1
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Cornejo-Páramo P, Petrova V, Zhang X, Young RS, Wong ES. Emergence of enhancers at late DNA replicating regions. Nat Commun 2024; 15:3451. [PMID: 38658544 PMCID: PMC11043393 DOI: 10.1038/s41467-024-47391-5] [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: 10/23/2023] [Accepted: 03/26/2024] [Indexed: 04/26/2024] Open
Abstract
Enhancers are fast-evolving genomic sequences that control spatiotemporal gene expression patterns. By examining enhancer turnover across mammalian species and in multiple tissue types, we uncover a relationship between the emergence of enhancers and genome organization as a function of germline DNA replication time. While enhancers are most abundant in euchromatic regions, enhancers emerge almost twice as often in late compared to early germline replicating regions, independent of transposable elements. Using a deep learning sequence model, we demonstrate that new enhancers are enriched for mutations that alter transcription factor (TF) binding. Recently evolved enhancers appear to be mostly neutrally evolving and enriched in eQTLs. They also show more tissue specificity than conserved enhancers, and the TFs that bind to these elements, as inferred by binding sequences, also show increased tissue-specific gene expression. We find a similar relationship with DNA replication time in cancer, suggesting that these observations may be time-invariant principles of genome evolution. Our work underscores that genome organization has a profound impact in shaping mammalian gene regulation.
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Affiliation(s)
- Paola Cornejo-Páramo
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia
- School of Biotechnology and Biomolecular Sciences, Sydney, NSW, Australia
| | - Veronika Petrova
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia
- School of Biotechnology and Biomolecular Sciences, Sydney, NSW, Australia
| | - Xuan Zhang
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia
| | - Robert S Young
- Usher Institute, University of Edinburgh, Teviot Place, Edinburgh, EH8 9AG, United Kingdom
- Zhejiang University - University of Edinburgh Institute, Zhejiang University, 718 East Haizhou Road, 314400, Haining, PR China
| | - Emily S Wong
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia.
- School of Biotechnology and Biomolecular Sciences, Sydney, NSW, Australia.
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2
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Giurato G, Terenzi I, Chiuso F, Salvati A, Rizzo F, Tarallo R, Weisz A, Nassa G. Genome-wide DNA methylation changes upon DOT1L inhibition in hormone-responsive breast cancer cells. Front Cell Dev Biol 2023; 11:1308025. [PMID: 38099289 PMCID: PMC10720356 DOI: 10.3389/fcell.2023.1308025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 11/13/2023] [Indexed: 12/17/2023] Open
Affiliation(s)
- Giorgio Giurato
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry “Scuola Medica Salernitana”, University of Salerno, Baronissi, Italy
- Genome Research Center for Health - CRGS, Baronissi, Italy
| | - Ilaria Terenzi
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry “Scuola Medica Salernitana”, University of Salerno, Baronissi, Italy
| | - Francesco Chiuso
- Department of Molecular Medicine and Medical Biotechnologies, University Federico II, Naples, Italy
| | - Annamaria Salvati
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry “Scuola Medica Salernitana”, University of Salerno, Baronissi, Italy
- Molecular Pathology and Medical Genomics Program, Division of Oncology, AOU 'S. Giovanni di Dio e Ruggi d'Aragona', Università di Salerno, Salerno, Italy
| | - Francesca Rizzo
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry “Scuola Medica Salernitana”, University of Salerno, Baronissi, Italy
- Genome Research Center for Health - CRGS, Baronissi, Italy
| | - Roberta Tarallo
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry “Scuola Medica Salernitana”, University of Salerno, Baronissi, Italy
- Genome Research Center for Health - CRGS, Baronissi, Italy
| | - Alessandro Weisz
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry “Scuola Medica Salernitana”, University of Salerno, Baronissi, Italy
- Genome Research Center for Health - CRGS, Baronissi, Italy
- Molecular Pathology and Medical Genomics Program, Division of Oncology, AOU 'S. Giovanni di Dio e Ruggi d'Aragona', Università di Salerno, Salerno, Italy
| | - Giovanni Nassa
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry “Scuola Medica Salernitana”, University of Salerno, Baronissi, Italy
- Genome Research Center for Health - CRGS, Baronissi, Italy
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3
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Petrova V, Song R, Nordström KJV, Walter J, Wong JJL, Armstrong N, Rasko JEJ, Schmitz U. Increased chromatin accessibility facilitates intron retention in specific cell differentiation states. Nucleic Acids Res 2022; 50:11563-11579. [PMID: 36354002 PMCID: PMC9723627 DOI: 10.1093/nar/gkac994] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 10/05/2022] [Accepted: 10/18/2022] [Indexed: 11/11/2022] Open
Abstract
Dynamic intron retention (IR) in vertebrate cells is of widespread biological importance. Aberrant IR is associated with numerous human diseases including several cancers. Despite consistent reports demonstrating that intrinsic sequence features can help introns evade splicing, conflicting findings about cell type- or condition-specific IR regulation by trans-regulatory and epigenetic mechanisms demand an unbiased and systematic analysis of IR in a controlled experimental setting. We integrated matched mRNA sequencing (mRNA-Seq), whole-genome bisulfite sequencing (WGBS), nucleosome occupancy methylome sequencing (NOMe-Seq) and chromatin immunoprecipitation sequencing (ChIP-Seq) data from primary human myeloid and lymphoid cells. Using these multi-omics data and machine learning, we trained two complementary models to determine the role of epigenetic factors in the regulation of IR in cells of the innate immune system. We show that increased chromatin accessibility, as revealed by nucleosome-free regions, contributes substantially to the retention of introns in a cell-specific manner. We also confirm that intrinsic characteristics of introns are key for them to evade splicing. This study suggests an important role for chromatin architecture in IR regulation. With an increasing appreciation that pathogenic alterations are linked to RNA processing, our findings may provide useful insights for the development of novel therapeutic approaches that target aberrant splicing.
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Affiliation(s)
- Veronika Petrova
- Computational BioMedicine Laboratory Centenary Institute, The University of Sydney, Camperdown 2050, Australia,Gene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown 2050, Australia
| | - Renhua Song
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown 2050, Australia,Faculty of Medicine and Health, The University of Sydney, Camperdown 2050, Australia
| | | | - Karl J V Nordström
- Laboratory of EpiGenetics, Saarland University, Campus A2 4, D-66123 Saarbrücken, Germany
| | - Jörn Walter
- Laboratory of EpiGenetics, Saarland University, Campus A2 4, D-66123 Saarbrücken, Germany
| | - Justin J L Wong
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown 2050, Australia,Faculty of Medicine and Health, The University of Sydney, Camperdown 2050, Australia
| | - Nicola J Armstrong
- Mathematics and Statistics, Curtin University, Bentley, WA 6102, Australia
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4
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Kong S, Lu Y, Tan S, Li R, Gao Y, Li K, Zhang Y. Nucleosome-Omics: A Perspective on the Epigenetic Code and 3D Genome Landscape. Genes (Basel) 2022; 13:genes13071114. [PMID: 35885897 PMCID: PMC9323251 DOI: 10.3390/genes13071114] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 06/14/2022] [Accepted: 06/17/2022] [Indexed: 12/04/2022] Open
Abstract
Genetic information is loaded on chromatin, which involves DNA sequence arrangement and the epigenetic landscape. The epigenetic information including DNA methylation, nucleosome positioning, histone modification, 3D chromatin conformation, and so on, has a crucial impact on gene transcriptional regulation. Out of them, nucleosomes, as basal chromatin structural units, play an important central role in epigenetic code. With the discovery of nucleosomes, various nucleosome-level technologies have been developed and applied, pushing epigenetics to a new climax. As the underlying methodology, next-generation sequencing technology has emerged and allowed scientists to understand the epigenetic landscape at a genome-wide level. Combining with NGS, nucleosome-omics (or nucleosomics) provides a fresh perspective on the epigenetic code and 3D genome landscape. Here, we summarized and discussed research progress in technology development and application of nucleosome-omics. We foresee the future directions of epigenetic development at the nucleosome level.
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5
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Gray JS, Wani SA, Campbell MJ. Epigenomic alterations in cancer: mechanisms and therapeutic potential. Clin Sci (Lond) 2022; 136:473-492. [PMID: 35383835 DOI: 10.1042/cs20210449] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 03/11/2022] [Accepted: 03/21/2022] [Indexed: 11/17/2022]
Abstract
The human cell requires ways to specify its transcriptome without altering the essential sequence of DNA; this is achieved through mechanisms which govern the epigenetic state of DNA and epitranscriptomic state of RNA. These alterations can be found as modified histone proteins, cytosine DNA methylation, non-coding RNAs, and mRNA modifications, such as N6-methyladenosine (m6A). The different aspects of epigenomic and epitranscriptomic modifications require protein complexes to write, read, and erase these chemical alterations. Reflecting these important roles, many of these reader/writer/eraser proteins are either frequently mutated or differentially expressed in cancer. The disruption of epigenetic regulation in the cell can both contribute to cancer initiation and progression, and increase the likelihood of developing resistance to chemotherapies. Development of therapeutics to target proteins involved in epigenomic/epitranscriptomic modifications has been intensive, but further refinement is necessary to achieve ideal treatment outcomes without too many off-target effects for cancer patients. Therefore, further integration of clinical outcomes combined with large-scale genomic analyses is imperative for furthering understanding of epigenomic mechanisms in cancer.
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Affiliation(s)
- Jaimie S Gray
- Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, OH 43210, U.S.A
| | - Sajad A Wani
- Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, OH 43210, U.S.A
| | - Moray J Campbell
- Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, OH 43210, U.S.A
- Biomedical Informatics Shared Resource, The Ohio State University, Columbus, OH 43210, U.S.A
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6
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BAF complex-mediated chromatin relaxation is required for establishment of X chromosome inactivation. Nat Commun 2022; 13:1658. [PMID: 35351876 PMCID: PMC8964718 DOI: 10.1038/s41467-022-29333-1] [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: 01/10/2021] [Accepted: 03/10/2022] [Indexed: 12/12/2022] Open
Abstract
The process of epigenetic silencing, while fundamentally important, is not yet completely understood. Here we report a replenishable female mouse embryonic stem cell (mESC) system, Xmas, that allows rapid assessment of X chromosome inactivation (XCI), the epigenetic silencing mechanism of one of the two X chromosomes that enables dosage compensation in female mammals. Through a targeted genetic screen in differentiating Xmas mESCs, we reveal that the BAF complex is required to create nucleosome-depleted regions at promoters on the inactive X chromosome during the earliest stages of establishment of XCI. Without this action gene silencing fails. Xmas mESCs provide a tractable model for screen-based approaches that enable the discovery of unknown facets of the female-specific process of XCI and epigenetic silencing more broadly. Female embryonic stem cells (ESCs) are the ideal model to study X chromosome inactivation (XCI) establishment; however, these cells are challenging to keep in culture. Here the authors create fluorescent ‘Xmas’ reporter mice as a renewable source of ESCs and show nucleosome remodelers Smarcc1 and Smarca4 create a nucleosome-free promoter region prior to the establishment of silencing.
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7
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Whole-genome methods to define DNA and histone accessibility and long-range interactions in chromatin. Biochem Soc Trans 2022; 50:199-212. [PMID: 35166326 PMCID: PMC9847230 DOI: 10.1042/bst20210959] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 12/30/2021] [Accepted: 01/24/2022] [Indexed: 02/08/2023]
Abstract
Defining the genome-wide chromatin landscape has been a goal of experimentalists for decades. Here we review highlights of these efforts, from seminal experiments showing discontinuities in chromatin structure related to gene activation to extensions of these methods elucidating general features of chromatin related to gene states by exploiting deep sequencing methods. We also review chromatin conformational capture methods to identify patterns in long-range interactions between genomic loci.
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8
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Xue Y, Yang Y, Tian H, Quan H, Liu S, Zhang L, Yang L, Zhu H, Wu H, Gao YQ. Computational characterization of domain-segregated 3D chromatin structure and segmented DNA methylation status in carcinogenesis. Mol Oncol 2022; 16:699-716. [PMID: 34708506 PMCID: PMC8807360 DOI: 10.1002/1878-0261.13127] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 09/17/2021] [Accepted: 10/26/2021] [Indexed: 12/12/2022] Open
Abstract
The high-order chromatin structure, together with DNA methylation and other epigenetic marks, plays a vital role in gene regulation and displays abnormal status in cancer cells. Theoretical analyses are expected to provide a more unified understanding of the multi-omics data on the large variety of samples, and hopefully a common picture of carcinogenesis. In particular, we are interested in the question of whether an underlying origin DNA sequence exists for these epigenetic alterations. The human genome consists of two types of megabase-sized domain based on the distribution of CpG islands (CGIs) that show distinct structural, epigenetic, and transcriptional properties: CGI-rich and CGI-poor domains. Through an integrated analysis of chromatin structure, DNA methylation, and RNA sequencing data, we found that, in carcinogenesis, the two different types of domain display different structural changes and have an increased number of DNA methylation differences and transcriptional-level differences, compared with in noncancer cells. We also compared the structural features among carcinogenesis, senescence, and mitosis, showing the possible connection between chromatin structure and cell state, which could affect vital cancer-related properties. In summary, chromatin structure, DNA methylation, and gene expression, as well as their changes observed in several types of cancers, show a dependence on multiscale DNA sequence heterogeneity.
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Affiliation(s)
- Yue Xue
- Beijing National Laboratory for Molecular SciencesCollege of Chemistry and Molecular EngineeringPeking UniversityBeijingChina
| | - Ying Yang
- Beijing National Laboratory for Molecular SciencesCollege of Chemistry and Molecular EngineeringPeking UniversityBeijingChina
| | - Hao Tian
- Beijing National Laboratory for Molecular SciencesCollege of Chemistry and Molecular EngineeringPeking UniversityBeijingChina
| | - Hui Quan
- Beijing National Laboratory for Molecular SciencesCollege of Chemistry and Molecular EngineeringPeking UniversityBeijingChina
| | - Sirui Liu
- Beijing National Laboratory for Molecular SciencesCollege of Chemistry and Molecular EngineeringPeking UniversityBeijingChina
| | - Ling Zhang
- Beijing National Laboratory for Molecular SciencesCollege of Chemistry and Molecular EngineeringPeking UniversityBeijingChina
| | - Lu Yang
- The MOE Key Laboratory of Cell Proliferation and DifferentiationSchool of Life SciencesPeking UniversityBeijingChina
- Peking‐Tsinghua Center for Life SciencesPeking UniversityBeijingChina
| | - Haichuan Zhu
- The MOE Key Laboratory of Cell Proliferation and DifferentiationSchool of Life SciencesPeking UniversityBeijingChina
- Peking‐Tsinghua Center for Life SciencesPeking UniversityBeijingChina
| | - Hong Wu
- The MOE Key Laboratory of Cell Proliferation and DifferentiationSchool of Life SciencesPeking UniversityBeijingChina
- Peking‐Tsinghua Center for Life SciencesPeking UniversityBeijingChina
- Peking University Institute of HematologyNational Clinical Research Center for Hematologic DiseasePeking University People’s HospitalBeijingChina
| | - Yi Qin Gao
- Beijing National Laboratory for Molecular SciencesCollege of Chemistry and Molecular EngineeringPeking UniversityBeijingChina
- Biomedical Pioneering Innovation Center (BIOPIC)Peking UniversityBeijingChina
- Beijing Advanced Innovation Center for Genomics (ICG)Peking UniversityBeijingChina
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9
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Chen E, Liu N, Zhao Y, Tang M, Ou L, Wu X, Luo C. Panobinostat reverses HepaCAM gene expression and suppresses proliferation by increasing histone acetylation in prostate cancer. Gene 2022; 808:145977. [PMID: 34592353 DOI: 10.1016/j.gene.2021.145977] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 09/16/2021] [Accepted: 09/24/2021] [Indexed: 12/22/2022]
Abstract
Increased expression of histone deacetylases (HDACs) affiliated to the epigenetic regulation is common aberration in prostate cancer (PCa). We have confirmed that hepatocyte cell adhesion molecule (hepaCAM), acting as a tumor suppressor gene, is rarely expressed in PCa previously, However, the mechanisms of which is still unknown. The level of histone acetylation reportedly may involve anti-oncogene transcription and expression. In this study, we investigated the effect of panobinostat, the broad-spectrum histone deacetylases inhibitor, on PCa LNCaP and DU145 cell growth, and observed re-expression of hepaCAM when treated with panobinostat. We demonstrated that intranuclear acetylation of lys9 of histone H3 (Ac-H3K9) were increased, while that of both mRNA and protein of HDAC1, HDAC3, and HDAC4 were decreased when the treating concentration of panobinostat increased. We confirmed the relationship between histone acetylation and the expression of hepaCAM and AR in prostate cancer tissues. We also confirmed that panobinostat could overcome the resistance for androgen deprivation therapy (ADT). Further, we combined panobinostat with Ad-hepaCAM, which resulted in significantly increased antitumor activity and significant attenuation of the proliferation-associated genes CCND1 and PCNA compared to each single treatment. In conclusion, panobinostat may enhance the acetylation of lys9 of histone 3 and reverse the hepaCAM expression through its inhibitory effect on HDACs activity in PCa LNCaP and DU145 cells; Ad-hepaCAM combined with panobinostat may synergistically inhibit the growth of LNCaP and DU145 cells, via a potential mechanism associated with the down-regulation of the expression of CCND1 and PCNA. These findings suggest that this therapeutic strategy should be further developed in clinical trials.
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Affiliation(s)
- E Chen
- The Key Laboratory of Diagnostics Medicine, Ministry of Education, Chongqing Medical University, Chongqing 400016, People's Republic of China; Center for Clinical Molecular Medicine, Children's Hospital, Chongqing Medical University, Chongqing 400015, People's Republic of China
| | - NanJing Liu
- The Key Laboratory of Diagnostics Medicine, Ministry of Education, Chongqing Medical University, Chongqing 400016, People's Republic of China
| | - Yan Zhao
- The Key Laboratory of Diagnostics Medicine, Ministry of Education, Chongqing Medical University, Chongqing 400016, People's Republic of China
| | - Min Tang
- The Key Laboratory of Diagnostics Medicine, Ministry of Education, Chongqing Medical University, Chongqing 400016, People's Republic of China
| | - LiPing Ou
- The Key Laboratory of Diagnostics Medicine, Ministry of Education, Chongqing Medical University, Chongqing 400016, People's Republic of China
| | - XiaoHou Wu
- Department of Urology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400042, People's Republic of China
| | - ChunLi Luo
- The Key Laboratory of Diagnostics Medicine, Ministry of Education, Chongqing Medical University, Chongqing 400016, People's Republic of China
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10
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Vu H, Ernst J. Universal annotation of the human genome through integration of over a thousand epigenomic datasets. Genome Biol 2022; 23:9. [PMID: 34991667 PMCID: PMC8734071 DOI: 10.1186/s13059-021-02572-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 12/08/2021] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Genome-wide maps of chromatin marks such as histone modifications and open chromatin sites provide valuable information for annotating the non-coding genome, including identifying regulatory elements. Computational approaches such as ChromHMM have been applied to discover and annotate chromatin states defined by combinatorial and spatial patterns of chromatin marks within the same cell type. An alternative "stacked modeling" approach was previously suggested, where chromatin states are defined jointly from datasets of multiple cell types to produce a single universal genome annotation based on all datasets. Despite its potential benefits for applications that are not specific to one cell type, such an approach was previously applied only for small-scale specialized purposes. Large-scale applications of stacked modeling have previously posed scalability challenges. RESULTS Using a version of ChromHMM enhanced for large-scale applications, we apply the stacked modeling approach to produce a universal chromatin state annotation of the human genome using over 1000 datasets from more than 100 cell types, with the learned model denoted as the full-stack model. The full-stack model states show distinct enrichments for external genomic annotations, which we use in characterizing each state. Compared to per-cell-type annotations, the full-stack annotations directly differentiate constitutive from cell type-specific activity and is more predictive of locations of external genomic annotations. CONCLUSIONS The full-stack ChromHMM model provides a universal chromatin state annotation of the genome and a unified global view of over 1000 datasets. We expect this to be a useful resource that complements existing per-cell-type annotations for studying the non-coding human genome.
