz
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 1L3, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 2B5, Canada
| | - Kieran O'Neill
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 1L3, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 2B5, Canada; Terry Fox Laboratory, BC Cancer, Vancouver, BC V5Z 1L3, Canada
| | - Colin A Hammond
- Terry Fox Laboratory, BC Cancer, Vancouver, BC V5Z 1L3, Canada; Department of Medicine, University of British Columbia, Vancouver, BC V5Z 1M9, Canada
| | - David J H F Knapp
- Terry Fox Laboratory, BC Cancer, Vancouver, BC V5Z 1L3, Canada; Department of Medicine, University of British Columbia, Vancouver, BC V5Z 1M9, Canada
| | - Emma Laks
- Department of Molecular Oncology, BC Cancer, Vancouver, BC V5Z 1L3, Canada
| | - Michelle Moksa
- Department of Microbiology and Immunology and Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Samuel Aparicio
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 2B5, Canada; Department of Molecular Oncology, BC Cancer, Vancouver, BC V5Z 1L3, Canada
| | - Connie J Eaves
- Terry Fox Laboratory, BC Cancer, Vancouver, BC V5Z 1L3, Canada; Department of Medicine, University of British Columbia, Vancouver, BC V5Z 1M9, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, BC V6H 3N1, Canada
| | - Aly Karsan
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 1L3, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 2B5, Canada; Terry Fox Laboratory, BC Cancer, Vancouver, BC V5Z 1L3, Canada
| | - Martin Hirst
- Department of Microbiology and Immunology and Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 1L3, Canada.
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32
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RUNX1 promotes cell growth in human T-cell acute lymphoblastic leukemia by transcriptional regulation of key target genes. Exp Hematol 2018; 64:84-96. [DOI: 10.1016/j.exphem.2018.04.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 04/19/2018] [Accepted: 04/27/2018] [Indexed: 11/23/2022]
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Casey AE, Sinha A, Singhania R, Livingstone J, Waterhouse P, Tharmapalan P, Cruickshank J, Shehata M, Drysdale E, Fang H, Kim H, Isserlin R, Bailey S, Medina T, Deblois G, Shiah YJ, Barsyte-Lovejoy D, Hofer S, Bader G, Lupien M, Arrowsmith C, Knapp S, De Carvalho D, Berman H, Boutros PC, Kislinger T, Khokha R. Mammary molecular portraits reveal lineage-specific features and progenitor cell vulnerabilities. J Cell Biol 2018; 217:2951-2974. [PMID: 29921600 PMCID: PMC6080920 DOI: 10.1083/jcb.201804042] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 05/14/2018] [Accepted: 05/17/2018] [Indexed: 12/15/2022] Open
Abstract
Casey et al. integrate epigenomic, transcriptomic, and proteomic profiling of primary basal and luminal mammary cells to identify master epigenetic regulators of the mammary epithelium and uncover stem and progenitor cell vulnerabilities. They develop a pipeline to identify drugs that abrogate progenitor cell activity in normal and high-risk breast cancer patient samples in vitro and in vivo. The mammary epithelium depends on specific lineages and their stem and progenitor function to accommodate hormone-triggered physiological demands in the adult female. Perturbations of these lineages underpin breast cancer risk, yet our understanding of normal mammary cell composition is incomplete. Here, we build a multimodal resource for the adult gland through comprehensive profiling of primary cell epigenomes, transcriptomes, and proteomes. We define systems-level relationships between chromatin–DNA–RNA–protein states, identify lineage-specific DNA methylation of transcription factor binding sites, and pinpoint proteins underlying progesterone responsiveness. Comparative proteomics of estrogen and progesterone receptor–positive and –negative cell populations, extensive target validation, and drug testing lead to discovery of stem and progenitor cell vulnerabilities. Top epigenetic drugs exert cytostatic effects; prevent adult mammary cell expansion, clonogenicity, and mammopoiesis; and deplete stem cell frequency. Select drugs also abrogate human breast progenitor cell activity in normal and high-risk patient samples. This integrative computational and functional study provides fundamental insight into mammary lineage and stem cell biology.
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Affiliation(s)
| | - Ankit Sinha
- Princess Margaret Cancer Centre, Toronto, ON, Canada
| | | | - Julie Livingstone
- Informatics and Biocomputing Program, Ontario Institute for Cancer Research, Toronto, ON, Canada
| | | | | | | | - Mona Shehata
- Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - Erik Drysdale
- Informatics and Biocomputing Program, Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Hui Fang
- Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - Hyeyeon Kim
- Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - Ruth Isserlin
- The Donnelly Centre, University of Toronto, Toronto, ON, Canada
| | - Swneke Bailey
- Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - Tiago Medina
- Princess Margaret Cancer Centre, Toronto, ON, Canada
| | | | - Yu-Jia Shiah
- Informatics and Biocomputing Program, Ontario Institute for Cancer Research, Toronto, ON, Canada
| | | | - Stefan Hofer
- Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - Gary Bader
- The Donnelly Centre, University of Toronto, Toronto, ON, Canada
| | - Mathieu Lupien
- Princess Margaret Cancer Centre, Toronto, ON, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Cheryl Arrowsmith
- Princess Margaret Cancer Centre, Toronto, ON, Canada.,Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Stefan Knapp
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford, Oxford, UK
| | - Daniel De Carvalho
- Princess Margaret Cancer Centre, Toronto, ON, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Hal Berman
- Princess Margaret Cancer Centre, Toronto, ON, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, ON, Canada
| | - Paul C Boutros
- Informatics and Biocomputing Program, Ontario Institute for Cancer Research, Toronto, ON, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.,Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, Canada
| | - Thomas Kislinger
- Princess Margaret Cancer Centre, Toronto, ON, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Rama Khokha
- Princess Margaret Cancer Centre, Toronto, ON, Canada .,Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
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34
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Dvinge H. Regulation of alternative
mRNA
splicing: old players and new perspectives. FEBS Lett 2018; 592:2987-3006. [DOI: 10.1002/1873-3468.13119] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2018] [Revised: 05/23/2018] [Accepted: 05/29/2018] [Indexed: 12/22/2022]
Affiliation(s)
- Heidi Dvinge
- Department of Biomolecular Chemistry School of Medicine and Public Health University of Wisconsin‐Madison WI USA
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35
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Vanichkina DP, Schmitz U, Wong JJL, Rasko JE. Challenges in defining the role of intron retention in normal biology and disease. Semin Cell Dev Biol 2018; 75:40-49. [DOI: 10.1016/j.semcdb.2017.07.030] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 07/19/2017] [Accepted: 07/19/2017] [Indexed: 10/19/2022]
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36
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Chu C, Liu X, Bai X, Zhao T, Wang M, Xu R, Li M, Hu Y, Li W, Yang L, Qin Y, Yang M, Yan C, Zhang Y. MiR-519d suppresses breast cancer tumorigenesis and metastasis via targeting MMP3. Int J Biol Sci 2018; 14:228-236. [PMID: 29483840 PMCID: PMC5821043 DOI: 10.7150/ijbs.22849] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2017] [Accepted: 12/28/2017] [Indexed: 01/10/2023] Open
Abstract
Breast cancer (BC) is the most common cause of death in women throughout the world. Although microRNAs (miRNAs) have been identified as novel regulators in carcinogenesis, there are still abundant hidden treasure needed to be excavated. In the present study, we found that miR-519d expression was remarkably decreased in both human BC tissues and MCF-7 cells. CCK8 and 5-Ethynyl-2'-deoxyuridine (EdU) assays were used to evaluate cell proliferation. Wound-healing and transwell assays were performed for detection of cell migration and invasion. The results demonstrated miR-519d overexpression dramatically suppressed MCF-7 cells proliferation, migration and invasion. While downregulation of miR-519d by miR-519d inhibitor substantially increased MCF-7 cell carcinogenesis. Further analysis identified Matrix Metalloproteinase-3 (MMP3) as a direct target of miR-519d. QRT-PCR and western blot results indicated the correlative expression of miR-519d and MMP3 in BC tissues and MCF-7 cells. In summary, our data uncovered the novel molecular interaction between miR-519d and MMP3, indicating a therapeutic strategy of miR-519d for BC.
