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Qu X, Lin Z, Jayawickramarajah J, Alsager JS, Schmidt E, Nephew KP, Fang F, Balasubramanian S, Shan B. G-quadruplex is critical to epigenetic activation of the lncRNA HOTAIR in cancer cells. iScience 2023; 26:108559. [PMID: 38144452 PMCID: PMC10746524 DOI: 10.1016/j.isci.2023.108559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 07/29/2023] [Accepted: 11/20/2023] [Indexed: 12/26/2023] Open
Abstract
The cancer-promoting lncRNA HOTAIR has multiple isoforms. Which isoform of HOTAIR accounts for its expression and functions in cancer is unknown. Unlike HOTAIR's canonical intergenic isoform NR_003716 (HOTAIR-C), the novel isoform NR_047517 (HOTAIR-N) forms an overlapping antisense transcription locus with HOXC11. We identified HOTAIR-N as the dominant isoform that regulates the gene expression programs and networks for cell proliferation, survival, and death in cancer cells. The CpG island in the HOTAIR-N promoter was marked with epigenetic markers for active transcription. We identified a G-quadruplex (G4) motif rich region in the HOTAIR-N CpG island. Our findings indicate that G4s in HOTAIR-N CpG island is critical for expression of HOTAIR-N in cancer cells. Disruption of G4 may represent a novel therapeutic approach for cancer. The transcriptomes regulated by HOTAIR-N and Bloom in cancer cells as provided herein are important resources for the exploration of lncRNA, DNA helicases, and G4 in cancer.
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Affiliation(s)
- Xiaohan Qu
- Department of Thoracic Surgery, The First Hospital of China Medical University, Shenyang, Liaoning 110001, China
| | - Zhen Lin
- Deparmtent of Pathology, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | | | - John S. Alsager
- Department of Biomedical Sciences, Elson S Floyd College of Medicine, Washington State University, Spokane, WA 99202, USA
| | - Emily Schmidt
- Department of Chemistry, Tulane University, New Orleans, LA 70118, USA
| | - Kenneth P. Nephew
- Medical Sciences, Cell and Molecular Cancer Biology Program, Indiana University School of Medicine, Bloomington, IN 47405, USA
| | - Fang Fang
- Medical Sciences, Cell and Molecular Cancer Biology Program, Indiana University School of Medicine, Bloomington, IN 47405, USA
| | - Shankar Balasubramanian
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
- Cancer Research UK, Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK
| | - Bin Shan
- Department of Biomedical Sciences, Elson S Floyd College of Medicine, Washington State University, Spokane, WA 99202, USA
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2
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Li AM, He B, Karagiannis D, Li Y, Jiang H, Srinivasan P, Ramirez Y, Zhou MN, Curtis C, Gruber JJ, Lu C, Rankin EB, Ye J. Serine starvation silences estrogen receptor signaling through histone hypoacetylation. Proc Natl Acad Sci U S A 2023; 120:e2302489120. [PMID: 37695911 PMCID: PMC10515173 DOI: 10.1073/pnas.2302489120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 08/07/2023] [Indexed: 09/13/2023] Open
Abstract
Loss of estrogen receptor (ER) pathway activity promotes breast cancer progression, yet how this occurs remains poorly understood. Here, we show that serine starvation, a metabolic stress often found in breast cancer, represses estrogen receptor alpha (ERα) signaling by reprogramming glucose metabolism and epigenetics. Using isotope tracing and time-resolved metabolomic analyses, we demonstrate that serine is required to maintain glucose flux through glycolysis and the TCA cycle to support acetyl-CoA generation for histone acetylation. Consequently, limiting serine depletes histone H3 lysine 27 acetylation (H3K27ac), particularly at the promoter region of ER pathway genes including the gene encoding ERα, ESR1. Mechanistically, serine starvation impairs acetyl-CoA-dependent gene expression by inhibiting the entry of glycolytic carbon into the TCA cycle and down-regulating the mitochondrial citrate exporter SLC25A1, a critical enzyme in the production of nucleocytosolic acetyl-CoA from glucose. Consistent with this model, total H3K27ac and ERα expression are suppressed by SLC25A1 inhibition and restored by acetate, an alternate source of acetyl-CoA, in serine-free conditions. We thus uncover an unexpected role for serine in sustaining ER signaling through the regulation of acetyl-CoA metabolism.
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Affiliation(s)
- Albert M Li
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305
- Cancer Biology Program, Stanford University School of Medicine, Stanford, CA 94305
| | - Bo He
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305
| | - Dimitris Karagiannis
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032
| | - Yang Li
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305
| | - Haowen Jiang
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305
| | - Preethi Srinivasan
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305
| | - Yaniel Ramirez
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305
| | - Meng-Ning Zhou
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305
| | - Christina Curtis
- Cancer Biology Program, Stanford University School of Medicine, Stanford, CA 94305
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305
| | - Joshua J Gruber
- Department of Internal Medicine, Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75235
| | - Chao Lu
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032
| | - Erinn B Rankin
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305
- Cancer Biology Program, Stanford University School of Medicine, Stanford, CA 94305
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305
| | - Jiangbin Ye
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305
- Cancer Biology Program, Stanford University School of Medicine, Stanford, CA 94305
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305
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3
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Lee BH, Wu Z, Rhie SK. Characterizing chromatin interactions of regulatory elements and nucleosome positions, using Hi-C, Micro-C, and promoter capture Micro-C. Epigenetics Chromatin 2022; 15:41. [PMID: 36544209 PMCID: PMC9768916 DOI: 10.1186/s13072-022-00473-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 12/08/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Regulatory elements such as promoters, enhancers, and insulators interact each other to mediate molecular processes. To capture chromatin interactions of regulatory elements, 3C-derived methods such as Hi-C and Micro-C are developed. Here, we generated and analyzed Hi-C, Micro-C, and promoter capture Micro-C datasets with different sequencing depths to study chromatin interactions of regulatory elements and nucleosome positions in human prostate cancer cells. RESULTS Compared to Hi-C, Micro-C identifies more high-resolution loops, including ones around structural variants. By evaluating the effect of sequencing depth, we revealed that more than 2 billion reads of Micro-C are needed to detect chromatin interactions at 1 kb resolution. Moreover, we found that deep-sequencing identifies additional long-range loops that are longer than 1 Mb in distance. Furthermore, we found that more than 50% of the loops are involved in insulators while less than 10% of the loops are promoter-enhancer loops. To comprehensively capture chromatin interactions that promoters are involved in, we performed promoter capture Micro-C. Promoter capture Micro-C identifies loops near promoters with a lower amount of sequencing reads. Sequencing of 160 million reads of promoter capture Micro-C resulted in reaching a plateau of identifying loops. However, there was still a subset of promoters that are not involved in loops even after deep-sequencing. By integrating Micro-C with NOMe-seq and ChIP-seq, we found that active promoters involved in loops have a more accessible region with lower levels of DNA methylation and more highly phased nucleosomes, compared to active promoters that are not involved in loops. CONCLUSION We determined the required sequencing depth for Micro-C and promoter capture Micro-C to generate high-resolution chromatin interaction maps and loops. We also investigated the effect of sequencing coverage of Hi-C, Micro-C, and promoter capture Micro-C on detecting chromatin loops. Our analyses suggest the presence of distinct regulatory element groups, which are differently involved in nucleosome positions and chromatin interactions. This study does not only provide valuable insights on understanding chromatin interactions of regulatory elements, but also present guidelines for designing research projects on chromatin interactions among regulatory elements.
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Affiliation(s)
- Beoung Hun Lee
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089, USA
| | - Zexun Wu
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089, USA
| | - Suhn K Rhie
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089, USA.
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4
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Prahl JD, Pierce SE, van der Schans EJC, Coetzee GA, Tyson T. The Parkinson's disease variant rs356182 regulates neuronal differentiation independently from alpha-synuclein. Hum Mol Genet 2022; 32:1-14. [PMID: 35866299 PMCID: PMC9837835 DOI: 10.1093/hmg/ddac161] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 06/16/2022] [Accepted: 07/10/2022] [Indexed: 01/25/2023] Open
Abstract
One of the most significant risk variants for Parkinson's disease (PD), rs356182, is located at the PD-associated locus near the alpha-synuclein (α-syn) encoding gene, SNCA. SNCA-proximal variants, including rs356182, are thought to function in PD risk through enhancers via allele-specific regulatory effects on SNCA expression. However, this interpretation discounts the complex activity of genetic enhancers and possible non-conical functions of α-syn. Here we investigated a novel risk mechanism for rs356182. We use CRISPR-Cas9 in LUHMES cells, a model for dopaminergic midbrain neurons, to generate precise hemizygous lesions at rs356182. The PD-protective (A/-), PD-risk (G/-) and wild-type (A/G) clones were neuronally differentiated and then compared transcriptionally and morphologically. Among the affected genes was SNCA, whose expression was promoted by the PD-protective allele (A) and repressed in its absence. In addition to SNCA, hundreds of genes were differentially expressed and associated with neurogenesis and axonogenesis-an effect not typically ascribed to α-syn. We also found that the transcription factor FOXO3 specifically binds to the rs356182 A-allele in differentiated LUHMES cells. Finally, we compared the results from the rs356182-edited cells to our previously published knockouts of SNCA and found only minimal overlap between the sets of significant differentially expressed genes. Together, the data implicate a risk mechanism for rs356182 in which the risk-allele (G) is associated with abnormal neuron development, independent of SNCA expression. We speculate that these pathological effects manifest as a diminished population of dopaminergic neurons during development leading to the predisposition for PD later in life.
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Affiliation(s)
- Jordan D Prahl
- To whom correspondence should be addressed. Tel: +1 6162345793; Fax: +1 6162345001;
| | - Steven E Pierce
- Department of Neurodegenerative Research, Van Andel Institute, 333 Bostwick Ave NE, Grand Rapids MI 49503, USA
| | - Edwin J C van der Schans
- Department of Neurodegenerative Research, Van Andel Institute, 333 Bostwick Ave NE, Grand Rapids MI 49503, USA
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5
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Fang W, Liao C, Shi R, Simon JM, Ptacek TS, Zurlo G, Ye Y, Han L, Fan C, Bao L, Ortiz CL, Lin HR, Manocha U, Luo W, Peng Y, Kim WY, Yang LW, Zhang Q. ZHX2 promotes HIF1α oncogenic signaling in triple-negative breast cancer. eLife 2021; 10:e70412. [PMID: 34779768 PMCID: PMC8673836 DOI: 10.7554/elife.70412] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Accepted: 11/14/2021] [Indexed: 12/24/2022] Open
Abstract
Triple-negative breast cancer (TNBC) is an aggressive and highly lethal disease, which warrants the critical need to identify new therapeutic targets. We show that Zinc Fingers and Homeoboxes 2 (ZHX2) is amplified or overexpressed in TNBC cell lines and patients. Functionally, depletion of ZHX2 inhibited TNBC cell growth and invasion in vitro, orthotopic tumor growth, and spontaneous lung metastasis in vivo. Mechanistically, ZHX2 bound with hypoxia-inducible factor (HIF) family members and positively regulated HIF1α activity in TNBC. Integrated ChIP-seq and gene expression profiling demonstrated that ZHX2 co-occupied with HIF1α on transcriptionally active promoters marked by H3K4me3 and H3K27ac, thereby promoting gene expression. Among the identified ZHX2 and HIF1α coregulated genes, overexpression of AP2B1, COX20, KDM3A, or PTGES3L could partially rescue TNBC cell growth defect by ZHX2 depletion, suggested that these downstream targets contribute to the oncogenic role of ZHX2 in an accumulative fashion. Furthermore, multiple residues (R491, R581, and R674) on ZHX2 are important in regulating its phenotype, which correspond with their roles on controlling ZHX2 transcriptional activity in TNBC cells. These studies establish that ZHX2 activates oncogenic HIF1α signaling, therefore serving as a potential therapeutic target for TNBC.
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Affiliation(s)
- Wentong Fang
- Department of Pharmacy, The First Affiliated Hospital of Nanjing Medical UniversityNanjingChina
- Lineberger Comprehensive Cancer Center, University of North Carolina School of MedicineChapel hillUnited States
| | - Chengheng Liao
- Department of Pathology, University of Texas Southwestern Medical CenterDallasUnited States
| | - Rachel Shi
- Department of Pathology, University of Texas Southwestern Medical CenterDallasUnited States
| | - Jeremy M Simon
- Lineberger Comprehensive Cancer Center, University of North Carolina School of MedicineChapel hillUnited States
- Department of Genetics, Neuroscience Center; University of North Carolina School of MedicineChapel HillUnited States
| | - Travis S Ptacek
- Lineberger Comprehensive Cancer Center, University of North Carolina School of MedicineChapel hillUnited States
- UNC Neuroscience Center, Carolina Institute for Developmental Disabilities, University of North CarolinaChapel HillUnited States
| | - Giada Zurlo
- Department of Pathology, University of Texas Southwestern Medical CenterDallasUnited States
| | - Youqiong Ye
- Shanghai Institute of Immunology, Faculty of Basic Medicine, Shanghai Jiao Tong University School of MedicineShanghaiChina
| | - Leng Han
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston McGovern Medical SchoolHoustonUnited States
| | - Cheng Fan
- Lineberger Comprehensive Cancer Center, University of North Carolina School of MedicineChapel hillUnited States
| | - Lei Bao
- Department of Pathology, University of Texas Southwestern Medical CenterDallasUnited States
| | - Christopher Llynard Ortiz
- Institute of Bioinformatics and Structural Biology, National Tsing Hua UniversityHsinchuTaiwan
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Institute of ChemistryAcademia SinicaTaiwan
- Department of Chemistry, National Tsing-Hua UniversityHsinchuTaiwan
| | - Hong-Rui Lin
- Institute of Bioinformatics and Structural Biology, National Tsing Hua UniversityHsinchuTaiwan
| | - Ujjawal Manocha
- Lineberger Comprehensive Cancer Center, University of North Carolina School of MedicineChapel hillUnited States
| | - Weibo Luo
- Department of Pathology, University of Texas Southwestern Medical CenterDallasUnited States
| | - Yan Peng
- Department of Pathology, University of Texas Southwestern Medical CenterDallasUnited States
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical CenterDallasUnited States
| | - William Y Kim
- Lineberger Comprehensive Cancer Center, University of North Carolina School of MedicineChapel hillUnited States
| | - Lee-Wei Yang
- Institute of Bioinformatics and Structural Biology, National Tsing Hua UniversityHsinchuTaiwan
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Institute of ChemistryAcademia SinicaTaiwan
- Physics Division, National Center for Theoretical SciencesHsinchuTaiwan
| | - Qing Zhang
- Department of Pathology, University of Texas Southwestern Medical CenterDallasUnited States
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6
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Vershinin Z, Feldman M, Werner T, Weil LE, Kublanovsky M, Abaev-Schneiderman E, Sklarz M, Lam EYN, Alasad K, Picaud S, Rotblat B, McAdam RA, Chalifa-Caspi V, Bantscheff M, Chapman T, Lewis HD, Filippakopoulos P, Dawson MA, Grandi P, Prinjha RK, Levy D. BRD4 methylation by the methyltransferase SETD6 regulates selective transcription to control mRNA translation. SCIENCE ADVANCES 2021; 7:7/22/eabf5374. [PMID: 34039605 PMCID: PMC8153730 DOI: 10.1126/sciadv.abf5374] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 04/06/2021] [Indexed: 05/14/2023]
Abstract
The transcriptional coactivator BRD4 has a fundamental role in transcription regulation and thus became a promising epigenetic therapeutic candidate to target diverse pathologies. However, the regulation of BRD4 by posttranslational modifications has been largely unexplored. Here, we show that BRD4 is methylated on chromatin at lysine-99 by the protein lysine methyltransferase SETD6. BRD4 methylation negatively regulates the expression of genes that are involved in translation and inhibits total mRNA translation in cells. Mechanistically, we provide evidence that supports a model where BRD4 methylation by SETD6 does not have a direct role in the association with acetylated histone H4 at chromatin. However, this methylation specifically determines the recruitment of the transcription factor E2F1 to selected target genes that are involved in mRNA translation. Together, our findings reveal a previously unknown molecular mechanism for BRD4 methylation-dependent gene-specific targeting, which may serve as a new direction for the development of therapeutic applications.