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Affiliation(s)
- Ha Vu
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, CA, 90095, USA
- Department of Biological Chemistry, University of California, Los Angeles, CA, 90095, USA
| | - Jason Ernst
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, CA, 90095, USA
- Department of Biological Chemistry, University of California, Los Angeles, CA, 90095, USA
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research at University of California, Los Angeles, CA, 90095, USA
- Computer Science Department, University of California, Los Angeles, CA, 90095, USA
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, CA, 90095, USA
- Molecular Biology Institute, University of California, Los Angeles, CA, 90095, USA
- Department of Computational Medicine, University of California, Los Angeles, CA, 90095, USA
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11
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Xu L, Zhou Y, Chen L, Bissessur AS, Chen J, Mao M, Ju S, Chen L, Chen C, Li Z, Zhang X, Chen F, Cao F, Wang L, Wang Q. Deoxyribonucleic Acid 5-Hydroxymethylation in Cell-Free Deoxyribonucleic Acid, a Novel Cancer Biomarker in the Era of Precision Medicine. Front Cell Dev Biol 2021; 9:744990. [PMID: 34957093 PMCID: PMC8703110 DOI: 10.3389/fcell.2021.744990] [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: 07/21/2021] [Accepted: 11/29/2021] [Indexed: 11/13/2022] Open
Abstract
Aberrant methylation has been regarded as a hallmark of cancer. 5-hydroxymethylcytosine (5hmC) is recently identified as the ten-eleven translocase (ten-eleven translocase)-mediated oxidized form of 5-methylcytosine, which plays a substantial role in DNA demethylation. Cell-free DNA has been introduced as a promising tool in the liquid biopsy of cancer. There are increasing evidence indicating that 5hmC in cell-free DNA play an active role during carcinogenesis. However, it remains unclear whether 5hmC could surpass classical markers in cancer detection, treatment, and prognosis. Here, we systematically reviewed the recent advances in the clinic and basic research of DNA 5-hydroxymethylation in cancer, especially in cell-free DNA. We further discuss the mechanisms underlying aberrant 5hmC patterns and carcinogenesis. Synergistically, 5-hydroxymethylation may act as a promising biomarker, unleashing great potential in early cancer detection, prognosis, and therapeutic strategies in precision oncology.
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Affiliation(s)
- Ling Xu
- Department of Surgical Oncology, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, China.,School of Medicine, Zhejiang University, Hangzhou, China
| | - Yixin Zhou
- Department of Thyroid and Breast Surgery, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Luqiao, China
| | - Lijie Chen
- Department of Thyroid and Breast Surgery, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Luqiao, China
| | - Abdul Saad Bissessur
- Department of Surgical Oncology, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, China.,School of Medicine, Zhejiang University, Hangzhou, China
| | - Jida Chen
- Department of Surgical Oncology, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, China
| | - Misha Mao
- Department of Surgical Oncology, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, China.,School of Medicine, Zhejiang University, Hangzhou, China
| | - Siwei Ju
- Department of Surgical Oncology, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, China.,School of Medicine, Zhejiang University, Hangzhou, China
| | - Lini Chen
- Department of Surgical Oncology, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, China.,School of Medicine, Zhejiang University, Hangzhou, China
| | - Cong Chen
- Department of Surgical Oncology, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, China.,School of Medicine, Zhejiang University, Hangzhou, China
| | - Zhaoqin Li
- Department of Surgical Oncology, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, China.,School of Medicine, Zhejiang University, Hangzhou, China
| | - Xun Zhang
- Department of Surgical Oncology, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, China.,School of Medicine, Zhejiang University, Hangzhou, China
| | - Fei Chen
- Department of Surgical Oncology, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, China.,School of Medicine, Zhejiang University, Hangzhou, China
| | - Feilin Cao
- Department of Thyroid and Breast Surgery, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Luqiao, China
| | - Linbo Wang
- Department of Surgical Oncology, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, China
| | - Qinchuan Wang
- Department of Surgical Oncology, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, China
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12
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Wang J, Nakato R. HiC1Dmetrics: framework to extract various one-dimensional features from chromosome structure data. Brief Bioinform 2021; 23:6446983. [PMID: 34850813 PMCID: PMC8769930 DOI: 10.1093/bib/bbab509] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 11/03/2021] [Accepted: 11/05/2021] [Indexed: 01/06/2023] Open
Abstract
Eukaryotic genomes are organized in a three-dimensional spatial structure. In this regard, the development of chromosome conformation capture methods has enabled studies of chromosome organization on a genomic scale. Hi-C, the high-throughput chromosome conformation capture method, can reveal a population-averaged, hierarchical chromatin structure. The typical Hi-C analysis uses a two-dimensional (2D) contact matrix that indicates contact frequencies between all possible genomic position pairs. Oftentimes, however, such a 2D matrix is not amenable to handling quantitative comparisons, visualizations and integrations across multiple datasets. Although several one-dimensional (1D) metrics have been proposed to depict structural information in Hi-C data, their effectiveness is still underappreciated. Here, we first review the currently available 1D metrics for individual Hi-C samples or two-sample comparisons and then discuss their validity and suitable analysis scenarios. We also propose several new 1D metrics to identify additional unique features of chromosome structures. We highlight that the 1D metrics are reproducible and robust for comparing and visualizing multiple Hi-C samples. Moreover, we show that 1D metrics can be easily combined with epigenome tracks to annotate chromatin states in greater details. We develop a new framework, called HiC1Dmetrics, to summarize all 1D metrics discussed in this study. HiC1Dmetrics is open-source (github.com/wangjk321/HiC1Dmetrics) and can be accessed from both command-line and web-based interfaces. Our tool constitutes a useful resource for the community of chromosome-organization researchers.
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Affiliation(s)
- Jiankang Wang
- Institute for Quantitative Biosciences, The University of Tokyo, Japan.,Graduate School of Medicine, The University of Tokyo, Japan
| | - Ryuichiro Nakato
- Institute for Quantitative Biosciences, The University of Tokyo, Japan.,Graduate School of Medicine, The University of Tokyo, Japan
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13
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Arslan E, Schulz J, Rai K. Machine Learning in Epigenomics: Insights into Cancer Biology and Medicine. Biochim Biophys Acta Rev Cancer 2021; 1876:188588. [PMID: 34245839 PMCID: PMC8595561 DOI: 10.1016/j.bbcan.2021.188588] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 05/29/2021] [Accepted: 07/02/2021] [Indexed: 02/01/2023]
Abstract
The recent deluge of genome-wide technologies for the mapping of the epigenome and resulting data in cancer samples has provided the opportunity for gaining insights into and understanding the roles of epigenetic processes in cancer. However, the complexity, high-dimensionality, sparsity, and noise associated with these data pose challenges for extensive integrative analyses. Machine Learning (ML) algorithms are particularly suited for epigenomic data analyses due to their flexibility and ability to learn underlying hidden structures. We will discuss four overlapping but distinct major categories under ML: dimensionality reduction, unsupervised methods, supervised methods, and deep learning (DL). We review the preferred use cases of these algorithms in analyses of cancer epigenomics data with the hope to provide an overview of how ML approaches can be used to explore fundamental questions on the roles of epigenome in cancer biology and medicine.
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Affiliation(s)
- Emre Arslan
- Department of Genomic Medicine, MD Anderson Cancer Center, Houston, TX 77030, United States of America
| | - Jonathan Schulz
- Department of Genomic Medicine, MD Anderson Cancer Center, Houston, TX 77030, United States of America
| | - Kunal Rai
- Department of Genomic Medicine, MD Anderson Cancer Center, Houston, TX 77030, United States of America.
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14
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Head and Neck Cancers Are Not Alike When Tarred with the Same Brush: An Epigenetic Perspective from the Cancerization Field to Prognosis. Cancers (Basel) 2021; 13:cancers13225630. [PMID: 34830785 PMCID: PMC8616074 DOI: 10.3390/cancers13225630] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/30/2021] [Accepted: 11/02/2021] [Indexed: 12/26/2022] Open
Abstract
Simple Summary Squamous cell carcinomas affect different head and neck subsites and, although these tumors arise from the same epithelial lining and share risk factors, they differ in terms of clinical behavior and molecular carcinogenesis mechanisms. Differences between HPV-negative and HPV-positive tumors are those most frequently explored, but further data suggest that the molecular heterogeneity observed among head and neck subsites may go beyond HPV infection. In this review, we explore how alterations of DNA methylation and microRNA expression contribute to head and neck squamous cell carcinoma (HNSCC) development and progression. The association of these epigenetic alterations with risk factor exposure, early carcinogenesis steps, transformation risk, and prognosis are described. Finally, we discuss the potential application of the use of epigenetic biomarkers in HNSCC. Abstract Head and neck squamous cell carcinomas (HNSCC) are among the ten most frequent types of cancer worldwide and, despite all efforts, are still diagnosed at late stages and show poor overall survival. Furthermore, HNSCC patients often experience relapses and the development of second primary tumors, as a consequence of the field cancerization process. Therefore, a better comprehension of the molecular mechanisms involved in HNSCC development and progression may enable diagnosis anticipation and provide valuable tools for prediction of prognosis and response to therapy. However, the different biological behavior of these tumors depending on the affected anatomical site and risk factor exposure, as well as the high genetic heterogeneity observed in HNSCC are major obstacles in this pursue. In this context, epigenetic alterations have been shown to be common in HNSCC, to discriminate the tumor anatomical subsites, to be responsive to risk factor exposure, and show promising results in biomarker development. Based on this, this review brings together the current knowledge on alterations of DNA methylation and microRNA expression in HNSCC natural history, focusing on how they contribute to each step of the process and on their applicability as biomarkers of exposure, HNSCC development, progression, and response to therapy.
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15
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Sklias A, Halaburkova A, Vanzan L, Jimenez NF, Cuenin C, Bouaoun L, Cahais V, Ythier V, Sallé A, Renard C, Durand G, Le Calvez-Kelm F, Khoueiry R, Murr R, Herceg Z. Epigenetic remodelling of enhancers in response to estrogen deprivation and re-stimulation. Nucleic Acids Res 2021; 49:9738-9754. [PMID: 34403459 PMCID: PMC8464064 DOI: 10.1093/nar/gkab697] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 08/14/2021] [Indexed: 12/24/2022] Open
Abstract
Estrogen hormones are implicated in a majority of breast cancers and estrogen receptor alpha (ER), the main nuclear factor mediating estrogen signaling, orchestrates a complex molecular circuitry that is not yet fully elucidated. Here, we investigated genome-wide DNA methylation, histone acetylation and transcription after estradiol (E2) deprivation and re-stimulation to better characterize the ability of ER to coordinate gene regulation. We found that E2 deprivation mostly resulted in DNA hypermethylation and histone deacetylation in enhancers. Transcriptome analysis revealed that E2 deprivation leads to a global down-regulation in gene expression, and more specifically of TET2 demethylase that may be involved in the DNA hypermethylation following short-term E2 deprivation. Further enrichment analysis of transcription factor (TF) binding and motif occurrence highlights the importance of ER connection mainly with two partner TF families, AP-1 and FOX. These interactions take place in the proximity of E2 deprivation-mediated differentially methylated and histone acetylated enhancers. Finally, while most deprivation-dependent epigenetic changes were reversed following E2 re-stimulation, DNA hypermethylation and H3K27 deacetylation at certain enhancers were partially retained. Overall, these results show that inactivation of ER mediates rapid and mostly reversible epigenetic changes at enhancers, and bring new insight into early events, which may ultimately lead to endocrine resistance.
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Affiliation(s)
- Athena Sklias
- Epigenetics Group, International Agency for Research on Cancer (IARC), 69372 Lyon Cedex 08, France
| | - Andrea Halaburkova
- Epigenetics Group, International Agency for Research on Cancer (IARC), 69372 Lyon Cedex 08, France
| | - Ludovica Vanzan
- Department of Genetic Medicine and Development (GEDEV), University of Geneva, Geneva, Switzerland
| | - Nora Fernandez Jimenez
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Biocruces-Bizkaia Health Research Institute, Leioa, Basque Country 48940, Spain
| | - Cyrille Cuenin
- Epigenetics Group, International Agency for Research on Cancer (IARC), 69372 Lyon Cedex 08, France
| | - Liacine Bouaoun
- Section of Environment and Radiation, International Agency for Research on Cancer (IARC), 69372 Lyon Cedex 08, France
| | - Vincent Cahais
- Epigenetics Group, International Agency for Research on Cancer (IARC), 69372 Lyon Cedex 08, France
| | - Victor Ythier
- Department of Genetic Medicine and Development (GEDEV), University of Geneva, Geneva, Switzerland
| | - Aurélie Sallé
- Epigenetics Group, International Agency for Research on Cancer (IARC), 69372 Lyon Cedex 08, France
| | - Claire Renard
- Epigenetics Group, International Agency for Research on Cancer (IARC), 69372 Lyon Cedex 08, France
| | - Geoffroy Durand
- Genetic Cancer Susceptibility Group, International Agency for Research on Cancer (IARC), Lyon, France
| | - Florence Le Calvez-Kelm
- Genetic Cancer Susceptibility Group, International Agency for Research on Cancer (IARC), Lyon, France
| | - Rita Khoueiry
- Epigenetics Group, International Agency for Research on Cancer (IARC), 69372 Lyon Cedex 08, France
| | - Rabih Murr
- Department of Genetic Medicine and Development (GEDEV), University of Geneva, Geneva, Switzerland
- Institute for Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, Switzerland
| | - Zdenko Herceg
- Epigenetics Group, International Agency for Research on Cancer (IARC), 69372 Lyon Cedex 08, France
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16
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Du Q, Smith GC, Luu PL, Ferguson JM, Armstrong NJ, Caldon CE, Campbell EM, Nair SS, Zotenko E, Gould CM, Buckley M, Chia KM, Portman N, Lim E, Kaczorowski D, Chan CL, Barton K, Deveson IW, Smith MA, Powell JE, Skvortsova K, Stirzaker C, Achinger-Kawecka J, Clark SJ. DNA methylation is required to maintain both DNA replication timing precision and 3D genome organization integrity. Cell Rep 2021; 36:109722. [PMID: 34551299 DOI: 10.1016/j.celrep.2021.109722] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 06/22/2021] [Accepted: 08/25/2021] [Indexed: 02/08/2023] Open
Abstract
DNA replication timing and three-dimensional (3D) genome organization are associated with distinct epigenome patterns across large domains. However, whether alterations in the epigenome, in particular cancer-related DNA hypomethylation, affects higher-order levels of genome architecture is still unclear. Here, using Repli-Seq, single-cell Repli-Seq, and Hi-C, we show that genome-wide methylation loss is associated with both concordant loss of replication timing precision and deregulation of 3D genome organization. Notably, we find distinct disruption in 3D genome compartmentalization, striking gains in cell-to-cell replication timing heterogeneity and loss of allelic replication timing in cancer hypomethylation models, potentially through the gene deregulation of DNA replication and genome organization pathways. Finally, we identify ectopic H3K4me3-H3K9me3 domains from across large hypomethylated domains, where late replication is maintained, which we purport serves to protect against catastrophic genome reorganization and aberrant gene transcription. Our results highlight a potential role for the methylome in the maintenance of 3D genome regulation.
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Affiliation(s)
- Qian Du
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia; St Vincent's Clinical School, University of New South Wales, Sydney, NSW 2010, Australia
| | - Grady C Smith
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
| | - Phuc Loi Luu
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia; St Vincent's Clinical School, University of New South Wales, Sydney, NSW 2010, Australia
| | - James M Ferguson
- The Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
| | - Nicola J Armstrong
- Mathematics and Statistics, Murdoch University, Murdoch, WA 6150, Australia
| | - C Elizabeth Caldon
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia; St Vincent's Clinical School, University of New South Wales, Sydney, NSW 2010, Australia
| | | | - Shalima S Nair
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia; St Vincent's Clinical School, University of New South Wales, Sydney, NSW 2010, Australia
| | - Elena Zotenko
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
| | - Cathryn M Gould
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
| | - Michael Buckley
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
| | - Kee-Ming Chia
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
| | - Neil Portman
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
| | - Elgene Lim
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia; St Vincent's Clinical School, University of New South Wales, Sydney, NSW 2010, Australia
| | - Dominik Kaczorowski
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
| | - Chia-Ling Chan
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
| | - Kirston Barton
- The Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
| | - Ira W Deveson
- St Vincent's Clinical School, University of New South Wales, Sydney, NSW 2010, Australia; The Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
| | - Martin A Smith
- St Vincent's Clinical School, University of New South Wales, Sydney, NSW 2010, Australia; The Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
| | - Joseph E Powell
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia; UNSW Cellular Genomics Futures Institute, School of Medical Sciences, UNSW Sydney, NSW 2010, Australia
| | - Ksenia Skvortsova
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia; St Vincent's Clinical School, University of New South Wales, Sydney, NSW 2010, Australia
| | - Clare Stirzaker
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia; St Vincent's Clinical School, University of New South Wales, Sydney, NSW 2010, Australia
| | - Joanna Achinger-Kawecka
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia; St Vincent's Clinical School, University of New South Wales, Sydney, NSW 2010, Australia
| | - Susan J Clark
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia; St Vincent's Clinical School, University of New South Wales, Sydney, NSW 2010, Australia.
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17
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Predicting pathogenic non-coding SVs disrupting the 3D genome in 1646 whole cancer genomes using multiple instance learning. Sci Rep 2021; 11:14411. [PMID: 34257393 PMCID: PMC8277903 DOI: 10.1038/s41598-021-93917-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 07/01/2021] [Indexed: 11/21/2022] Open
Abstract
Over the past years, large consortia have been established to fuel the sequencing of whole genomes of many cancer patients. Despite the increased abundance in tools to study the impact of SNVs, non-coding SVs have been largely ignored in these data. Here, we introduce svMIL2, an improved version of our Multiple Instance Learning-based method to study the effect of somatic non-coding SVs disrupting boundaries of TADs and CTCF loops in 1646 cancer genomes. We demonstrate that svMIL2 predicts pathogenic non-coding SVs with an average AUC of 0.86 across 12 cancer types, and identifies non-coding SVs affecting well-known driver genes. The disruption of active (super) enhancers in open chromatin regions appears to be a common mechanism by which non-coding SVs exert their pathogenicity. Finally, our results reveal that the contribution of pathogenic non-coding SVs as opposed to driver SNVs may highly vary between cancers, with notably high numbers of genes being disrupted by pathogenic non-coding SVs in ovarian and pancreatic cancer. Taken together, our machine learning method offers a potent way to prioritize putatively pathogenic non-coding SVs and leverage non-coding SVs to identify driver genes. Moreover, our analysis of 1646 cancer genomes demonstrates the importance of including non-coding SVs in cancer diagnostics.
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18
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AlAbdi L, Saha D, He M, Dar MS, Utturkar SM, Sudyanti PA, McCune S, Spears BH, Breedlove JA, Lanman NA, Gowher H. Oct4-Mediated Inhibition of Lsd1 Activity Promotes the Active and Primed State of Pluripotency Enhancers. Cell Rep 2021; 30:1478-1490.e6. [PMID: 32023463 DOI: 10.1016/j.celrep.2019.11.040] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 07/30/2019] [Accepted: 12/19/2019] [Indexed: 12/16/2022] Open
Abstract
An aberrant increase in pluripotency gene (PpG) expression due to enhancer reactivation could induce stemness and enhance the tumorigenicity of cancer stem cells. Silencing of PpG enhancers (PpGe) during embryonic stem cell differentiation involves Lsd1-mediated H3K4me1 demethylation and DNA methylation. Here, we observed retention of H3K4me1 and DNA hypomethylation at PpGe associated with a partial repression of PpGs in F9 embryonal carcinoma cells (ECCs) post-differentiation. H3K4me1 demethylation in F9 ECCs could not be rescued by Lsd1 overexpression. Given our observation that H3K4me1 demethylation is accompanied by strong Oct4 repression in P19 ECCs, we tested if Oct4 interaction with Lsd1 affects its catalytic activity. Our data show a dose-dependent inhibition of Lsd1 activity by Oct4 and retention of H3K4me1 at PpGe in Oct4-overexpressing P19 ECCs. These data suggest that Lsd1-Oct4 interaction in cancer stem cells could establish a "primed" enhancer state that is susceptible to reactivation, leading to aberrant PpG expression.