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Affiliation(s)
- Chengling Chu
- Department of Oncology, The First Affiliated Hospital of Harbin Medical University, Harbin 150001, China
| | - Xin Liu
- Department of Pharmacology (the State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin 150081, China
| | - Xue Bai
- Department of Pharmacology (the State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin 150081, China
| | - Tong Zhao
- Department of Pharmacology (the State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin 150081, China
| | - Mengxue Wang
- Department of Pharmacology (the State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin 150081, China
| | - Ranchen Xu
- Department of Pharmacology (the State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin 150081, China
| | - Mingqi Li
- Department of Pharmacology (the State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin 150081, China
| | - Yingying Hu
- Department of Pharmacy, The First Affiliated Hospital of Harbin Medical University, Harbin 150001, China
| | - Weihua Li
- Department of Pharmacy, The First Affiliated Hospital of Harbin Medical University, Harbin 150001, China
| | - Lida Yang
- Department of Pharmacology (the State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin 150081, China
| | - Youyou Qin
- Department of Breast Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin 150086, China
| | - Meng Yang
- Department of Oncology, The First Affiliated Hospital of Harbin Medical University, Harbin 150001, China
| | - Chaoqi Yan
- Department of Breast Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin 150086, China
| | - Yong Zhang
- Department of Pharmacology (the State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin 150081, China.,Institute of Metabolic Disease, Heilongjiang Academy of Medical Science, Harbin 150086, China
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37
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Pellacani D, Bilenky M, Kannan N, Heravi-Moussavi A, Knapp DJHF, Gakkhar S, Moksa M, Carles A, Moore R, Mungall AJ, Marra MA, Jones SJM, Aparicio S, Hirst M, Eaves CJ. Analysis of Normal Human Mammary Epigenomes Reveals Cell-Specific Active Enhancer States and Associated Transcription Factor Networks. Cell Rep 2017; 17:2060-2074. [PMID: 27851968 DOI: 10.1016/j.celrep.2016.10.058] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Revised: 08/10/2016] [Accepted: 09/30/2016] [Indexed: 01/06/2023] Open
Abstract
The normal adult human mammary gland is a continuous bilayered epithelial system. Bipotent and myoepithelial progenitors are prominent and unique components of the outer (basal) layer. The inner (luminal) layer includes both luminal-restricted progenitors and a phenotypically separable fraction that lacks progenitor activity. We now report an epigenomic comparison of these three subsets with one another, with their associated stromal cells, and with three immortalized, non-tumorigenic human mammary cell lines. Each genome-wide analysis contains profiles for six histone marks, methylated DNA, and RNA transcripts. Analysis of these datasets shows that each cell type has unique features, primarily within genomic regulatory regions, and that the cell lines group together. Analyses of the promoter and enhancer profiles place the luminal progenitors in between the basal cells and the non-progenitor luminal subset. Integrative analysis reveals networks of subset-specific transcription factors.
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Affiliation(s)
- Davide Pellacani
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - Misha Bilenky
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - Nagarajan Kannan
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - Alireza Heravi-Moussavi
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - David J H F Knapp
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - Sitanshu Gakkhar
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - Michelle Moksa
- Michael Smith Laboratories, Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Annaick Carles
- Michael Smith Laboratories, Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Richard Moore
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - Andrew J Mungall
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - Marco A Marra
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - Steven J M Jones
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - Samuel Aparicio
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, BC V5Z 1L3, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 2B5, Canada
| | - Martin Hirst
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC V5Z 1L3, Canada; Michael Smith Laboratories, Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
| | - Connie J Eaves
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC V5Z 1L3, Canada.
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38
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Ebata KT, Mesh K, Liu S, Bilenky M, Fekete A, Acker MG, Hirst M, Garcia BA, Ramalho-Santos M. Vitamin C induces specific demethylation of H3K9me2 in mouse embryonic stem cells via Kdm3a/b. Epigenetics Chromatin 2017; 10:36. [PMID: 28706564 PMCID: PMC5506665 DOI: 10.1186/s13072-017-0143-3] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2017] [Accepted: 07/03/2017] [Indexed: 01/06/2023] Open
Abstract
Background Histone methylation patterns regulate gene expression and are highly dynamic during development. The erasure of histone methylation is carried out by histone demethylase enzymes. We had previously shown that vitamin C enhances the activity of Tet enzymes in embryonic stem (ES) cells, leading to DNA demethylation and activation of germline genes. Results We report here that vitamin C induces a remarkably specific demethylation of histone H3 lysine 9 dimethylation (H3K9me2) in naïve ES cells. Vitamin C treatment reduces global levels of H3K9me2, but not other histone methylation marks analyzed, as measured by western blot, immunofluorescence and mass spectrometry. Vitamin C leads to widespread loss of H3K9me2 at large chromosomal domains as well as gene promoters and repeat elements. Vitamin C-induced loss of H3K9me2 occurs rapidly within 24 h and is reversible. Importantly, we found that the histone demethylases Kdm3a and Kdm3b are required for vitamin C-induced demethylation of H3K9me2. Moreover, we show that vitamin C-induced Kdm3a/b-mediated H3K9me2 demethylation and Tet-mediated DNA demethylation are independent processes at specific loci. Lastly, we document Kdm3a/b are partially required for the upregulation of germline genes by vitamin C. Conclusions These results reveal a specific role for vitamin C in histone demethylation in ES cells and document that DNA methylation and H3K9me2 cooperate to silence germline genes in pluripotent cells. Electronic supplementary material The online version of this article (doi:10.1186/s13072-017-0143-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kevin T Ebata
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA USA
| | - Kathryn Mesh
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA USA
| | - Shichong Liu
- Epigenetics Program, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA USA
| | - Misha Bilenky
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC Canada
| | | | - Michael G Acker
- Novartis Institutes for Biomedical Research, Cambridge, MA USA
| | - Martin Hirst
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC Canada.,Department of Microbiology and Immunology, Centre for High-Throughput Biology, University of British Columbia, Vancouver, BC Canada
| | - Benjamin A Garcia
- Epigenetics Program, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA USA
| | - Miguel Ramalho-Santos
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA USA
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39
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Zhang X, Chiang HC, Wang Y, Zhang C, Smith S, Zhao X, Nair SJ, Michalek J, Jatoi I, Lautner M, Oliver B, Wang H, Petit A, Soler T, Brunet J, Mateo F, Angel Pujana M, Poggi E, Chaldekas K, Isaacs C, Peshkin BN, Ochoa O, Chedin F, Theoharis C, Sun LZ, Curiel TJ, Elledge R, Jin VX, Hu Y, Li R. Attenuation of RNA polymerase II pausing mitigates BRCA1-associated R-loop accumulation and tumorigenesis. Nat Commun 2017; 8:15908. [PMID: 28649985 PMCID: PMC5490191 DOI: 10.1038/ncomms15908] [Citation(s) in RCA: 103] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 05/12/2017] [Indexed: 01/08/2023] Open
Abstract
Most BRCA1-associated breast tumours are basal-like yet originate from luminal progenitors. BRCA1 is best known for its functions in double-strand break repair and resolution of DNA replication stress. However, it is unclear whether loss of these ubiquitously important functions fully explains the cell lineage-specific tumorigenesis. In vitro studies implicate BRCA1 in elimination of R-loops, DNA-RNA hybrid structures involved in transcription and genetic instability. Here we show that R-loops accumulate preferentially in breast luminal epithelial cells, not in basal epithelial or stromal cells, of BRCA1 mutation carriers. Furthermore, R-loops are enriched at the 5' end of those genes with promoter-proximal RNA polymerase II (Pol II) pausing. Genetic ablation of Cobra1, which encodes a Pol II-pausing and BRCA1-binding protein, ameliorates R-loop accumulation and reduces tumorigenesis in Brca1-knockout mouse mammary epithelium. Our studies show that Pol II pausing is an important contributor to BRCA1-associated R-loop accumulation and breast cancer development.