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Affiliation(s)
- Zlata Vershinin
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Ben-Gurion University of the Negev, P.O.B. 653, Be'er-Sheva 84105, Israel
- National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, P.O.B. 653, Be'er-Sheva 84105, Israel
| | - Michal Feldman
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Ben-Gurion University of the Negev, P.O.B. 653, Be'er-Sheva 84105, Israel
- National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, P.O.B. 653, Be'er-Sheva 84105, Israel
| | - Thilo Werner
- GSK Cellzome GmbH, Functional Genomics R&D, 69117 Heidelberg, Germany
| | - Lital Estrella Weil
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Ben-Gurion University of the Negev, P.O.B. 653, Be'er-Sheva 84105, Israel
- National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, P.O.B. 653, Be'er-Sheva 84105, Israel
| | - Margarita Kublanovsky
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Ben-Gurion University of the Negev, P.O.B. 653, Be'er-Sheva 84105, Israel
- National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, P.O.B. 653, Be'er-Sheva 84105, Israel
| | - Elina Abaev-Schneiderman
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Ben-Gurion University of the Negev, P.O.B. 653, Be'er-Sheva 84105, Israel
- National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, P.O.B. 653, Be'er-Sheva 84105, Israel
| | - Menachem Sklarz
- National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, P.O.B. 653, Be'er-Sheva 84105, Israel
| | - Enid Y N Lam
- Sir Peter MacCallum Department of Oncology and Centre for Cancer Research, University of Melbourne, Melbourne, Australia
| | - Khawla Alasad
- National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, P.O.B. 653, Be'er-Sheva 84105, Israel
- Department of Life Sciences, Ben-Gurion University of the Negev, Be'er-Sheva 84105, Israel
| | - Sarah Picaud
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7DQ, UK
| | - Barak Rotblat
- National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, P.O.B. 653, Be'er-Sheva 84105, Israel
- Department of Life Sciences, Ben-Gurion University of the Negev, Be'er-Sheva 84105, Israel
| | - Ruth A McAdam
- GSK, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, UK
| | - Vered Chalifa-Caspi
- National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, P.O.B. 653, Be'er-Sheva 84105, Israel
| | - Marcus Bantscheff
- GSK Cellzome GmbH, Functional Genomics R&D, 69117 Heidelberg, Germany
| | - Trevor Chapman
- GSK, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, UK
| | - Huw D Lewis
- GSK, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, UK
| | - Panagis Filippakopoulos
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7DQ, UK
| | - Mark A Dawson
- Sir Peter MacCallum Department of Oncology and Centre for Cancer Research, University of Melbourne, Melbourne, Australia
| | - Paola Grandi
- GSK Cellzome GmbH, Functional Genomics R&D, 69117 Heidelberg, Germany
| | - Rab K Prinjha
- GSK, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, UK
| | - Dan Levy
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Ben-Gurion University of the Negev, P.O.B. 653, Be'er-Sheva 84105, Israel.
- National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, P.O.B. 653, Be'er-Sheva 84105, Israel
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7
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Yi M, Tan Y, Wang L, Cai J, Li X, Zeng Z, Xiong W, Li G, Li X, Tan P, Xiang B. TP63 links chromatin remodeling and enhancer reprogramming to epidermal differentiation and squamous cell carcinoma development. Cell Mol Life Sci 2020; 77:4325-4346. [PMID: 32447427 PMCID: PMC7588389 DOI: 10.1007/s00018-020-03539-2] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 02/21/2020] [Accepted: 04/24/2020] [Indexed: 12/19/2022]
Abstract
Squamous cell carcinoma (SCC) is an aggressive malignancy that can originate from various organs. TP63 is a master regulator that plays an essential role in epidermal differentiation. It is also a lineage-dependent oncogene in SCC. ΔNp63α is the prominent isoform of TP63 expressed in epidermal cells and SCC, and overexpression promotes SCC development through a variety of mechanisms. Recently, ΔNp63α was highlighted to act as an epidermal-specific pioneer factor that binds closed chromatin and enhances chromatin accessibility at epidermal enhancers. ΔNp63α coordinates chromatin-remodeling enzymes to orchestrate the tissue-specific enhancer landscape and three-dimensional high-order architecture of chromatin. Moreover, ΔNp63α establishes squamous-like enhancer landscapes to drive oncogenic target expression during SCC development. Importantly, ΔNp63α acts as an upstream regulator of super enhancers to activate a number of oncogenic transcripts linked to poor prognosis in SCC. Mechanistically, ΔNp63α activates genes transcription through physically interacting with a number of epigenetic modulators to establish enhancers and enhance chromatin accessibility. In contrast, ΔNp63α also represses gene transcription via interacting with repressive epigenetic regulators. ΔNp63α expression is regulated at multiple levels, including transcriptional, post-transcriptional, and post-translational levels. In this review, we summarize recent advances of p63 in epigenomic and transcriptional control, as well as the mechanistic regulation of p63.
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Affiliation(s)
- Mei Yi
- NHC Key Laboratory of Carcinogenesis, Hunan Provincial Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
- Hunan Key Laboratory of Nonresolving Inflammation and Cancer, The Third Xiangya Hospital, Central South University, Changsha, 410013, Hunan, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, 410078, Hunan, China
| | - Yixin Tan
- Department of Dermatology, The Second Xiangya Hospital, The Central South University, Changsha, 410011, Hunan, China
| | - Li Wang
- Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China
| | - Jing Cai
- NHC Key Laboratory of Carcinogenesis, Hunan Provincial Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
- Hunan Key Laboratory of Nonresolving Inflammation and Cancer, The Third Xiangya Hospital, Central South University, Changsha, 410013, Hunan, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, 410078, Hunan, China
| | - Xiaoling Li
- NHC Key Laboratory of Carcinogenesis, Hunan Provincial Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China
- Hunan Key Laboratory of Nonresolving Inflammation and Cancer, The Third Xiangya Hospital, Central South University, Changsha, 410013, Hunan, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, 410078, Hunan, China
| | - Zhaoyang Zeng
- NHC Key Laboratory of Carcinogenesis, Hunan Provincial Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China
- Hunan Key Laboratory of Nonresolving Inflammation and Cancer, The Third Xiangya Hospital, Central South University, Changsha, 410013, Hunan, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, 410078, Hunan, China
| | - Wei Xiong
- NHC Key Laboratory of Carcinogenesis, Hunan Provincial Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China
- Hunan Key Laboratory of Nonresolving Inflammation and Cancer, The Third Xiangya Hospital, Central South University, Changsha, 410013, Hunan, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, 410078, Hunan, China
| | - Guiyuan Li
- NHC Key Laboratory of Carcinogenesis, Hunan Provincial Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China
- Hunan Key Laboratory of Nonresolving Inflammation and Cancer, The Third Xiangya Hospital, Central South University, Changsha, 410013, Hunan, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, 410078, Hunan, China
| | - Xiayu Li
- Hunan Key Laboratory of Nonresolving Inflammation and Cancer, The Third Xiangya Hospital, Central South University, Changsha, 410013, Hunan, China.
| | - Pingqing Tan
- NHC Key Laboratory of Carcinogenesis, Hunan Provincial Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China.
- Department of Head and Neck Surgery, Hunan Provincial Cancer Hospital and Cancer Hospital Affiliated to Xiangya Medical School, Central South University, Changsha, 410013, Hunan, China.
| | - Bo Xiang
- NHC Key Laboratory of Carcinogenesis, Hunan Provincial Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China.
- Hunan Key Laboratory of Nonresolving Inflammation and Cancer, The Third Xiangya Hospital, Central South University, Changsha, 410013, Hunan, China.
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, 410078, Hunan, China.
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8
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Mullen DJ, Yan C, Kang DS, Zhou B, Borok Z, Marconett CN, Farnham PJ, Offringa IA, Rhie SK. TENET 2.0: Identification of key transcriptional regulators and enhancers in lung adenocarcinoma. PLoS Genet 2020; 16:e1009023. [PMID: 32925947 PMCID: PMC7515200 DOI: 10.1371/journal.pgen.1009023] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 09/24/2020] [Accepted: 08/02/2020] [Indexed: 01/09/2023] Open
Abstract
Lung cancer is the leading cause of cancer-related death and lung adenocarcinoma is its most common subtype. Although genetic alterations have been identified as drivers in subsets of lung adenocarcinoma, they do not fully explain tumor development. Epigenetic alterations have been implicated in the pathogenesis of tumors. To identify epigenetic alterations driving lung adenocarcinoma, we used an improved version of the Tracing Enhancer Networks using Epigenetic Traits method (TENET 2.0) in primary normal lung and lung adenocarcinoma cells. We found over 32,000 enhancers that appear differentially activated between normal lung and lung adenocarcinoma. Among the identified transcriptional regulators inactivated in lung adenocarcinoma vs. normal lung, NKX2-1 was linked to a large number of silenced enhancers. Among the activated transcriptional regulators identified, CENPA, FOXM1, and MYBL2 were linked to numerous cancer-specific enhancers. High expression of CENPA, FOXM1, and MYBL2 is particularly observed in a subgroup of lung adenocarcinomas and is associated with poor patient survival. Notably, CENPA, FOXM1, and MYBL2 are also key regulators of cancer-specific enhancers in breast adenocarcinoma of the basal subtype, but they are associated with distinct sets of activated enhancers. We identified individual lung adenocarcinoma enhancers linked to CENPA, FOXM1, or MYBL2 that were associated with poor patient survival. Knockdown experiments of FOXM1 and MYBL2 suggest that these factors regulate genes involved in controlling cell cycle progression and cell division. For example, we found that expression of TK1, a potential target gene of a MYBL2-linked enhancer, is associated with poor patient survival. Identification and characterization of key transcriptional regulators and associated enhancers in lung adenocarcinoma provides important insights into the deregulation of lung adenocarcinoma epigenomes, highlighting novel potential targets for clinical intervention.
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Affiliation(s)
- Daniel J. Mullen
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, CA, United States of America
- Department of Surgery, Keck School of Medicine, University of Southern California, CA, United States of America
| | - Chunli Yan
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, CA, United States of America
- Department of Surgery, Keck School of Medicine, University of Southern California, CA, United States of America
| | - Diane S. Kang
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, CA, United States of America
- Department of Surgery, Keck School of Medicine, University of Southern California, CA, United States of America
| | - Beiyun Zhou
- Hastings Center for Pulmonary Research and Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Keck School of Medicine, University of Southern California, CA, United States of America
| | - Zea Borok
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, CA, United States of America
- Hastings Center for Pulmonary Research and Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Keck School of Medicine, University of Southern California, CA, United States of America
| | - Crystal N. Marconett
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, CA, United States of America
- Department of Surgery, Keck School of Medicine, University of Southern California, CA, United States of America
| | - Peggy J. Farnham
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, CA, United States of America
| | - Ite A. Offringa
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, CA, United States of America
- Department of Surgery, Keck School of Medicine, University of Southern California, CA, United States of America
| | - Suhn Kyong Rhie
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, CA, United States of America
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9
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Yamamoto T, Hirosue A, Nakamoto M, Yoshida R, Sakata J, Matsuoka Y, Kawahara K, Nagao Y, Nagata M, Takahashi N, Hiraki A, Shinohara M, Nakao M, Saitoh N, Nakayama H. BRD4 promotes metastatic potential in oral squamous cell carcinoma through the epigenetic regulation of the MMP2 gene. Br J Cancer 2020; 123:580-590. [PMID: 32499570 PMCID: PMC7435185 DOI: 10.1038/s41416-020-0907-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 04/29/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Oral squamous cell carcinoma (OSCC) has increased morbidity, and its high metastatic potential affects patient survival. Bromodomain containing 4 (BRD4) is a chromatin protein that associates with acetylated histone lysines and facilitates transcription. BRD4 has been implicated in cell proliferation, metastasis, and prognosis in several types of cancer. However, the role of BRD4 in OSCC remains to be elucidated. METHODS We investigated the role of BRD4 and its potential utility as a therapeutic target in OSCC. RESULTS JQ1, the BRD4 inhibitor, suppressed the cell proliferation, migration, and invasion in the OSCC cell lines and in vivo. JQ1 reduced the expression levels of 15 metastasis genes in OSCC, including matrix metallopeptidase 2 (MMP2). Our chromatin immunoprecipitation assay showed that JQ1 reduced the BRD4 binding to the histone H3 lysine 27 acetylation-enriched sites in the MMP2 locus. Analyses of biopsy specimens from OSCC patients revealed that the BRD4 and MMP2 expression levels were correlated in the cancerous regions, and both were highly expressed in lymph node metastasis cases, including delayed metastasis. CONCLUSIONS BRD4 contributes to metastasis in OSCC, through the epigenetic regulation of the MMP2 gene, and thus BRD4 may represent a therapeutic target and a novel prediction indicator for metastasis.
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Affiliation(s)
- Tatsuro Yamamoto
- Department of Oral and Maxillofacial Surgery, Faculty of Life Sciences, Kumamoto University, Kumamoto, 860-8556, Japan
- Division of Cancer Biology, The Cancer Institute of JFCR, Tokyo, 135-8550, Japan
- Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto, 860-0811, Japan
| | - Akiyuki Hirosue
- Department of Oral and Maxillofacial Surgery, Faculty of Life Sciences, Kumamoto University, Kumamoto, 860-8556, Japan.
| | - Masafumi Nakamoto
- Department of Oral and Maxillofacial Surgery, Faculty of Life Sciences, Kumamoto University, Kumamoto, 860-8556, Japan
| | - Ryoji Yoshida
- Department of Oral and Maxillofacial Surgery, Faculty of Life Sciences, Kumamoto University, Kumamoto, 860-8556, Japan
| | - Junki Sakata
- Department of Oral and Maxillofacial Surgery, Faculty of Life Sciences, Kumamoto University, Kumamoto, 860-8556, Japan
| | - Yuichiro Matsuoka
- Department of Oral and Maxillofacial Surgery, Faculty of Life Sciences, Kumamoto University, Kumamoto, 860-8556, Japan
| | - Kenta Kawahara
- Department of Oral and Maxillofacial Surgery, Faculty of Life Sciences, Kumamoto University, Kumamoto, 860-8556, Japan
| | - Yuka Nagao
- Department of Oral and Maxillofacial Surgery, Faculty of Life Sciences, Kumamoto University, Kumamoto, 860-8556, Japan
| | - Masashi Nagata
- Department of Oral and Maxillofacial Surgery, Faculty of Life Sciences, Kumamoto University, Kumamoto, 860-8556, Japan
| | - Nozomu Takahashi
- Department of Oral and Maxillofacial Surgery, Faculty of Life Sciences, Kumamoto University, Kumamoto, 860-8556, Japan
| | - Akimitsu Hiraki
- Section of Oral Oncology, Department of Oral and Maxillofacial Surgery, Fukuoka Dental College, Fukuoka, 814-0193, Japan
| | - Masanori Shinohara
- Department of Oral and Maxillofacial Surgery, Faculty of Life Sciences, Kumamoto University, Kumamoto, 860-8556, Japan
| | - Mitsuyoshi Nakao
- Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto, 860-0811, Japan
| | - Noriko Saitoh
- Division of Cancer Biology, The Cancer Institute of JFCR, Tokyo, 135-8550, Japan.
| | - Hideki Nakayama
- Department of Oral and Maxillofacial Surgery, Faculty of Life Sciences, Kumamoto University, Kumamoto, 860-8556, Japan
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10
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Stallcup MR, Poulard C. Gene-Specific Actions of Transcriptional Coregulators Facilitate Physiological Plasticity: Evidence for a Physiological Coregulator Code. Trends Biochem Sci 2020; 45:497-510. [PMID: 32413325 DOI: 10.1016/j.tibs.2020.02.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 01/24/2020] [Accepted: 02/10/2020] [Indexed: 01/14/2023]
Abstract
The actions of transcriptional coregulators are highly gene-specific, that is, each coregulator is required only for a subset of the genes regulated by a specific transcription factor. These coregulator-specific gene subsets often represent selected physiological responses among multiple pathways targeted by a transcription factor. Regulating the activity of a coregulator via post-translational modifications would thus affect only a subset of the transcription factor's physiological actions. Using the context of transcriptional regulation by steroid hormone receptors, this review focuses on gene-specific actions of coregulators and evidence linking individual coregulators with specific physiological pathways. Such evidence suggests that there is a 'physiological coregulator code', which represents a fertile area for future research with important clinical implications.