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Affiliation(s)
- Lama AlAbdi
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Debapriya Saha
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Ming He
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Mohd Saleem Dar
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Sagar M Utturkar
- Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA
| | - Putu Ayu Sudyanti
- Department of Statistics, Purdue University, West Lafayette, IN 47907, USA
| | - Stephen McCune
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Brice H Spears
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - James A Breedlove
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Nadia A Lanman
- Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA; Department of Comparative Pathobiology, Purdue University, West Lafayette, IN 47907, USA
| | - Humaira Gowher
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA; Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA.
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19
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Su SF, Liu CH, Cheng CL, Ho CC, Yang TY, Chen KC, Hsu KH, Tseng JS, Chen HW, Chang GC, Yu SL, Li KC. Genome-Wide Epigenetic Landscape of Lung Adenocarcinoma Links HOXB9 DNA Methylation to Intrinsic EGFR-TKI Resistance and Heterogeneous Responses. JCO Precis Oncol 2021; 5:PO.20.00151. [PMID: 34036228 PMCID: PMC8140798 DOI: 10.1200/po.20.00151] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 10/15/2020] [Accepted: 01/08/2021] [Indexed: 12/11/2022] Open
Abstract
PURPOSE Epidermal growth factor receptor (EGFR)-tyrosine kinase inhibitors (TKIs) show efficacy in treating patients with lung adenocarcinoma with EGFR-activating mutations. However, a significant subset of targeted patients fail to respond. Unlike acquired resistance (AR), intrinsic resistance (IR) remains poorly understood. We investigated whether epigenomic factors contribute to patient-to-patient heterogeneity in the EGFR-TKI response and aimed to characterize the IR subpopulation that obtains no benefit from EGFR-TKIs. PATIENTS AND METHODS We conducted genome-wide DNA methylation profiling of 79 tumors sampled from patients with advanced lung adenocarcinoma before they received EGFR-TKI treatment and analyzed the patient responses. Pyrosequencing was performed in a validation cohort of 163 patients with EGFR-activating mutations. RESULTS A DNA methylation landscape of 216 CpG sites with differential methylation was established to elucidate the association of DNA methylation with the characteristics and EGFR-TKI response status of the patients. Functional analysis of 37 transcription-repressive sites identified the enrichment of transcription factors, notably homeobox (HOX) genes. DNA methylation of HOXB9 (cg13643585) in the enhancer region yielded 88% sensitivity for predicting drug response (odds ratio [OR], 6.64; 95% CI, 1.98 to 25.23; P = .0009). Pyrosequencing validated that HOXB9 gained methylation in patients with a poor EGFR-TKI response (OR, 3.06; 95% CI, 1.13 to 8.19; P = .019). CONCLUSION Our data suggest that homeobox DNA methylation could be a novel tumor cellular state that can aid the precise categorization of tumor heterogeneity in the study of IR to EGFR-TKIs. We identified, for the first time, an epigenomic factor that can potentially complement DNA mutation status in discriminating patients with lung adenocarcinoma who are less likely to benefit from EGFR-TKI treatment, thereby leading to improved patient management in precision medicine.
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Affiliation(s)
- Sheng-Fang Su
- Institute of Statistical Sciences, Academia Sinica, Taipei, Taiwan.,Graduate Institute of Oncology, National Taiwan University, College of Medicine, Taipei, Taiwan.,YongLin Institute of Health, YongLin Scholar, National Taiwan University, Taipei, Taiwan
| | - Chia-Hsin Liu
- Institute of Statistical Sciences, Academia Sinica, Taipei, Taiwan.,Bioinformatics Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan.,Institute of Biomedical Informatics, National Yang-Ming University, Taipei, Taiwan
| | - Chiou-Ling Cheng
- NTU Centers for Genomic and Precision Medicine, National Taiwan University, College of Medicine, Taipei, Taiwan
| | - Chao-Chi Ho
- Department of Internal Medicine, National Taiwan University Hospital and National Taiwan University, College of Medicine, Taipei, Taiwan
| | - Tsung-Ying Yang
- Department of Internal Medicine, Division of Chest Medicine, Taichung Veterans General Hospital, Taichung, Taiwan.,School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Kun-Chieh Chen
- Department of Internal Medicine, Division of Chest Medicine, Taichung Veterans General Hospital, Taichung, Taiwan.,Department of Applied Chemistry, National Chi Nan University, Nantou, Taiwan
| | - Kuo-Hsuan Hsu
- Institute of Biomedical Sciences, National Chung Hsing University, Taichung, Taiwan.,Internal Medicine, Division of Critical Care and Respiratory Therapy, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Jeng-Sen Tseng
- Department of Internal Medicine, Division of Chest Medicine, Taichung Veterans General Hospital, Taichung, Taiwan.,School of Medicine, National Yang-Ming University, Taipei, Taiwan.,Institute of Biomedical Sciences, National Chung Hsing University, Taichung, Taiwan
| | - Huei-Wen Chen
- Graduate Institute of Toxicology, National Taiwan University, College of Medicine, Taipei, Taiwan
| | - Gee-Chen Chang
- Department of Internal Medicine, Division of Chest Medicine, Taichung Veterans General Hospital, Taichung, Taiwan.,School of Medicine, National Yang-Ming University, Taipei, Taiwan.,Institute of Biomedical Sciences, National Chung Hsing University, Taichung, Taiwan.,Division of Pulmonary Medicine, Department of Internal Medicine, Chung Shan Medical University Hospital, Taichung, Taiwan.,Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan.,School of Medicine, Chung Shan Medical University, Taichung, Taiwan
| | - Sung-Liang Yu
- NTU Centers for Genomic and Precision Medicine, National Taiwan University, College of Medicine, Taipei, Taiwan.,Department of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan University, College of Medicine, Taipei, Taiwan.,Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan.,Department of Pathology and Graduate Institute of Pathology, National Taiwan University, College of Medicine, Taipei, Taiwan.,Institute of Medical Device and Imaging, National Taiwan University, College of Medicine, Taipei, Taiwan.,Graduate Institute of Clinical Medicine, National Taiwan University, College of Medicine, Taipei, Taiwan
| | - Ker-Chau Li
- Institute of Statistical Sciences, Academia Sinica, Taipei, Taiwan.,Department of Statistics, University of California, Los Angeles, Los Angeles, CA
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20
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Giles KA, Gould CM, Achinger-Kawecka J, Page SG, Kafer GR, Rogers S, Luu PL, Cesare AJ, Clark SJ, Taberlay PC. BRG1 knockdown inhibits proliferation through multiple cellular pathways in prostate cancer. Clin Epigenetics 2021; 13:37. [PMID: 33596994 PMCID: PMC7888175 DOI: 10.1186/s13148-021-01023-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 02/04/2021] [Indexed: 12/13/2022] Open
Abstract
Background BRG1 (encoded by SMARCA4) is a catalytic component of the SWI/SNF chromatin remodelling complex, with key roles in modulating DNA accessibility. Dysregulation of BRG1 is observed, but functionally uncharacterised, in a wide range of malignancies. We have probed the functions of BRG1 on a background of prostate cancer to investigate how BRG1 controls gene expression programmes and cancer cell behaviour. Results Our investigation of SMARCA4 revealed that BRG1 is over-expressed in the majority of the 486 tumours from The Cancer Genome Atlas prostate cohort, as well as in a complementary panel of 21 prostate cell lines. Next, we utilised a temporal model of BRG1 depletion to investigate the molecular effects on global transcription programmes. Depleting BRG1 had no impact on alternative splicing and conferred only modest effect on global expression. However, of the transcriptional changes that occurred, most manifested as down-regulated expression. Deeper examination found the common thread linking down-regulated genes was involvement in proliferation, including several known to increase prostate cancer proliferation (KLK2, PCAT1 and VAV3). Interestingly, the promoters of genes driving proliferation were bound by BRG1 as well as the transcription factors, AR and FOXA1. We also noted that BRG1 depletion repressed genes involved in cell cycle progression and DNA replication, but intriguingly, these pathways operated independently of AR and FOXA1. In agreement with transcriptional changes, depleting BRG1 conferred G1 arrest. Conclusions Our data have revealed that BRG1 promotes cell cycle progression and DNA replication, consistent with the increased cell proliferation associated with oncogenesis. Supplementary Information The online version contains supplementary material available at 10.1186/s13148-021-01023-7.
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Affiliation(s)
- Katherine A Giles
- Epigenetics Laboratory, Genomics and Epigenetics Theme, Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia.,Genome Integrity Unit, Children's Medical Research Institute, University of Sydney, Westmead, NSW, 2145, Australia.,Tasmanian School of Medicine, College of Health and Medicine, University of Tasmania, TAS, Hobart, 7000, Australia
| | - Cathryn M Gould
- Epigenetics Laboratory, Genomics and Epigenetics Theme, Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia
| | - Joanna Achinger-Kawecka
- Epigenetics Laboratory, Genomics and Epigenetics Theme, Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia.,St Vincent's Clinical School, UNSW Sydney, Sydney, NSW, 2000, Australia
| | - Scott G Page
- Genome Integrity Unit, Children's Medical Research Institute, University of Sydney, Westmead, NSW, 2145, Australia
| | - Georgia R Kafer
- Genome Integrity Unit, Children's Medical Research Institute, University of Sydney, Westmead, NSW, 2145, Australia
| | - Samuel Rogers
- Genome Integrity Unit, Children's Medical Research Institute, University of Sydney, Westmead, NSW, 2145, Australia
| | - Phuc-Loi Luu
- Epigenetics Laboratory, Genomics and Epigenetics Theme, Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia.,St Vincent's Clinical School, UNSW Sydney, Sydney, NSW, 2000, Australia
| | - Anthony J Cesare
- Genome Integrity Unit, Children's Medical Research Institute, University of Sydney, Westmead, NSW, 2145, Australia
| | - Susan J Clark
- Epigenetics Laboratory, Genomics and Epigenetics Theme, Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia.,St Vincent's Clinical School, UNSW Sydney, Sydney, NSW, 2000, Australia
| | - Phillippa C Taberlay
- Tasmanian School of Medicine, College of Health and Medicine, University of Tasmania, TAS, Hobart, 7000, Australia.
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21
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The Role of H3K4 Trimethylation in CpG Islands Hypermethylation in Cancer. Biomolecules 2021; 11:biom11020143. [PMID: 33499170 PMCID: PMC7912453 DOI: 10.3390/biom11020143] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 12/30/2020] [Accepted: 01/15/2021] [Indexed: 01/01/2023] Open
Abstract
CpG methylation in transposons, exons, introns and intergenic regions is important for long-term silencing, silencing of parasitic sequences and alternative promoters, regulating imprinted gene expression and determining X chromosome inactivation. Promoter CpG islands, although rich in CpG dinucleotides, are unmethylated and remain so during all phases of mammalian embryogenesis and development, except in specific cases. The biological mechanisms that contribute to the maintenance of the unmethylated state of CpG islands remain elusive, but the modification of established DNA methylation patterns is a common feature in all types of tumors and is considered as an event that intrinsically, or in association with genetic lesions, feeds carcinogenesis. In this review, we focus on the latest results describing the role that the levels of H3K4 trimethylation may have in determining the aberrant hypermethylation of CpG islands in tumors.
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22
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Gray JS, Campbell MJ. Challenges and Opportunities of Genomic Approaches in Therapeutics Development. Methods Mol Biol 2021; 2194:107-126. [PMID: 32926364 DOI: 10.1007/978-1-0716-0849-4_7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The magnitude of all therapeutic responses is significantly determined by genome structure, variation, and functional interactions. This determination occurs at many levels which are discussed in the current review. Well-established examples of structural variation between individuals are known to dictate an individual's response to numerous drugs, as clearly illustrated by warfarin. The exponential rate of genomic-based interrogation is coupled with an expanding repertoire of genomic technologies and applications. This is leading to an ever more sophisticated appreciation of how structural variation, regulation of transcription and genomic structure, both individually and collectively, define cell therapeutic responses.
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Affiliation(s)
- Jaimie S Gray
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, OH, USA
| | - Moray J Campbell
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, OH, USA.
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23
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Nieboer MM, de Ridder J. svMIL: predicting the pathogenic effect of TAD boundary-disrupting somatic structural variants through multiple instance learning. Bioinformatics 2020; 36:i692-i699. [DOI: 10.1093/bioinformatics/btaa802] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/08/2020] [Indexed: 12/21/2022] Open
Abstract
Abstract
Motivation
Despite the fact that structural variants (SVs) play an important role in cancer, methods to predict their effect, especially for SVs in non-coding regions, are lacking, leaving them often overlooked in the clinic. Non-coding SVs may disrupt the boundaries of Topologically Associated Domains (TADs), thereby affecting interactions between genes and regulatory elements such as enhancers. However, it is not known when such alterations are pathogenic. Although machine learning techniques are a promising solution to answer this question, representing the large number of interactions that an SV can disrupt in a single feature matrix is not trivial.
Results
We introduce svMIL: a method to predict pathogenic TAD boundary-disrupting SV effects based on multiple instance learning, which circumvents the need for a traditional feature matrix by grouping SVs into bags that can contain any number of disruptions. We demonstrate that svMIL can predict SV pathogenicity, measured through same-sample gene expression aberration, for various cancer types. In addition, our approach reveals that somatic pathogenic SVs alter different regulatory interactions than somatic non-pathogenic SVs and germline SVs.
Availability and implementation
All code for svMIL is publicly available on GitHub: https://github.com/UMCUGenetics/svMIL.
Supplementary information
Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Marleen M. Nieboer
- Center for Molecular Medicine, Oncode Institute, University Medical Center Utrecht, Utrecht 3584 CG, The Netherlands
| | - Jeroen de Ridder
- Center for Molecular Medicine, Oncode Institute, University Medical Center Utrecht, Utrecht 3584 CG, The Netherlands
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24
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Schwartz M, Portugez AS, Attia BZ, Tannenbaum M, Cohen L, Loza O, Chase E, Turman Y, Kaplan T, Salah Z, Hakim O. Genomic retargeting of p53 and CTCF is associated with transcriptional changes during oncogenic HRas-induced transformation. Commun Biol 2020; 3:696. [PMID: 33239721 PMCID: PMC7809021 DOI: 10.1038/s42003-020-01398-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Accepted: 10/16/2020] [Indexed: 12/15/2022] Open
Abstract
Gene transcription is regulated by distant regulatory elements via combinatorial binding of transcription factors. It is increasingly recognized that alterations in chromatin state and transcription factor binding in these distant regulatory elements may have key roles in cancer development. Here we focused on the first stages of oncogene-induced carcinogenic transformation, and characterized the regulatory network underlying transcriptional changes associated with this process. Using Hi-C data, we observe spatial coupling between differentially expressed genes and their differentially accessible regulatory elements and reveal two candidate transcription factors, p53 and CTCF, as determinants of transcriptional alterations at the early stages of oncogenic HRas-induced transformation in human mammary epithelial cells. Strikingly, the malignant transcriptional reprograming is promoted by redistribution of chromatin binding of these factors without major variation in their expression level. Our results demonstrate that alterations in the regulatory landscape have a major role in driving oncogene-induced transcriptional reprogramming.
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Affiliation(s)
- Michal Schwartz
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Avital Sarusi Portugez
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Bracha Zukerman Attia
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Miriam Tannenbaum
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Leslie Cohen
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Olga Loza
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Emily Chase
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Yousef Turman
- Al-Quds-Bard College for Arts and Sciences, Al-Quds University, Abu Dis, Palestinian Terretories, Palestine
| | - Tommy Kaplan
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Zaidoun Salah
- Al-Quds-Bard College for Arts and Sciences, Al-Quds University, Abu Dis, Palestinian Terretories, Palestine
| | - Ofir Hakim
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel.
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25
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Gómez Acuña LI, Nazer E, Rodríguez-Seguí SA, Pozzi B, Buggiano V, Marasco LE, Agirre E, He C, Alló M, Kornblihtt AR. Nuclear role for human Argonaute-1 as an estrogen-dependent transcription coactivator. J Cell Biol 2020; 219:e201908097. [PMID: 32673398 PMCID: PMC7480116 DOI: 10.1083/jcb.201908097] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 04/20/2020] [Accepted: 05/20/2020] [Indexed: 01/07/2023] Open
Abstract
In mammals, argonaute (AGO) proteins have been characterized for their roles in small RNA-mediated posttranscriptional and also in transcriptional gene silencing. Here, we report a different role for AGO1 in estradiol-triggered transcriptional activation in human cells. We show that in MCF-7 mammary gland cells, AGO1 associates with transcriptional enhancers of estrogen receptor α (ERα) and that this association is up-regulated by treating the cells with estrogen (E2), displaying a positive correlation with the activation of these enhancers. Moreover, we show that AGO1 interacts with ERα and that this interaction is also increased by E2 treatment, but occurs in the absence of RNA. We show that AGO1 acts positively as a coactivator in estradiol-triggered transcription regulation by promoting ERα binding to its enhancers. Consistently, AGO1 depletion decreases long-range contacts between ERα enhancers and their target promoters. Our results point to a role of AGO1 in transcriptional regulation in human cells that is independent from small RNA binding.
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Affiliation(s)
- Luciana I Gómez Acuña
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología, Biología Molecular y Celular and Consejo Nacional de Investigaciones Científicas y Técnicas of Argentina, Instituto de Fisiología, Biología Molecular y Neurociencias, Buenos Aires, Argentina
| | - Ezequiel Nazer
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología, Biología Molecular y Celular and Consejo Nacional de Investigaciones Científicas y Técnicas of Argentina, Instituto de Fisiología, Biología Molecular y Neurociencias, Buenos Aires, Argentina
| | - Santiago A Rodríguez-Seguí
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología, Biología Molecular y Celular and Consejo Nacional de Investigaciones Científicas y Técnicas of Argentina, Instituto de Fisiología, Biología Molecular y Neurociencias, Buenos Aires, Argentina
| | - Berta Pozzi
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología, Biología Molecular y Celular and Consejo Nacional de Investigaciones Científicas y Técnicas of Argentina, Instituto de Fisiología, Biología Molecular y Neurociencias, Buenos Aires, Argentina
| | - Valeria Buggiano
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología, Biología Molecular y Celular and Consejo Nacional de Investigaciones Científicas y Técnicas of Argentina, Instituto de Fisiología, Biología Molecular y Neurociencias, Buenos Aires, Argentina
| | - Luciano E Marasco
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología, Biología Molecular y Celular and Consejo Nacional de Investigaciones Científicas y Técnicas of Argentina, Instituto de Fisiología, Biología Molecular y Neurociencias, Buenos Aires, Argentina
| | | | - Cody He
- Pritzker School of Medicine, University of Chicago, Chicago, IL
| | - Mariano Alló
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología, Biología Molecular y Celular and Consejo Nacional de Investigaciones Científicas y Técnicas of Argentina, Instituto de Fisiología, Biología Molecular y Neurociencias, Buenos Aires, Argentina
| | - Alberto R Kornblihtt
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología, Biología Molecular y Celular and Consejo Nacional de Investigaciones Científicas y Técnicas of Argentina, Instituto de Fisiología, Biología Molecular y Neurociencias, Buenos Aires, Argentina
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26
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Dissecting the epigenomic dynamics of human fetal germ cell development at single-cell resolution. Cell Res 2020; 31:463-477. [PMID: 32884136 PMCID: PMC8115345 DOI: 10.1038/s41422-020-00401-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 08/09/2020] [Indexed: 12/14/2022] Open
Abstract
Proper development of fetal germ cells (FGCs) is vital for the precise transmission of genetic and epigenetic information through generations. The transcriptional landscapes of human FGC development have been revealed; however, the epigenetic reprogramming process of FGCs remains elusive. Here, we profiled the genome-wide DNA methylation and chromatin accessibility of human FGCs at different phases as well as gonadal niche cells at single-cell resolution. First, we found that DNA methylation levels of FGCs changed in a temporal manner, whereas FGCs at different phases in the same embryo exhibited comparable DNA methylation levels and patterns. Second, we revealed the phase-specific chromatin accessibility signatures at the promoter regions of a large set of critical transcription factors and signaling pathway genes. We also identified potential distal regulatory elements including enhancers in FGCs. Third, compared with other hominid-specific retrotransposons, SVA_D might have a broad spectrum of binding capacity for transcription factors, including SOX15 and SOX17. Finally, using an in vitro culture system of human FGCs, we showed that the BMP signaling pathway promoted the cell proliferation of FGCs, and regulated the WNT signaling pathway by orchestrating the chromatin accessibility of its ligand genes. Our single-cell epigenomic atlas and functional assays provide valuable insights for understanding the strongly heterogeneous, unsynchronized, yet highly robust nature of human germ cell development.