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Affiliation(s)
- Xiaowen Zhang
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, 8403 Floyd Curl Drive, San Antonio, Texas 78229, USA
| | - Huai-Chin Chiang
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, 8403 Floyd Curl Drive, San Antonio, Texas 78229, USA
| | - Yao Wang
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, 8403 Floyd Curl Drive, San Antonio, Texas 78229, USA
| | - Chi Zhang
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, 8403 Floyd Curl Drive, San Antonio, Texas 78229, USA
| | - Sabrina Smith
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, 8403 Floyd Curl Drive, San Antonio, Texas 78229, USA
| | - Xiayan Zhao
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, 8403 Floyd Curl Drive, San Antonio, Texas 78229, USA
| | - Sreejith J. Nair
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, 8403 Floyd Curl Drive, San Antonio, Texas 78229, USA
| | - Joel Michalek
- Department of Epidemiology and Biostatistics, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, USA
| | - Ismail Jatoi
- Department of Surgery, Cancer Therapy and Research Center, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, USA
| | - Meeghan Lautner
- Department of Surgery, Cancer Therapy and Research Center, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, USA
| | - Boyce Oliver
- Department of Surgery, Cancer Therapy and Research Center, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, USA
| | - Howard Wang
- Department of Surgery, Cancer Therapy and Research Center, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, USA
| | - Anna Petit
- Department of Pathology, University Hospital of Bellvitge, Bellvitge Institute for Biomedical Research (IDIBELL), L’Hospitalet del Llobregat, Barcelona 08908, Spain
| | - Teresa Soler
- Department of Pathology, University Hospital of Bellvitge, Bellvitge Institute for Biomedical Research (IDIBELL), L’Hospitalet del Llobregat, Barcelona 08908, Spain
| | - Joan Brunet
- Hereditary Cancer Program, Catalan Institute of Oncology (ICO), Girona Biomedical Research Institute (IDIBGI), Girona 17007, Spain
| | - Francesca Mateo
- Breast Cancer and Systems Biology Lab, Program Against Cancer Therapeutic Resistance (ProCURE), Catalan Institute of Oncology (ICO), Bellvitge Institute for Biomedical Research (IDIBELL), L’Hospitalet del Llobregat, Barcelona 08908, Spain
| | - Miguel Angel Pujana
- Breast Cancer and Systems Biology Lab, Program Against Cancer Therapeutic Resistance (ProCURE), Catalan Institute of Oncology (ICO), Bellvitge Institute for Biomedical Research (IDIBELL), L’Hospitalet del Llobregat, Barcelona 08908, Spain
| | - Elizabeth Poggi
- Lombardi Comprehensive Cancer Center, Georgetown University, Washington, District of Columbia 20007, USA
| | - Krysta Chaldekas
- Lombardi Comprehensive Cancer Center, Georgetown University, Washington, District of Columbia 20007, USA
| | - Claudine Isaacs
- Lombardi Comprehensive Cancer Center, Georgetown University, Washington, District of Columbia 20007, USA
| | - Beth N. Peshkin
- Lombardi Comprehensive Cancer Center, Georgetown University, Washington, District of Columbia 20007, USA
| | - Oscar Ochoa
- PRMA Plastic Surgery, San Antonio, Texas 78240, USA
| | - Frederic Chedin
- Department of Molecular and Cellular Biology, University of California, Davis, California 95616, USA
| | | | - Lu-Zhe Sun
- Department of Cell Systems and Anatomy, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, USA
| | - Tyler J. Curiel
- Department of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, USA
| | - Richard Elledge
- Department of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, USA
| | - Victor X. Jin
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, 8403 Floyd Curl Drive, San Antonio, Texas 78229, USA
| | - Yanfen Hu
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, 8403 Floyd Curl Drive, San Antonio, Texas 78229, USA
| | - Rong Li
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, 8403 Floyd Curl Drive, San Antonio, Texas 78229, USA
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40
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Intron retention is regulated by altered MeCP2-mediated splicing factor recruitment. Nat Commun 2017; 8:15134. [PMID: 28480880 PMCID: PMC5424149 DOI: 10.1038/ncomms15134] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 03/02/2017] [Indexed: 01/07/2023] Open
Abstract
While intron retention (IR) is considered a widely conserved and distinct mechanism of gene expression control, its regulation is poorly understood. Here we show that DNA methylation directly regulates IR. We also find reduced occupancy of MeCP2 near the splice junctions of retained introns, mirroring the reduced DNA methylation at these sites. Accordingly, MeCP2 depletion in tissues and cells enhances IR. By analysing the MeCP2 interactome using mass spectrometry and RNA co-precipitation, we demonstrate that decreased MeCP2 binding near splice junctions facilitates IR via reduced recruitment of splicing factors, including Tra2b, and increased RNA polymerase II stalling. These results suggest an association between IR and a slower rate of transcription elongation, which reflects inefficient splicing factor recruitment. In summary, our results reinforce the interdependency between alternative splicing involving IR and epigenetic controls of gene expression. Intron retention is a conserved mechanism that controls gene expression but its regulation is poorly understood. Here, the authors provide evidence that DNA methylation regulates intron retention and find reduced MeCP2 occupancy and splicing factor recruitment near affected splice junctions.