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Affiliation(s)
- Michael R Stallcup
- Department of Biochemistry and Molecular Medicine, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA90089-9176, USA.
| | - Coralie Poulard
- Université de Lyon, F-69000 Lyon, France; Inserm U1052, Centre de Recherche en Cancérologie de Lyon, F-69000 Lyon, France; CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, F-69000 Lyon, France
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11
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Beesley J, Sivakumaran H, Moradi Marjaneh M, Lima LG, Hillman KM, Kaufmann S, Tuano N, Hussein N, Ham S, Mukhopadhyay P, Kazakoff S, Lee JS, Michailidou K, Barnes DR, Antoniou AC, Fachal L, Dunning AM, Easton DF, Waddell N, Rosenbluh J, Möller A, Chenevix-Trench G, French JD, Edwards SL. Chromatin interactome mapping at 139 independent breast cancer risk signals. Genome Biol 2020; 21:8. [PMID: 31910858 PMCID: PMC6947858 DOI: 10.1186/s13059-019-1877-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 11/01/2019] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Genome-wide association studies have identified 196 high confidence independent signals associated with breast cancer susceptibility. Variants within these signals frequently fall in distal regulatory DNA elements that control gene expression. RESULTS We designed a Capture Hi-C array to enrich for chromatin interactions between the credible causal variants and target genes in six human mammary epithelial and breast cancer cell lines. We show that interacting regions are enriched for open chromatin, histone marks for active enhancers, and transcription factors relevant to breast biology. We exploit this comprehensive resource to identify candidate target genes at 139 independent breast cancer risk signals and explore the functional mechanism underlying altered risk at the 12q24 risk region. CONCLUSIONS Our results demonstrate the power of combining genetics, computational genomics, and molecular studies to rationalize the identification of key variants and candidate target genes at breast cancer GWAS signals.
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Affiliation(s)
- Jonathan Beesley
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Haran Sivakumaran
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Mahdi Moradi Marjaneh
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia
- Current address: UK Dementia Research Institute, Imperial College London, London, UK
| | - Luize G Lima
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Kristine M Hillman
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Susanne Kaufmann
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Natasha Tuano
- Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Australia
| | - Nehal Hussein
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia
- Faculty of Medicine, The University of Queensland, Brisbane, Australia
| | - Sunyoung Ham
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Pamela Mukhopadhyay
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Stephen Kazakoff
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Jason S Lee
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - 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, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Daniel R Barnes
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Antonis C Antoniou
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Laura Fachal
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Alison M Dunning
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Douglas F Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Nicola Waddell
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Joseph Rosenbluh
- Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Australia
| | - Andreas Möller
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | | | - Juliet D French
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia.
| | - Stacey L Edwards
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia.
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12
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Li M, Tang L, Wu FX, Pan Y, Wang J. CSA: a web service for the complete process of ChIP-Seq analysis. BMC Bioinformatics 2019; 20:515. [PMID: 31874601 PMCID: PMC6929326 DOI: 10.1186/s12859-019-3090-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 09/10/2019] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Chromatin immunoprecipitation sequencing (ChIP-seq) is a technology that combines chromatin immunoprecipitation (ChIP) with next generation of sequencing technology (NGS) to analyze protein interactions with DNA. At present, most ChIP-seq analysis tools adopt the command line, which lacks user-friendly interfaces. Although some web services with graphical interfaces have been developed for ChIP-seq analysis, these sites cannot provide a comprehensive analysis of ChIP-seq from raw data to downstream analysis. RESULTS In this study, we develop a web service for the whole process of ChIP-Seq Analysis (CSA), which covers mapping, quality control, peak calling, and downstream analysis. In addition, CSA provides a customization function for users to define their own workflows. And the visualization of mapping, peak calling, motif finding, and pathway analysis results are also provided in CSA. For the different types of ChIP-seq datasets, CSA can provide the corresponding tool to perform the analysis. Moreover, CSA can detect differences in ChIP signals between ChIP samples and controls to identify absolute binding sites. CONCLUSIONS The two case studies demonstrate the effectiveness of CSA, which can complete the whole procedure of ChIP-seq analysis. CSA provides a web interface for users, and implements the visualization of every analysis step. The website of CSA is available at http://CompuBio.csu.edu.cn.
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Affiliation(s)
- Min Li
- School of Computer Science and Engineering, Central South University, Changsha, China
| | - Li Tang
- School of Computer Science and Engineering, Central South University, Changsha, China
| | - Fang-Xiang Wu
- Division of Biomedical Engineering and Department of Mechanical Engineering, University of Saskatchewan, SKS7N5A9, Saskatoon, Canada
| | - Yi Pan
- Department of Computer Science, Georgia State University, GA30303, Atlanta, USA
| | - Jianxin Wang
- School of Computer Science and Engineering, Central South University, Changsha, China
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13
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Kong T, Ahn R, Yang K, Zhu X, Fu Z, Morin G, Bramley R, Cliffe NC, Xue Y, Kuasne H, Li Q, Jung S, Gonzalez AV, Camilleri-Broet S, Guiot MC, Park M, Ursini-Siegel J, Huang S. CD44 Promotes PD-L1 Expression and Its Tumor-Intrinsic Function in Breast and Lung Cancers. Cancer Res 2019; 80:444-457. [PMID: 31722999 DOI: 10.1158/0008-5472.can-19-1108] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 09/18/2019] [Accepted: 11/08/2019] [Indexed: 11/16/2022]
Abstract
The PD-L1 (CD274) immune-checkpoint ligand is often upregulated in cancers to inhibit T cells and elicit immunosuppression. Independent of this activity, PD-L1 has recently been shown to also exert a cancer cell-intrinsic function promoting tumorigenesis. Here, we establish this tumor-intrinsic role of PD-L1 in triple-negative breast cancer (TNBC) and non-small cell lung cancer (NSCLC). Using FACS-assisted shRNA screens, we identified the cell-surface adhesion receptor CD44 as a key positive regulator of PD-L1 expression in these cancers. Mechanistically, CD44 activated PD-L1 transcription in part through its cleaved intracytoplasmic domain (ICD), which bound to a regulatory region of the PD-L1 locus containing a consensus CD44-ICD binding site. Supporting this genetic interaction, CD44 positively correlated with PD-L1 expression at the mRNA and protein levels in primary tumor samples of TNBC and NSCLC patients. These data provide a novel basis for CD44 as a critical therapeutic target to suppress PD-L1 tumor-intrinsic function. SIGNIFICANCE: CD44 is a potential target to suppress PD-L1 function in TNBC. This finding has the potential to open a new area of therapy for TNBC.
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Affiliation(s)
- Tim Kong
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada.,Goodman Cancer Research Centre, McGill University, Montreal, Quebec, Canada
| | - Ryuhjin Ahn
- Lady Davis Institute for Medical Research, Montréal, Quebec, Canada.,Department of Experimental Medicine, McGill University, Montréal, Quebec, Canada
| | - Kangning Yang
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada.,Goodman Cancer Research Centre, McGill University, Montreal, Quebec, Canada
| | - Xianbing Zhu
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada.,Goodman Cancer Research Centre, McGill University, Montreal, Quebec, Canada
| | - Zheng Fu
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada.,Goodman Cancer Research Centre, McGill University, Montreal, Quebec, Canada
| | - Geneviève Morin
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada.,Goodman Cancer Research Centre, McGill University, Montreal, Quebec, Canada
| | - Rachel Bramley
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada.,Goodman Cancer Research Centre, McGill University, Montreal, Quebec, Canada
| | - Nikki C Cliffe
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada.,Goodman Cancer Research Centre, McGill University, Montreal, Quebec, Canada
| | - Yibo Xue
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada.,Goodman Cancer Research Centre, McGill University, Montreal, Quebec, Canada
| | - Hellen Kuasne
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada.,Goodman Cancer Research Centre, McGill University, Montreal, Quebec, Canada
| | - Qinghao Li
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada.,Goodman Cancer Research Centre, McGill University, Montreal, Quebec, Canada
| | - Sungmi Jung
- Department of Pathology, Glen Site, McGill University Health Centre Montreal, Quebec, Canada
| | - Anne V Gonzalez
- Department of Medicine, Division of Respiratory Medicine, McGill University Health Centre, Montreal Chest Institute, Montreal, Quebec, Canada
| | - Sophie Camilleri-Broet
- Department of Pathology, Glen Site, McGill University Health Centre Montreal, Quebec, Canada
| | - Marie-Christine Guiot
- Departments of Pathology, Montreal Neurological Hospital/Institute, McGill University Health Centre, Montreal, Quebec, Canada
| | - Morag Park
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada.,Goodman Cancer Research Centre, McGill University, Montreal, Quebec, Canada
| | - Josie Ursini-Siegel
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada. .,Lady Davis Institute for Medical Research, Montréal, Quebec, Canada.,Department of Experimental Medicine, McGill University, Montréal, Quebec, Canada.,Department of Oncology, McGill University, Montréal, Quebec, Canada
| | - Sidong Huang
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada. .,Goodman Cancer Research Centre, McGill University, Montreal, Quebec, Canada
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14
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Rhie SK, Perez AA, Lay FD, Schreiner S, Shi J, Polin J, Farnham PJ. A high-resolution 3D epigenomic map reveals insights into the creation of the prostate cancer transcriptome. Nat Commun 2019; 10:4154. [PMID: 31515496 PMCID: PMC6742760 DOI: 10.1038/s41467-019-12079-8] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 08/15/2019] [Indexed: 12/27/2022] Open
Abstract
To better understand the impact of chromatin structure on regulation of the prostate cancer transcriptome, we develop high-resolution chromatin interaction maps in normal and prostate cancer cells using in situ Hi-C. By combining the in situ Hi-C data with active and repressive histone marks, CTCF binding sites, nucleosome-depleted regions, and transcriptome profiling, we identify topologically associating domains (TADs) that change in size and epigenetic states between normal and prostate cancer cells. Moreover, we identify normal and prostate cancer-specific enhancer-promoter loops and involved transcription factors. For example, we show that FOXA1 is enriched in prostate cancer-specific enhancer-promoter loop anchors. We also find that the chromatin structure surrounding the androgen receptor (AR) locus is altered in the prostate cancer cells with many cancer-specific enhancer-promoter loops. This creation of 3D epigenomic maps enables a better understanding of prostate cancer biology and mechanisms of gene regulation. In prostate cancer, chromatin structure can impact the transcriptome. Here, the authors develop high resolution chromatin interaction maps in prostate cancer cells using in situ Hi-C, revealing prostate cancer-specific TADs and enhancer-promoter loops surrounding the androgen receptor (AR) locus.
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Affiliation(s)
- Suhn Kyong Rhie
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089, USA.
| | - Andrew A Perez
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089, USA
| | - Fides D Lay
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089, USA
| | - Shannon Schreiner
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089, USA
| | - Jiani Shi
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089, USA
| | - Jenevieve Polin
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089, USA
| | - Peggy J Farnham
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089, USA.
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15
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Booms A, Coetzee GA, Pierce SE. MCF-7 as a Model for Functional Analysis of Breast Cancer Risk Variants. Cancer Epidemiol Biomarkers Prev 2019; 28:1735-1745. [PMID: 31292138 DOI: 10.1158/1055-9965.epi-19-0066] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 05/17/2019] [Accepted: 07/02/2019] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Breast cancer genetic predisposition is governed by more than 142 loci as revealed by genome-wide association studies (GWAS). The functional contribution of these risk loci to breast cancer remains unclear, and additional post-GWAS analyses are required. METHODS We identified active regulatory elements (enhancers, promoters, and chromatin organizing elements) by histone H3K27 acetylation and CTCF occupancy and determined the enrichment of risk variants at these sites. We compared these results with previously published data and for other cell lines, including human mammary epithelial cells, and related these data to gene expression. RESULTS In terms of mapping accuracy and resolution, our data augment previous annotations of the MCF-7 epigenome. After intersection with GWAS risk variants, we found 39 enhancers and 15 CTCF occupancy sites that, between them, overlapped 96 breast cancer credible risk variants at 42 loci. These risk enhancers likely regulate the expression of dozens of genes, which are enriched for GO categories, including estrogen and prolactin signaling. CONCLUSIONS Ten (of 142) breast cancer risk loci likely function via enhancers that are active in MCF-7 and are well suited to targeted manipulation in this system. In contrast, risk loci cannot be mapped to specific CTCF-binding sites, and the genes linked to risk CTCF sites did not show functional enrichment. The identity of risk enhancers and their associated genes suggests that some risk may function during later processes in cancer progression. IMPACT Here, we report how the ER+ cell line MCF-7 can be used to dissect risk mechanisms for breast cancer.
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Affiliation(s)
- Alix Booms
- Center for Neurodegenerative Science, Van Andel Research Institute, Grand Rapids, Michigan
| | - Gerhard A Coetzee
- Center for Neurodegenerative Science, Van Andel Research Institute, Grand Rapids, Michigan.
| | - Steven E Pierce
- Center for Neurodegenerative Science, Van Andel Research Institute, Grand Rapids, Michigan
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16
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Rhie SK, Schreiner S, Witt H, Armoskus C, Lay FD, Camarena A, Spitsyna VN, Guo Y, Berman BP, Evgrafov OV, Knowles JA, Farnham PJ. Using 3D epigenomic maps of primary olfactory neuronal cells from living individuals to understand gene regulation. SCIENCE ADVANCES 2018; 4:eaav8550. [PMID: 30555922 PMCID: PMC6292713 DOI: 10.1126/sciadv.aav8550] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 11/16/2018] [Indexed: 05/20/2023]
Abstract
As part of PsychENCODE, we developed a three-dimensional (3D) epigenomic map of primary cultured neuronal cells derived from olfactory neuroepithelium (CNON). We mapped topologically associating domains and high-resolution chromatin interactions using Hi-C and identified regulatory elements using chromatin immunoprecipitation and nucleosome positioning assays. Using epigenomic datasets from biopsies of 63 living individuals, we found that epigenetic marks at distal regulatory elements are more variable than marks at proximal regulatory elements. By integrating genotype and metadata, we identified enhancers that have different levels corresponding to differences in genetic variation, gender, smoking, and schizophrenia. Motif searches revealed that many CNON enhancers are bound by neuronal-related transcription factors. Last, we combined 3D epigenomic maps and gene expression profiles to predict enhancer-target gene interactions on a genome-wide scale. This study not only provides a framework for understanding individual epigenetic variation using a primary cell model system but also contributes valuable data resources for epigenomic studies of neuronal epithelium.
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Affiliation(s)
- Suhn K. Rhie
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Shannon Schreiner
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Heather Witt
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Chris Armoskus
- Department of Psychiatry and the Behavioral Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Fides D. Lay
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Adrian Camarena
- Department of Psychiatry and the Behavioral Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Valeria N. Spitsyna
- Department of Psychiatry and the Behavioral Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Yu Guo
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Benjamin P. Berman
- Department of Biomedical Sciences, Bioinformatics and Computational Biology Research Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Oleg V. Evgrafov
- Department of Cell Biology, SUNY Downstate Medical Center, Brooklyn, NY, USA
| | - James A. Knowles
- Department of Cell Biology, SUNY Downstate Medical Center, Brooklyn, NY, USA
| | - Peggy J. Farnham
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
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17
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DeVaux RS, Herschkowitz JI. Beyond DNA: the Role of Epigenetics in the Premalignant Progression of Breast Cancer. J Mammary Gland Biol Neoplasia 2018; 23:223-235. [PMID: 30306389 PMCID: PMC6244889 DOI: 10.1007/s10911-018-9414-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 09/18/2018] [Indexed: 12/19/2022] Open
Abstract
Ductal Carcinoma in Situ (DCIS) is an early breast cancer lesion that is considered a nonobligate precursor to development of invasive ductal carcinoma (IDC). Although only a small subset of DCIS lesions are predicted to progress into a breast cancer, distinguishing innocuous from minacious DCIS lesions remains a clinical challenge. Thus, patients diagnosed with DCIS will undergo surgery with the potential for radiation and hormone therapy. This has led to a current state of overdiagnosis and overtreatment. Interrogating the transcriptome alone has yet to define clear functional determinants of progression from DCIS to IDC. Epigenetic changes, critical for imprinting and tissue specific development, in the incorrect context can lead to global signaling rewiring driving pathological phenotypes. Epigenetic signaling pathways, and the molecular players that interpret and sustain their signals, are critical to understanding the underlying pathology of breast cancer progression. The types of epigenetic changes, as well as the molecular players, are expanding. In addition to DNA methylation, histone modifications, and chromatin remodeling, we must also consider enhancers as well as the growing field of noncoding RNAs. Herein we will review the epigenetic interactions that have been uncovered in early stage lesions that impact breast cancer progression, and how these players may be utilized as biomarkers to mitigate overdiagnosis and overtreatment.