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27
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D'Anna F, Van Dyck L, Xiong J, Zhao H, Berrens RV, Qian J, Bieniasz-Krzywiec P, Chandra V, Schoonjans L, Matthews J, De Smedt J, Minnoye L, Amorim R, Khorasanizadeh S, Yu Q, Zhao L, De Borre M, Savvides SN, Simon MC, Carmeliet P, Reik W, Rastinejad F, Mazzone M, Thienpont B, Lambrechts D. DNA methylation repels binding of hypoxia-inducible transcription factors to maintain tumor immunotolerance. Genome Biol 2020; 21:182. [PMID: 32718321 PMCID: PMC7384226 DOI: 10.1186/s13059-020-02087-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 06/29/2020] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Hypoxia is pervasive in cancer and other diseases. Cells sense and adapt to hypoxia by activating hypoxia-inducible transcription factors (HIFs), but it is still an outstanding question why cell types differ in their transcriptional response to hypoxia. RESULTS We report that HIFs fail to bind CpG dinucleotides that are methylated in their consensus binding sequence, both in in vitro biochemical binding assays and in vivo studies of differentially methylated isogenic cell lines. Based on in silico structural modeling, we show that 5-methylcytosine indeed causes steric hindrance in the HIF binding pocket. A model wherein cell-type-specific methylation landscapes, as laid down by the differential expression and binding of other transcription factors under normoxia, control cell-type-specific hypoxia responses is observed. We also discover ectopic HIF binding sites in repeat regions which are normally methylated. Genetic and pharmacological DNA demethylation, but also cancer-associated DNA hypomethylation, expose these binding sites, inducing HIF-dependent expression of cryptic transcripts. In line with such cryptic transcripts being more prone to cause double-stranded RNA and viral mimicry, we observe low DNA methylation and high cryptic transcript expression in tumors with high immune checkpoint expression, but not in tumors with low immune checkpoint expression, where they would compromise tumor immunotolerance. In a low-immunogenic tumor model, DNA demethylation upregulates cryptic transcript expression in a HIF-dependent manner, causing immune activation and reducing tumor growth. CONCLUSIONS Our data elucidate the mechanism underlying cell-type-specific responses to hypoxia and suggest DNA methylation and hypoxia to underlie tumor immunotolerance.
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Affiliation(s)
- Flora D'Anna
- Center for Cancer Biology, VIB, 3000, Leuven, Belgium
- Laboratory of Translational Genetics, Department of Human Genetics, KU Leuven, 3000, Leuven, Belgium
| | - Laurien Van Dyck
- Center for Cancer Biology, VIB, 3000, Leuven, Belgium
- Laboratory of Translational Genetics, Department of Human Genetics, KU Leuven, 3000, Leuven, Belgium
| | - Jieyi Xiong
- Center for Cancer Biology, VIB, 3000, Leuven, Belgium
- Laboratory of Translational Genetics, Department of Human Genetics, KU Leuven, 3000, Leuven, Belgium
| | - Hui Zhao
- Center for Cancer Biology, VIB, 3000, Leuven, Belgium
- Laboratory of Translational Genetics, Department of Human Genetics, KU Leuven, 3000, Leuven, Belgium
| | - Rebecca V Berrens
- Epigenetics Programme, Babraham Institute, Cambridge, CB22 3AT, UK
- The Old Schools, University of Cambridge, Trinity Lane Cambridge, CB2 1TN, UK
| | - Junbin Qian
- Center for Cancer Biology, VIB, 3000, Leuven, Belgium
- Laboratory of Translational Genetics, Department of Human Genetics, KU Leuven, 3000, Leuven, Belgium
| | - Pawel Bieniasz-Krzywiec
- Center for Cancer Biology, VIB, 3000, Leuven, Belgium
- Laboratory of Tumor Inflammation and Angiogenesis, Department of Oncology, KU Leuven, 3000, Leuven, Belgium
| | - Vikas Chandra
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Luc Schoonjans
- Center for Cancer Biology, VIB, 3000, Leuven, Belgium
- State Key Laboratory of Ophthalmology, Zhongsan Ophthalmic Center, Sun Yat-Sen University, Guangzhou, China
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology, Leuven Cancer Institute, KU Leuven, 3000, Leuven, Belgium
| | - Jason Matthews
- Institute of Basic Medical Sciences, University of Oslo, 0372, Oslo, Norway
| | - Julie De Smedt
- Laboratory of Dermatology, Department of Oncology, KU Leuven, 3000, Leuven, Belgium
| | - Liesbeth Minnoye
- Center for Cancer Biology, VIB, 3000, Leuven, Belgium
- Laboratory of Translational Genetics, Department of Human Genetics, KU Leuven, 3000, Leuven, Belgium
| | - Ricardo Amorim
- Center for Cancer Biology, VIB, 3000, Leuven, Belgium
- Laboratory of Tumor Inflammation and Angiogenesis, Department of Oncology, KU Leuven, 3000, Leuven, Belgium
| | - Sepideh Khorasanizadeh
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Qian Yu
- Laboratory for Functional Epigenetics, Department of Human Genetics, KU Leuven, 3000, Leuven, Belgium
| | - Liyun Zhao
- Laboratory for Functional Epigenetics, Department of Human Genetics, KU Leuven, 3000, Leuven, Belgium
| | - Marie De Borre
- Laboratory for Functional Epigenetics, Department of Human Genetics, KU Leuven, 3000, Leuven, Belgium
| | - Savvas N Savvides
- Unit for Structural Biology, Department of Biochemistry and Microbiology, Ghent University, 9052, Ghent, Belgium
- VIB Center for Inflammation Research, 9052, Ghent, Belgium
| | - M Celeste Simon
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Peter Carmeliet
- Center for Cancer Biology, VIB, 3000, Leuven, Belgium
- State Key Laboratory of Ophthalmology, Zhongsan Ophthalmic Center, Sun Yat-Sen University, Guangzhou, China
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology, Leuven Cancer Institute, KU Leuven, 3000, Leuven, Belgium
| | - Wolf Reik
- Epigenetics Programme, Babraham Institute, Cambridge, CB22 3AT, UK
- Centre for Trophoblast Research, University of Cambridge, Cambridge, CB2 3EG, UK
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, CB2 3EG, UK
| | - Fraydoon Rastinejad
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Clinical and Experimental Endocrinology, Department of Chronic Diseases, Metabolism and Ageing, KU Leuven, 3000, Leuven, Belgium
| | - Massimiliano Mazzone
- Center for Cancer Biology, VIB, 3000, Leuven, Belgium
- Laboratory of Tumor Inflammation and Angiogenesis, Department of Oncology, KU Leuven, 3000, Leuven, Belgium
| | - Bernard Thienpont
- Center for Cancer Biology, VIB, 3000, Leuven, Belgium.
- Laboratory of Translational Genetics, Department of Human Genetics, KU Leuven, 3000, Leuven, Belgium.
- Laboratory for Functional Epigenetics, Department of Human Genetics, KU Leuven, 3000, Leuven, Belgium.
| | - Diether Lambrechts
- Center for Cancer Biology, VIB, 3000, Leuven, Belgium.
- Laboratory of Translational Genetics, Department of Human Genetics, KU Leuven, 3000, Leuven, Belgium.
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28
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崔 颖, 徐 泽, 李 建. [Identification of nucleosome positioning using support vector machine method based on comprehensive DNA sequence feature]. SHENG WU YI XUE GONG CHENG XUE ZA ZHI = JOURNAL OF BIOMEDICAL ENGINEERING = SHENGWU YIXUE GONGCHENGXUE ZAZHI 2020; 37:496-501. [PMID: 32597092 PMCID: PMC10319573 DOI: 10.7507/1001-5515.201911064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Indexed: 11/03/2022]
Abstract
In this article, based on z-curve theory and position weight matrix (PWM), a model for nucleosome sequences was constructed. Nucleosome sequence dataset was transformed into three-dimensional coordinates, PWM of the nucleosome sequences was calculated and the similarity score was obtained. After integrating them, a nucleosome feature model based on the comprehensive DNA sequences was obtained and named CSeqFM. We calculated the Euclidean distance between nucleosome sequence candidates or linker sequences and CSeqFM model as the feature dataset, and put the feature datasets into the support vector machine (SVM) for training and testing by ten-fold cross-validation. The results showed that the sensitivity, specificity, accuracy and Matthews correlation coefficient (MCC) of identifying nucleosome positioning for S. cerevisiae were 97.1%, 96.9%, 94.2% and 0.89, respectively, and the area under the receiver operating characteristic curve (AUC) was 0.980 1. Compared with another z-curve method, it was found that our method had better identifying effect and each evaluation performance showed better superiority. CSeqFM method was applied to identify nucleosome positioning for other three species, including C. elegans, H. sapiens and D. melanogaster. The results showed that AUCs of the three species were all higher than 0.90, and CSeqFM method also showed better stability and effectiveness compared with iNuc-STNC and iNuc-PseKNC methods, which is further demonstrated that CSeqFM method has strong reliability and good identification performance.
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Affiliation(s)
- 颖 崔
- 黑龙江大学 电子工程学院(哈尔滨 150080)Electronic Engineering College, Heilongjiang University, Harbin 150080, P.R.China
- 哈尔滨医科大学 生物信息科学与技术学院(哈尔滨 150081)School of Bioinformatics Sciences and Technology, Harbin Medical University, Harbin 150081, P.R.China
| | - 泽龙 徐
- 黑龙江大学 电子工程学院(哈尔滨 150080)Electronic Engineering College, Heilongjiang University, Harbin 150080, P.R.China
| | - 建中 李
- 黑龙江大学 电子工程学院(哈尔滨 150080)Electronic Engineering College, Heilongjiang University, Harbin 150080, P.R.China
- 哈尔滨医科大学 生物信息科学与技术学院(哈尔滨 150081)School of Bioinformatics Sciences and Technology, Harbin Medical University, Harbin 150081, P.R.China
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29
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The DNA methylation landscape in cancer. Essays Biochem 2020; 63:797-811. [PMID: 31845735 PMCID: PMC6923322 DOI: 10.1042/ebc20190037] [Citation(s) in RCA: 154] [Impact Index Per Article: 38.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 11/26/2019] [Accepted: 11/26/2019] [Indexed: 12/13/2022]
Abstract
As one of the most abundant and well-studied epigenetic modifications, DNA methylation plays an essential role in normal development and cellular biology. Global alterations to the DNA methylation landscape contribute to alterations in the transcriptome and deregulation of cellular pathways. Indeed, improved methods to study DNA methylation patterning and dynamics at base pair resolution and across individual DNA molecules on a genome-wide scale has highlighted the scope of change to the DNA methylation landscape in disease states, particularly during tumorigenesis. More recently has been the development of DNA hydroxymethylation profiling techniques, which allows differentiation between 5mC and 5hmC profiles and provides further insights into DNA methylation dynamics and remodeling in tumorigenesis. In this review, we describe the distribution of DNA methylation and DNA hydroxymethylation in different genomic contexts, first in normal cells, and how this is altered in cancer. Finally, we discuss DNA methylation profiling technologies and the most recent advances in single-cell methods, bisulfite-free approaches and ultra-long read sequencing techniques.
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30
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Nordström KJV, Schmidt F, Gasparoni N, Salhab A, Gasparoni G, Kattler K, Müller F, Ebert P, Costa IG, Pfeifer N, Lengauer T, Schulz MH, Walter J. Unique and assay specific features of NOMe-, ATAC- and DNase I-seq data. Nucleic Acids Res 2020; 47:10580-10596. [PMID: 31584093 PMCID: PMC6847574 DOI: 10.1093/nar/gkz799] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 08/31/2019] [Accepted: 09/11/2019] [Indexed: 01/01/2023] Open
Abstract
Chromatin accessibility maps are important for the functional interpretation of the genome. Here, we systematically analysed assay specific differences between DNase I-seq, ATAC-seq and NOMe-seq in a side by side experimental and bioinformatic setup. We observe that most prominent nucleosome depleted regions (NDRs, e.g. in promoters) are roboustly called by all three or at least two assays. However, we also find a high proportion of assay specific NDRs that are often ‘called’ by only one of the assays. We show evidence that these assay specific NDRs are indeed genuine open chromatin sites and contribute important information for accurate gene expression prediction. While technically ATAC-seq and DNase I-seq provide a superb high NDR calling rate for relatively low sequencing costs in comparison to NOMe-seq, NOMe-seq singles out for its genome-wide coverage allowing to not only detect NDRs but also endogenous DNA methylation and as we show here genome wide segmentation into heterochromatic B domains and local phasing of nucleosomes outside of NDRs. In summary, our comparisons strongly suggest to consider assay specific differences for the experimental design and for generalized and comparative functional interpretations.
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Affiliation(s)
| | - Florian Schmidt
- Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, 66123 Saarbrücken, Germany.,Excellence Cluster on Multimodal Computing and Interaction, Saarland University, 66123 Saarbrücken, Germany
| | - Nina Gasparoni
- Department of Genetics, Saarland University, 66123 Saarbrücken, Germany
| | | | - Gilles Gasparoni
- Department of Genetics, Saarland University, 66123 Saarbrücken, Germany
| | - Kathrin Kattler
- Department of Genetics, Saarland University, 66123 Saarbrücken, Germany
| | - Fabian Müller
- Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, 66123 Saarbrücken, Germany
| | - Peter Ebert
- Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, 66123 Saarbrücken, Germany
| | - Ivan G Costa
- Institute for Computational Genomics, Joint Research Center for Computational Biomedicine, RWTH Aachen University Medical School, 52074 Aachen, Germany
| | | | - Nico Pfeifer
- Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, 66123 Saarbrücken, Germany
| | - Thomas Lengauer
- Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, 66123 Saarbrücken, Germany
| | - Marcel H Schulz
- Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, 66123 Saarbrücken, Germany.,Excellence Cluster on Multimodal Computing and Interaction, Saarland University, 66123 Saarbrücken, Germany
| | - Jörn Walter
- Department of Genetics, Saarland University, 66123 Saarbrücken, Germany
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31
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Nagasawa M, Tomimatsu K, Terada K, Kondo K, Miyazaki K, Miyazaki M, Motooka D, Okuzaki D, Yoshida T, Kageyama S, Kawamoto H, Kawauchi A, Agata Y. Long non-coding RNA MANCR is a target of BET bromodomain protein BRD4 and plays a critical role in cellular migration and invasion abilities of prostate cancer. Biochem Biophys Res Commun 2020; 526:128-134. [PMID: 32199616 DOI: 10.1016/j.bbrc.2020.03.043] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Accepted: 03/09/2020] [Indexed: 01/03/2023]
Abstract
Androgen receptor (AR)-negative castration-resistant prostate cancer (CRPC) is highly aggressive and is resistant to most of the current therapies. Bromodomain and extra terminal domain (BET) protein BRD4 binds to super-enhancers (SEs) that drive high expression of oncogenes in many cancers. A BET inhibitor, JQ1, has been found to suppress the malignant phenotypes of prostate cancer cells, however, the target genes of JQ1 remain largely unknown. Here we show that SE-associated genes specific for AR-negative CRPC PC3 cells include genes involved in migration and invasion, and that JQ1 impairs migration and invasion of PC3 cells. We identified a long non-coding RNA, MANCR, which was markedly down-regulated by JQ1, and found that BRD4 binds to the MANCR locus. MANCR knockdown led to a significant decrease in migration and invasion of PC3 cells. Furthermore, RNA sequencing analysis revealed that expression of the genes involved in migration and invasion was altered by MANCR knockdown. In summary, our data demonstrate that MANCR plays a critical role in migration and invasion of PC3 cells.
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Affiliation(s)
- Masayuki Nagasawa
- Department of Biochemistry and Molecular Biology, Shiga University of Medical Science, Shiga, Japan; Department of Urology, Shiga University of Medical Science, Shiga, Japan
| | - Kosuke Tomimatsu
- Department of Biochemistry and Molecular Biology, Shiga University of Medical Science, Shiga, Japan
| | - Koji Terada
- Department of Biochemistry and Molecular Biology, Shiga University of Medical Science, Shiga, Japan
| | - Kenta Kondo
- Department of Biochemistry and Molecular Biology, Shiga University of Medical Science, Shiga, Japan
| | - Kazuko Miyazaki
- Laboratory of Immunology, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Masaki Miyazaki
- Laboratory of Immunology, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Daisuke Motooka
- Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Daisuke Okuzaki
- Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Tetsuya Yoshida
- Department of Urology, Shiga University of Medical Science, Shiga, Japan
| | - Susumu Kageyama
- Department of Urology, Shiga University of Medical Science, Shiga, Japan
| | - Hiroshi Kawamoto
- Laboratory of Immunology, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Akihiro Kawauchi
- Department of Urology, Shiga University of Medical Science, Shiga, Japan
| | - Yasutoshi Agata
- Department of Biochemistry and Molecular Biology, Shiga University of Medical Science, Shiga, Japan.
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Chakraborty S, Canzar S, Marschall T, Schulz MH. Chromatyping: Reconstructing Nucleosome Profiles from NOMe Sequencing Data. J Comput Biol 2020; 27:330-341. [PMID: 32160036 DOI: 10.1089/cmb.2019.0457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Measuring nucleosome positioning in cells is crucial for the analysis of epigenetic gene regulation. Reconstruction of nucleosome profiles of individual cells or subpopulations of cells remains challenging because most genome-wide assays measure nucleosome positioning and DNA accessibility for thousands of cells using bulk sequencing. In this study we use characteristics of the NOMe (nucleosome occupancy and methylation)-sequencing assay to derive a new approach, called ChromaClique, for deconvolution of different nucleosome profiles (chromatypes) from cell subpopulations of one NOMe-seq measurement. ChromaClique uses a maximal clique enumeration algorithm on a newly defined NOMe read graph that is able to group reads according to their nucleosome profiles. We show that the edge probabilities of that graph can be efficiently computed using hidden Markov models. We demonstrate using simulated data that ChromaClique is more accurate than a related method and scales favorably, allowing genome-wide analyses of chromatypes in cell subpopulations.
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Affiliation(s)
- Shounak Chakraborty
- Cluster of Excellence for Multimodal Computing and Interaction, Saarland University, Saarland Informatics Campus E1.7, Saarbrücken, Germany.,Max Planck Institute for Informatics, Saarland Informatics Campus E1.4, Saarbrücken, Germany.,Center for Bioinformatics, Saarland University, Saarland Informatics Campus E2.1, Saarbrücken, Germany.,Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Stefan Canzar
- Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Tobias Marschall
- Max Planck Institute for Informatics, Saarland Informatics Campus E1.4, Saarbrücken, Germany.,Center for Bioinformatics, Saarland University, Saarland Informatics Campus E2.1, Saarbrücken, Germany
| | - Marcel H Schulz
- Cluster of Excellence for Multimodal Computing and Interaction, Saarland University, Saarland Informatics Campus E1.7, Saarbrücken, Germany.,Max Planck Institute for Informatics, Saarland Informatics Campus E1.4, Saarbrücken, Germany.,Center for Bioinformatics, Saarland University, Saarland Informatics Campus E2.1, Saarbrücken, Germany
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33
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Constitutively bound CTCF sites maintain 3D chromatin architecture and long-range epigenetically regulated domains. Nat Commun 2020; 11:54. [PMID: 31911579 PMCID: PMC6946690 DOI: 10.1038/s41467-019-13753-7] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 11/25/2019] [Indexed: 12/19/2022] Open
Abstract
The architectural protein CTCF is a mediator of chromatin conformation, but how CTCF binding to DNA is orchestrated to maintain long-range gene expression is poorly understood. Here we perform RNAi knockdown to reduce CTCF levels and reveal a shared subset of CTCF-bound sites are robustly resistant to protein depletion. The ‘persistent’ CTCF sites are enriched at domain boundaries and chromatin loops constitutive to all cell types. CRISPR-Cas9 deletion of 2 persistent CTCF sites at the boundary between a long-range epigenetically active (LREA) and silenced (LRES) region, within the Kallikrein (KLK) locus, results in concordant activation of all 8 KLK genes within the LRES region. CTCF genome-wide depletion results in alteration in Topologically Associating Domain (TAD) structure, including the merging of TADs, whereas TAD boundaries are not altered where persistent sites are maintained. We propose that the subset of essential CTCF sites are involved in cell-type constitutive, higher order chromatin architecture. The architectural protein CTCF is a mediator of chromatin conformation, but how CTCF binding to DNA is regulated remains poorly understood. Here the authors find that there is a shared subset of CTCF-bound sites resistant to protein depletion in different cell lines, which are enriched at domain boundaries and chromatin loops constitutive to all cell types.