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41
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Jacob AG, Smith CWJ. Intron retention as a component of regulated gene expression programs. Hum Genet 2017; 136:1043-1057. [PMID: 28391524 PMCID: PMC5602073 DOI: 10.1007/s00439-017-1791-x] [Citation(s) in RCA: 178] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 03/29/2017] [Indexed: 12/16/2022]
Abstract
Intron retention has long been an exemplar of regulated splicing with case studies of individual events serving as models that provided key mechanistic insights into the process of splicing control. In organisms such as plants and budding yeast, intron retention is well understood as a major mechanism of gene expression regulation. In contrast, in mammalian systems, the extent and functional significance of intron retention have, until recently, remained greatly underappreciated. Technical challenges to the global detection and quantitation of transcripts with retained introns have often led to intron retention being overlooked or dismissed as “noise”. Now, however, with the wealth of information available from high-throughput deep sequencing, combined with focused computational and statistical analyses, we are able to distinguish clear intron retention patterns in various physiological and pathological contexts. Several recent studies have demonstrated intron retention as a central component of gene expression programs during normal development as well as in response to stress and disease. Furthermore, these studies revealed various ways in which intron retention regulates protein isoform production, RNA stability and translation efficiency, and rapid induction of expression via post-transcriptional splicing of retained introns. In this review, we highlight critical findings from these transcriptomic studies and discuss commonalties in the patterns prevalent in intron retention networks at the functional and regulatory levels.
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Affiliation(s)
- Aishwarya G Jacob
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QW, UK
| | - Christopher W J Smith
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QW, UK.
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42
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Feng Y, Rhie SK, Huo D, Ruiz-Narvaez EA, Haddad SA, Ambrosone CB, John EM, Bernstein L, Zheng W, Hu JJ, Ziegler RG, Nyante S, Bandera EV, Ingles SA, Press MF, Deming SL, Rodriguez-Gil JL, Zheng Y, Yao S, Han YJ, Ogundiran TO, Rebbeck TR, Adebamowo C, Ojengbede O, Falusi AG, Hennis A, Nemesure B, Ambs S, Blot W, Cai Q, Signorello L, Nathanson KL, Lunetta KL, Sucheston-Campbell LE, Bensen JT, Chanock SJ, Marchand LL, Olshan AF, Kolonel LN, Conti DV, Coetzee GA, Stram DO, Olopade OI, Palmer JR, Haiman CA. Characterizing Genetic Susceptibility to Breast Cancer in Women of African Ancestry. Cancer Epidemiol Biomarkers Prev 2017; 26:1016-1026. [PMID: 28377418 DOI: 10.1158/1055-9965.epi-16-0567] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Revised: 10/07/2016] [Accepted: 03/15/2017] [Indexed: 01/01/2023] Open
Abstract
Background: Genome-wide association studies have identified approximately 100 common genetic variants associated with breast cancer risk, the majority of which were discovered in women of European ancestry. Because of different patterns of linkage disequilibrium, many of these genetic markers may not represent signals in populations of African ancestry.Methods: We tested 74 breast cancer risk variants and conducted fine-mapping of these susceptibility regions in 6,522 breast cancer cases and 7,643 controls of African ancestry from three genetic consortia (AABC, AMBER, and ROOT).Results: Fifty-four of the 74 variants (73%) were found to have ORs that were directionally consistent with those previously reported, of which 12 were nominally statistically significant (P < 0.05). Through fine-mapping, in six regions (3p24, 12p11, 14q13, 16q12/FTO, 16q23, 19p13), we observed seven markers that better represent the underlying risk variant for overall breast cancer or breast cancer subtypes, whereas in another two regions (11q13, 16q12/TOX3), we identified suggestive evidence of signals that are independent of the reported index variant. Overlapping chromatin features and regulatory elements suggest that many of the risk alleles lie in regions with biological functionality.Conclusions: Through fine-mapping of known susceptibility regions, we have revealed alleles that better characterize breast cancer risk in women of African ancestry.Impact: The risk alleles identified represent genetic markers for modeling and stratifying breast cancer risk in women of African ancestry. Cancer Epidemiol Biomarkers Prev; 26(7); 1016-26. ©2017 AACR.
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Affiliation(s)
- Ye Feng
- Department of Preventive Medicine, Keck School of Medicine and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California.
| | - Suhn Kyong Rhie
- Department of Preventive Medicine, Keck School of Medicine and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California
| | - Dezheng Huo
- Department of Public Health Sciences, University of Chicago, Chicago, Illinois
| | | | - Stephen A Haddad
- Slone Epidemiology Center at Boston University, Boston, Massachusetts
| | - Christine B Ambrosone
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, New York
| | - Esther M John
- Cancer Prevention Institute of California, Fremont, California.,Department of Health Research and Policy (Epidemiology) and Stanford Cancer Institute, Stanford University School of Medicine, Stanford, California
| | - Leslie Bernstein
- Division of Cancer Etiology, Department of Population Sciences, Beckman Research Institute, City of Hope, Duarte, California
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, and Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Jennifer J Hu
- Sylvester Comprehensive Cancer Center and Department of Epidemiology and Public Health, University of Miami Miller School of Medicine, Miami, Florida
| | - Regina G Ziegler
- Epidemiology and Biostatistics Program, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
| | - Sarah Nyante
- Department of Epidemiology, Gillings School of Global Public Health and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina
| | - Elisa V Bandera
- Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey
| | - Sue A Ingles
- Department of Preventive Medicine, Keck School of Medicine and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California
| | - Michael F Press
- Department of Pathology, Keck School of Medicine and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California
| | - Sandra L Deming
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, and Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Jorge L Rodriguez-Gil
- Sylvester Comprehensive Cancer Center and Department of Epidemiology and Public Health, University of Miami Miller School of Medicine, Miami, Florida
| | - Yonglan Zheng
- Department of Medicine, University of Chicago, Chicago, Illinois
| | - Song Yao
- Roswell Park Cancer Institute, Buffalo, New York
| | - Yoo-Jeong Han
- Department of Medicine, University of Chicago, Chicago, Illinois
| | - Temidayo O Ogundiran
- Department of Surgery, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Timothy R Rebbeck
- Dana Farber Cancer Institute & Harvard T. H. Chan School of Public Health, Boston, Maryland
| | - Clement Adebamowo
- Department of Epidemiology & Preventive Medicine, University of Maryland, Baltimore, Maryland
| | - Oladosu Ojengbede
- Center for Population and Reproductive Health, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Adeyinka G Falusi
- Institute for Medical Research and Training, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Anselm Hennis
- Chronic Disease Research Centre, Tropical Medicine Research Institute, University of the West Indies, Bridgetown, Barbados.,Department of Preventive Medicine, State University of New York at Stony Brook, Stony Brook, New York
| | - Barbara Nemesure
- Department of Preventive Medicine, State University of New York at Stony Brook, Stony Brook, New York
| | - Stefan Ambs
- Laboratory of Human Carcinogenesis, National Cancer Institute, Bethesda, Maryland
| | - William Blot
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, and Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Qiuyin Cai
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, and Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Lisa Signorello
- Cancer Prevention Fellowship Program, National Cancer Institute, Bethesda, Maryland
| | | | - Kathryn L Lunetta
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts
| | | | - Jeannette T Bensen
- Department of Epidemiology, Gillings School of Global Public Health and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina
| | - Stephen J Chanock
- Epidemiology and Biostatistics Program, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
| | - Loic Le Marchand
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, Hawaii
| | - Andrew F Olshan
- Department of Epidemiology, Gillings School of Global Public Health and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina
| | - Laurence N Kolonel
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, Hawaii
| | - David V Conti
- Department of Preventive Medicine, Keck School of Medicine and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California
| | - Gerhard A Coetzee
- Department of Preventive Medicine, Keck School of Medicine and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California
| | - Daniel O Stram
- Department of Preventive Medicine, Keck School of Medicine and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California
| | | | - Julie R Palmer
- Slone Epidemiology Center at Boston University, Boston, Massachusetts
| | - Christopher A Haiman
- Department of Preventive Medicine, Keck School of Medicine and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California.