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Affiliation(s)
- Rebecca S DeVaux
- Department of Biomedical Sciences, Cancer Research Center, University at Albany, State University of New York, Rensselaer, NY, USA
| | - Jason I Herschkowitz
- Department of Biomedical Sciences, Cancer Research Center, University at Albany, State University of New York, Rensselaer, NY, USA.
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18
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Genetics and Expression Profile of the Tubulin Gene Superfamily in Breast Cancer Subtypes and Its Relation to Taxane Resistance. Cancers (Basel) 2018; 10:cancers10080274. [PMID: 30126203 PMCID: PMC6116153 DOI: 10.3390/cancers10080274] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 08/13/2018] [Accepted: 08/16/2018] [Indexed: 01/15/2023] Open
Abstract
Taxanes are a class of chemotherapeutic agents that inhibit cell division by disrupting the mitotic spindle through the stabilization of microtubules. Most breast cancer (BC) tumors show resistance against taxanes partially due to alterations in tubulin genes. In this project we investigated tubulin isoforms in BC to explore any correlation between tubulin alterations and taxane resistance. Genetic alteration and expression profiling of 28 tubulin isoforms in 6714 BC tumor samples from 4205 BC cases were analyzed. Protein-protein, drug-protein and alterations neighbor genes in tubulin pathways were examined in the tumor samples. To study correlation between promoter activity and expression of the tubulin isoforms in BC, we analyzed the ChIP-seq enrichment of active promoter histone mark H3K4me3 and mRNA expression profile of MCF-7, ZR-75-30, SKBR-3 and MDA-MB-231 cell lines. Potential correlation between tubulin alterations and taxane resistance, were investigated by studying the expression profile of taxane-sensitive and resistant BC tumors also the MDA-MB-231 cells acquired resistance to paclitaxel. All genomic data were obtained from public databases. Results showed that TUBD1 and TUBB3 were the most frequently amplified and deleted tubulin genes in the BC tumors respectively. The interaction analysis showed physical interactions of α-, β- and γ-tubulin isoforms with each other. The most of FDA-approved tubulin inhibitor drugs including taxanes target only β-tubulins. The analysis also revealed sex tubulin-interacting neighbor proteins including ENCCT3, NEK2, PFDN2, PTP4A3, SDCCAG8 and TBCE which were altered in at least 20% of the tumors. Three of them are tubulin-specific chaperons responsible for tubulin protein folding. Expression of tubulin genes in BC cell lines were correlated with H3K4me3 enrichment on their promoter chromatin. Analyzing expression profile of BC tumors and tumor-adjacent normal breast tissues showed upregulation of TUBA1A, TUBA1C, TUBB and TUBB3 and downregulation of TUBB2A, TUBB2B, TUBB6, TUBB7P pseudogene, and TUBGCP2 in the tumor tissues compared to the normal breast tissues. Analyzing taxane-sensitive versus taxane-resistant tumors revealed that expression of TUBB3 and TUBB6 was significantly downregulated in the taxane-resistant tumors. Our results suggest that downregulation of tumor βIII- and βV-tubulins is correlated with taxane resistance in BC. Based on our results, we conclude that aberrant protein folding of tubulins due to mutation and/or dysfunction of tubulin-specific chaperons may be potential mechanisms of taxane resistance. Thus, we propose studying the molecular pathology of tubulin mutations and folding in BC and their impacts on taxane resistance.
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19
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Genetics and Expression Profile of the Tubulin Gene Superfamily in Breast Cancer Subtypes and Its Relation to Taxane Resistance. Cancers (Basel) 2018. [DOI: 10.10.3390/cancers10080274] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Taxanes are a class of chemotherapeutic agents that inhibit cell division by disrupting the mitotic spindle through the stabilization of microtubules. Most breast cancer (BC) tumors show resistance against taxanes partially due to alterations in tubulin genes. In this project we investigated tubulin isoforms in BC to explore any correlation between tubulin alterations and taxane resistance. Genetic alteration and expression profiling of 28 tubulin isoforms in 6714 BC tumor samples from 4205 BC cases were analyzed. Protein-protein, drug-protein and alterations neighbor genes in tubulin pathways were examined in the tumor samples. To study correlation between promoter activity and expression of the tubulin isoforms in BC, we analyzed the ChIP-seq enrichment of active promoter histone mark H3K4me3 and mRNA expression profile of MCF-7, ZR-75-30, SKBR-3 and MDA-MB-231 cell lines. Potential correlation between tubulin alterations and taxane resistance, were investigated by studying the expression profile of taxane-sensitive and resistant BC tumors also the MDA-MB-231 cells acquired resistance to paclitaxel. All genomic data were obtained from public databases. Results showed that TUBD1 and TUBB3 were the most frequently amplified and deleted tubulin genes in the BC tumors respectively. The interaction analysis showed physical interactions of α-, β- and γ-tubulin isoforms with each other. The most of FDA-approved tubulin inhibitor drugs including taxanes target only β-tubulins. The analysis also revealed sex tubulin-interacting neighbor proteins including ENCCT3, NEK2, PFDN2, PTP4A3, SDCCAG8 and TBCE which were altered in at least 20% of the tumors. Three of them are tubulin-specific chaperons responsible for tubulin protein folding. Expression of tubulin genes in BC cell lines were correlated with H3K4me3 enrichment on their promoter chromatin. Analyzing expression profile of BC tumors and tumor-adjacent normal breast tissues showed upregulation of TUBA1A, TUBA1C, TUBB and TUBB3 and downregulation of TUBB2A, TUBB2B, TUBB6, TUBB7P pseudogene, and TUBGCP2 in the tumor tissues compared to the normal breast tissues. Analyzing taxane-sensitive versus taxane-resistant tumors revealed that expression of TUBB3 and TUBB6 was significantly downregulated in the taxane-resistant tumors. Our results suggest that downregulation of tumor βIII- and βV-tubulins is correlated with taxane resistance in BC. Based on our results, we conclude that aberrant protein folding of tubulins due to mutation and/or dysfunction of tubulin-specific chaperons may be potential mechanisms of taxane resistance. Thus, we propose studying the molecular pathology of tubulin mutations and folding in BC and their impacts on taxane resistance.
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20
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Parkinson's disease genetic risk in a midbrain neuronal cell line. Neurobiol Dis 2018; 114:53-64. [DOI: 10.1016/j.nbd.2018.02.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 01/30/2018] [Accepted: 02/21/2018] [Indexed: 12/16/2022] Open
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21
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Rhie SK, Yao L, Luo Z, Witt H, Schreiner S, Guo Y, Perez AA, Farnham PJ. ZFX acts as a transcriptional activator in multiple types of human tumors by binding downstream from transcription start sites at the majority of CpG island promoters. Genome Res 2018; 28:310-320. [PMID: 29429977 PMCID: PMC5848610 DOI: 10.1101/gr.228809.117] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 01/26/2018] [Indexed: 12/29/2022]
Abstract
High expression of the transcription factor ZFX is correlated with proliferation, tumorigenesis, and patient survival in multiple types of human cancers. However, the mechanism by which ZFX influences transcriptional regulation has not been determined. We performed ChIP-seq in four cancer cell lines (representing kidney, colon, prostate, and breast cancers) to identify ZFX binding sites throughout the human genome. We identified roughly 9000 ZFX binding sites and found that most of the sites are in CpG island promoters. Moreover, genes with promoters bound by ZFX are expressed at higher levels than genes with promoters not bound by ZFX. To determine if ZFX contributes to regulation of the promoters to which it is bound, we performed RNA-seq analysis after knockdown of ZFX by siRNA in prostate and breast cancer cells. Many genes with promoters bound by ZFX were down-regulated upon ZFX knockdown, supporting the hypothesis that ZFX acts as a transcriptional activator. Surprisingly, ZFX binds at +240 bp downstream from the TSS of the responsive promoters. Using Nucleosome Occupancy and Methylome Sequencing (NOMe-seq), we show that ZFX binds between the open chromatin region at the TSS and the first downstream nucleosome, suggesting that ZFX may play a critical role in promoter architecture. We have also shown that a closely related zinc finger protein ZNF711 has a similar binding pattern at CpG island promoters, but ZNF711 may play a subordinate role to ZFX. This functional characterization of ZFX provides important new insights into transcription, chromatin structure, and the regulation of the cancer transcriptome.
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Affiliation(s)
- Suhn Kyong Rhie
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California 90089, USA
| | - Lijun Yao
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California 90089, USA
| | - Zhifei Luo
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California 90089, USA
| | - Heather Witt
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California 90089, USA
| | - Shannon Schreiner
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California 90089, USA
| | - Yu Guo
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California 90089, USA
| | - Andrew A Perez
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California 90089, USA
| | - Peggy J Farnham
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California 90089, USA
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22
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Targeting the Epigenome as a Novel Therapeutic Approach for Breast Cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1026:287-313. [DOI: 10.1007/978-981-10-6020-5_14] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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23
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Kalender Atak Z, Imrichova H, Svetlichnyy D, Hulselmans G, Christiaens V, Reumers J, Ceulemans H, Aerts S. Identification of cis-regulatory mutations generating de novo edges in personalized cancer gene regulatory networks. Genome Med 2017; 9:80. [PMID: 28854983 PMCID: PMC5575942 DOI: 10.1186/s13073-017-0464-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Accepted: 08/02/2017] [Indexed: 01/05/2023] Open
Abstract
The identification of functional non-coding mutations is a key challenge in the field of genomics. Here we introduce μ-cisTarget to filter, annotate and prioritize cis-regulatory mutations based on their putative effect on the underlying "personal" gene regulatory network. We validated μ-cisTarget by re-analyzing the TAL1 and LMO1 enhancer mutations in T-ALL, and the TERT promoter mutation in melanoma. Next, we re-sequenced the full genomes of ten cancer cell lines and used matched transcriptome data and motif discovery to identify master regulators with de novo binding sites that result in the up-regulation of nearby oncogenic drivers. μ-cisTarget is available from http://mucistarget.aertslab.org .
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Affiliation(s)
- Zeynep Kalender Atak
- Laboratory of Computational Biology, VIB Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Hana Imrichova
- Laboratory of Computational Biology, VIB Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Dmitry Svetlichnyy
- Laboratory of Computational Biology, VIB Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Gert Hulselmans
- Laboratory of Computational Biology, VIB Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Valerie Christiaens
- Laboratory of Computational Biology, VIB Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Joke Reumers
- Discovery Sciences, Janssen Research & Development, Turnhoutseweg 30, 2340, Beerse, Belgium
| | - Hugo Ceulemans
- Discovery Sciences, Janssen Research & Development, Turnhoutseweg 30, 2340, Beerse, Belgium
| | - Stein Aerts
- Laboratory of Computational Biology, VIB Center for Brain & Disease Research, Leuven, Belgium.
- Department of Human Genetics, KU Leuven, Leuven, Belgium.
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24
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Gallenne T, Ross KN, Visser NL, Salony, Desmet CJ, Wittner BS, Wessels LFA, Ramaswamy S, Peeper DS. Systematic functional perturbations uncover a prognostic genetic network driving human breast cancer. Oncotarget 2017; 8:20572-20587. [PMID: 28411283 PMCID: PMC5400527 DOI: 10.18632/oncotarget.16244] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 01/28/2017] [Indexed: 12/12/2022] Open
Abstract
Prognostic classifiers conceivably comprise biomarker genes that functionally contribute to the oncogenic and metastatic properties of cancer, but this has not been investigated systematically. The transcription factor Fra-1 not only has an essential role in breast cancer, but also drives the expression of a highly prognostic gene set. Here, we systematically perturbed the function of 31 individual Fra-1-dependent poor-prognosis genes and examined their impact on breast cancer growth in vivo. We find that stable shRNA depletion of each of nine individual signature genes strongly inhibits breast cancer growth and aggressiveness. Several factors within this nine-gene set regulate each others expression, suggesting that together they form a network. The nine-gene set is regulated by estrogen, ERBB2 and EGF signaling, all established breast cancer factors. We also uncover three transcription factors, MYC, E2F1 and TP53, which act alongside Fra-1 at the core of this network. ChIP-Seq analysis reveals that a substantial number of genes are bound, and regulated, by all four transcription factors. The nine-gene set retains significant prognostic power and includes several potential therapeutic targets, including the bifunctional enzyme PAICS, which catalyzes purine biosynthesis. Depletion of PAICS largely cancelled breast cancer expansion, exemplifying a prognostic gene with breast cancer activity. Our data uncover a core genetic and prognostic network driving human breast cancer. We propose that pharmacological inhibition of components within this network, such as PAICS, may be used in conjunction with the Fra-1 prognostic classifier towards personalized management of poor prognosis breast cancer.
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Affiliation(s)
- Tristan Gallenne
- Department of Molecular Oncology, The Netherlands Cancer Institute, Plesmanlaan, CX, Amsterdam, The Netherlands.,Current address: Merus B.V., Padualaan, CH Utrecht, The Netherlands
| | - Kenneth N Ross
- Massachusetts General Hospital Cancer Center, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Nils L Visser
- Department of Molecular Oncology, The Netherlands Cancer Institute, Plesmanlaan, CX, Amsterdam, The Netherlands
| | - Salony
- Massachusetts General Hospital Cancer Center, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Christophe J Desmet
- Department of Molecular Oncology, The Netherlands Cancer Institute, Plesmanlaan, CX, Amsterdam, The Netherlands
| | - Ben S Wittner
- Massachusetts General Hospital Cancer Center, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Lodewyk F A Wessels
- Department of Molecular Carcinogenesis, The Netherlands Cancer Institute, Plesmanlaan, CX, Amsterdam, The Netherlands.,Faculty of EEMCS Delft University of Technology, Delft, The Netherlands
| | - Sridhar Ramaswamy
- Massachusetts General Hospital Cancer Center, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA.,Broad Institute of Harvard & MIT, Cambridge, MA, USA.,Harvard Stem Cell Institute, Cambridge, MA, USA.,Harvard-Ludwig Center for Cancer Research, Boston, MA, USA
| | - Daniel S Peeper
- Department of Molecular Oncology, The Netherlands Cancer Institute, Plesmanlaan, CX, Amsterdam, The Netherlands
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25
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Feng Y, Rhie SK, Huo D, Ruiz-Narvaez EA, Haddad SA, Ambrosone CB, John EM, Bernstein L, Zheng W, Hu JJ, Ziegler RG, Nyante S, Bandera EV, Ingles SA, Press MF, Deming SL, Rodriguez-Gil JL, Zheng Y, Yao S, Han YJ, Ogundiran TO, Rebbeck TR, Adebamowo C, Ojengbede O, Falusi AG, Hennis A, Nemesure B, Ambs S, Blot W, Cai Q, Signorello L, Nathanson KL, Lunetta KL, Sucheston-Campbell LE, Bensen JT, Chanock SJ, Marchand LL, Olshan AF, Kolonel LN, Conti DV, Coetzee GA, Stram DO, Olopade OI, Palmer JR, Haiman CA. Characterizing Genetic Susceptibility to Breast Cancer in Women of African Ancestry. Cancer Epidemiol Biomarkers Prev 2017; 26:1016-1026. [PMID: 28377418 DOI: 10.1158/1055-9965.epi-16-0567] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Revised: 10/07/2016] [Accepted: 03/15/2017] [Indexed: 01/01/2023] Open
Abstract
Background: Genome-wide association studies have identified approximately 100 common genetic variants associated with breast cancer risk, the majority of which were discovered in women of European ancestry. Because of different patterns of linkage disequilibrium, many of these genetic markers may not represent signals in populations of African ancestry.Methods: We tested 74 breast cancer risk variants and conducted fine-mapping of these susceptibility regions in 6,522 breast cancer cases and 7,643 controls of African ancestry from three genetic consortia (AABC, AMBER, and ROOT).Results: Fifty-four of the 74 variants (73%) were found to have ORs that were directionally consistent with those previously reported, of which 12 were nominally statistically significant (P < 0.05). Through fine-mapping, in six regions (3p24, 12p11, 14q13, 16q12/FTO, 16q23, 19p13), we observed seven markers that better represent the underlying risk variant for overall breast cancer or breast cancer subtypes, whereas in another two regions (11q13, 16q12/TOX3), we identified suggestive evidence of signals that are independent of the reported index variant. Overlapping chromatin features and regulatory elements suggest that many of the risk alleles lie in regions with biological functionality.Conclusions: Through fine-mapping of known susceptibility regions, we have revealed alleles that better characterize breast cancer risk in women of African ancestry.Impact: The risk alleles identified represent genetic markers for modeling and stratifying breast cancer risk in women of African ancestry. Cancer Epidemiol Biomarkers Prev; 26(7); 1016-26. ©2017 AACR.