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34
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Yu J, Hua R, Zhang Y, Tao R, Wang Q, Ni Q. DNA hypomethylation promotes invasion and metastasis of gastric cancer cells by regulating the binding of SP1 to the CDCA3 promoter. J Cell Biochem 2020; 121:142-151. [PMID: 31211445 DOI: 10.1002/jcb.28993] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Revised: 03/21/2019] [Accepted: 04/01/2019] [Indexed: 12/16/2022]
Abstract
BACKGROUND Cell division cycle associated protein-3 (CDCA3) has been reported frequently upregulated in various cancers. It has been progressively realized that changed DNA methylations occur in diverse carcinomas. However, the concrete involvement of CDCA3 and DNA methylation in gastric cancer (GC) still needs to be further elucidated. METHODS In this study, quantitative reverse-transcription polymerase chain reaction (PCR) was utilized to determine the relative expressions of CDCA3 in GC and normal tissue samples. The methylation condition of CDCA3 was determined by bisulfite-sequencing PCR (BSP) and methylation-specific PCR (MSP). A chromatin immunoprecipitation (ChIP) assay and luciferase activity assay was used for the interaction between transcription factors and promoters and binding site determination, respectively. The effects of knockdown or overexpression of specificity protein 1 (SP1) or CDCA3 on GC cells in vitro were further assessed via wound healing assay, colony formation assay, and matrigel invasion assay. RESULTS In comparison to paired normal tissues, CDCA3 expressions were significantly increased in the GC tissues. The CDCA3 expression was regulated by DNA methylation, with the CpG island hypomethylation responsible for CDCA3 upregulation of GC. ChIP assays verified that the activity of SP1 binding to the CDCA3 promoter was dramatically increased. When the CDCA3 expression was downregulated in MKN45 cells by knockdown SP1, the proliferation ability, healing ability, and invasive ability were significantly suppressed. CONCLUSION The process by which SP1 bound to the nearest promoter region was expedited in GC cells, by which DNA was hypomethylated and CDCA3 expression was promoted. The effect on cell proliferation and invasion by CDCA3 was under the regulation of SP1 and also affected by hypomethylation of DNA.
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Affiliation(s)
- Jiawei Yu
- Department of General Surgery, Affiliated Hospital of Nantong University, Nantong, China
| | - Ruheng Hua
- Department of General Surgery, Affiliated Hospital of Nantong University, Nantong, China
| | - Yan Zhang
- Department of Chemotherapy, Affiliated Hospital of Nantong University, Nantong, China
| | - Ran Tao
- Department of General Surgery, Affiliated Hospital of Nantong University, Nantong, China
| | - Quhui Wang
- Department of General Surgery, Affiliated Hospital of Nantong University, Nantong, China
| | - Qingfeng Ni
- Department of General Surgery, Affiliated Hospital of Nantong University, Nantong, China
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35
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Fachal L, Aschard H, Beesley J, Barnes DR, Allen J, Kar S, Pooley KA, Dennis J, Michailidou K, Turman C, Soucy P, Lemaçon A, Lush M, Tyrer JP, Ghoussaini M, Moradi Marjaneh M, Jiang X, Agata S, Aittomäki K, Alonso MR, Andrulis IL, Anton-Culver H, Antonenkova NN, Arason A, Arndt V, Aronson KJ, Arun BK, Auber B, Auer PL, Azzollini J, Balmaña J, Barkardottir RB, Barrowdale D, Beeghly-Fadiel A, Benitez J, Bermisheva M, Białkowska K, Blanco AM, Blomqvist C, Blot W, Bogdanova NV, Bojesen SE, Bolla MK, Bonanni B, Borg A, Bosse K, Brauch H, Brenner H, Briceno I, Brock IW, Brooks-Wilson A, Brüning T, Burwinkel B, Buys SS, Cai Q, Caldés T, Caligo MA, Camp NJ, Campbell I, Canzian F, Carroll JS, Carter BD, Castelao JE, Chiquette J, Christiansen H, Chung WK, Claes KBM, Clarke CL, Collée JM, Cornelissen S, Couch FJ, Cox A, Cross SS, Cybulski C, Czene K, Daly MB, de la Hoya M, Devilee P, Diez O, Ding YC, Dite GS, Domchek SM, Dörk T, Dos-Santos-Silva I, Droit A, Dubois S, Dumont M, Duran M, Durcan L, Dwek M, Eccles DM, Engel C, Eriksson M, Evans DG, Fasching PA, Fletcher O, Floris G, Flyger H, Foretova L, Foulkes WD, Friedman E, Fritschi L, Frost D, Gabrielson M, Gago-Dominguez M, Gambino G, Ganz PA, Gapstur SM, Garber J, García-Sáenz JA, Gaudet MM, Georgoulias V, Giles GG, Glendon G, Godwin AK, Goldberg MS, Goldgar DE, González-Neira A, Tibiletti MG, Greene MH, Grip M, Gronwald J, Grundy A, Guénel P, Hahnen E, Haiman CA, Håkansson N, Hall P, Hamann U, Harrington PA, Hartikainen JM, Hartman M, He W, Healey CS, Heemskerk-Gerritsen BAM, Heyworth J, Hillemanns P, Hogervorst FBL, Hollestelle A, Hooning MJ, Hopper JL, Howell A, Huang G, Hulick PJ, Imyanitov EN, Isaacs C, Iwasaki M, Jager A, Jakimovska M, Jakubowska A, James PA, Janavicius R, Jankowitz RC, John EM, Johnson N, Jones ME, Jukkola-Vuorinen A, Jung A, Kaaks R, Kang D, Kapoor PM, Karlan BY, Keeman R, Kerin MJ, Khusnutdinova E, Kiiski JI, Kirk J, Kitahara CM, Ko YD, Konstantopoulou I, Kosma VM, Koutros S, Kubelka-Sabit K, Kwong A, Kyriacou K, Laitman Y, Lambrechts D, Lee E, Leslie G, Lester J, Lesueur F, Lindblom A, Lo WY, Long J, Lophatananon A, Loud JT, Lubiński J, MacInnis RJ, Maishman T, Makalic E, Mannermaa A, Manoochehri M, Manoukian S, Margolin S, Martinez ME, Matsuo K, Maurer T, Mavroudis D, Mayes R, McGuffog L, McLean C, Mebirouk N, Meindl A, Miller A, Miller N, Montagna M, Moreno F, Muir K, Mulligan AM, Muñoz-Garzon VM, Muranen TA, Narod SA, Nassir R, Nathanson KL, Neuhausen SL, Nevanlinna H, Neven P, Nielsen FC, Nikitina-Zake L, Norman A, Offit K, Olah E, Olopade OI, Olsson H, Orr N, Osorio A, Pankratz VS, Papp J, Park SK, Park-Simon TW, Parsons MT, Paul J, Pedersen IS, Peissel B, Peshkin B, Peterlongo P, Peto J, Plaseska-Karanfilska D, Prajzendanc K, Prentice R, Presneau N, Prokofyeva D, Pujana MA, Pylkäs K, Radice P, Ramus SJ, Rantala J, Rau-Murthy R, Rennert G, Risch HA, Robson M, Romero A, Rossing M, Saloustros E, Sánchez-Herrero E, Sandler DP, Santamariña M, Saunders C, Sawyer EJ, Scheuner MT, Schmidt DF, Schmutzler RK, Schneeweiss A, Schoemaker MJ, Schöttker B, Schürmann P, Scott C, Scott RJ, Senter L, Seynaeve CM, Shah M, Sharma P, Shen CY, Shu XO, Singer CF, Slavin TP, Smichkoska S, Southey MC, Spinelli JJ, Spurdle AB, Stone J, Stoppa-Lyonnet D, Sutter C, Swerdlow AJ, Tamimi RM, Tan YY, Tapper WJ, Taylor JA, Teixeira MR, Tengström M, Teo SH, Terry MB, Teulé A, Thomassen M, Thull DL, Tischkowitz M, Toland AE, Tollenaar RAEM, Tomlinson I, Torres D, Torres-Mejía G, Troester MA, Truong T, Tung N, Tzardi M, Ulmer HU, Vachon CM, van Asperen CJ, van der Kolk LE, van Rensburg EJ, Vega A, Viel A, Vijai J, Vogel MJ, Wang Q, Wappenschmidt B, Weinberg CR, Weitzel JN, Wendt C, Wildiers H, Winqvist R, Wolk A, Wu AH, Yannoukakos D, Zhang Y, Zheng W, Hunter D, Pharoah PDP, Chang-Claude J, García-Closas M, Schmidt MK, Milne RL, Kristensen VN, French JD, Edwards SL, Antoniou AC, Chenevix-Trench G, Simard J, Easton DF, Kraft P, Dunning AM. Fine-mapping of 150 breast cancer risk regions identifies 191 likely target genes. Nat Genet 2020; 52:56-73. [PMID: 31911677 PMCID: PMC6974400 DOI: 10.1038/s41588-019-0537-1] [Citation(s) in RCA: 96] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 10/24/2019] [Indexed: 02/08/2023]
Abstract
Genome-wide association studies have identified breast cancer risk variants in over 150 genomic regions, but the mechanisms underlying risk remain largely unknown. These regions were explored by combining association analysis with in silico genomic feature annotations. We defined 205 independent risk-associated signals with the set of credible causal variants in each one. In parallel, we used a Bayesian approach (PAINTOR) that combines genetic association, linkage disequilibrium and enriched genomic features to determine variants with high posterior probabilities of being causal. Potentially causal variants were significantly over-represented in active gene regulatory regions and transcription factor binding sites. We applied our INQUSIT pipeline for prioritizing genes as targets of those potentially causal variants, using gene expression (expression quantitative trait loci), chromatin interaction and functional annotations. Known cancer drivers, transcription factors and genes in the developmental, apoptosis, immune system and DNA integrity checkpoint gene ontology pathways were over-represented among the highest-confidence target genes.
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Affiliation(s)
- Laura Fachal
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Hugues Aschard
- Centre de Bioinformatique Biostatistique et Biologie Intégrative (C3BI), Institut Pasteur, Paris, France
- Program in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Jonathan Beesley
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Daniel R Barnes
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Jamie Allen
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Siddhartha Kar
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Karen A Pooley
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Joe Dennis
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Kyriaki Michailidou
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Department of Electron Microscopy/Molecular Pathology and The Cyprus School of Molecular Medicine, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Constance Turman
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Penny Soucy
- Genomics Center, Centre Hospitalier Universitaire de Québec, Université Laval Research Center, Québec City, Québec, Canada
| | - Audrey Lemaçon
- Genomics Center, Centre Hospitalier Universitaire de Québec, Université Laval Research Center, Québec City, Québec, Canada
| | - Michael Lush
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Jonathan P Tyrer
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Maya Ghoussaini
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Mahdi Moradi Marjaneh
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
- UK Dementia Research Institute, Imperial College London, London, UK
| | - Xia Jiang
- Program in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Simona Agata
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology (IOV), IRCCS, Padua, Italy
| | - Kristiina Aittomäki
- Department of Clinical Genetics, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - M Rosario Alonso
- Human Genotyping-CEGEN Unit, Human Cancer Genetic Program, Spanish National Cancer Research Centre, Madrid, Spain
| | - Irene L Andrulis
- Fred A. Litwin Center for Cancer Genetics, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Hoda Anton-Culver
- Department of Epidemiology, Genetic Epidemiology Research Institute, University of California, Irvine, Irvine, CA, USA
| | - Natalia N Antonenkova
- N.N. Alexandrov Research Institute of Oncology and Medical Radiology, Minsk, Belarus
| | - Adalgeir Arason
- Department of Pathology, Landspitali University Hospital, Reykjavik, Iceland
- BMC (Biomedical Centre), Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Volker Arndt
- Division of Clinical Epidemiology and Aging Research (C070), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Kristan J Aronson
- Department of Public Health Sciences and Cancer Research Institute, Queen's University, Kingston, Ontario, Canada
| | - Banu K Arun
- Department of Breast Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Bernd Auber
- Institute of Human Genetics, Hannover Medical School, Hannover, Germany
| | - Paul L Auer
- Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Zilber School of Public Health, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Jacopo Azzollini
- Unit of Medical Genetics, Department of Medical Oncology and Hematology, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milan, Italy
| | - Judith Balmaña
- High Risk and Cancer Prevention Group, Vall Hebron Institute of Oncology, Barcelona, Spain
- Department of Medical Oncology, Vall Hebron University Hospital, Barcelona, Spain
| | - Rosa B Barkardottir
- Department of Pathology, Landspitali University Hospital, Reykjavik, Iceland
- BMC (Biomedical Centre), Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Daniel Barrowdale
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Alicia Beeghly-Fadiel
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Javier Benitez
- Centro de Investigación en Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain
- Human Cancer Genetics Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Marina Bermisheva
- Institute of Biochemistry and Genetics, Ufa Federal Research Centre of the Russian Academy of Sciences, Ufa, Russia
| | - Katarzyna Białkowska
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Amie M Blanco
- Cancer Genetics and Prevention Program, University of California, San Francisco, San Francisco, CA, USA
| | - Carl Blomqvist
- Department of Oncology, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
- Department of Oncology, Örebro University Hospital, Örebro, Sweden
| | - William Blot
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
- International Epidemiology Institute, Rockville, MD, USA
| | - Natalia V Bogdanova
- N.N. Alexandrov Research Institute of Oncology and Medical Radiology, Minsk, Belarus
- Department of Radiation Oncology, Hannover Medical School, Hannover, Germany
- Gynaecology Research Unit, Hannover Medical School, Hannover, Germany
| | - Stig E Bojesen
- Copenhagen General Population Study, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Manjeet K Bolla
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Bernardo Bonanni
- Division of Cancer Prevention and Genetics, European Institute of Oncology (IEO), IRCCS, Milan, Italy
| | - Ake Borg
- Department of Oncology, Lund University and Skåne University Hospital, Lund, Sweden
| | - Kristin Bosse
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Hiltrud Brauch
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany
- iFIT Cluster of Excellence, University of Tuebingen, Tuebingen, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research (C070), German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Ignacio Briceno
- Institute of Human Genetics, Pontificia Universidad Javeriana, Bogota, Colombia
- Medical Faculty, Universidad de La Sabana, Bogota, Colombia
| | - Ian W Brock
- Sheffield Institute for Nucleic Acids (SInFoNiA), Department of Oncology and Metabolism, University of Sheffield, Sheffield, UK
| | - Angela Brooks-Wilson
- Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
- Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Thomas Brüning
- Institute for Prevention and Occupational Medicine of the German Social Accident Insurance, Institute of the Ruhr University Bochum (IPA), Bochum, Germany
| | - Barbara Burwinkel
- Molecular Epidemiology Group (C080), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Molecular Biology of Breast Cancer, University Womens Clinic Heidelberg, University of Heidelberg, Heidelberg, Germany
| | - Saundra S Buys
- Department of Medicine, Huntsman Cancer Institute, Salt Lake City, UT, USA
| | - Qiuyin Cai
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Trinidad Caldés
- Molecular Oncology Laboratory, CIBERONC, Hospital Clinico San Carlos, Instituto de Investigación Sanitaria del Hospital Clínico San Carlos (IdISSC), Madrid, Spain
| | - Maria A Caligo
- SOD Genetica Molecolare, University Hospital, Pisa, Italy
| | - Nicola J Camp
- Department of Internal Medicine, Huntsman Cancer Institute, Salt Lake City, UT, USA
| | - Ian Campbell
- Research Department, Peter MacCallum Cancer Center, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Federico Canzian
- Genomic Epidemiology Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jason S Carroll
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
| | - Brian D Carter
- Behavioral and Epidemiology Research Group, American Cancer Society, Atlanta, GA, USA
| | - Jose E Castelao
- Oncology and Genetics Unit, Instituto de Investigacion Sanitaria Galicia Sur (IISGS), Xerencia de Xestion Integrada de Vigo-SERGAS, Vigo, Spain
| | - Jocelyne Chiquette
- Axe Oncologie, Centre de Recherche, Centre Hospitalier Universitaire de Québec, Université Laval, Québec, Québec, Canada
| | - Hans Christiansen
- Department of Radiation Oncology, Hannover Medical School, Hannover, Germany
| | - Wendy K Chung
- Departments of Pediatrics and Medicine, Columbia University, New York, NY, USA
| | | | - Christine L Clarke
- Westmead Institute for Medical Research, University of Sydney, Sydney, New South Wales, Australia
| | - J Margriet Collée
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Sten Cornelissen
- Division of Molecular Pathology, Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
| | - Fergus J Couch
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Angela Cox
- Sheffield Institute for Nucleic Acids (SInFoNiA), Department of Oncology and Metabolism, University of Sheffield, Sheffield, UK
| | - Simon S Cross
- Academic Unit of Pathology, Department of Neuroscience, University of Sheffield, Sheffield, UK
| | - Cezary Cybulski
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Kamila Czene
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Mary B Daly
- Department of Clinical Genetics, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Miguel de la Hoya
- Molecular Oncology Laboratory, CIBERONC, Hospital Clinico San Carlos, Instituto de Investigación Sanitaria del Hospital Clínico San Carlos (IdISSC), Madrid, Spain
| | - Peter Devilee
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Orland Diez
- Oncogenetics Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain
- Clinical and Molecular Genetics Area, Vall Hebron University Hospital, Barcelona, Spain
| | - Yuan Chun Ding
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Gillian S Dite
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Susan M Domchek
- Basser Center for BRCA, Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA
| | - Thilo Dörk
- Gynaecology Research Unit, Hannover Medical School, Hannover, Germany
| | - Isabel Dos-Santos-Silva
- Department of Non-Communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
| | - Arnaud Droit
- Genomics Center, Centre Hospitalier Universitaire de Québec, Université Laval Research Center, Québec City, Québec, Canada
- Département de Médecine Moléculaire, Faculté de Médecine, Centre de Recherche, Centre Hospitalier Universitaire de Québec, Laval University, Québec City, Québec, Canada
| | - Stéphane Dubois
- Genomics Center, Centre Hospitalier Universitaire de Québec, Université Laval Research Center, Québec City, Québec, Canada
| | - Martine Dumont
- Genomics Center, Centre Hospitalier Universitaire de Québec, Université Laval Research Center, Québec City, Québec, Canada
| | - Mercedes Duran
- Cáncer Hereditario, Instituto de Biología y Genética Molecular (IBGM), Universidad de Valladolid Centro Superior de Investigaciones Científicas (UVA-CSIC), Valladolid, Spain
| | - Lorraine Durcan
- Southampton Clinical Trials Unit, Faculty of Medicine, University of Southampton, Southampton, UK
- Cancer Sciences Academic Unit, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Miriam Dwek
- School of Life Sciences, University of Westminster, London, UK
| | - Diana M Eccles
- Faculty of Medicine, University of Southampton, Southampton, UK
| | - Christoph Engel
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
| | - Mikael Eriksson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - D Gareth Evans
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
- North West Genomics Laboratory Hub, Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
| | - Peter A Fasching
- David Geffen School of Medicine, Department of Medicine, Division of Hematology and Oncology, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Gynecology and Obstetrics, Comprehensive Cancer Center ER-EMN, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Olivia Fletcher
- Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Giuseppe Floris
- Leuven Multidisciplinary Breast Center, Department of Oncology, Leuven Cancer Institute, University Hospitals Leuven, Leuven, Belgium
| | - Henrik Flyger
- Department of Breast Surgery, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark
| | - Lenka Foretova
- Department of Cancer Epidemiology and Genetics, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - William D Foulkes
- Program in Cancer Genetics, Departments of Human Genetics and Oncology, McGill University, Montréal, Québec, Canada
| | - Eitan Friedman
- The Suzanne Levy-Gertner Oncogenetics Unit, Chaim Sheba Medical Center, Ramat Gan, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv, Israel
| | - Lin Fritschi
- School of Public Health, Curtin University, Perth, Western Australia, Australia
| | - Debra Frost
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Marike Gabrielson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Manuela Gago-Dominguez
- Genomic Medicine Group, Galician Foundation of Genomic Medicine, Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Complejo Hospitalario Universitario de Santiago, SERGAS, Santiago de Compostela, Spain
- Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA
| | | | - Patricia A Ganz
- Schools of Medicine and Public Health, Division of Cancer Prevention and Control Research, Jonsson Comprehensive Cancer Centre, University of California, Los Angeles, Los Angeles, CA, USA
| | - Susan M Gapstur
- Behavioral and Epidemiology Research Group, American Cancer Society, Atlanta, GA, USA
| | - Judy Garber
- Cancer Risk and Prevention Clinic, Dana-Farber Cancer Institute, Boston, MA, USA
| | - José A García-Sáenz
- Medical Oncology Department, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria San Carlos (IdISSC), Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Mia M Gaudet
- Behavioral and Epidemiology Research Group, American Cancer Society, Atlanta, GA, USA
| | | | - Graham G Giles
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Melbourne, Victoria, Australia
| | - Gord Glendon
- Fred A. Litwin Center for Cancer Genetics, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Andrew K Godwin
- Department of Pathology and Laboratory Medicine, Kansas University Medical Center, Kansas City, KS, USA
| | - Mark S Goldberg
- Department of Medicine, McGill University, Montréal, Québec, Canada
- Division of Clinical Epidemiology, Royal Victoria Hospital, McGill University, Montréal, Québec, Canada
| | - David E Goldgar
- Department of Dermatology, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Anna González-Neira
- Human Cancer Genetics Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | | | - Mark H Greene
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Mervi Grip
- Department of Surgery, Oulu University Hospital, University of Oulu, Oulu, Finland
| | - Jacek Gronwald
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Anne Grundy
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CHUM), Université de Montréal, Montréal, Québec, Canada
| | - Pascal Guénel
- Cancer and Environment Group, Center for Research in Epidemiology and Population Health (CESP), INSERM, University Paris-Sud, University Paris-Saclay, Paris, France
| | - Eric Hahnen
- Center for Hereditary Breast and Ovarian Cancer, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Center for Integrated Oncology (CIO), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Christopher A Haiman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Niclas Håkansson
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Per Hall
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Department of Oncology, Södersjukhuset, Stockholm, Sweden
| | - Ute Hamann
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Patricia A Harrington
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Jaana M Hartikainen
- Translational Cancer Research Area, University of Eastern Finland, Kuopio, Finland
- Institute of Clinical Medicine, Pathology and Forensic Medicine, University of Eastern Finland, Kuopio, Finland
- Imaging Center, Department of Clinical Pathology, Kuopio University Hospital, Kuopio, Finland
| | - Mikael Hartman
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
- Department of Surgery, National University Health System, Singapore, Singapore
| | - Wei He
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Catherine S Healey
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | | | - Jane Heyworth
- School of Population and Global Health, The University of Western Australia, Perth, Western Australia, Australia
| | - Peter Hillemanns
- Gynaecology Research Unit, Hannover Medical School, Hannover, Germany
| | - Frans B L Hogervorst
- Family Cancer Clinic, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
| | - Antoinette Hollestelle