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Chae H, Lee S, Nephew KP, Kim S. Subtype-specific CpG island shore methylation and mutation patterns in 30 breast cancer cell lines. BMC SYSTEMS BIOLOGY 2016; 10:116. [PMID: 28155687 PMCID: PMC5259919 DOI: 10.1186/s12918-016-0356-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Background Aberrant epigenetic modifications, including DNA methylation, are key regulators of gene activity in tumorigenesis. Breast cancer is a heterogeneous disease, and large-scale analyses indicate that tumor from normal and benign tissues, as well as molecular subtypes of breast cancer, can be distinguished based on their distinct genomic, transcriptomic, and epigenomic profiles. In this study, we used affinity-based methylation sequencing data in 30 breast cancer cell lines representing functionally distinct cancer subtypes to investigate methylation and mutation patterns at the whole genome level. Results Our analysis revealed significant differences in CpG island (CpGI) shore methylation and mutation patterns among breast cancer subtypes. In particular, the basal-like B type, a highly aggressive form of the disease, displayed distinct CpGI shore hypomethylation patterns that were significantly associated with downstream gene regulation. We determined that mutation rates at CpG sites were highly correlated with DNA methylation status and observed distinct mutation rates among the breast cancer subtypes. These findings were validated by using targeted bisulfite sequencing of differentially expressed genes (n=85) among the cell lines. Conclusions Our results suggest that alterations in DNA methylation play critical roles in gene regulatory process as well as cytosine substitution rates at CpG sites in molecular subtypes of breast cancer. Electronic supplementary material The online version of this article (doi:10.1186/s12918-016-0356-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Heejoon Chae
- School of Informatics and Computing, Indiana University Bloomington, IN 47405, USA, Waterloo Road, Bloomington, IN, 47405, USA
| | - Sangseon Lee
- Department of Computer Science and Engineering, Seoul National University, Seoul, Republic of Korea
| | - Kenneth P Nephew
- Indiana University School of Medicine, Department of Cellular and Integrative Physiology, Medical Sciences Program, Bloomington, USA
| | - Sun Kim
- Department of Computer Science and Engineering, Seoul National University, Seoul, Republic of Korea. .,Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea. .,Bioinformatics Institute, Seoul National University, Seoul, Republic of Korea.
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44
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Abstract
Coupling chromosome conformation capture to molecular enrichment for promoter-containing DNA fragments enables the systematic mapping of interactions between individual distal regulatory sequences and their target genes. In this Minireview, we describe recent progress in the application of this technique and related complementary approaches to gain insight into the lineage- and cell-type-specific dynamics of interactions between regulators and gene promoters.
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Affiliation(s)
- Cailyn H Spurrell
- MS 84-171, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Diane E Dickel
- MS 84-171, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Axel Visel
- MS 84-171, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA; School of Natural Sciences, University of California, Merced, CA 95343, USA.
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45
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Mapping of Variable DNA Methylation Across Multiple Cell Types Defines a Dynamic Regulatory Landscape of the Human Genome. G3-GENES GENOMES GENETICS 2016; 6:973-86. [PMID: 26888867 PMCID: PMC4825665 DOI: 10.1534/g3.115.025437] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
DNA methylation is an important epigenetic modification involved in many biological processes and diseases. Many studies have mapped DNA methylation changes associated with embryogenesis, cell differentiation, and cancer at a genome-wide scale. Our understanding of genome-wide DNA methylation changes in a developmental or disease-related context has been steadily growing. However, the investigation of which CpGs are variably methylated in different normal cell or tissue types is still limited. Here, we present an in-depth analysis of 54 single-CpG-resolution DNA methylomes of normal human cell types by integrating high-throughput sequencing-based methylation data. We found that the ratio of methylated to unmethylated CpGs is relatively constant regardless of cell type. However, which CpGs made up the unmethylated complement was cell-type specific. We categorized the 26,000,000 human autosomal CpGs based on their methylation levels across multiple cell types to identify variably methylated CpGs and found that 22.6% exhibited variable DNA methylation. These variably methylated CpGs formed 660,000 variably methylated regions (VMRs), encompassing 11% of the genome. By integrating a multitude of genomic data, we found that VMRs enrich for histone modifications indicative of enhancers, suggesting their role as regulatory elements marking cell type specificity. VMRs enriched for transcription factor binding sites in a tissue-dependent manner. Importantly, they enriched for GWAS variants, suggesting that VMRs could potentially be implicated in disease and complex traits. Taken together, our results highlight the link between CpG methylation variation, genetic variation, and disease risk for many human cell types.
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46
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Gross K, Wronski A, Skibinski A, Phillips S, Kuperwasser C, Dettman RW, Wessels A. Cell Fate Decisions During Breast Cancer Development. J Dev Biol 2016; 4:4. [PMID: 27110512 PMCID: PMC4840277 DOI: 10.3390/jdb4010004] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2015] [Accepted: 01/20/2016] [Indexed: 01/07/2023] Open
Abstract
During the formation of breast cancer, many genes become altered as cells evolve progressively from normal to a pre-malignant to a malignant state of growth. How mutations in genes lead to specific subtypes of human breast cancer is only partially understood. Here we review how initial genetic or epigenetic alterations within mammary epithelial cells (MECs) can alter cell fate decisions and put pre-malignant cells on a path towards cancer development with specific phenotypes. Understanding the early stages of breast cancer initiation and progression and how normal developmental processes are hijacked during transformation has significant implications for improving early detection and prevention of breast cancer. In addition, insights gleaned from this understanding may also be important for developing subtype-specific treatment options.