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Affiliation(s)
- Ye Feng
- Department of Preventive Medicine, Keck School of Medicine and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California.
| | - Suhn Kyong Rhie
- Department of Preventive Medicine, Keck School of Medicine and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California
| | - Dezheng Huo
- Department of Public Health Sciences, University of Chicago, Chicago, Illinois
| | | | - Stephen A Haddad
- Slone Epidemiology Center at Boston University, Boston, Massachusetts
| | - Christine B Ambrosone
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, New York
| | - Esther M John
- Cancer Prevention Institute of California, Fremont, California.,Department of Health Research and Policy (Epidemiology) and Stanford Cancer Institute, Stanford University School of Medicine, Stanford, California
| | - Leslie Bernstein
- Division of Cancer Etiology, Department of Population Sciences, Beckman Research Institute, City of Hope, Duarte, California
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, and Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Jennifer J Hu
- Sylvester Comprehensive Cancer Center and Department of Epidemiology and Public Health, University of Miami Miller School of Medicine, Miami, Florida
| | - Regina G Ziegler
- Epidemiology and Biostatistics Program, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
| | - Sarah Nyante
- Department of Epidemiology, Gillings School of Global Public Health and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina
| | - Elisa V Bandera
- Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey
| | - Sue A Ingles
- Department of Preventive Medicine, Keck School of Medicine and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California
| | - Michael F Press
- Department of Pathology, Keck School of Medicine and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California
| | - Sandra L Deming
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, and Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Jorge L Rodriguez-Gil
- Sylvester Comprehensive Cancer Center and Department of Epidemiology and Public Health, University of Miami Miller School of Medicine, Miami, Florida
| | - Yonglan Zheng
- Department of Medicine, University of Chicago, Chicago, Illinois
| | - Song Yao
- Roswell Park Cancer Institute, Buffalo, New York
| | - Yoo-Jeong Han
- Department of Medicine, University of Chicago, Chicago, Illinois
| | - Temidayo O Ogundiran
- Department of Surgery, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Timothy R Rebbeck
- Dana Farber Cancer Institute & Harvard T. H. Chan School of Public Health, Boston, Maryland
| | - Clement Adebamowo
- Department of Epidemiology & Preventive Medicine, University of Maryland, Baltimore, Maryland
| | - Oladosu Ojengbede
- Center for Population and Reproductive Health, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Adeyinka G Falusi
- Institute for Medical Research and Training, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Anselm Hennis
- Chronic Disease Research Centre, Tropical Medicine Research Institute, University of the West Indies, Bridgetown, Barbados.,Department of Preventive Medicine, State University of New York at Stony Brook, Stony Brook, New York
| | - Barbara Nemesure
- Department of Preventive Medicine, State University of New York at Stony Brook, Stony Brook, New York
| | - Stefan Ambs
- Laboratory of Human Carcinogenesis, National Cancer Institute, Bethesda, Maryland
| | - William Blot
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, and Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Qiuyin Cai
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, and Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Lisa Signorello
- Cancer Prevention Fellowship Program, National Cancer Institute, Bethesda, Maryland
| | | | - Kathryn L Lunetta
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts
| | | | - Jeannette T Bensen
- Department of Epidemiology, Gillings School of Global Public Health and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina
| | - Stephen J Chanock
- Epidemiology and Biostatistics Program, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
| | - Loic Le Marchand
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, Hawaii
| | - Andrew F Olshan
- Department of Epidemiology, Gillings School of Global Public Health and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina
| | - Laurence N Kolonel
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, Hawaii
| | - David V Conti
- Department of Preventive Medicine, Keck School of Medicine and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California
| | - Gerhard A Coetzee
- Department of Preventive Medicine, Keck School of Medicine and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California
| | - Daniel O Stram
- Department of Preventive Medicine, Keck School of Medicine and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California
| | | | - Julie R Palmer
- Slone Epidemiology Center at Boston University, Boston, Massachusetts
| | - Christopher A Haiman
- Department of Preventive Medicine, Keck School of Medicine and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California.
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26
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Tu WJ, Hardy K, Sutton CR, McCuaig R, Li J, Dunn J, Tan A, Brezar V, Morris M, Denyer G, Lee SK, Turner SJ, Seddiki N, Smith C, Khanna R, Rao S. Priming of transcriptional memory responses via the chromatin accessibility landscape in T cells. Sci Rep 2017; 7:44825. [PMID: 28317936 PMCID: PMC5357947 DOI: 10.1038/srep44825] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 02/14/2017] [Indexed: 12/17/2022] Open
Abstract
Memory T cells exhibit transcriptional memory and “remember” their previous pathogenic encounter to increase transcription on re-infection. However, how this transcriptional priming response is regulated is unknown. Here we performed global FAIRE-seq profiling of chromatin accessibility in a human T cell transcriptional memory model. Primary activation induced persistent accessibility changes, and secondary activation induced secondary-specific opening of previously less accessible regions associated with enhanced expression of memory-responsive genes. Increased accessibility occurred largely in distal regulatory regions and was associated with increased histone acetylation and relative H3.3 deposition. The enhanced re-stimulation response was linked to the strength of initial PKC-induced signalling, and PKC-sensitive increases in accessibility upon initial stimulation showed higher accessibility on re-stimulation. While accessibility maintenance was associated with ETS-1, accessibility at re-stimulation-specific regions was linked to NFAT, especially in combination with ETS-1, EGR, GATA, NFκB, and NR4A. Furthermore, NFATC1 was directly regulated by ETS-1 at an enhancer region. In contrast to the factors that increased accessibility, signalling from bHLH and ZEB family members enhanced decreased accessibility upon re-stimulation. Interplay between distal regulatory elements, accessibility, and the combined action of sequence-specific transcription factors allows transcriptional memory-responsive genes to “remember” their initial environmental encounter.
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Affiliation(s)
- Wen Juan Tu
- Faculty of Education, Science, Technology &Mathematics, University of Canberra, Canberra, Australian Capital Territory 2617, Australia
| | - Kristine Hardy
- Faculty of Education, Science, Technology &Mathematics, University of Canberra, Canberra, Australian Capital Territory 2617, Australia
| | - Christopher R Sutton
- Faculty of Education, Science, Technology &Mathematics, University of Canberra, Canberra, Australian Capital Territory 2617, Australia
| | - Robert McCuaig
- Faculty of Education, Science, Technology &Mathematics, University of Canberra, Canberra, Australian Capital Territory 2617, Australia
| | - Jasmine Li
- Department of Microbiology, Biomedical Discovery Institute, Monash University, Clayton, Victoria 3800, Australia.,Department of Microbiology &Immunology, The Doherty Institute for Infection and Immunity, University of Melbourne, Victoria 3010, Australia
| | - Jenny Dunn
- Faculty of Education, Science, Technology &Mathematics, University of Canberra, Canberra, Australian Capital Territory 2617, Australia
| | - Abel Tan
- Faculty of Education, Science, Technology &Mathematics, University of Canberra, Canberra, Australian Capital Territory 2617, Australia
| | - Vedran Brezar
- INSERM U955 Eq16 Faculte de medicine Henri Mondor and Universite Paris-Est, Creteil/Vaccine Research Institute, Creteil 94010, France
| | - Melanie Morris
- Faculty of Education, Science, Technology &Mathematics, University of Canberra, Canberra, Australian Capital Territory 2617, Australia
| | - Gareth Denyer
- School of Molecular Bioscience, The University of Sydney, Sydney, NSW, Australia
| | - Sau Kuen Lee
- QIMR Berghofer Centre for Immunotherapy and Vaccine Development QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia.,Tumour Immunology Laboratory, Department of Immunology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Stephen J Turner
- Department of Microbiology, Biomedical Discovery Institute, Monash University, Clayton, Victoria 3800, Australia.,Department of Microbiology &Immunology, The Doherty Institute for Infection and Immunity, University of Melbourne, Victoria 3010, Australia
| | - Nabila Seddiki
- INSERM U955 Eq16 Faculte de medicine Henri Mondor and Universite Paris-Est, Creteil/Vaccine Research Institute, Creteil 94010, France
| | - Corey Smith
- QIMR Berghofer Centre for Immunotherapy and Vaccine Development QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia.,Tumour Immunology Laboratory, Department of Immunology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Rajiv Khanna
- QIMR Berghofer Centre for Immunotherapy and Vaccine Development QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia.,Tumour Immunology Laboratory, Department of Immunology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Sudha Rao
- Faculty of Education, Science, Technology &Mathematics, University of Canberra, Canberra, Australian Capital Territory 2617, Australia
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27
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Abraham BJ, Hnisz D, Weintraub AS, Kwiatkowski N, Li CH, Li Z, Weichert-Leahey N, Rahman S, Liu Y, Etchin J, Li B, Shen S, Lee TI, Zhang J, Look AT, Mansour MR, Young RA. Small genomic insertions form enhancers that misregulate oncogenes. Nat Commun 2017; 8:14385. [PMID: 28181482 PMCID: PMC5309821 DOI: 10.1038/ncomms14385] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 12/22/2016] [Indexed: 01/04/2023] Open
Abstract
The non-coding regions of tumour cell genomes harbour a considerable fraction of total DNA sequence variation, but the functional contribution of these variants to tumorigenesis is ill-defined. Among these non-coding variants, somatic insertions are among the least well characterized due to challenges with interpreting short-read DNA sequences. Here, using a combination of Chip-seq to enrich enhancer DNA and a computational approach with multiple DNA alignment procedures, we identify enhancer-associated small insertion variants. Among the 102 tumour cell genomes we analyse, small insertions are frequently observed in enhancer DNA sequences near known oncogenes. Further study of one insertion, somatically acquired in primary leukaemia tumour genomes, reveals that it nucleates formation of an active enhancer that drives expression of the LMO2 oncogene. The approach described here to identify enhancer-associated small insertion variants provides a foundation for further study of these abnormalities across human cancers. Sequencing initiatives have detected multiple types of mutations in cancer. Here the authors, analysing enhancer-targeting sequence data, show that small insertions in transcriptional enhancers are frequently found near oncogenes, and demonstrate how one mutation deregulates expression of LMO2 in leukemia cells.
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Affiliation(s)
- Brian J Abraham
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, Massachusetts 02142, USA
| | - Denes Hnisz
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, Massachusetts 02142, USA
| | - Abraham S Weintraub
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, Massachusetts 02142, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Nicholas Kwiatkowski
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, Massachusetts 02142, USA
| | - Charles H Li
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, Massachusetts 02142, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Zhaodong Li
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02215, USA.,Division of Hematology/Oncology, Children's Hospital, Boston, Massachusetts 02115, USA
| | - Nina Weichert-Leahey
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02215, USA.,Division of Hematology/Oncology, Children's Hospital, Boston, Massachusetts 02115, USA
| | - Sunniyat Rahman
- Department of Haematology, UCL Cancer Institute, University College London, London WC1E 6DD, UK
| | - Yu Liu
- Department of Computational Biology, St Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Julia Etchin
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02215, USA.,Division of Hematology/Oncology, Children's Hospital, Boston, Massachusetts 02115, USA
| | - Benshang Li
- Key Laboratory of Pediatric Hematology &Oncology Ministry of Health, Department of Hematology &Oncology, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China.,Pediatric Translational Medicine Institute, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
| | - Shuhong Shen
- Key Laboratory of Pediatric Hematology &Oncology Ministry of Health, Department of Hematology &Oncology, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China.,Pediatric Translational Medicine Institute, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
| | - Tong Ihn Lee
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, Massachusetts 02142, USA
| | - Jinghui Zhang
- Department of Computational Biology, St Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - A Thomas Look
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02215, USA.,Division of Hematology/Oncology, Children's Hospital, Boston, Massachusetts 02115, USA
| | - Marc R Mansour
- Department of Haematology, UCL Cancer Institute, University College London, London WC1E 6DD, UK
| | - Richard A Young
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, Massachusetts 02142, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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28
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Rhie SK, Guo Y, Tak YG, Yao L, Shen H, Coetzee GA, Laird PW, Farnham PJ. Identification of activated enhancers and linked transcription factors in breast, prostate, and kidney tumors by tracing enhancer networks using epigenetic traits. Epigenetics Chromatin 2016; 9:50. [PMID: 27833659 PMCID: PMC5103450 DOI: 10.1186/s13072-016-0102-4] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 10/28/2016] [Indexed: 12/22/2022] Open
Abstract
Background Although technological advances now allow increased tumor profiling, a detailed understanding of the mechanisms leading to the development of different cancers remains elusive. Our approach toward understanding the molecular events that lead to cancer is to characterize changes in transcriptional regulatory networks between normal and tumor tissue. Because enhancer activity is thought to be critical in regulating cell fate decisions, we have focused our studies on distal regulatory elements and transcription factors that bind to these elements. Results Using DNA methylation data, we identified more than 25,000 enhancers that are differentially activated in breast, prostate, and kidney tumor tissues, as compared to normal tissues. We then developed an analytical approach called Tracing Enhancer Networks using Epigenetic Traits that correlates DNA methylation levels at enhancers with gene expression to identify more than 800,000 genome-wide links from enhancers to genes and from genes to enhancers. We found more than 1200 transcription factors to be involved in these tumor-specific enhancer networks. We further characterized several transcription factors linked to a large number of enhancers in each tumor type, including GATA3 in non-basal breast tumors, HOXC6 and DLX1 in prostate tumors, and ZNF395 in kidney tumors. We showed that HOXC6 and DLX1 are associated with different clusters of prostate tumor-specific enhancers and confer distinct transcriptomic changes upon knockdown in C42B prostate cancer cells. We also discovered de novo motifs enriched in enhancers linked to ZNF395 in kidney tumors. Conclusions Our studies characterized tumor-specific enhancers and revealed key transcription factors involved in enhancer networks for specific tumor types and subgroups. Our findings, which include a large set of identified enhancers and transcription factors linked to those enhancers in breast, prostate, and kidney cancers, will facilitate understanding of enhancer networks and mechanisms leading to the development of these cancers. Electronic supplementary material The online version of this article (doi:10.1186/s13072-016-0102-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Suhn Kyong Rhie
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, 1450 Biggy Street, NRT G511B, Los Angeles, CA 90089-9601 USA
| | - Yu Guo
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, 1450 Biggy Street, NRT G511B, Los Angeles, CA 90089-9601 USA
| | - Yu Gyoung Tak
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, 1450 Biggy Street, NRT G511B, Los Angeles, CA 90089-9601 USA
| | - Lijing Yao
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, 1450 Biggy Street, NRT G511B, Los Angeles, CA 90089-9601 USA
| | - Hui Shen
- Van Andel Research Institute, Grand Rapids, MI 49503 USA
| | | | - Peter W Laird
- Van Andel Research Institute, Grand Rapids, MI 49503 USA
| | - Peggy J Farnham
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, 1450 Biggy Street, NRT G511B, Los Angeles, CA 90089-9601 USA
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29
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Functional characterization of open chromatin in bidirectional promoters of rice. Sci Rep 2016; 6:32088. [PMID: 27558448 PMCID: PMC4997330 DOI: 10.1038/srep32088] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 08/02/2016] [Indexed: 02/05/2023] Open
Abstract
Bidirectional gene pairs tend to be highly coregulated and function in similar biological processes in eukaryotic genomes. Structural features and functional consequences of bidirectional promoters (BDPs) have received considerable attention among diverse species. However, the underlying mechanisms responsible for the bidirectional transcription and coexpression of BDPs remain poorly understood in plants. In this study, we integrated DNase-seq, RNA-seq, ChIP-seq and MNase-seq data and investigated the effect of physical DNase I hypersensitive site (DHS) positions on the transcription of rice BDPs. We found that the physical position of a DHS relative to the TSS of bidirectional gene pairs can affect the expression of the corresponding genes: the closer a DHS is to the TSS, the higher is the expression level of the genes. Most importantly, we observed that the distribution of DHSs plays a significant role in the regulation of transcription and the coexpression of gene pairs, which are possibly mediated by orchestrating the positioning of histone marks and canonical nucleosomes around BDPs. Our results demonstrate that the combined actions of chromatin structures with DHSs, which contain functional cis-elements for interaction with transcriptional machinery, may play an important role in the regulation of the bidirectional transcription or coexpression in rice BDPs. Our findings may help to enhance the understanding of DHSs in the regulation of bidirectional gene pairs.