- Department of Medical Oncology, Family Cancer Clinic, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Maartje J Hooning
- Department of Medical Oncology, Family Cancer Clinic, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - John L Hopper
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Anthony Howell
- Division of Cancer Sciences, University of Manchester, Manchester, UK
| | - Guanmengqian Huang
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Peter J Hulick
- Center for Medical Genetics, NorthShore University HealthSystem, Evanston, IL, USA
- The University of Chicago Pritzker School of Medicine, Chicago, IL, USA
| | | | - Claudine Isaacs
- Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA
| | - Motoki Iwasaki
- Division of Epidemiology, Center for Public Health Sciences, National Cancer Center, Tokyo, Japan
| | - Agnes Jager
- Department of Medical Oncology, Family Cancer Clinic, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Milena Jakimovska
- Research Centre for Genetic Engineering and Biotechnology 'Georgi D. Efremov', Macedonian Academy of Sciences and Arts, Skopje, Republic of North Macedonia
| | - Anna Jakubowska
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
- Independent Laboratory of Molecular Biology and Genetic Diagnostics, Pomeranian Medical University, Szczecin, Poland
| | - Paul A James
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia
- Parkville Familial Cancer Centre, Peter MacCallum Cancer Center, Melbourne, Victoria, Australia
| | - Ramunas Janavicius
- Hematology, Oncology and Transfusion Medicine Center, Department of Molecular and Regenerative Medicine, Vilnius University Hospital Santariskiu Clinics, Vilnius, Lithuania
- State Research Institute Centre for Innovative Medicine, Vilnius, Lithuania
| | - Rachel C Jankowitz
- Department of Medicine, Division of Hematology/Oncology, UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Esther M John
- Department of Medicine, Division of Oncology, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Nichola Johnson
- Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Michael E Jones
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Arja Jukkola-Vuorinen
- Department of Oncology, Tampere University Hospital, Tampere University and Tampere Cancer Center, Tampere, Finland
| | - Audrey Jung
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Rudolf Kaaks
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Daehee Kang
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, Korea
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul, Korea
- Cancer Research Institute, Seoul National University, Seoul, Korea
| | - Pooja Middha Kapoor
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Faculty of Medicine, University of Heidelberg, Heidelberg, Germany
| | - Beth Y Karlan
- David Geffen School of Medicine, Department of Obstetrics and Gynecology, University of California, Los Angeles, Los Angeles, CA, USA
- Women's Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Renske Keeman
- Division of Molecular Pathology, Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
| | - Michael J Kerin
- Surgery, School of Medicine, National University of Ireland, Galway, Ireland
| | - Elza Khusnutdinova
- Institute of Biochemistry and Genetics, Ufa Federal Research Centre of the Russian Academy of Sciences, Ufa, Russia
- Department of Genetics and Fundamental Medicine, Bashkir State Medical University, Ufa, Russia
| | - Johanna I Kiiski
- Department of Obstetrics and Gynecology, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - Judy Kirk
- Familial Cancer Service, Weatmead Hospital, Sydney, New South Wales, Australia
| | - Cari M Kitahara
- Radiation Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Yon-Dschun Ko
- Department of Internal Medicine, Evangelische Kliniken Bonn, Johanniter Krankenhaus, Bonn, Germany
| | - Irene Konstantopoulou
- Molecular Diagnostics Laboratory, INRASTES, National Centre for Scientific Research 'Demokritos', Athens, Greece
| | - Veli-Matti Kosma
- Translational Cancer Research Area, University of Eastern Finland, Kuopio, Finland
- Institute of Clinical Medicine, Pathology and Forensic Medicine, University of Eastern Finland, Kuopio, Finland
- Imaging Center, Department of Clinical Pathology, Kuopio University Hospital, Kuopio, Finland
| | - Stella Koutros
- Division of Cancer Epidemiology and Genetics, Department of Health and Human Services, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Katerina Kubelka-Sabit
- Department of Histopathology and Cytology, Clinical Hospital 'Acibadem Sistina', Skopje, Republic of North Macedonia
| | - Ava Kwong
- Hong Kong Hereditary Breast Cancer Family Registry, Cancer Genetics Centre, Happy Valley, Hong Kong
- Department of Surgery, The University of Hong Kong, Pok Fu Lam, Hong Kong
- Department of Surgery, Hong Kong Sanatorium and Hospital, Happy Valley, Hong Kong
| | - Kyriacos Kyriacou
- Department of Electron Microscopy/Molecular Pathology and The Cyprus School of Molecular Medicine, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Yael Laitman
- The Suzanne Levy-Gertner Oncogenetics Unit, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Diether Lambrechts
- VIB Center for Cancer Biology, VIB, Leuven, Belgium
- Laboratory for Translational Genetics, Department of Human Genetics, University of Leuven, Leuven, Belgium
| | - Eunjung Lee
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Goska Leslie
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Jenny Lester
- David Geffen School of Medicine, Department of Obstetrics and Gynecology, University of California, Los Angeles, Los Angeles, CA, USA
- Women's Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Fabienne Lesueur
- Institut Curie, Paris, France
- Mines ParisTech, Paris, France
- Genetic Epidemiology of Cancer Team, INSERM U900, Paris, France
| | - Annika Lindblom
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Wing-Yee Lo
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany
| | - Jirong Long
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Artitaya Lophatananon
- Division of Population Health, Health Services Research and Primary Care, School of Health Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
| | - Jennifer T Loud
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jan Lubiński
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Robert J MacInnis
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia
| | - Tom Maishman
- Southampton Clinical Trials Unit, Faculty of Medicine, University of Southampton, Southampton, UK
- Cancer Sciences Academic Unit, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Enes Makalic
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Arto Mannermaa
- Translational Cancer Research Area, University of Eastern Finland, Kuopio, Finland
- Institute of Clinical Medicine, Pathology and Forensic Medicine, University of Eastern Finland, Kuopio, Finland
- Imaging Center, Department of Clinical Pathology, Kuopio University Hospital, Kuopio, Finland
| | - Mehdi Manoochehri
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Siranoush Manoukian
- Unit of Medical Genetics, Department of Medical Oncology and Hematology, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milan, Italy
| | - Sara Margolin
- Department of Oncology, Södersjukhuset, Stockholm, Sweden
- Department of Clinical Science and Education, Södersjukhuset, Karolinska Institutet, Stockholm, Sweden
| | - Maria Elena Martinez
- Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA
- Department of Family Medicine and Public Health, University of California, San Diego, La Jolla, CA, USA
| | - Keitaro Matsuo
- Division of Cancer Epidemiology and Prevention, Aichi Cancer Center Research Institute, Nagoya, Japan
- Division of Cancer Epidemiology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Tabea Maurer
- Cancer Epidemiology Group, University Cancer Center Hamburg (UCCH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Dimitrios Mavroudis
- Department of Medical Oncology, University Hospital of Heraklion, Heraklion, Greece
| | - Rebecca Mayes
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Lesley McGuffog
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Catriona McLean
- Anatomical Pathology, The Alfred Hospital, Melbourne, Victoria, Australia
| | - Noura Mebirouk
- Institut Curie, Paris, France
- Mines ParisTech, Paris, France
- Department of Tumour Biology, INSERM U830, Paris, France
| | - Alfons Meindl
- Department of Gynecology and Obstetrics, University of Munich, Munich, Germany
| | - Austin Miller
- NRG Oncology, Statistics and Data Management Center, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Nicola Miller
- Surgery, School of Medicine, National University of Ireland, Galway, Ireland
| | - Marco Montagna
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology (IOV), IRCCS, Padua, Italy
| | - Fernando Moreno
- Medical Oncology Department, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria San Carlos (IdISSC), Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Kenneth Muir
- Division of Population Health, Health Services Research and Primary Care, School of Health Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
| | - Anna Marie Mulligan
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Laboratory Medicine Program, University Health Network, Toronto, Ontario, Canada
| | | | - Taru A Muranen
- Department of Obstetrics and Gynecology, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - Steven A Narod
- Women's College Research Institute, University of Toronto, Toronto, Ontario, Canada
| | - Rami Nassir
- Department of Pathology, School of Medicine, Umm Al-Qura University, Holy Makkah, Saudi Arabia
| | - Katherine L Nathanson
- Basser Center for BRCA, Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA
| | - Susan L Neuhausen
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Heli Nevanlinna
- Department of Obstetrics and Gynecology, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - Patrick Neven
- Leuven Multidisciplinary Breast Center, Department of Oncology, Leuven Cancer Institute, University Hospitals Leuven, Leuven, Belgium
| | - Finn C Nielsen
- Center for Genomic Medicine at Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | | | - Aaron Norman
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Kenneth Offit
- Clinical Genetics Research Laboratory, Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Edith Olah
- Department of Molecular Genetics, National Institute of Oncology, Budapest, Hungary
| | | | - Håkan Olsson
- Department of Cancer Epidemiology, Clinical Sciences, Lund University, Lund, Sweden
| | - Nick Orr
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK
| | - Ana Osorio
- Centro de Investigación en Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain
- Human Cancer Genetics Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - V Shane Pankratz
- University of New Mexico Health Sciences Center, University of New Mexico, Albuquerque, NM, USA
| | - Janos Papp
- Department of Molecular Genetics, National Institute of Oncology, Budapest, Hungary
| | - Sue K Park
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, Korea
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul, Korea
- Cancer Research Institute, Seoul National University, Seoul, Korea
| | | | - Michael T Parsons
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - James Paul
- Cancer Research UK Clinical Trials Unit, Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Inge Sokilde Pedersen
- Molecular Diagnostics, Aalborg University Hospital, Aalborg, Denmark
- Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, Denmark
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
| | - Bernard Peissel
- Unit of Medical Genetics, Department of Medical Oncology and Hematology, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milan, Italy
| | - Beth Peshkin
- Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA
| | - Paolo Peterlongo
- Genome Diagnostics Program, IFOM-the FIRC (Italian Foundation for Cancer Research) Institute of Molecular Oncology, Milan, Italy
| | - Julian Peto
- Department of Non-Communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
| | - Dijana Plaseska-Karanfilska
- Research Centre for Genetic Engineering and Biotechnology 'Georgi D. Efremov', Macedonian Academy of Sciences and Arts, Skopje, Republic of North Macedonia
| | - Karolina Prajzendanc
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Ross Prentice
- Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Nadege Presneau
- School of Life Sciences, University of Westminster, London, UK
| | - Darya Prokofyeva
- Department of Genetics and Fundamental Medicine, Bashkir State Medical University, Ufa, Russia
| | - Miquel Angel Pujana
- ProCURE, Catalan Institute of Oncology, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain
| | - Katri Pylkäs
- Laboratory of Cancer Genetics and Tumor Biology, Cancer and Translational Medicine Research Unit, Biocenter Oulu, University of Oulu, Oulu, Finland
- Laboratory of Cancer Genetics and Tumor Biology, Northern Finland Laboratory Centre Oulu, Oulu, Finland
| | - Paolo Radice
- Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori (INT), Milan, Italy
| | - Susan J Ramus
- School of Women's and Children's Health, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | | | - Rohini Rau-Murthy
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Gad Rennert
- Clalit National Israeli Cancer Control Center, Carmel Medical Center and Technion Faculty of Medicine, Haifa, Israel
| | - Harvey A Risch
- Chronic Disease Epidemiology, Yale School of Public Health, New Haven, CT, USA
| | - Mark Robson
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Atocha Romero
- Medical Oncology Department, Hospital Universitario Puerta de Hierro, Madrid, Spain
| | - Maria Rossing
- Center for Genomic Medicine at Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | | | | | - Dale P Sandler
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Marta Santamariña
- Centro de Investigación en Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain
- Fundación Pública Galega de Medicina Xenómica, Santiago de Compostela, Spain
- Instituto de Investigación Sanitaria de Santiago de Compostela, Santiago de Compostela, Spain
| | - Christobel Saunders
- School of Medicine, University of Western Australia, Perth, Western Australia, Australia
| | - Elinor J Sawyer
- Research Oncology, Guy's Hospital, King's College London, London, UK
| | - Maren T Scheuner
- Cancer Genetics and Prevention Program, University of California, San Francisco, San Francisco, CA, USA
| | - Daniel F Schmidt
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
- Faculty of Information Technology, Monash University, Melbourne, Victoria, Australia
| | - Rita K Schmutzler
- Center for Hereditary Breast and Ovarian Cancer, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Center for Integrated Oncology (CIO), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Andreas Schneeweiss
- Molecular Biology of Breast Cancer, University Womens Clinic Heidelberg, University of Heidelberg, Heidelberg, Germany
- National Center for Tumor Diseases, University Hospital and German Cancer Research Center, Heidelberg, Germany
| | - Minouk J Schoemaker
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Ben Schöttker
- Division of Clinical Epidemiology and Aging Research (C070), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Network Aging Research, University of Heidelberg, Heidelberg, Germany
| | - Peter Schürmann
- Gynaecology Research Unit, Hannover Medical School, Hannover, Germany
| | - Christopher Scott
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Rodney J Scott
- Division of Molecular Medicine, Pathology North, John Hunter Hospital, Newcastle, New South Wales, Australia
- Discipline of Medical Genetics, School of Biomedical Sciences and Pharmacy, Faculty of Health, University of Newcastle, Newcastle, New South Wales, Australia
- Hunter Medical Research Institute, John Hunter Hospital, Newcastle, New South Wales, Australia
| | - Leigha Senter
- Clinical Cancer Genetics Program, Division of Human Genetics, Department of Internal Medicine, The Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Caroline M Seynaeve
- Department of Medical Oncology, Family Cancer Clinic, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Mitul Shah
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Priyanka Sharma
- Department of Internal Medicine, Division of Medical Oncology, University of Kansas Medical Center, Westwood, KS, USA
| | - Chen-Yang Shen
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
- School of Public Health, China Medical University, Taichung, Taiwan
| | - Xiao-Ou Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Christian F Singer
- Department of Obstetrics and Gynecology and Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | | | - Snezhana Smichkoska
- University Clinic of Radiotherapy and Oncology, Medical Faculty, Ss. Cyril and Methodius University in Skopje, Skopje, Republic of North Macedonia
| | - Melissa C Southey
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Melbourne, Victoria, Australia
- Department of Clinical Pathology, The University of Melbourne, Melbourne, Victoria, Australia
| | - John J Spinelli
- Population Oncology, BC Cancer, Vancouver, British Columbia, Canada
- School of Population and Public Health, University of British Columbia, Vancouver, British Columbia, Canada
| | - Amanda B Spurdle
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Jennifer Stone
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
- The Curtin UWA Centre for Genetic Origins of Health and Disease, Curtin University and University of Western Australia, Perth, Western Australia, Australia
| | - Dominique Stoppa-Lyonnet
- Department of Tumour Biology, INSERM U830, Paris, France
- Service de Génétique, Institut Curie, Paris, France
- Université Paris Descartes, Paris, France
| | - Christian Sutter
- Institute of Human Genetics, University Hospital Heidelberg, Heidelberg, Germany
| | - Anthony J Swerdlow
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
- Division of Breast Cancer Research, The Institute of Cancer Research, London, UK
| | - Rulla M Tamimi
- Program in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Yen Yen Tan
- Department of Obstetrics and Gynecology, Medical University of Vienna, Vienna, Austria
| | | | - Jack A Taylor
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
- Epigenetic and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Manuel R Teixeira
- Department of Genetics, Portuguese Oncology Institute, Porto, Portugal
- Biomedical Sciences Institute (ICBAS), University of Porto, Porto, Portugal
| | - Maria Tengström
- Translational Cancer Research Area, University of Eastern Finland, Kuopio, Finland
- Cancer Center, Kuopio University Hospital, Kuopio, Finland
- Institute of Clinical Medicine, Oncology, University of Eastern Finland, Kuopio, Finland
| | - Soo Hwang Teo
- Breast Cancer Research Programme, Cancer Research Malaysia, Kuala Lumpur, Malaysia
- Department of Surgery, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Mary Beth Terry
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Alex Teulé
- Hereditary Cancer Program, ONCOBELL-IDIBELL-IDIBGI-IGTP, Catalan Institute of Oncology, CIBERONC, Barcelona, Spain
| | - Mads Thomassen
- Department of Clinical Genetics, Odense University Hospital, Odence, Denmark
| | - Darcy L Thull
- Department of Medicine, Magee-Womens Hospital, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Marc Tischkowitz
- Program in Cancer Genetics, Departments of Human Genetics and Oncology, McGill University, Montréal, Québec, Canada
- Department of Medical Genetics, University of Cambridge, Cambridge, UK
| | - Amanda E Toland
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, USA
| | - Rob A E M Tollenaar
- Department of Surgery, Leiden University Medical Center, Leiden, the Netherlands
| | - Ian Tomlinson
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
- Wellcome Trust Centre for Human Genetics and NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Diana Torres
- Institute of Human Genetics, Pontificia Universidad Javeriana, Bogota, Colombia
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Gabriela Torres-Mejía
- Center for Population Health Research, National Institute of Public Health, Cuernavaca, Mexico
| | - Melissa A Troester
- Department of Epidemiology, Gillings School of Global Public Health and UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Thérèse Truong
- Cancer and Environment Group, Center for Research in Epidemiology and Population Health (CESP), INSERM, University Paris-Sud, University Paris-Saclay, Paris, France
| | - Nadine Tung
- Department of Medical Oncology, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Maria Tzardi
- Department of Pathology, University Hospital of Heraklion, Heraklion, Greece
| | | | - Celine M Vachon
- Department of Health Science Research, Division of Epidemiology, Mayo Clinic, Rochester, MN, USA
| | - Christi J van Asperen
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Lizet E van der Kolk
- Family Cancer Clinic, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
| | | | - Ana Vega
- Fundación Pública Galega de Medicina Xenómica-SERGAS, Grupo de Medicina Xenómica-USC, CIBERER, IDIS, Santiago de Compostela, Spain
| | - Alessandra Viel
- Division of Functional Onco-genomics and Genetics, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, Aviano, Italy
| | - Joseph Vijai
- Clinical Genetics Research Laboratory, Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Maartje J Vogel
- Family Cancer Clinic, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
| | - Qin Wang
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Barbara Wappenschmidt
- Center for Hereditary Breast and Ovarian Cancer, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Center for Integrated Oncology (CIO), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Clarice R Weinberg
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, USA
| | | | - Camilla Wendt
- Department of Clinical Science and Education, Södersjukhuset, Karolinska Institutet, Stockholm, Sweden
| | - Hans Wildiers
- Leuven Multidisciplinary Breast Center, Department of Oncology, Leuven Cancer Institute, University Hospitals Leuven, Leuven, Belgium
| | - Robert Winqvist
- Laboratory of Cancer Genetics and Tumor Biology, Cancer and Translational Medicine Research Unit, Biocenter Oulu, University of Oulu, Oulu, Finland
- Laboratory of Cancer Genetics and Tumor Biology, Northern Finland Laboratory Centre Oulu, Oulu, Finland
| | - Alicja Wolk
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Anna H Wu
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Drakoulis Yannoukakos
- Molecular Diagnostics Laboratory, INRASTES, National Centre for Scientific Research 'Demokritos', Athens, Greece
| | - Yan Zhang
- Division of Clinical Epidemiology and Aging Research (C070), German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - David Hunter
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Paul D P Pharoah
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Cancer Epidemiology Group, University Cancer Center Hamburg (UCCH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Montserrat García-Closas
- Division of Cancer Epidemiology and Genetics, Department of Health and Human Services, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | - Marjanka K Schmidt
- Division of Molecular Pathology, Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
- Division of Psychosocial Research and Epidemiology, The Netherlands Cancer Institute-Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
| | - Roger L Milne
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Melbourne, Victoria, Australia
| | - Vessela N Kristensen
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital-Radiumhospitalet, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- The Hereditary Breast and Ovarian Cancer Research Group Netherlands (HEBON) Coordinating Center, The Netherlands Cancer Institute, Amsterdam, the Netherlands
- Australian Breast Cancer Tissue Bank, Westmead Institute for Medical Research, University of Sydney, Sydney, New South Wales, Australia
| | - Juliet D French
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Stacey L Edwards
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Antonis C Antoniou
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Georgia Chenevix-Trench
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Jacques Simard
- Genomics Center, Centre Hospitalier Universitaire de Québec, Université Laval Research Center, Québec City, Québec, Canada
| | - Douglas F Easton
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Peter Kraft
- Program in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
| | - Alison M Dunning
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK.