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Affiliation(s)
- Kayla Gross
- Department of Developmental, Molecular and Chemical Biology, Sackler School of Graduate Biomedical Sciences, Tufts University School of Medicine, 136 Harrison Ave., Boston, MA 02111, USA
- Raymond and Beverly Sackler Convergence Laboratory, Tufts University School of Medicine, 145 Harrison Ave., Boston, MA 02111, USA
- Molecular Oncology Research Institute, Tufts Medical Center, 800 Washington St., Boston, MA 02111, USA
| | - Ania Wronski
- Department of Developmental, Molecular and Chemical Biology, Sackler School of Graduate Biomedical Sciences, Tufts University School of Medicine, 136 Harrison Ave., Boston, MA 02111, USA
- Raymond and Beverly Sackler Convergence Laboratory, Tufts University School of Medicine, 145 Harrison Ave., Boston, MA 02111, USA
- Molecular Oncology Research Institute, Tufts Medical Center, 800 Washington St., Boston, MA 02111, USA
| | - Adam Skibinski
- Department of Developmental, Molecular and Chemical Biology, Sackler School of Graduate Biomedical Sciences, Tufts University School of Medicine, 136 Harrison Ave., Boston, MA 02111, USA
- Molecular Oncology Research Institute, Tufts Medical Center, 800 Washington St., Boston, MA 02111, USA
| | - Sarah Phillips
- Department of Developmental, Molecular and Chemical Biology, Sackler School of Graduate Biomedical Sciences, Tufts University School of Medicine, 136 Harrison Ave., Boston, MA 02111, USA
- Molecular Oncology Research Institute, Tufts Medical Center, 800 Washington St., Boston, MA 02111, USA
| | - Charlotte Kuperwasser
- Department of Developmental, Molecular and Chemical Biology, Sackler School of Graduate Biomedical Sciences, Tufts University School of Medicine, 136 Harrison Ave., Boston, MA 02111, USA
- Raymond and Beverly Sackler Convergence Laboratory, Tufts University School of Medicine, 145 Harrison Ave., Boston, MA 02111, USA
- Molecular Oncology Research Institute, Tufts Medical Center, 800 Washington St., Boston, MA 02111, USA
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47
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Barcoding reveals complex clonal dynamics of de novo transformed human mammary cells. Nature 2015; 528:267-71. [PMID: 26633636 DOI: 10.1038/nature15742] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Accepted: 09/22/2015] [Indexed: 02/06/2023]
Abstract
Most human breast cancers have diversified genomically and biologically by the time they become clinically evident. Early events involved in their genesis and the cellular context in which these events occur have thus been difficult to characterize. Here we present the first formal evidence of the shared and independent ability of basal cells and luminal progenitors, isolated from normal human mammary tissue and transduced with a single oncogene (KRAS(G12D)), to produce serially transplantable, polyclonal, invasive ductal carcinomas within 8 weeks of being introduced either subrenally or subcutaneously into immunodeficient mice. DNA barcoding of the initial cells revealed a dramatic change in the numbers and sizes of clones generated from them within 2 weeks, and the first appearance of many 'new' clones in tumours passaged into secondary recipients. Both primary and secondary tumours were phenotypically heterogeneous and primary tumours were categorized transcriptionally as 'normal-like'. This system challenges previous concepts that carcinogenesis in normal human epithelia is necessarily a slow process requiring the acquisition of multiple driver mutations. It also presents the first description of initial events that accompany the genesis and evolution of malignant human mammary cell populations, thereby contributing new understanding of the rapidity with which heterogeneity in their properties can develop.
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48
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Affiliation(s)
- Justin J.-L. Wong
- Gene and Stem Cell Therapy Program, Centenary Institute; Royal Prince Alfred Hospital; Camperdown Australia
- Sydney Medical School; University of Sydney; Camperdown Australia
| | - Amy Y. M. Au
- Gene and Stem Cell Therapy Program, Centenary Institute; Royal Prince Alfred Hospital; Camperdown Australia
- Sydney Medical School; University of Sydney; Camperdown Australia
| | - William Ritchie
- Gene and Stem Cell Therapy Program, Centenary Institute; Royal Prince Alfred Hospital; Camperdown Australia
- Sydney Medical School; University of Sydney; Camperdown Australia
- Department of Bioinformatics, Centenary Institute; Royal Prince Alfred Hospital; Camperdown Australia
| | - John E. J. Rasko
- Gene and Stem Cell Therapy Program, Centenary Institute; Royal Prince Alfred Hospital; Camperdown Australia
- Sydney Medical School; University of Sydney; Camperdown Australia
- Cell and Molecular Therapies; Royal Prince Alfred Hospital; Camperdown Australia
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49
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FOROOTAN SHIVASEYED, BUTLER JOEM, GARDENER DEREK, BAIRD ALISONE, DODSON ANDREW, DARBY ALISTAIR, KENNY JOHN, HALL NEIL, COSSINS ANDREWR, FOSTER CHRISTOPHERS, GOSDEN CHRISTINEM. Transcriptome sequencing of human breast cancer reveals aberrant intronic transcription in amplicons and dysregulation of alternative splicing with major therapeutic implications. Int J Oncol 2015; 48:130-44. [DOI: 10.3892/ijo.2015.3222] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 07/31/2015] [Indexed: 11/05/2022] Open
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50
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Kundaje A, Meuleman W, Ernst J, Bilenky M, Yen A, Heravi-Moussavi A, Kheradpour P, Zhang Z, Wang J, Ziller MJ, Amin V, Whitaker JW, Schultz MD, Ward LD, Sarkar A, Quon G, Sandstrom RS, Eaton ML, Wu YC, Pfenning AR, Wang X, Claussnitzer M, Liu Y, Coarfa C, Harris RA, Shoresh N, Epstein CB, Gjoneska E, Leung D, Xie W, Hawkins RD, Lister R, Hong C, Gascard P, Mungall AJ, Moore R, Chuah E, Tam A, Canfield TK, Hansen RS, Kaul R, Sabo PJ, Bansal MS, Carles A, Dixon JR, Farh KH, Feizi S, Karlic R, Kim AR, Kulkarni A, Li D, Lowdon R, Elliott G, Mercer TR, Neph SJ, Onuchic V, Polak P, Rajagopal N, Ray P, Sallari RC, Siebenthall KT, Sinnott-Armstrong NA, Stevens M, Thurman RE, Wu J, Zhang B, Zhou X, Beaudet AE, Boyer LA, De Jager PL, Farnham PJ, Fisher SJ, Haussler D, Jones SJM, Li W, Marra MA, McManus MT, Sunyaev S, Thomson JA, Tlsty TD, Tsai LH, Wang W, Waterland RA, Zhang MQ, Chadwick LH, Bernstein BE, Costello JF, Ecker JR, Hirst M, Meissner A, Milosavljevic A, Ren B, Stamatoyannopoulos JA, Wang T, Kellis M. Integrative analysis of 111 reference human epigenomes. Nature 2015; 518:317-30. [PMID: 25693563 PMCID: PMC4530010 DOI: 10.1038/nature14248] [Citation(s) in RCA: 4112] [Impact Index Per Article: 456.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Accepted: 01/21/2015] [Indexed: 02/06/2023]
Abstract
The reference human genome sequence set the stage for studies of genetic variation and its association with human disease, but epigenomic studies lack a similar reference. To address this need, the NIH Roadmap Epigenomics Consortium generated the largest collection so far of human epigenomes for primary cells and tissues. Here we describe the integrative analysis of 111 reference human epigenomes generated as part of the programme, profiled for histone modification patterns, DNA accessibility, DNA methylation and RNA expression. We establish global maps of regulatory elements, define regulatory modules of coordinated activity, and their likely activators and repressors. We show that disease- and trait-associated genetic variants are enriched in tissue-specific epigenomic marks, revealing biologically relevant cell types for diverse human traits, and providing a resource for interpreting the molecular basis of human disease. Our results demonstrate the central role of epigenomic information for understanding gene regulation, cellular differentiation and human disease.