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30
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Longacre M, Snyder NA, Housman G, Leary M, Lapinska K, Heerboth S, Willbanks A, Sarkar S. A Comparative Analysis of Genetic and Epigenetic Events of Breast and Ovarian Cancer Related to Tumorigenesis. Int J Mol Sci 2016; 17:E759. [PMID: 27213343 PMCID: PMC4881580 DOI: 10.3390/ijms17050759] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Revised: 05/02/2016] [Accepted: 05/12/2016] [Indexed: 01/02/2023] Open
Abstract
Breast cancer persists as the most common cause of cancer death in women worldwide. Ovarian cancer is also a significant source of morbidity and mortality, as the fifth leading cause of cancer death among women. This reflects the continued need for further understanding and innovation in cancer treatment. Though breast and ovarian cancer usually present as distinct clinical entities, the recent explosion of large-scale -omics research has uncovered many overlaps, particularly with respect to genetic and epigenetic alterations. We compared genetic, microenvironmental, stromal, and epigenetic changes common between breast and ovarian cancer cells, as well as the clinical relevance of these changes. Some of the most striking commonalities include genetic alterations of BRCA1 and 2, TP53, RB1, NF1, FAT3, MYC, PTEN, and PIK3CA; down regulation of miRNAs 9, 100, 125a, 125b, and 214; and epigenetic alterations such as H3K27me3, H3K9me2, H3K9me3, H4K20me3, and H3K4me. These parallels suggest shared features of pathogenesis. Furthermore, preliminary evidence suggests a shared epigenetic mechanism of oncogenesis. These similarities, warrant further investigation in order to ultimately inform development of more effective chemotherapeutics, as well as strategies to circumvent drug resistance.
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Affiliation(s)
| | - Nicole A Snyder
- Department of Genetics and Complex Diseases, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA.
| | - Genevieve Housman
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ 85281, USA.
| | - Meghan Leary
- Cancer Center, Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA.
| | - Karolina Lapinska
- Cancer Center, Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA.
| | - Sarah Heerboth
- School of Medicine, Vanderbilt University, Nashville, TN 37240, USA.
| | - Amber Willbanks
- Cancer Center, Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA.
| | - Sibaji Sarkar
- Cancer Center, Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA.
- Genome Science Institute, Boston University School of Medicine, Boston, MA 02118, USA.
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31
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Couch FJ, Kuchenbaecker KB, Michailidou K, Mendoza-Fandino GA, Nord S, Lilyquist J, Olswold C, Hallberg E, Agata S, Ahsan H, Aittomäki K, Ambrosone C, Andrulis IL, Anton-Culver H, Arndt V, Arun BK, Arver B, Barile M, Barkardottir RB, Barrowdale D, Beckmann L, Beckmann MW, Benitez J, Blank SV, Blomqvist C, Bogdanova NV, Bojesen SE, Bolla MK, Bonanni B, Brauch H, Brenner H, Burwinkel B, Buys SS, Caldes T, Caligo MA, Canzian F, Carpenter J, Chang-Claude J, Chanock SJ, Chung WK, Claes KBM, Cox A, Cross SS, Cunningham JM, Czene K, Daly MB, Damiola F, Darabi H, de la Hoya M, Devilee P, Diez O, Ding YC, Dolcetti R, Domchek SM, Dorfling CM, dos-Santos-Silva I, Dumont M, Dunning AM, Eccles DM, Ehrencrona H, Ekici AB, Eliassen H, Ellis S, Fasching PA, Figueroa J, Flesch-Janys D, Försti A, Fostira F, Foulkes WD, Friebel T, Friedman E, Frost D, Gabrielson M, Gammon MD, Ganz PA, Gapstur SM, Garber J, Gaudet MM, Gayther SA, Gerdes AM, Ghoussaini M, Giles GG, Glendon G, Godwin AK, Goldberg MS, Goldgar DE, González-Neira A, Greene MH, Gronwald J, Guénel P, Gunter M, Haeberle L, Haiman CA, Hamann U, Hansen TVO, Hart S, Healey S, Heikkinen T, Henderson BE, Herzog J, Hogervorst FBL, Hollestelle A, Hooning MJ, Hoover RN, Hopper JL, Humphreys K, Hunter DJ, Huzarski T, Imyanitov EN, Isaacs C, Jakubowska A, James P, Janavicius R, Jensen UB, John EM, Jones M, Kabisch M, Kar S, Karlan BY, Khan S, Khaw KT, Kibriya MG, Knight JA, Ko YD, Konstantopoulou I, Kosma VM, Kristensen V, Kwong A, Laitman Y, Lambrechts D, Lazaro C, Lee E, Le Marchand L, Lester J, Lindblom A, Lindor N, Lindstrom S, Liu J, Long J, Lubinski J, Mai PL, Makalic E, Malone KE, Mannermaa A, Manoukian S, Margolin S, Marme F, Martens JWM, McGuffog L, Meindl A, Miller A, Milne RL, Miron P, Montagna M, Mazoyer S, Mulligan AM, Muranen TA, Nathanson KL, Neuhausen SL, Nevanlinna H, Nordestgaard BG, Nussbaum RL, Offit K, Olah E, Olopade OI, Olson JE, Osorio A, Park SK, Peeters PH, Peissel B, Peterlongo P, Peto J, Phelan CM, Pilarski R, Poppe B, Pylkäs K, Radice P, Rahman N, Rantala J, Rappaport C, Rennert G, Richardson A, Robson M, Romieu I, Rudolph A, Rutgers EJ, Sanchez MJ, Santella RM, Sawyer EJ, Schmidt DF, Schmidt MK, Schmutzler RK, Schumacher F, Scott R, Senter L, Sharma P, Simard J, Singer CF, Sinilnikova OM, Soucy P, Southey M, Steinemann D, Stenmark-Askmalm M, Stoppa-Lyonnet D, Swerdlow A, Szabo CI, Tamimi R, Tapper W, Teixeira MR, Teo SH, Terry MB, Thomassen M, Thompson D, Tihomirova L, Toland AE, Tollenaar RAEM, Tomlinson I, Truong T, Tsimiklis H, Teulé A, Tumino R, Tung N, Turnbull C, Ursin G, van Deurzen CHM, van Rensburg EJ, Varon-Mateeva R, Wang Z, Wang-Gohrke S, Weiderpass E, Weitzel JN, Whittemore A, Wildiers H, Winqvist R, Yang XR, Yannoukakos D, Yao S, Zamora MP, Zheng W, Hall P, Kraft P, Vachon C, Slager S, Chenevix-Trench G, Pharoah PDP, Monteiro AAN, García-Closas M, Easton DF, Antoniou AC. Identification of four novel susceptibility loci for oestrogen receptor negative breast cancer. Nat Commun 2016; 7:11375. [PMID: 27117709 PMCID: PMC4853421 DOI: 10.1038/ncomms11375] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 03/21/2016] [Indexed: 02/02/2023] Open
Abstract
Common variants in 94 loci have been associated with breast cancer including 15 loci with genome-wide significant associations (P<5 × 10(-8)) with oestrogen receptor (ER)-negative breast cancer and BRCA1-associated breast cancer risk. In this study, to identify new ER-negative susceptibility loci, we performed a meta-analysis of 11 genome-wide association studies (GWAS) consisting of 4,939 ER-negative cases and 14,352 controls, combined with 7,333 ER-negative cases and 42,468 controls and 15,252 BRCA1 mutation carriers genotyped on the iCOGS array. We identify four previously unidentified loci including two loci at 13q22 near KLF5, a 2p23.2 locus near WDR43 and a 2q33 locus near PPIL3 that display genome-wide significant associations with ER-negative breast cancer. In addition, 19 known breast cancer risk loci have genome-wide significant associations and 40 had moderate associations (P<0.05) with ER-negative disease. Using functional and eQTL studies we implicate TRMT61B and WDR43 at 2p23.2 and PPIL3 at 2q33 in ER-negative breast cancer aetiology. All ER-negative loci combined account for ∼11% of familial relative risk for ER-negative disease and may contribute to improved ER-negative and BRCA1 breast cancer risk prediction.
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Affiliation(s)
- Fergus J. Couch
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota 55905, USA
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Karoline B. Kuchenbaecker
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Kyriaki Michailidou
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Gustavo A. Mendoza-Fandino
- Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida 33612, USA
| | - Silje Nord
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital, Radiumhospitalet, N-0310 Oslo, Norway
| | - Janna Lilyquist
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Curtis Olswold
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Emily Hallberg
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Simona Agata
- Immunology and Molecular Oncology Unit, Istituto Oncologico Veneto IOV—IRCCS, 20133 Padua, Italy
| | - Habibul Ahsan
- Department of Health Studies, The University of Chicago, Chicago, Illinois 60637, USA
- Comprehensive Cancer Center, The University of Chicago, Chicago, Illinois 60637, USA
- Departments of Medicine and Human Genetics, The University of Chicago, Chicago, Illinois 60637, USA
| | - Kristiina Aittomäki
- Department of Clinical Genetics, Helsinki University Central Hospital, 00029 Helsinki, Finland
| | - Christine Ambrosone
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, New York 14263, USA
| | - Irene L. Andrulis
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, Ontario, Canada M5G 1X5
- Departments of Molecular Genetics and Laboratory Medicine and Pathobiology, University of Toronto, Ontario, Canada M5B 1W8
| | - Hoda Anton-Culver
- Department of Epidemiology, University of California Irvine, Irvine, California, 92697, USA
| | - Volker Arndt
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Banu K. Arun
- University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Brita Arver
- Department of Oncology, Karolinska University Hospital, SE-17176 Stockholm, Sweden
| | - Monica Barile
- Division of Cancer Prevention and Genetics, Istituto Europeo di Oncologia, 20141 Milan, Italy
| | - Rosa B. Barkardottir
- Department of Pathology, Landspitali University Hospital and University of Iceland School of Medicine, 101 Reykjavik, Iceland
| | - Daniel Barrowdale
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Lars Beckmann
- Institute for Quality and Efficiency in Health Care (IQWiG), 50670 Cologne, Germany
| | - Matthias W. Beckmann
- University Breast Center Franconia, Department of Gynecology and Obstetrics, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Comprehensive Cancer Center Erlangen-EMN, 91054 Erlangen, Germany
| | - Javier Benitez
- Human Genetics Group, Human Cancer Genetics Program, Spanish National Cancer Centre (CNIO), 28029 Madrid, Spain
- Genotyping Unit (CeGen), Human Cancer Genetics Program, Spanish National Cancer Centre (CNIO), 28029 Madrid, Spain
- Biomedical Network on Rare Diseases (CIBERER), 28029 Madrid, Spain
| | - Stephanie V. Blank
- NYU Women's Cancer Program, New York University School of Medicine, New York, New York 10016, USA
| | - Carl Blomqvist
- Department of Oncology, University of Helsinki and Helsinki University Central Hospital, FI-00029 Helsinki, Finland
| | - Natalia V. Bogdanova
- Department of Radiation Oncology, Hannover Medical School, 30625 Hannover, Germany
| | - Stig E. Bojesen
- Copenhagen General Population Study, Herlev Hospital, Copenhagen University Hospital, 2730 Herlev, Denmark
| | - Manjeet K. Bolla
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Bernardo Bonanni
- Division of Cancer Prevention and Genetics, Istituto Europeo di Oncologia, 20141 Milan, Italy
| | - Hiltrud Brauch
- Dr Margarete Fischer-Bosch-Institute of Clinical Pharmacology, 70376 Stuttgart, Germany
- University of Tübingen 72074 Tübingen, Germany
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany
| | - Barbara Burwinkel
- Department of Obstetrics and Gynecology, University of Heidelberg, 69120 Heidelberg, Germany
| | - Saundra S. Buys
- Department of Medicine, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City Utah 84112, USA
| | - Trinidad Caldes
- Molecular Oncology Laboratory, Hospital Clinico San Carlos, IdISSC, Madrid 28040, Spain
| | - Maria A. Caligo
- Section of Genetic Oncology, Department of Laboratory Medicine, University and University Hospital of Pisa, I-56126 Pisa, Italy
| | - Federico Canzian
- Genomic Epidemiology Group, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Jane Carpenter
- Australian Breast Cancer Tissue Bank, Westmead Millennium Institute, University of Sydney, Sydney, New South Wales 2145, Australia
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Stephen J. Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland 20850, USA
| | - Wendy K. Chung
- Departments of Pediatrics and Medicine, Columbia University, New York, New York 10032, USA
| | | | - Angela Cox
- Sheffield Cancer Research Centre, Department of Oncology, University of Sheffield, Sheffield S10 2RX, UK
| | - Simon S. Cross
- Academic Unit of Pathology, Department of Neuroscience, University of Sheffield, Sheffield S10 2HQ, UK
| | - Julie M. Cunningham
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Kamila Czene
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, SE-17177 Stockholm, Sweden
| | - Mary B. Daly
- Department of Clinical Genetics, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
| | - Francesca Damiola
- INSERM U1052, CNRS UMR5286, Université Lyon, Centre de Recherche en Cancérologie de Lyon, 69373 Lyon, France
| | - Hatef Darabi
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, SE-17177 Stockholm, Sweden
| | - Miguel de la Hoya
- Molecular Oncology Laboratory, Hospital Clinico San Carlos, IdISSC, Madrid 28040, Spain
| | - Peter Devilee
- Department of Human Genetics and Department of Pathology, Leiden University Medical Center, Leiden 2333 ZC, The Netherlands
| | - Orland Diez
- Oncogenetics Group, University Hospital Vall d'Hebron, Vall d'Hebron Institute of Oncology (VHIO) and Universitat Autònoma de Barcelona, 08035 Barcelona, Spain
| | - Yuan C. Ding
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, California 91010, USA
| | - Riccardo Dolcetti
- Cancer Bioimmunotherapy Unit, CRO Aviano National Cancer Institute, 33081 Aviano , Italy
| | - Susan M. Domchek
- Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Pennsylvania 19104, USA
| | | | - Isabel dos-Santos-Silva
- Department of Non-Communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Martine Dumont
- Cancer Genomics Laboratory, Centre Hospitalier Universitaire de Québec and Laval University, Quebec City, Quebec, Canada G1V 4G2
| | - Alison M. Dunning
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Diana M. Eccles
- Faculty of Medicine, University of Southampton, University Hospital Southampton, Southampton, Hampshire SO16 6YD, UK
| | - Hans Ehrencrona
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala SE-751 85, Sweden
- Department of Clinical Genetics, Lund University Hospital, SE-22185 Lund, Sweden
| | - Arif B. Ekici
- Institute of Human Genetics, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, 91054 Erlangen, Germany
- Comprehensive Cancer Center -EMN, 91054 Erlangen, Germany
| | - Heather Eliassen
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
- Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts 02115, USA
| | - Steve Ellis
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Peter A. Fasching
- University Breast Center Franconia, Department of Gynecology and Obstetrics, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Comprehensive Cancer Center Erlangen-EMN, 91054 Erlangen, Germany
| | - Jonine Figueroa
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland 20850, USA
| | - Dieter Flesch-Janys
- Department of Cancer Epidemiology/Clinical Cancer Registry and Institute for Medical Biometrics and Epidemiology, University Clinic Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Asta Försti
- Division of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Center for Primary Health Care Research, Lund University, SE-221 00 Malmö, Sweden
| | - Florentia Fostira
- Molecular Diagnostics Laboratory, INRASTES, National Centre for Scientific Research ‘Demokritos', Aghia Paraskevi Attikis, 15310 Athens, Greece
| | - William D. Foulkes
- Program in Cancer Genetics, McGill University, Montreal, Quebec, Canada H3A 0G4
| | - Tara Friebel
- University of, Philadelphia, Pennsylvania 19104, USA
| | - Eitan Friedman
- Susanne Levy Gertner Oncogenetics Unit, Sheba Medical Center, Tel-Hashomer 52621, Israel
| | - Debra Frost
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Marike Gabrielson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, SE-17177 Stockholm, Sweden
| | - Marilie D. Gammon
- Department of Epidemiology, University of, Chapel Hill, North Carolina 27599-7400, USA
| | - Patricia A. Ganz
- UCLA Schools of Medicine and Public Health, Division of Cancer Prevention and Control Research, Jonsson Comprehensive Cancer Center, Los Angeles, California 90095-6900, USA
| | - Susan M. Gapstur
- Epidemiology Research Program, American Cancer Society, Atlanta, Georgia 30303, USA
| | - Judy Garber
- Cancer Risk and Prevention Clinic, Dana Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Mia M. Gaudet
- Epidemiology Research Program, American Cancer Society, Atlanta, Georgia 30303, USA
| | - Simon A. Gayther
- Department of Biomedical Sciences, Cedars Sinai Medical Center, Los Angeles, California 90048, USA
| | - Anne-Marie Gerdes
- Department of Clinical Genetics, Rigshospitalet, Copenhagen University Hospital, DK-2100 Copenhagen, Denmark
| | - Maya Ghoussaini
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Graham G. Giles
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Victoria 3010, Australia
| | - Gord Glendon
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, Ontario, Canada M5G 1X5
| | - Andrew K. Godwin
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, Kansas, 66205, USA