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Piggin CL, Roden DL, Law AMK, Molloy MP, Krisp C, Swarbrick A, Naylor MJ, Kalyuga M, Kaplan W, Oakes SR, Gallego-Ortega D, Clark SJ, Carroll JS, Bartonicek N, Ormandy CJ. ELF5 modulates the estrogen receptor cistrome in breast cancer. PLoS Genet 2020; 16:e1008531. [PMID: 31895944 PMCID: PMC6959601 DOI: 10.1371/journal.pgen.1008531] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 01/14/2020] [Accepted: 11/20/2019] [Indexed: 11/28/2022] Open
Abstract
Acquired resistance to endocrine therapy is responsible for half of the therapeutic failures in the treatment of breast cancer. Recent findings have implicated increased expression of the ETS transcription factor ELF5 as a potential modulator of estrogen action and driver of endocrine resistance, and here we provide the first insight into the mechanisms by which ELF5 modulates estrogen sensitivity. Using chromatin immunoprecipitation sequencing we found that ELF5 binding overlapped with FOXA1 and ER at super enhancers, enhancers and promoters, and when elevated, caused FOXA1 and ER to bind to new regions of the genome, in a pattern that replicated the alterations to the ER/FOXA1 cistrome caused by the acquisition of resistance to endocrine therapy. RNA sequencing demonstrated that these changes altered estrogen-driven patterns of gene expression, the expression of ER transcription-complex members, and 6 genes known to be involved in driving the acquisition of endocrine resistance. Using rapid immunoprecipitation mass spectrometry of endogenous proteins, and proximity ligation assays, we found that ELF5 interacted physically with members of the ER transcription complex, such as DNA-PKcs. We found 2 cases of endocrine-resistant brain metastases where ELF5 levels were greatly increased and ELF5 patterns of gene expression were enriched, compared to the matched primary tumour. Thus ELF5 alters ER-driven gene expression by modulating the ER/FOXA1 cistrome, by interacting with it, and by modulating the expression of members of the ER transcriptional complex, providing multiple mechanisms by which ELF5 can drive endocrine resistance.
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Affiliation(s)
- Catherine L. Piggin
- Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Victoria Street Darlinghurst Sydney, NSW, Australia
- St Vincent’s Clinical School, Faculty of Medicine, UNSW Sydney, Australia
| | - Daniel L. Roden
- Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Victoria Street Darlinghurst Sydney, NSW, Australia
- St Vincent’s Clinical School, Faculty of Medicine, UNSW Sydney, Australia
| | - Andrew M. K. Law
- Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Victoria Street Darlinghurst Sydney, NSW, Australia
- St Vincent’s Clinical School, Faculty of Medicine, UNSW Sydney, Australia
| | - Mark P. Molloy
- Australian Proteome Analysis Facility, Macquarie University, Sydney, Australia
| | - Christoph Krisp
- Australian Proteome Analysis Facility, Macquarie University, Sydney, Australia
| | - Alexander Swarbrick
- Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Victoria Street Darlinghurst Sydney, NSW, Australia
- St Vincent’s Clinical School, Faculty of Medicine, UNSW Sydney, Australia
| | - Matthew J. Naylor
- Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Victoria Street Darlinghurst Sydney, NSW, Australia
- St Vincent’s Clinical School, Faculty of Medicine, UNSW Sydney, Australia
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, Australia
| | - Maria Kalyuga
- Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Victoria Street Darlinghurst Sydney, NSW, Australia
- St Vincent’s Clinical School, Faculty of Medicine, UNSW Sydney, Australia
| | - Warren Kaplan
- Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Victoria Street Darlinghurst Sydney, NSW, Australia
- St Vincent’s Clinical School, Faculty of Medicine, UNSW Sydney, Australia
| | - Samantha R. Oakes
- Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Victoria Street Darlinghurst Sydney, NSW, Australia
- St Vincent’s Clinical School, Faculty of Medicine, UNSW Sydney, Australia
| | - David Gallego-Ortega
- Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Victoria Street Darlinghurst Sydney, NSW, Australia
- St Vincent’s Clinical School, Faculty of Medicine, UNSW Sydney, Australia
| | - Susan J. Clark
- Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Victoria Street Darlinghurst Sydney, NSW, Australia
- St Vincent’s Clinical School, Faculty of Medicine, UNSW Sydney, Australia
| | - Jason S. Carroll
- Cancer Research UK Cambridge Research Institute, Li Ka Shing Centre Robinson Way, Cambridge, United Kingdom
| | - Nenad Bartonicek
- Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Victoria Street Darlinghurst Sydney, NSW, Australia
- St Vincent’s Clinical School, Faculty of Medicine, UNSW Sydney, Australia
| | - Christopher J. Ormandy
- Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Victoria Street Darlinghurst Sydney, NSW, Australia
- St Vincent’s Clinical School, Faculty of Medicine, UNSW Sydney, Australia
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Tarbell ED, Liu T. HMMRATAC: a Hidden Markov ModeleR for ATAC-seq. Nucleic Acids Res 2019; 47:e91. [PMID: 31199868 PMCID: PMC6895260 DOI: 10.1093/nar/gkz533] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 05/23/2019] [Accepted: 06/04/2019] [Indexed: 12/12/2022] Open
Abstract
ATAC-seq has been widely adopted to identify accessible chromatin regions across the genome. However, current data analysis still utilizes approaches initially designed for ChIP-seq or DNase-seq, without considering the transposase digested DNA fragments that contain additional nucleosome positioning information. We present the first dedicated ATAC-seq analysis tool, a semi-supervised machine learning approach named HMMRATAC. HMMRATAC splits a single ATAC-seq dataset into nucleosome-free and nucleosome-enriched signals, learns the unique chromatin structure around accessible regions, and then predicts accessible regions across the entire genome. We show that HMMRATAC outperforms the popular peak-calling algorithms on published human ATAC-seq datasets. We find that single-end sequenced or size-selected ATAC-seq datasets result in a loss of sensitivity compared to paired-end datasets without size-selection.
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Affiliation(s)
- Evan D Tarbell
- Department of Biochemistry, University at Buffalo, Buffalo, NY 14203, USA.,Enhanced Pharmacodynamics LLC, Buffalo, NY 14203, USA
| | - Tao Liu
- Department of Biochemistry, University at Buffalo, Buffalo, NY 14203, USA.,Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
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Campbell MJ. Tales from topographic oceans: topologically associated domains and cancer. Endocr Relat Cancer 2019; 26:R611-R626. [PMID: 31505466 PMCID: PMC7664306 DOI: 10.1530/erc-19-0348] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 09/09/2019] [Indexed: 01/03/2023]
Abstract
The 3D organization of the genome within the cell nucleus has come into sharp focus over the last decade. This has largely arisen because of the application of genomic approaches that have revealed numerous levels of genomic and chromatin interactions, including topologically associated domains (TADs). The current review examines how these domains were identified, are organized, how their boundaries arise and are regulated, and how genes within TADs are coordinately regulated. There are many examples of the disruption to TAD structure in cancer and the altered regulation, structure and function of TADs are discussed in the context of hormone responsive cancers, including breast, prostate and ovarian cancer. Finally, some aspects of the statistical insight and computational skills required to interrogate TAD organization are considered and future directions discussed.
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Affiliation(s)
- Moray J Campbell
- Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, Ohio, USA
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Scalea S, Maresca C, Catalanotto C, Marino R, Cogoni C, Reale A, Zampieri M, Zardo G. Modifications of H3K4 methylation levels are associated with DNA hypermethylation in acute myeloid leukemia. FEBS J 2019; 287:1155-1175. [PMID: 31599112 DOI: 10.1111/febs.15086] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 08/02/2019] [Accepted: 10/06/2019] [Indexed: 01/07/2023]
Abstract
The 'instructive model' of aberrant DNA methylation in human tumors is based on the observation that CpG islands prone to hypermethylation in cancers are embedded in chromatin enriched in H3K27me3 in human embryonic stem cells (hESC). Recent studies also link methylation of CpG islands to the methylation status of H3K4, where H3K4me3 is inversely correlated with DNA methylation. To provide insight into these conflicting findings, we generated DNA methylation profiles for acute myeloid leukemia samples from patients and leukemic cell lines and integrated them with publicly available ChIp-seq data, containing H3K4me3 and H3K27me3 CpG island occupation in hESC, or hematopoietic stem or progenitor cells (hHSC/MPP). Hypermethylated CpG islands in AML samples displayed H3K27me3 enrichments in hESC and hHSC/MPP; however, ChIp analysis of specific hypermethylated CpG islands revealed a significant reduction in H3K4me3 signal with a concomitant increase in H3K4me0 levels as opposed to a nonsignificant increase in H3K27me3 marks. The integration of AML DNA methylation profiles with the ChIp-seq data in hESC and hHSC/MPP also led to the identification of Iroquois homeobox 2 (IRX2) as a previously unknown factor promoting differentiation of leukemic cells. Our results indicate that in contrast to the 'instructive model', H3K4me3 levels are strongly associated with DNA methylation patterns in AML and have a role in the regulation of critical genes, such as the putative tumor suppressor IRX2.
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Affiliation(s)
- Stefania Scalea
- Department of Experimental Medicine, University of Rome, Sapienza, Italy
| | - Carmen Maresca
- Oncogenomic and Epigenetic Unit, Regina Elena National Cancer Institute, Rome, Italy
| | | | - Rachele Marino
- Department of Molecular Medicine, University of Rome, Sapienza, Italy
| | - Carlo Cogoni
- Department of Molecular Medicine, University of Rome, Sapienza, Italy
| | - Anna Reale
- Department of Experimental Medicine, University of Rome, Sapienza, Italy
| | - Michele Zampieri
- Department of Experimental Medicine, University of Rome, Sapienza, Italy
| | - Giuseppe Zardo
- Department of Experimental Medicine, University of Rome, Sapienza, Italy
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Hadad N, Masser DR, Blanco-Berdugo L, Stanford DR, Freeman WM. Early-life DNA methylation profiles are indicative of age-related transcriptome changes. Epigenetics Chromatin 2019; 12:58. [PMID: 31594536 PMCID: PMC6781367 DOI: 10.1186/s13072-019-0306-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Accepted: 09/14/2019] [Indexed: 12/15/2022] Open
Abstract
Background Alterations to cellular and molecular programs with brain aging result in cognitive impairment and susceptibility to neurodegenerative disease. Changes in DNA methylation patterns, an epigenetic modification required for various CNS functions are observed with brain aging and can be prevented by anti-aging interventions, but the relationship of altered methylation to gene expression is poorly understood. Results Paired analysis of the hippocampal methylome and transcriptome with aging of male and female mice demonstrates that age-related differences in methylation and gene expression are anti-correlated within gene bodies and enhancers. Altered promoter methylation with aging was found to be generally un-related to altered gene expression. A more striking relationship was found between methylation levels at young age and differential gene expression with aging. Highly methylated gene bodies and promoters in early life were associated with age-related increases in gene expression even in the absence of significant methylation changes with aging. As well, low levels of methylation in early life were correlated to decreased expression with aging. This relationship was also observed in genes altered in two mouse Alzheimer’s models. Conclusion DNA methylation patterns established in youth, in combination with other epigenetic marks, were able to accurately predict changes in transcript trajectories with aging. These findings are consistent with the developmental origins of disease hypothesis and indicate that epigenetic variability in early life may explain differences in aging trajectories and age-related disease.
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Affiliation(s)
- Niran Hadad
- Oklahoma Center for Neuroscience, Oklahoma City, OK, USA.,Reynolds Oklahoma Center on Aging, SLY-BRC 1370, 975 NE 10th St, Oklahoma City, OK, 73104, USA.,The Jackson Laboratory, Bar Harbor, ME, 04609, USA
| | - Dustin R Masser
- Reynolds Oklahoma Center on Aging, SLY-BRC 1370, 975 NE 10th St, Oklahoma City, OK, 73104, USA.,Department of Physiology, Oklahoma City, OK, USA
| | | | - David R Stanford
- Reynolds Oklahoma Center on Aging, SLY-BRC 1370, 975 NE 10th St, Oklahoma City, OK, 73104, USA.,Department of Physiology, Oklahoma City, OK, USA.,Oklahoma Nathan Shock Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Willard M Freeman
- Oklahoma Center for Neuroscience, Oklahoma City, OK, USA. .,Reynolds Oklahoma Center on Aging, SLY-BRC 1370, 975 NE 10th St, Oklahoma City, OK, 73104, USA. .,Department of Physiology, Oklahoma City, OK, USA. .,Oklahoma Nathan Shock Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA. .,Oklahoma City VA Medical Center, Oklahoma City, OK, 73104, USA.
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41
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Houlahan KE, Shiah YJ, Gusev A, Yuan J, Ahmed M, Shetty A, Ramanand SG, Yao CQ, Bell C, O'Connor E, Huang V, Fraser M, Heisler LE, Livingstone J, Yamaguchi TN, Rouette A, Foucal A, Espiritu SMG, Sinha A, Sam M, Timms L, Johns J, Wong A, Murison A, Orain M, Picard V, Hovington H, Bergeron A, Lacombe L, Lupien M, Fradet Y, Têtu B, McPherson JD, Pasaniuc B, Kislinger T, Chua MLK, Pomerantz MM, van der Kwast T, Freedman ML, Mani RS, He HH, Bristow RG, Boutros PC. Genome-wide germline correlates of the epigenetic landscape of prostate cancer. Nat Med 2019; 25:1615-1626. [PMID: 31591588 PMCID: PMC7418214 DOI: 10.1038/s41591-019-0579-z] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 08/13/2019] [Indexed: 12/16/2022]
Abstract
Oncogenesis is driven by germline, environmental and stochastic factors. It is unknown how these interact to produce the molecular phenotypes of tumors. We therefore quantified the influence of germline polymorphisms on the somatic epigenome of 589 localized prostate tumors. Predisposition risk loci influence a tumor's epigenome, uncovering a mechanism for cancer susceptibility. We identified and validated 1,178 loci associated with altered methylation in tumoral but not nonmalignant tissue. These tumor methylation quantitative trait loci influence chromatin structure, as well as RNA and protein abundance. One prominent tumor methylation quantitative trait locus is associated with AKT1 expression and is predictive of relapse after definitive local therapy in both discovery and validation cohorts. These data reveal intricate crosstalk between the germ line and the epigenome of primary tumors, which may help identify germline biomarkers of aggressive disease to aid patient triage and optimize the use of more invasive or expensive diagnostic assays.
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Affiliation(s)
- Kathleen E Houlahan
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Vector Institute, Toronto, Ontario, Canada
| | - Yu-Jia Shiah
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Alexander Gusev
- Division of Population Sciences, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Jiapei Yuan
- Department of Pathology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Musaddeque Ahmed
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Anamay Shetty
- Division of Population Sciences, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- University of Cambridge, Cambridge, UK
| | - Susmita G Ramanand
- Department of Pathology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Cindy Q Yao
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Connor Bell
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Edward O'Connor
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Vincent Huang
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Michael Fraser
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | | | | | | | | | - Adrien Foucal
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | | | - Ankit Sinha
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Michelle Sam
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Lee Timms
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Jeremy Johns
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Ada Wong
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Alex Murison
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Michèle Orain
- Department of Pathology, Centre de recheche du CHU de Québec-Université Laval, Québec City, Québec, Canada
| | - Valérie Picard
- Division of Urology, Centre de recheche du CHU de Québec-Université Laval, Québec City, Québec, Canada
| | - Hélène Hovington
- Division of Urology, Centre de recheche du CHU de Québec-Université Laval, Québec City, Québec, Canada
| | - Alain Bergeron
- Division of Urology, Centre de recheche du CHU de Québec-Université Laval, Québec City, Québec, Canada
| | - Louis Lacombe
- Division of Urology, Centre de recheche du CHU de Québec-Université Laval, Québec City, Québec, Canada
| | - Mathieu Lupien
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Yves Fradet
- Division of Urology, Centre de recheche du CHU de Québec-Université Laval, Québec City, Québec, Canada
| | - Bernard Têtu
- Department of Pathology, Centre de recheche du CHU de Québec-Université Laval, Québec City, Québec, Canada
| | | | - Bogdan Pasaniuc
- Department of Computational Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Thomas Kislinger
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Melvin L K Chua
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Division of Radiation Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Mark M Pomerantz
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Theodorus van der Kwast
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Laboratory Medicine Program, University Health Network, Toronto, Ontario, Canada
| | - Matthew L Freedman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- The Eli and Edythe L. Broad Institute, Cambridge, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Ram S Mani
- Department of Pathology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Housheng H He
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Robert G Bristow
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.
- Department of Radiation Oncology, University of Toronto, Toronto, Ontario, Canada.
- Division of Cancer Sciences, Faculty of Biology, Health and Medicine, University of Manchester, Manchester, UK.
- The Christie NHS Foundation Trust, Manchester, UK.
- Cancer Research UK Manchester Institute, Manchester, UK.
- Manchester Cancer Research Centre, Manchester, UK.
| | - Paul C Boutros
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada.
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.
- Vector Institute, Toronto, Ontario, Canada.
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA.
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, Canada.
- Department of Urology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.
- Institute for Precision Health, University of California, Los Angeles, Los Angeles, CA, USA.