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Affiliation(s)
- Anshul Kundaje
- 1] Computer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology, 32 Vassar St, Cambridge, Massachusetts 02139, USA. [2] The Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA. [3] Department of Genetics, Department of Computer Science, 300 Pasteur Dr., Lane Building, L301, Stanford, California 94305-5120, USA
| | - Wouter Meuleman
- 1] Computer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology, 32 Vassar St, Cambridge, Massachusetts 02139, USA. [2] The Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - Jason Ernst
- 1] Computer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology, 32 Vassar St, Cambridge, Massachusetts 02139, USA. [2] The Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA. [3] Department of Biological Chemistry, University of California, Los Angeles, 615 Charles E Young Dr South, Los Angeles, California 90095, USA
| | - Misha Bilenky
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, 675 West 10th Avenue, Vancouver, British Columbia V5Z 1L3, Canada
| | - Angela Yen
- 1] Computer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology, 32 Vassar St, Cambridge, Massachusetts 02139, USA. [2] The Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - Alireza Heravi-Moussavi
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, 675 West 10th Avenue, Vancouver, British Columbia V5Z 1L3, Canada
| | - Pouya Kheradpour
- 1] Computer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology, 32 Vassar St, Cambridge, Massachusetts 02139, USA. [2] The Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - Zhizhuo Zhang
- 1] Computer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology, 32 Vassar St, Cambridge, Massachusetts 02139, USA. [2] The Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - Jianrong Wang
- 1] Computer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology, 32 Vassar St, Cambridge, Massachusetts 02139, USA. [2] The Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - Michael J Ziller
- 1] The Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA. [2] Department of Stem Cell and Regenerative Biology, 7 Divinity Ave, Cambridge, Massachusetts 02138, USA
| | - Viren Amin
- Epigenome Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
| | - John W Whitaker
- Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, Moores Cancer Center, Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA
| | - Matthew D Schultz
- Genomic Analysis Laboratory, Howard Hughes Medical Institute &The Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, California 92037, USA
| | - Lucas D Ward
- 1] Computer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology, 32 Vassar St, Cambridge, Massachusetts 02139, USA. [2] The Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - Abhishek Sarkar
- 1] Computer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology, 32 Vassar St, Cambridge, Massachusetts 02139, USA. [2] The Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - Gerald Quon
- 1] Computer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology, 32 Vassar St, Cambridge, Massachusetts 02139, USA. [2] The Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - Richard S Sandstrom
- Department of Genome Sciences, University of Washington, 3720 15th Ave. NE, Seattle, Washington 98195, USA
| | - Matthew L Eaton
- 1] Computer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology, 32 Vassar St, Cambridge, Massachusetts 02139, USA. [2] The Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - Yi-Chieh Wu
- 1] Computer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology, 32 Vassar St, Cambridge, Massachusetts 02139, USA. [2] The Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - Andreas R Pfenning
- 1] Computer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology, 32 Vassar St, Cambridge, Massachusetts 02139, USA. [2] The Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - Xinchen Wang
- 1] Computer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology, 32 Vassar St, Cambridge, Massachusetts 02139, USA. [2] The Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA. [3] Biology Department, Massachusetts Institute of Technology, 31 Ames St, Cambridge, Massachusetts 02142, USA
| | - Melina Claussnitzer
- 1] Computer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology, 32 Vassar St, Cambridge, Massachusetts 02139, USA. [2] The Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - Yaping Liu
- 1] Computer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology, 32 Vassar St, Cambridge, Massachusetts 02139, USA. [2] The Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - Cristian Coarfa
- Epigenome Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
| | - R Alan Harris
- Epigenome Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
| | - Noam Shoresh
- The Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - Charles B Epstein
- The Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - Elizabeta Gjoneska
- 1] The Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA. [2] The Picower Institute for Learning and Memory, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, 43 Vassar St, Cambridge, Massachusetts 02139, USA
| | - Danny Leung
- 1] Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, Moores Cancer Center, Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA. [2] Ludwig Institute for Cancer Research, 9500 Gilman Drive, La Jolla, California 92093, USA
| | - Wei Xie
- 1] Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, Moores Cancer Center, Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA. [2] Ludwig Institute for Cancer Research, 9500 Gilman Drive, La Jolla, California 92093, USA
| | - R David Hawkins
- 1] Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, Moores Cancer Center, Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA. [2] Ludwig Institute for Cancer Research, 9500 Gilman Drive, La Jolla, California 92093, USA
| | - Ryan Lister
- Genomic Analysis Laboratory, Howard Hughes Medical Institute &The Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, California 92037, USA
| | - Chibo Hong
- Department of Neurosurgery, Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, 1450 3rd Street, San Francisco, California 94158, USA
| | - Philippe Gascard
- Department of Pathology, University of California San Francisco, 513 Parnassus Avenue, San Francisco, California 94143-0511, USA
| | - Andrew J Mungall
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, 675 West 10th Avenue, Vancouver, British Columbia V5Z 1L3, Canada
| | - Richard Moore
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, 675 West 10th Avenue, Vancouver, British Columbia V5Z 1L3, Canada
| | - Eric Chuah
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, 675 West 10th Avenue, Vancouver, British Columbia V5Z 1L3, Canada
| | - Angela Tam
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, 675 West 10th Avenue, Vancouver, British Columbia V5Z 1L3, Canada
| | - Theresa K Canfield
- Department of Genome Sciences, University of Washington, 3720 15th Ave. NE, Seattle, Washington 98195, USA
| | - R Scott Hansen
- Department of Medicine, Division of Medical Genetics, University of Washington, 2211 Elliot Avenue, Seattle, Washington 98121, USA
| | - Rajinder Kaul
- Department of Medicine, Division of Medical Genetics, University of Washington, 2211 Elliot Avenue, Seattle, Washington 98121, USA
| | - Peter J Sabo
- Department of Genome Sciences, University of Washington, 3720 15th Ave. NE, Seattle, Washington 98195, USA
| | - Mukul S Bansal
- 1] Computer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology, 32 Vassar St, Cambridge, Massachusetts 02139, USA. [2] The Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA. [3] Department of Computer Science &Engineering, University of Connecticut, 371 Fairfield Way, Storrs, Connecticut 06269, USA
| | - Annaick Carles
- Department of Microbiology and Immunology and Centre for High-Throughput Biology, University of British Columbia, 2125 East Mall, Vancouver, British Columbia V6T 1Z4, Canada
| | - Jesse R Dixon
- 1] Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, Moores Cancer Center, Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA. [2] Ludwig Institute for Cancer Research, 9500 Gilman Drive, La Jolla, California 92093, USA
| | - Kai-How Farh
- The Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - Soheil Feizi
- 1] Computer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology, 32 Vassar St, Cambridge, Massachusetts 02139, USA. [2] The Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - Rosa Karlic