| | - Mark S. Goldberg
- Department of Medicine, McGill University, Montreal, Quebec, Canada H3G 2M1
- Division of Clinical Epidemiology, McGill University Health Centre, Royal Victoria Hospital, Montreal, Quebec, Canada H4A 3J1
| | - David E. Goldgar
- Department of Dermatology, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah 84132, USA
| | - Anna González-Neira
- Human Genotyping-CEGEN Unit, Human Cancer Genetics Program, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain
| | - Mark H. Greene
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, Maryland 20850-9772, USA
| | - Jacek Gronwald
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Pascal Guénel
- Inserm (National Institute of Health and Medical Research), CESP (Center for Research in Epidemiology and Population Health), U1018, Environmental Epidemiology of Cancer, 70-115 Villejuif, France
| | - Marc Gunter
- Department of of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, SW7 2AZ, UK
| | - Lothar Haeberle
- University Breast Center Franconia, Department of Gynecology and Obstetrics, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Comprehensive Cancer Center Erlangen-EMN, 91054 Erlangen, Germany
| | - Christopher A. Haiman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, California 90033, USA
| | - Ute Hamann
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Thomas V. O. Hansen
- Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, DK-2100 Copenhagen, Denmark
| | - Steven Hart
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Sue Healey
- Department of Genetics, QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4029, Australia
| | - Tuomas Heikkinen
- Department of Obstetrics and Gynecology, University of Heidelberg, 69120 Heidelberg, Germany
- Helsinki University Central Hospital, FI-00029 Helsinki, Finland
| | - Brian E. Henderson
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, California 90033, USA
| | - Josef Herzog
- Clinical Cancer Genetics, for the City of Hope Clinical Cancer Genetics Community Research Network, Duarte, California 91010, USA
| | | | - Antoinette Hollestelle
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam 3008 AE, The Netherlands
| | - Maartje J. Hooning
- Department of Medical Oncology, Family Cancer Clinic, Erasmus University Medical Center, Rotterdam 3008 AE, The Netherlands
| | - Robert N. Hoover
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland 20850, USA
| | - John L. Hopper
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Keith Humphreys
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, SE-17177 Stockholm, Sweden
| | - David J. Hunter
- Program in Molecular and Genetic Epidemiology, Harvard School of Public Health, Boston, Massachusetts 02115, USA
| | - Tomasz Huzarski
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | | | - Claudine Isaacs
- Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20007, USA
| | - Anna Jakubowska
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Paul James
- Familial Cancer Centre, Peter MacCallum Cancer Centre, Melbourne, Victoria 8006, Australia
- Department of Oncology, The University of Melbourne, Melbourne, Victoria 8006, Australia
| | - Ramunas Janavicius
- State Research Institute Centre for Innovative Medicine, LT-08661 Vilnius, Lithuania
| | - Uffe Birk Jensen
- Department of Clinical Genetics, Aarhus University Hospital, 8200 Aarhus N, Denmark
| | - Esther M. John
- Department of Epidemiology, Cancer Prevention Institute of California, Fremont, California 94538, USA
| | - Michael Jones
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton SM2 5NG, UK
| | - Maria Kabisch
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Siddhartha Kar
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Beth Y. Karlan
- Women's Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California, 90048, USA
| | - Sofia Khan
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Central Hospital, FI-00029 Helsinki, Finland
| | - Kay-Tee Khaw
- Department of Public Health and Primary Care, University of Cambridge, Strangeways Research Laboratory, Cambridge CB1 8RN, UK
| | - Muhammad G. Kibriya
- Department of Health Studies, The University of Chicago, Chicago, Illinois 60637, USA
| | - Julia A. Knight
- Prosserman Centre for Health Research, Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, Ontario, Canada M5G 1X5
| | - Yon-Dschun Ko
- Department of Internal Medicine, Evangelische Kliniken Bonn gGmbH, Johanniter Krankenhaus, 53113 Bonn, Germany
| | - Irene Konstantopoulou
- Molecular Diagnostics Laboratory, INRASTES, National Centre for Scientific Research ‘Demokritos', Aghia Paraskevi Attikis, 15310 Athens, Greece
| | - Veli-Matti Kosma
- School of Medicine, Institute of Clinical Medicine, Pathology and Forensic Medicine, University of Eastern Finland, FI-70211 Kuopio, Finland
| | - Vessela Kristensen
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital, Radiumhospitalet, N-0310 Oslo, Norway
| | - Ava Kwong
- The Hong Kong Hereditary Breast Cancer Family Registry, Cancer Genetics Center, Hong Kong Sanatorium and Hospital, Hong Kong
- Department of Surgery, The University of Hong Kong, Hong Kong, China
| | - Yael Laitman
- Susanne Levy Gertner Oncogenetics Unit, Sheba Medical Center, Tel-Hashomer 52621, Israel
| | | | - Conxi Lazaro
- Molecular Diagnostic Unit, Hereditary Cancer Program, IDIBELL-Catalan Institute of Oncology, 08908 Barcelona, Spain
| | - Eunjung Lee
- Department of Preventive Medicine, University of Southern California, Los Angeles, California 90032, USA
| | - Loic Le Marchand
- Cancer Epidemiology Program, University of Cancer Center, Honolulu, Hawaii 96813, USA
| | - Jenny Lester
- Women's Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California, 90048, USA
| | - Annika Lindblom
- Department of Molecular Medicine and Surgery, Karolinska Institutet, SE-17177 Stockholm, Sweden
| | - Noralane Lindor
- Health Sciences Research, Mayo Clinic, Scotsdale, Arizona 85259, USA
| | - Sara Lindstrom
- Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts 02115, USA
- Program in Genetic Epidemiology and Statistical Genetics, Harvard School of Public Health, Boston, Massachusetts 02115, USA
| | - Jianjun Liu
- Human Genetics Division, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Jirong Long
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center and Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee 37203, USA
| | - Jan Lubinski
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Phuong L. Mai
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, Maryland 20850-9772, USA
| | - Enes Makalic
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Kathleen E. Malone
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
- Department of Epidemiology, School of Public Health and Community Medicine, University of Washington, Seattle, Washington 98195, USA
| | - Arto Mannermaa
- School of Medicine, Institute of Clinical Medicine, Pathology and Forensic Medicine, University of Eastern Finland, FI-70211 Kuopio, Finland
| | - Siranoush Manoukian
- Unit of Medical Genetics, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale Tumori (INT), 20133 Milan, Italy
| | - Sara Margolin
- Department of Oncology, Karolinska University Hospital, SE-17176 Stockholm, Sweden
| | - Frederik Marme
- Department of Obstetrics and Gynecology, University of Heidelberg, 69120 Heidelberg, Germany
| | - John W. M. Martens
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam 3008 AE, The Netherlands
| | - Lesley McGuffog
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Alfons Meindl
- Department of Gynaecology and Obstetrics, Technical University of Munich, 81675 Munich, Germany
| | - Austin Miller
- NRG Oncology Statistics and Data Management Center, Roswell Park Cancer Institute, Buffalo, New York 14263, USA
| | - Roger L. Milne
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Victoria 3010, Australia
| | - Penelope Miron
- Department of Genomics and Genome Sciences, Case Western Reserve University Medical School, Cleveland, Ohio 44106, USA
| | - Marco Montagna
- Immunology and Molecular Oncology Unit, Istituto Oncologico Veneto IOV—IRCCS, 20133 Padua, Italy
| | - Sylvie Mazoyer
- INSERM U1052, CNRS UMR5286, Université Lyon, Centre de Recherche en Cancérologie de Lyon, 69373 Lyon, France
| | - Anna M. Mulligan
- Laboratory Medicine Program, University Health Network, Toronto, Ontario, Canada M5B 1W8
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada M5B 1W8
| | - Taru A. Muranen
- Department of Obstetrics and Gynecology, University of Heidelberg, 69120 Heidelberg, Germany
- Helsinki University Central Hospital, FI-00029 Helsinki, Finland
| | - Katherine L. Nathanson
- Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Pennsylvania 19104, USA
| | - Susan L. Neuhausen
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, California 91010, USA
| | - Heli Nevanlinna
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Central Hospital, FI-00029 Helsinki, Finland
| | - Børge G. Nordestgaard
- Copenhagen General Population Study, Herlev Hospital, Copenhagen University Hospital, 2730 Herlev, Denmark
| | | | - Kenneth Offit
- Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA
| | - Edith Olah
- Department of Molecular Genetics, National Institute of Oncology, H-1122 Budapest, Hungary
| | - Olufunmilayo I. Olopade
- Center for Clinical Cancer Genetics and Global Health, University of Chicago Medical Center, Chicago, Illinois 60637, USA
| | - Janet E. Olson
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Ana Osorio
- Human Genetics Group, Human Cancer Genetics Program, Spanish National Cancer Centre (CNIO), 28029 Madrid, Spain
| | - Sue K. Park
- Department of Preventive Medicine and Biomedical Science, Seoul National University College of Medicine and Cancer Research Institute, Seoul National University, 110-799 Seoul, Republic of Korea
| | - Petra H. Peeters
- Department of Epidemiology, Julius Center for Health Sciences and Primary Care, University Medical Center, Utrecht 3508 GA, The Netherlands
- MRC-PHE Centre for Environment and Health, Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London SW7 2AZ, UK
| | - Bernard Peissel
- Unit of Medical Genetics, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale Tumori (INT), 20133 Milan, Italy
| | - Paolo Peterlongo
- IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, 20133 Milan, Italy
| | - Julian Peto
- Department of Non-Communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Catherine M. Phelan
- Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida 33612, USA
| | - Robert Pilarski
- Divison of Human Genetics, Department of Internal Medicine, The Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, USA
| | - Bruce Poppe
- Center for Medical Genetics, Ghent University, 9000 Ghent, Belgium
| | - Katri Pylkäs
- Laboratory of Cancer Genetics and Tumor Biology, Department of Clinical Chemistry and Biocenter Oulu, University of Oulu, NordLab Oulu/Oulu University Hospital, FI-90220 Oulu, Finland
| | - Paolo Radice
- Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale Tumori (INT), 20133 Milan, Italy
| | - Nazneen Rahman
- Section of Cancer Genetics, Institute of Cancer Research, Sutton SM2 5NG, UK
| | - Johanna Rantala
- Department of Clinical Genetics, Karolinska University Hospital, SE-17176 Stockholm, Sweden
| | - Christine Rappaport
- Department of Obstetrics and Gynecology, Comprehensive Cancer Center, Medical University of Vienna, A 1090 Vienna, Austria
| | - Gad Rennert
- Clalit National Israeli Cancer Control Center and Department of Community Medicine and Epidemiology, Carmel Medical Center and B. Rappaport Faculty of Medicine, Haifa 34362, Israel
| | - Andrea Richardson
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, 21205, USA
| | - Mark Robson
- Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA
| | - Isabelle Romieu
- International Agency for Research on Cancer, 69008 Lyon, France
| | - Anja Rudolph
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Emiel J. Rutgers
- Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, Amsterdam 1006 BE, The Netherlands
| | - Maria-Jose Sanchez
- Escuela Andaluza de Salud Pública. Instituto de Investigación Biosanitaria ibs.GRANADA, Hospitales Universitarios de Granada/Universidad de Granada, 18014 Granada, Spain
- CIBER de Epidemiología y Salud Pública (CIBERESP), Spain
| | - Regina M. Santella
- Department of Environmental Health Sciences, Columbia University, New York, New York, 10032, USA
| | - Elinor J. Sawyer
- Research Oncology, Division of Cancer Studies, King's College London, Guy's Hospital, London SE1 9RT, UK
| | - Daniel F. Schmidt
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Marjanka K. Schmidt
- Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, Amsterdam 1006 BE, The Netherlands
| | - Rita K. Schmutzler
- Center for Hereditary Breast and Ovarian Cancer, Medical Faculty, University Hospital Cologne, Cologne 50931, Germany
- Center for Integrated Oncology (CIO), Medical Faculty, University Hospital Cologne, 50931 Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany
| | - Fredrick Schumacher
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, California 90033, USA
| | - Rodney Scott
- Division of Genetics, Hunter Area Pathology Service, John Hunter Hospital, Newcastle, New South Wales 2305, Australia
| | - Leigha Senter
- Divison of Human Genetics, Department of Internal Medicine, The Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, USA
| | - Priyanka Sharma
- Department of Hematology and Oncology, University of Kansas Medical Center, Kansas City, Kansas 66205, USA
| | - Jacques Simard
- Centre Hospitalier Universitaire de Québec Research Center, Laval University, Quebec City, Quebec, Canada G1V 4G2
| | - Christian F. Singer
- Department of Obstetrics and Gynecology, Comprehensive Cancer Center, Medical University of Vienna, A 1090 Vienna, Austria
| | - Olga M. Sinilnikova
- INSERM U1052, CNRS UMR5286, Université Lyon, Centre de Recherche en Cancérologie de Lyon, 69373 Lyon, France
- Unité Mixte de Génétique Constitutionnelle des Cancers Fréquents, Hospices Civils de Lyon—Centre Léon Bérard, 69373 Lyon, France
| | - Penny Soucy
- Centre Hospitalier Universitaire de Québec Research Center, Laval University, Quebec City, Quebec, Canada G1V 4G2
| | - Melissa Southey
- Department of Pathology, The University of Melbourne, Melbourne, Victoria, Australia
| | | | - Marie Stenmark-Askmalm
- Division of Clinical Genetics, Department of Clinical and Experimental Medicine, Linköping University, SE-58185 Linköping, Sweden
| | - Dominique Stoppa-Lyonnet
- Institut Curie, Department of Tumour Biology, 75248 Paris, France
- Université Paris Descartes, Sorbonne Paris Cité, 75248 Paris, France
| | - Anthony Swerdlow
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton SM2 5NG, UK
| | - Csilla I. Szabo
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892-2152, USA
| | - Rulla Tamimi
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
- Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts 02115, USA
- Program in Genetic Epidemiology and Statistical Genetics, Harvard School of Public Health, Boston, Massachusetts 02115, USA
| | - William Tapper
- Faculty of Medicine, University of Southampton, University Hospital Southampton, Southampton, Hampshire SO16 6YD, UK
| | - Manuel R. Teixeira
- Department of Genetics, Portuguese Oncology Institute, Porto, 4200-072, Portugal
- Biomedical Sciences Institute (ICBAS), Porto University, 4200-072 Porto, Portugal
| | - Soo-Hwang Teo
- Cancer Research Initiatives Foundation, Sime Darby Medical Centre, Subang Jaya 47500, Malaysia
- University Malaya Cancer Research Institute, Faculty of Medicine, University Malaya Medical Centre, University Malaya, Kuala Lumpur 50603, Malaysia
| | - Mary B. Terry
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, New York, 10032, USA
| | - Mads Thomassen
- Department of Clinical Genetics, Odense University Hospital, 5000 Odense C, Denmark
| | - Deborah Thompson
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Laima Tihomirova
- Latvian Biomedical Research and Study Centre, LV-1067 Riga, Latvia
| | - Amanda E. Toland
- Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State University, Columbus, Ohio, 43210, USA
| | | | - Ian Tomlinson
- Wellcome Trust Centre for Human Genetics and Oxford Biomedical Research Centre, University of Oxford, Oxford OX3 7BN, UK
| | - Thérèse Truong
- Inserm (National Institute of Health and Medical Research), CESP (Center for Research in Epidemiology and Population Health), U1018, Environmental Epidemiology of Cancer, 70-115 Villejuif, France
| | - Helen Tsimiklis
- Department of Pathology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Alex Teulé
- Genetic Counseling Unit, Hereditary Cancer Program, IDIBELL-Catalan Institute of Oncology, 08908 Barcelona, Spain
| | - Rosario Tumino
- Cancer Registry and Histopathology Unit, ‘Civic—M.P. Arezzo' Hospital, 97100 ASP Ragusa, Italy
| | - Nadine Tung
- Department of Medical Oncology, Beth Israel Deaconess Medical Center, Boston, Massachusetts, 02215, USA
| | - Clare Turnbull
- Section of Cancer Genetics, Institute of Cancer Research, Sutton SM2 5NG, UK