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ZCMM: A Novel Method Using Z-Curve Theory- Based and Position Weight Matrix for Predicting Nucleosome Positioning. Genes (Basel) 2019; 10:genes10100765. [PMID: 31569414 PMCID: PMC6827144 DOI: 10.3390/genes10100765] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Revised: 09/25/2019] [Accepted: 09/26/2019] [Indexed: 02/04/2023] Open
Abstract
Nucleosomes are the basic units of eukaryotes. The accurate positioning of nucleosomes plays a significant role in understanding many biological processes such as transcriptional regulation mechanisms and DNA replication and repair. Here, we describe the development of a novel method, termed ZCMM, based on Z-curve theory and position weight matrix (PWM). The ZCMM was trained and tested using the nucleosomal and linker sequences determined by support vector machine (SVM) in Saccharomyces cerevisiae (S. cerevisiae), and experimental results showed that the sensitivity (Sn), specificity (Sp), accuracy (Acc), and Matthews correlation coefficient (MCC) values for ZCMM were 91.40%, 96.56%, 96.75%, and 0.88, respectively, and the average area under the receiver operating characteristic curve (AUC) value was 0.972. A ZCMM predictor was developed to predict nucleosome positioning in Homo sapiens (H. sapiens), Caenorhabditis elegans (C. elegans), and Drosophila melanogaster (D. melanogaster) genomes, and the accuracy (Acc) values were 77.72%, 85.34%, and 93.62%, respectively. The maximum AUC values of the four species were 0.982, 0.861, 0.912 and 0.911, respectively. Another independent dataset for S. cerevisiae was used to predict nucleosome positioning. Compared with the results of Wu's method, it was found that the Sn, Sp, Acc, and MCC of ZCMM results for S. cerevisiae were all higher, reaching 96.72%, 96.54%, 94.10%, and 0.88. Compared with the Guo's method 'iNuc-PseKNC', the results of ZCMM for D. melanogaster were better. Meanwhile, the ZCMM was compared with some experimental data in vitro and in vivo for S. cerevisiae, and the results showed that the nucleosomes predicted by ZCMM were highly consistent with those confirmed by these experiments. Therefore, it was further confirmed that the ZCMM method has good accuracy and reliability in predicting nucleosome positioning.
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Ordoñez R, Martínez-Calle N, Agirre X, Prosper F. DNA Methylation of Enhancer Elements in Myeloid Neoplasms: Think Outside the Promoters? Cancers (Basel) 2019; 11:cancers11101424. [PMID: 31554341 PMCID: PMC6827153 DOI: 10.3390/cancers11101424] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 09/15/2019] [Accepted: 09/18/2019] [Indexed: 12/19/2022] Open
Abstract
Gene regulation through DNA methylation is a well described phenomenon that has a prominent role in physiological and pathological cell-states. This epigenetic modification is usually grouped in regions denominated CpG islands, which frequently co-localize with gene promoters, silencing the transcription of those genes. Recent genome-wide DNA methylation studies have challenged this paradigm, demonstrating that DNA methylation of regulatory regions outside promoters is able to influence cell-type specific gene expression programs under physiologic or pathologic conditions. Coupling genome-wide DNA methylation assays with histone mark annotation has allowed for the identification of specific epigenomic changes that affect enhancer regulatory regions, revealing an additional layer of complexity to the epigenetic regulation of gene expression. In this review, we summarize the novel evidence for the molecular and biological regulation of DNA methylation in enhancer regions and the dynamism of these changes contributing to the fine-tuning of gene expression. We also analyze the contribution of enhancer DNA methylation on the expression of relevant genes in acute myeloid leukemia and chronic myeloproliferative neoplasms. The characterization of the aberrant enhancer DNA methylation provides not only a novel pathogenic mechanism for different tumors but also highlights novel potential therapeutic targets for myeloid derived neoplasms.
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Affiliation(s)
- Raquel Ordoñez
- Área de Hemato-Oncología, Centro de Investigación Médica Aplicada, IDISNA, Universidad de Navarra, Avenida Pío XII-55, 31008 Pamplona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain
| | - Nicolás Martínez-Calle
- Área de Hemato-Oncología, Centro de Investigación Médica Aplicada, IDISNA, Universidad de Navarra, Avenida Pío XII-55, 31008 Pamplona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain
| | - Xabier Agirre
- Área de Hemato-Oncología, Centro de Investigación Médica Aplicada, IDISNA, Universidad de Navarra, Avenida Pío XII-55, 31008 Pamplona, Spain.
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain.
| | - Felipe Prosper
- Área de Hemato-Oncología, Centro de Investigación Médica Aplicada, IDISNA, Universidad de Navarra, Avenida Pío XII-55, 31008 Pamplona, Spain.
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain.
- Departamento de Hematología, Clínica Universidad de Navarra, Universidad de Navarra, Avenida Pío XII-36, 31008 Pamplona, Spain.
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Wang Y, Liu Q, Tang F, Yan L, Qiao J. Epigenetic Regulation and Risk Factors During the Development of Human Gametes and Early Embryos. Annu Rev Genomics Hum Genet 2019; 20:21-40. [DOI: 10.1146/annurev-genom-083118-015143] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Drastic epigenetic reprogramming occurs during human gametogenesis and early embryo development. Advances in low-input and single-cell epigenetic techniques have provided powerful tools to dissect the genome-wide dynamics of different epigenetic molecular layers in these processes. In this review, we focus mainly on the most recent progress in understanding the dynamics of DNA methylation, chromatin accessibility, and histone modifications in human gametogenesis and early embryo development. Deficiencies in remodeling of the epigenomes can cause severe developmental defects, infertility, and long-term health issues in offspring. Aspects of the external environment, including assisted reproductive technology procedures, parental diets, and unhealthy parental habits, may disturb the epigenetic reprogramming processes and lead to an aberrant epigenome in the offspring. Here, we review the current knowledge of the potential risk factors of aberrant epigenomes in humans.
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Affiliation(s)
- Yang Wang
- Beijing Advanced Innovation Center for Genomics, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China;, , ,
- Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing 100191, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing 100191, China
| | - Qiang Liu
- Beijing Advanced Innovation Center for Genomics, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China;, , ,
- Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing 100191, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing 100191, China
| | - Fuchou Tang
- Beijing Advanced Innovation Center for Genomics, Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking University, Beijing 100871, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Liying Yan
- Beijing Advanced Innovation Center for Genomics, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China;, , ,
- Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing 100191, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing 100191, China
| | - Jie Qiao
- Beijing Advanced Innovation Center for Genomics, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China;, , ,
- Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing 100191, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing 100191, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
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45
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Su W, Han HH, Wang Y, Zhang B, Zhou B, Cheng Y, Rumandla A, Gurrapu S, Chakraborty G, Su J, Yang G, Liang X, Wang G, Rosen N, Scher HI, Ouerfelli O, Giancotti FG. The Polycomb Repressor Complex 1 Drives Double-Negative Prostate Cancer Metastasis by Coordinating Stemness and Immune Suppression. Cancer Cell 2019; 36:139-155.e10. [PMID: 31327655 PMCID: PMC7210785 DOI: 10.1016/j.ccell.2019.06.009] [Citation(s) in RCA: 126] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 04/28/2019] [Accepted: 06/17/2019] [Indexed: 12/14/2022]
Abstract
The mechanisms that enable immune evasion at metastatic sites are poorly understood. We show that the Polycomb Repressor Complex 1 (PRC1) drives colonization of the bones and visceral organs in double-negative prostate cancer (DNPC). In vivo genetic screening identifies CCL2 as the top prometastatic gene induced by PRC1. CCL2 governs self-renewal and induces the recruitment of M2-like tumor-associated macrophages and regulatory T cells, thus coordinating metastasis initiation with immune suppression and neoangiogenesis. A catalytic inhibitor of PRC1 cooperates with immune checkpoint therapy to reverse these processes and suppress metastasis in genetically engineered mouse transplantation models of DNPC. These results reveal that PRC1 coordinates stemness with immune evasion and neoangiogenesis and point to the potential clinical utility of targeting PRC1 in DNPC.
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MESH Headings
- Adenocarcinoma/drug therapy
- Adenocarcinoma/immunology
- Adenocarcinoma/metabolism
- Adenocarcinoma/secondary
- Animals
- Antineoplastic Agents, Immunological/pharmacology
- Antineoplastic Combined Chemotherapy Protocols/pharmacology
- Cell Movement/drug effects
- Cell Self Renewal/drug effects
- Chemokine CCL2/genetics
- Chemokine CCL2/metabolism
- Enzyme Inhibitors/pharmacology
- Gene Expression Regulation, Neoplastic
- Humans
- Lymphocytes, Tumor-Infiltrating/immunology
- Lymphocytes, Tumor-Infiltrating/metabolism
- Macrophages/immunology
- Macrophages/metabolism
- Male
- Mice, Inbred BALB C
- Mice, Inbred C57BL
- Mice, Inbred NOD
- Mice, Knockout
- Mice, Nude
- Mice, SCID
- Neoplasm Metastasis
- Neoplastic Stem Cells/immunology
- Neoplastic Stem Cells/metabolism
- Neoplastic Stem Cells/pathology
- PC-3 Cells
- Polycomb Repressive Complex 1/antagonists & inhibitors
- Polycomb Repressive Complex 1/genetics
- Polycomb Repressive Complex 1/metabolism
- Prostatic Neoplasms/drug therapy
- Prostatic Neoplasms/immunology
- Prostatic Neoplasms/metabolism
- Prostatic Neoplasms/pathology
- Receptors, Androgen/deficiency
- Receptors, Androgen/genetics
- Receptors, CCR4/genetics
- Receptors, CCR4/metabolism
- Signal Transduction
- T-Lymphocytes, Regulatory/immunology
- T-Lymphocytes, Regulatory/metabolism
- Tumor Escape/drug effects
- Xenograft Model Antitumor Assays
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Affiliation(s)
- Wenjing Su
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center (MSKCC), New York, NY 10065, USA
| | - Hyun Ho Han
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Unit 1906, PO Box 301429, Houston, TX 77054/77030-1429, USA; Department of Urology, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Yan Wang
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Unit 1906, PO Box 301429, Houston, TX 77054/77030-1429, USA
| | - Boyu Zhang
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Unit 1906, PO Box 301429, Houston, TX 77054/77030-1429, USA
| | - Bing Zhou
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yuanming Cheng
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center (MSKCC), New York, NY 10065, USA
| | - Alekya Rumandla
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Unit 1906, PO Box 301429, Houston, TX 77054/77030-1429, USA
| | - Sreeharsha Gurrapu
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Unit 1906, PO Box 301429, Houston, TX 77054/77030-1429, USA
| | - Goutam Chakraborty
- Department of Medicine, Memorial Sloan Kettering Cancer Center (MSKCC), New York, NY 10065, USA
| | - Jie Su
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center (MSKCC), New York, NY 10065, USA
| | - Guangli Yang
- Organic Synthesis Core Facility, Memorial Sloan Kettering Cancer Center (MSKCC), New York, NY 10065, USA
| | - Xin Liang
- Department of Genitourinary Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Guocan Wang
- Department of Genitourinary Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Neal Rosen
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center (MSKCC), New York, NY 10065, USA
| | - Howard I Scher
- Genitourinary Oncology Service, Department of Medicine, MSKCC, Department of Medicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Ouathek Ouerfelli
- Organic Synthesis Core Facility, Memorial Sloan Kettering Cancer Center (MSKCC), New York, NY 10065, USA
| | - Filippo G Giancotti
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Unit 1906, PO Box 301429, Houston, TX 77054/77030-1429, USA; Department of Genitourinary Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA.
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46
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Varizhuk A, Isaakova E, Pozmogova G. DNA G-Quadruplexes (G4s) Modulate Epigenetic (Re)Programming and Chromatin Remodeling: Transient Genomic G4s Assist in the Establishment and Maintenance of Epigenetic Marks, While Persistent G4s May Erase Epigenetic Marks. Bioessays 2019; 41:e1900091. [PMID: 31379012 DOI: 10.1002/bies.201900091] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 07/09/2019] [Indexed: 01/07/2023]
Abstract
Here, the emerging data on DNA G-quadruplexes (G4s) as epigenetic modulators are reviewed and integrated. This concept has appeared and evolved substantially in recent years. First, persistent G4s (e.g., those stabilized by exogenous ligands) were linked to the loss of the histone code. More recently, transient G4s (i.e., those formed upon replication or transcription and unfolded rapidly by helicases) were implicated in CpG island methylation maintenance and de novo CpG methylation control. The most recent data indicate that there are direct interactions between G4s and chromatin remodeling factors. Finally, multiple findings support the indirect participation of G4s in chromatin reshaping via interactions with remodeling-related transcription factors (TFs) or damage responders. Here, the links between the above processes are analyzed; also, how further elucidation of these processes may stimulate the progress of epigenetic therapy is discussed, and the remaining open questions are highlighted.
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Affiliation(s)
- Anna Varizhuk
- Biophysics Department, Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, 119435, Russia
| | - Ekaterina Isaakova
- Biophysics Department, Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, 119435, Russia
| | - Galina Pozmogova
- Biophysics Department, Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, 119435, Russia
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47
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Zhang P, Tillmans LS, Thibodeau SN, Wang L. Single-Nucleotide Polymorphisms Sequencing Identifies Candidate Functional Variants at Prostate Cancer Risk Loci. Genes (Basel) 2019; 10:genes10070547. [PMID: 31323811 PMCID: PMC6678189 DOI: 10.3390/genes10070547] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 07/10/2019] [Accepted: 07/16/2019] [Indexed: 01/22/2023] Open
Abstract
Genome-wide association studies have identified over 150 risk loci that increase prostate cancer risk. However, few causal variants and their regulatory mechanisms have been characterized. In this study, we utilized our previously developed single-nucleotide polymorphisms sequencing (SNPs-seq) technology to test allele-dependent protein binding at 903 SNP sites covering 28 genomic regions. All selected SNPs have shown significant cis-association with at least one nearby gene. After preparing nuclear extract using LNCaP cell line, we first mixed the extract with dsDNA oligo pool for protein–DNA binding incubation. We then performed sequencing analysis on protein-bound oligos. SNPs-seq analysis showed protein-binding differences (>1.5-fold) between reference and variant alleles in 380 (42%) of 903 SNPs with androgen treatment and 403 (45%) of 903 SNPs without treatment. From these significant SNPs, we performed a database search and further narrowed down to 74 promising SNPs. To validate this initial finding, we performed electrophoretic mobility shift assay in two SNPs (rs12246440 and rs7077275) at CTBP2 locus and one SNP (rs113082846) at NCOA4 locus. This analysis showed that all three SNPs demonstrated allele-dependent protein-binding differences that were consistent with the SNPs-seq. Finally, clinical association analysis of the two candidate genes showed that CTBP2 was upregulated, while NCOA4 was downregulated in prostate cancer (p < 0.02). Lower expression of CTBP2 was associated with poor recurrence-free survival in prostate cancer. Utilizing our experimental data along with bioinformatic tools provides a strategy for identifying candidate functional elements at prostate cancer susceptibility loci to help guide subsequent laboratory studies.
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Affiliation(s)
- Peng Zhang
- Department of Pathology, MCW Cancer Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA
| | - Lori S Tillmans
- Department of Laboratory Medicine and Pathology, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, MN 55905, USA
| | - Stephen N Thibodeau
- Department of Laboratory Medicine and Pathology, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, MN 55905, USA
| | - Liang Wang
- Department of Pathology, MCW Cancer Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA.
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48
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Pageaud Y, Plass C, Assenov Y. Enrichment analysis with EpiAnnotator. Bioinformatics 2019; 34:1781-1783. [PMID: 29329372 PMCID: PMC5946894 DOI: 10.1093/bioinformatics/bty007] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 01/09/2018] [Indexed: 12/29/2022] Open
Abstract
Motivation Deciphering relevant biological insights from epigenomic data can be a challenging task. One commonly used approach is to perform enrichment analysis. However, finding, downloading and using the publicly available functional annotations require time, programming skills and IT infrastructure. Here we describe the online tool EpiAnnotator for performing enrichment analyses on epigenomic data in a fast and user-friendly way. Results EpiAnnotator is an R Package accompanied by a web interface. It contains regularly updated annotations from 4 public databases: Blueprint, RoadMap, GENCODE and the UCSC Genome Browser. Annotations are hosted locally or in a server environment and automatically updated by scripts of our own design. Thousands of tracks are available, reflecting data on a variety of tissues, cell types and cell lines from the human and mouse genomes. Users need to upload sets of selected and background regions. Results are displayed in customizable and easily interpretable figures. Availability and implementation The R package and Shiny app are open source and available under the GPL v3 license. EpiAnnotator’s web interface is accessible at http://computational-epigenomics.com/en/epiannotator.
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Affiliation(s)
- Yoann Pageaud
- Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Christoph Plass
- Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Yassen Assenov
- Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.,German Centre for Cardiovascular Research (DZHK), Partner Site Heidelberg/Mannheim, 69120 Heidelberg, Germany
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49
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NOMePlot: analysis of DNA methylation and nucleosome occupancy at the single molecule. Sci Rep 2019; 9:8140. [PMID: 31148571 PMCID: PMC6544651 DOI: 10.1038/s41598-019-44597-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 05/20/2019] [Indexed: 11/15/2022] Open
Abstract
Recent technical advances highlight that to understand mammalian development and human disease we need to consider transcriptional and epigenetic cell-to-cell differences within cell populations. This is particularly important in key areas of biomedicine like stem cell differentiation and intratumor heterogeneity. The recently developed nucleosome occupancy and methylome (NOMe) assay facilitates the simultaneous study of DNA methylation and nucleosome positioning on the same DNA strand. NOMe-treated DNA can be sequenced by sanger (NOMe-PCR) or high throughput approaches (NOMe-seq). NOMe-PCR provides information for a single locus at the single molecule while NOMe-seq delivers genome-wide data that is usually interrogated to obtain population-averaged measures. Here, we have developed a bioinformatic tool that allow us to easily obtain locus-specific information at the single molecule using genome-wide NOMe-seq datasets obtained from bulk populations. We have used NOMePlot to study mouse embryonic stem cells and found that polycomb-repressed bivalent gene promoters coexist in two different epigenetic states, as defined by the nucleosome binding pattern detected around their transcriptional start site.
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50
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Wang R, Wang Y, Zhang X, Zhang Y, Du X, Fang Y, Li G. Hierarchical cooperation of transcription factors from integration analysis of DNA sequences, ChIP-Seq and ChIA-PET data. BMC Genomics 2019; 20:296. [PMID: 32039697 PMCID: PMC7226942 DOI: 10.1186/s12864-019-5535-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Background Chromosomal architecture, which is constituted by chromatin loops, plays an important role in cellular functions. Gene expression and cell identity can be regulated by the chromatin loop, which is formed by proximal or distal enhancers and promoters in linear DNA (1D). Enhancers and promoters are fundamental non-coding elements enriched with transcription factors (TFs) to form chromatin loops. However, the specific cooperation of TFs involved in forming chromatin loops is not fully understood. Results Here, we proposed a method for investigating the cooperation of TFs in four cell lines by the integrative analysis of DNA sequences, ChIP-Seq and ChIA-PET data. Results demonstrate that the interaction of enhancers and promoters is a hierarchical and dynamic complex process with cooperative interactions of different TFs synergistically regulating gene expression and chromatin structure. The TF cooperation involved in maintaining and regulating the chromatin loop of cells can be regulated by epigenetic factors, such as other TFs and DNA methylation. Conclusions Such cooperation among TFs provides the potential features that can affect chromatin’s 3D architecture in cells. The regulation of chromatin 3D organization and gene expression is a complex process associated with the hierarchical and dynamic prosperities of TFs. Electronic supplementary material The online version of this article (10.1186/s12864-019-5535-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ruimin Wang
- Agricultural Bioinformatics Key Laboratory of Hubei Province, Wuhan, 430070, China
| | - Yunlong Wang
- Agricultural Bioinformatics Key Laboratory of Hubei Province, Wuhan, 430070, China
| | - Xueying Zhang
- Agricultural Bioinformatics Key Laboratory of Hubei Province, Wuhan, 430070, China
| | - Yaliang Zhang
- Agricultural Bioinformatics Key Laboratory of Hubei Province, Wuhan, 430070, China
| | - Xiaoyong Du
- Agricultural Bioinformatics Key Laboratory of Hubei Province, Wuhan, 430070, China.,Huazhong Agricultural University, Wuhan, 430070, China
| | - Yaping Fang
- Agricultural Bioinformatics Key Laboratory of Hubei Province, Wuhan, 430070, China. .,Huazhong Agricultural University, Wuhan, 430070, China. .,College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Guoliang Li
- Agricultural Bioinformatics Key Laboratory of Hubei Province, Wuhan, 430070, China. .,Huazhong Agricultural University, Wuhan, 430070, China. .,College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China.
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