- Bioinformatics Group, Department of Molecular Biology, Division of Biology, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia
| | - Ah-Ram Kim
- 1] Computer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology, 32 Vassar St, Cambridge, Massachusetts 02139, USA. [2] The Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - Ashwinikumar Kulkarni
- Department of Molecular and Cell Biology, Center for Systems Biology, The University of Texas, Dallas, NSERL, RL10, 800 W Campbell Road, Richardson, Texas 75080, USA
| | - Daofeng Li
- Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University in St Louis, 4444 Forest Park Ave, St Louis, Missouri 63108, USA
| | - Rebecca Lowdon
- Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University in St Louis, 4444 Forest Park Ave, St Louis, Missouri 63108, USA
| | - GiNell Elliott
- Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University in St Louis, 4444 Forest Park Ave, St Louis, Missouri 63108, USA
| | - Tim R Mercer
- Institute for Molecular Bioscience, University of Queensland, St Lucia, Queensland 4072, Australia
| | - Shane J Neph
- Department of Genome Sciences, University of Washington, 3720 15th Ave. NE, Seattle, Washington 98195, USA
| | - Vitor Onuchic
- Epigenome Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
| | - Paz Polak
- 1] The Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA. [2] Brigham &Women's Hospital, 75 Francis Street, Boston, Massachusetts 02115, USA
| | - Nisha Rajagopal
- 1] Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, Moores Cancer Center, Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA. [2] Ludwig Institute for Cancer Research, 9500 Gilman Drive, La Jolla, California 92093, USA
| | - Pradipta Ray
- Department of Molecular and Cell Biology, Center for Systems Biology, The University of Texas, Dallas, NSERL, RL10, 800 W Campbell Road, Richardson, Texas 75080, USA
| | - Richard C Sallari
- 1] Computer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology, 32 Vassar St, Cambridge, Massachusetts 02139, USA. [2] The Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - Kyle T Siebenthall
- Department of Genome Sciences, University of Washington, 3720 15th Ave. NE, Seattle, Washington 98195, USA
| | - Nicholas A Sinnott-Armstrong
- 1] Computer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology, 32 Vassar St, Cambridge, Massachusetts 02139, USA. [2] The Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - Michael Stevens
- 1] Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University in St Louis, 4444 Forest Park Ave, St Louis, Missouri 63108, USA. [2] Department of Computer Science and Engineeering, Washington University in St. Louis, St. Louis, Missouri 63130, USA
| | - Robert E Thurman
- Department of Genome Sciences, University of Washington, 3720 15th Ave. NE, Seattle, Washington 98195, USA
| | - Jie Wu
- 1] Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York 11794-3600, USA. [2] Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Bo Zhang
- Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University in St Louis, 4444 Forest Park Ave, St Louis, Missouri 63108, USA
| | - Xin Zhou
- Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University in St Louis, 4444 Forest Park Ave, St Louis, Missouri 63108, USA
| | - Arthur E Beaudet
- Molecular and Human Genetics Department, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
| | - Laurie A Boyer
- Biology Department, Massachusetts Institute of Technology, 31 Ames St, Cambridge, Massachusetts 02142, USA
| | - Philip L De Jager
- 1] The Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA. [2] Brigham &Women's Hospital, 75 Francis Street, Boston, Massachusetts 02115, USA. [3] Harvard Medical School, 25 Shattuck St, Boston, Massachusetts 02115, USA
| | - Peggy J Farnham
- Department of Biochemistry, Keck School of Medicine, University of Southern California, 1450 Biggy Street, Los Angeles, California 90089-9601, USA
| | - Susan J Fisher
- ObGyn, Reproductive Sciences, University of California San Francisco, 35 Medical Center Way, San Francisco, California 94143, USA
| | - David Haussler
- Center for Biomolecular Sciences and Engineering, University of Santa Cruz, 1156 High Street, Santa Cruz, California 95064, USA
| | - Steven J M Jones
- 1] Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, 675 West 10th Avenue, Vancouver, British Columbia V5Z 1L3, Canada. [2] Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada. [3] Department of Medical Genetics, University of British Columbia, 2329 West Mall, Vancouver, BC, Canada, V6T 1Z4
| | - Wei Li
- Dan L. Duncan Cancer Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
| | - Marco A Marra
- 1] Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, 675 West 10th Avenue, Vancouver, British Columbia V5Z 1L3, Canada. [2] Department of Medical Genetics, University of British Columbia, 2329 West Mall, Vancouver, BC, Canada, V6T 1Z4
| | - Michael T McManus
- Department of Microbiology and Immunology, Diabetes Center, University of California, San Francisco, 513 Parnassus Ave, San Francisco, California 94143-0534, USA
| | - Shamil Sunyaev
- 1] The Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA. [2] Brigham &Women's Hospital, 75 Francis Street, Boston, Massachusetts 02115, USA. [3] Harvard Medical School, 25 Shattuck St, Boston, Massachusetts 02115, USA
| | - James A Thomson
- 1] University of Wisconsin, Madison, Wisconsin 53715, USA. [2] Morgridge Institute for Research, 330 N. Orchard Street, Madison, Wisconsin 53707, USA
| | - Thea D Tlsty
- Department of Pathology, University of California San Francisco, 513 Parnassus Avenue, San Francisco, California 94143-0511, USA
| | - Li-Huei Tsai
- 1] The Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA. [2] The Picower Institute for Learning and Memory, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, 43 Vassar St, Cambridge, Massachusetts 02139, USA
| | - Wei Wang
- Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, Moores Cancer Center, Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA
| | - Robert A Waterland
- USDA/ARS Children's Nutrition Research Center, Baylor College of Medicine, 1100 Bates Street, Houston, Texas 77030, USA
| | - Michael Q Zhang
- 1] Department of Molecular and Cell Biology, Center for Systems Biology, The University of Texas, Dallas, NSERL, RL10, 800 W Campbell Road, Richardson, Texas 75080, USA. [2] Bioinformatics Division, Center for Synthetic and Systems Biology, TNLIST, Tsinghua University, Beijing 100084, China
| | - Lisa H Chadwick
- National Institute of Environmental Health Sciences, 111 T.W. Alexander Drive, Research Triangle Park, North Carolina 27709, USA
| | - Bradley E Bernstein
- 1] The Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA. [2] Massachusetts General Hospital, 55 Fruit St, Boston, Massachusetts 02114, USA. [3] Howard Hughes Medical Institute, 4000 Jones Bridge Road, Chevy Chase, Maryland 20815-6789, USA
| | - Joseph F Costello
- Department of Neurosurgery, Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, 1450 3rd Street, San Francisco, California 94158, USA
| | - Joseph R Ecker
- Genomic Analysis Laboratory, Howard Hughes Medical Institute &The Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, California 92037, USA
| | - Martin Hirst
- 1] Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, 675 West 10th Avenue, Vancouver, British Columbia V5Z 1L3, Canada. [2] Department of Microbiology and Immunology and Centre for High-Throughput Biology, University of British Columbia, 2125 East Mall, Vancouver, British Columbia V6T 1Z4, Canada
| | - Alexander Meissner
- 1] The Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA. [2] Department of Stem Cell and Regenerative Biology, 7 Divinity Ave, Cambridge, Massachusetts 02138, USA
| | | | - Bing Ren
- 1] Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, Moores Cancer Center, Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA. [2] Ludwig Institute for Cancer Research, 9500 Gilman Drive, La Jolla, California 92093, USA
| | - John A Stamatoyannopoulos
- Department of Genome Sciences, University of Washington, 3720 15th Ave. NE, Seattle, Washington 98195, USA
| | - Ting Wang
- Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University in St Louis, 4444 Forest Park Ave, St Louis, Missouri 63108, USA
| | - Manolis Kellis
- 1] Computer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology, 32 Vassar St, Cambridge, Massachusetts 02139, USA. [2] The Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA
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