| | - Giski Ursin
- Cancer Registry of Norway, Institute of Population-Based Cancer Research, N-0304 Oslo, Norway
| | - Carolien H. M. van Deurzen
- Department of Pathology, Family Cancer Clinic, Erasmus University Medical Center, Rotterdam 3000 CA, The Netherlands
| | | | | | - Zhaoming Wang
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Gaithersburg, Maryland 20877, USA
| | | | - Elisabete Weiderpass
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, SE-17177 Stockholm, Sweden
- Cancer Registry of Norway, Institute of Population-Based Cancer Research, N-0304 Oslo, Norway
- Department of Community Medicine, Faculty of Health Sciences, University of Tromsø—The Arctic University of Norway, 9037 Tromsø, Norway
- Genetic Epidemiology Group, Folkhälsan Research Center, 2016 Helsinki, Finland
| | - Jeffrey N. Weitzel
- Clinical Cancer Genetics, for the City of Hope Clinical Cancer Genetics Community Research Network, Duarte, California 91010, USA
| | - Alice Whittemore
- Department of Health Research and Policy—Epidemiology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Hans Wildiers
- Multidisciplinary Breast Center, Department of General Medical Oncology, University Hospitals, B-3000 Leuven, Belgium
| | - Robert Winqvist
- Laboratory of Cancer Genetics and Tumor Biology, Department of Clinical Chemistry and Biocenter Oulu, University of Oulu, NordLab Oulu/Oulu University Hospital, FI-90220 Oulu, Finland
| | - Xiaohong R. Yang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Drakoulis Yannoukakos
- Molecular Diagnostics Laboratory, INRASTES, National Centre for Scientific Research ‘Demokritos', Aghia Paraskevi Attikis, 15310 Athens, Greece
| | - Song Yao
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, New York 14263, USA
| | - M Pilar Zamora
- Servicio de Oncología Médica, Hospital Universitario La Paz, 28046 Madrid, Spain
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center and Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee 37203, USA
| | - Per Hall
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, SE-17177 Stockholm, Sweden
| | - Peter Kraft
- Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts 02115, USA
- Program in Genetic Epidemiology and Statistical Genetics, Harvard School of Public Health, Boston, Massachusetts 02115, USA
- Department of Biostatistics, Harvard School Of Public Health, Boston, Massachusetts 02115, USA
| | - Celine Vachon
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Susan Slager
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Georgia Chenevix-Trench
- Cancer Division, QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4029, Australia
| | - Paul D. P. Pharoah
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Alvaro A. N. Monteiro
- Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida 33612, USA
| | - Montserrat García-Closas
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, Maryland 20850, USA
| | - Douglas F. Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Antonis C. Antoniou
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
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Hardy K, Wu F, Tu W, Zafar A, Boulding T, McCuaig R, Sutton CR, Theodoratos A, Rao S. Identification of chromatin accessibility domains in human breast cancer stem cells. Nucleus 2016; 7:50-67. [PMID: 26962893 PMCID: PMC4916893 DOI: 10.1080/19491034.2016.1150392] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Epithelial-to-mesenchymal transition (EMT) is physiological in embryogenesis and wound healing but also associated with the formation of cancer stem cells (CSCs). Many EMT signaling pathways are implicated in CSC formation, but the precise underlying mechanisms of CSC formation remain elusive. We have previously demonstrated that PKC is critical for EMT induction and CSC formation in inducible breast EMT/CSC models. Here, we used formaldehyde-assisted isolation of regulatory elements-sequencing (FAIRE-seq) to investigate DNA accessibility changes after PKC activation and determine how they influence EMT and CSC formation. During EMT, DNA accessibility principally increased in regions distant from transcription start sites, low in CpG content, and enriched with chromatin enhancer marks. ChIP-sequencing revealed that a subset of these regions changed from poised to active enhancers upon stimulation, with some even more acteylated in CSCs. While regions with increased accessibility were enriched for FOX, AP-1, TEAD, and TFAP2 motifs, those containing FOX and AP-1 motif were associated with increased expression of CSC-associated genes, while those with TFAP2 were associated with genes with increased expression in non-CSCs. Silencing of 2 members of the FOX family, FOXN2 and FOXQ1, repressed CSCs and the mesenchymal phenotype and inhibited the CSC gene signature. These novel, PKC-induced DNA accessibility regions help explain how the epigenomic plasticity of cells undergoing EMT leads to CSC gene activation.
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Affiliation(s)
- K Hardy
- a HRI, Faculty of ESTeM, University of Canberra , Bruce , Australia
| | - F Wu
- a HRI, Faculty of ESTeM, University of Canberra , Bruce , Australia
| | - W Tu
- a HRI, Faculty of ESTeM, University of Canberra , Bruce , Australia
| | - A Zafar
- a HRI, Faculty of ESTeM, University of Canberra , Bruce , Australia
| | - T Boulding
- a HRI, Faculty of ESTeM, University of Canberra , Bruce , Australia
| | - R McCuaig
- a HRI, Faculty of ESTeM, University of Canberra , Bruce , Australia
| | - C R Sutton
- a HRI, Faculty of ESTeM, University of Canberra , Bruce , Australia
| | - A Theodoratos
- b JCSMR, Australian National University , Canberra, Australia
| | - S Rao
- a HRI, Faculty of ESTeM, University of Canberra , Bruce , Australia
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Han Y, Hazelett DJ, Wiklund F, Schumacher FR, Stram DO, Berndt SI, Wang Z, Rand KA, Hoover RN, Machiela MJ, Yeager M, Burdette L, Chung CC, Hutchinson A, Yu K, Xu J, Travis RC, Key TJ, Siddiq A, Canzian F, Takahashi A, Kubo M, Stanford JL, Kolb S, Gapstur SM, Diver WR, Stevens VL, Strom SS, Pettaway CA, Al Olama AA, Kote-Jarai Z, Eeles RA, Yeboah ED, Tettey Y, Biritwum RB, Adjei AA, Tay E, Truelove A, Niwa S, Chokkalingam AP, Isaacs WB, Chen C, Lindstrom S, Le Marchand L, Giovannucci EL, Pomerantz M, Long H, Li F, Ma J, Stampfer M, John EM, Ingles SA, Kittles RA, Murphy AB, Blot WJ, Signorello LB, Zheng W, Albanes D, Virtamo J, Weinstein S, Nemesure B, Carpten J, Leske MC, Wu SY, Hennis AJM, Rybicki BA, Neslund-Dudas C, Hsing AW, Chu L, Goodman PJ, Klein EA, Zheng SL, Witte JS, Casey G, Riboli E, Li Q, Freedman ML, Hunter DJ, Gronberg H, Cook MB, Nakagawa H, Kraft P, Chanock SJ, Easton DF, Henderson BE, Coetzee GA, Conti DV, Haiman CA. Integration of multiethnic fine-mapping and genomic annotation to prioritize candidate functional SNPs at prostate cancer susceptibility regions. Hum Mol Genet 2015; 24:5603-18. [PMID: 26162851 PMCID: PMC4572069 DOI: 10.1093/hmg/ddv269] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Accepted: 07/07/2015] [Indexed: 01/27/2023] Open
Abstract
Interpretation of biological mechanisms underlying genetic risk associations for prostate cancer is complicated by the relatively large number of risk variants (n = 100) and the thousands of surrogate SNPs in linkage disequilibrium. Here, we combined three distinct approaches: multiethnic fine-mapping, putative functional annotation (based upon epigenetic data and genome-encoded features), and expression quantitative trait loci (eQTL) analyses, in an attempt to reduce this complexity. We examined 67 risk regions using genotyping and imputation-based fine-mapping in populations of European (cases/controls: 8600/6946), African (cases/controls: 5327/5136), Japanese (cases/controls: 2563/4391) and Latino (cases/controls: 1034/1046) ancestry. Markers at 55 regions passed a region-specific significance threshold (P-value cutoff range: 3.9 × 10(-4)-5.6 × 10(-3)) and in 30 regions we identified markers that were more significantly associated with risk than the previously reported variants in the multiethnic sample. Novel secondary signals (P < 5.0 × 10(-6)) were also detected in two regions (rs13062436/3q21 and rs17181170/3p12). Among 666 variants in the 55 regions with P-values within one order of magnitude of the most-associated marker, 193 variants (29%) in 48 regions overlapped with epigenetic or other putative functional marks. In 11 of the 55 regions, cis-eQTLs were detected with nearby genes. For 12 of the 55 regions (22%), the most significant region-specific, prostate-cancer associated variant represented the strongest candidate functional variant based on our annotations; the number of regions increased to 20 (36%) and 27 (49%) when examining the 2 and 3 most significantly associated variants in each region, respectively. These results have prioritized subsets of candidate variants for downstream functional evaluation.
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Affiliation(s)
- Ying Han
- Department of Preventive Medicine, Keck School of Medicine
| | | | - Fredrik Wiklund
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
| | - Fredrick R Schumacher
- Department of Preventive Medicine, Keck School of Medicine, Norris Comprehensive Cancer Center
| | - Daniel O Stram
- Department of Preventive Medicine, Keck School of Medicine, Norris Comprehensive Cancer Center
| | - Sonja I Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Zhaoming Wang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA, Cancer Genomics Research Laboratory, NCI-DCEG, SAIC-Frederick Inc., Frederick, MD, USA
| | - Kristin A Rand
- Department of Preventive Medicine, Keck School of Medicine
| | - Robert N Hoover
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Mitchell J Machiela
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Merideth Yeager
- Cancer Genomics Research Laboratory, NCI-DCEG, SAIC-Frederick Inc., Frederick, MD, USA
| | - Laurie Burdette
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA, Cancer Genomics Research Laboratory, NCI-DCEG, SAIC-Frederick Inc., Frederick, MD, USA
| | - Charles C Chung
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Amy Hutchinson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA, Cancer Genomics Research Laboratory, NCI-DCEG, SAIC-Frederick Inc., Frederick, MD, USA
| | - Kai Yu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jianfeng Xu
- Program for Personalized Cancer Care and Department of Surgery, NorthShore University HealthSystem, Evanston, IL, USA
| | - Ruth C Travis
- Cancer Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Timothy J Key
- Cancer Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Afshan Siddiq
- Department of Genomics of Common Disease, School of Public Health
| | - Federico Canzian
- Genomic Epidemiology Group, German Cancer Research Center, Heidelberg, Germany
| | | | | | - Janet L Stanford
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA, Department of Epidemiology, School of Public Health, University of Washington, Seattle, WA, USA
| | - Suzanne Kolb
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Susan M Gapstur
- Epidemiology Research Program, American Cancer Society, Atlanta, GA, USA
| | - W Ryan Diver
- Epidemiology Research Program, American Cancer Society, Atlanta, GA, USA
| | - Victoria L Stevens
- Epidemiology Research Program, American Cancer Society, Atlanta, GA, USA
| | | | - Curtis A Pettaway
- Department of Urology, University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Ali Amin Al Olama
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | | | - Rosalind A Eeles
- The Institute of Cancer Research, London, UK, Royal Marsden National Health Services (NHS) Foundation Trust, London and Sutton, UK
| | - Edward D Yeboah
- Korle Bu Teaching Hospital, Accra, Ghana, University of Ghana Medical School, Accra, Ghana
| | - Yao Tettey
- Korle Bu Teaching Hospital, Accra, Ghana, University of Ghana Medical School, Accra, Ghana
| | - Richard B Biritwum
- Korle Bu Teaching Hospital, Accra, Ghana, University of Ghana Medical School, Accra, Ghana
| | - Andrew A Adjei
- Korle Bu Teaching Hospital, Accra, Ghana, University of Ghana Medical School, Accra, Ghana
| | - Evelyn Tay
- Korle Bu Teaching Hospital, Accra, Ghana, University of Ghana Medical School, Accra, Ghana
| | | | | | | | - William B Isaacs
- James Buchanan Brady Urological Institute, Johns Hopkins Hospital and Medical Institution, Baltimore, MD, USA
| | - Constance Chen
- Program in Genetic Epidemiology and Statistical Genetics, Department of Epidemiology
| | - Sara Lindstrom
- Program in Genetic Epidemiology and Statistical Genetics, Department of Epidemiology
| | - Loic Le Marchand
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, USA
| | | | | | - Henry Long
- Department of Medical Oncology, Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Fugen Li
- Department of Medical Oncology, Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jing Ma
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Esther M John
- Cancer Prevention Institute of California, Fremont, CA, USA, Division of Epidemiology, Department of Health Research and Policy, and Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Sue A Ingles
- Department of Preventive Medicine, Keck School of Medicine, Norris Comprehensive Cancer Center
| | - Rick A Kittles
- University of Arizona College of Medicine and University of Arizona Cancer Center, Tucson, AZ, USA
| | - Adam B Murphy
- Department of Urology, Northwestern University, Chicago, IL, USA
| | - William J Blot
- International Epidemiology Institute, Rockville, MD, USA, Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | | | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Demetrius Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jarmo Virtamo
- Department of Chronic Disease Prevention, National Institute for Health and Welfare, Helsinki, Finland
| | - Stephanie Weinstein
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Barbara Nemesure
- Department of Preventive Medicine, Stony Brook University, Stony Brook, NY, USA
| | - John Carpten
- The Translational Genomics Research Institute, Phoenix, AZ, USA
| | - M Cristina Leske
- Department of Preventive Medicine, Stony Brook University, Stony Brook, NY, USA
| | - Suh-Yuh Wu
- Department of Preventive Medicine, Stony Brook University, Stony Brook, NY, USA
| | - Anselm J M Hennis
- Department of Preventive Medicine, Stony Brook University, Stony Brook, NY, USA, Chronic Disease Research Centre and Faculty of Medical Sciences, University of the West Indies, Bridgetown, Barbados
| | - Benjamin A Rybicki
- Department of Public Health Sciences, Henry Ford Hospital, Detroit, MI, USA
| | | | - Ann W Hsing
- Cancer Prevention Institute of California, Fremont, CA, USA, Division of Epidemiology, Department of Health Research and Policy, and Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Lisa Chu
- Cancer Prevention Institute of California, Fremont, CA, USA, Division of Epidemiology, Department of Health Research and Policy, and Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Phyllis J Goodman
- SWOG Statistical Center, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Eric A Klein
- Department of Urology, Glickman Urological and Kidney Institute, Cleveland Clinic, Cleveland, OH, USA
| | - S Lilly Zheng
- Center for Cancer Genomics, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - John S Witte
- Department of Epidemiology and Biostatistics, Institute for Human Genetics, University of California, San Francisco, CA, USA and
| | - Graham Casey
- Department of Preventive Medicine, Keck School of Medicine, Norris Comprehensive Cancer Center
| | - Elio Riboli
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College, London, UK
| | - Qiyuan Li
- Medical College, Xiamen University, Xiamen 361102, China
| | | | - David J Hunter
- Program in Genetic Epidemiology and Statistical Genetics, Department of Epidemiology
| | - Henrik Gronberg
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
| | - Michael B Cook
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Hidewaki Nakagawa
- Laboratory for Genome Sequencing Analysis, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan
| | - Peter Kraft
- Program in Genetic Epidemiology and Statistical Genetics, Department of Epidemiology, Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Douglas F Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Brian E Henderson
- Department of Preventive Medicine, Keck School of Medicine, Norris Comprehensive Cancer Center
| | - Gerhard A Coetzee
- Department of Preventive Medicine, Keck School of Medicine, Norris Comprehensive Cancer Center, Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - David V Conti
- Department of Preventive Medicine, Keck School of Medicine, Norris Comprehensive Cancer Center
| | - Christopher A Haiman
- Department of Preventive Medicine, Keck School of Medicine, Norris Comprehensive Cancer Center,
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Zanconato F, Forcato M, Battilana G, Azzolin L, Quaranta E, Bodega B, Rosato A, Bicciato S, Cordenonsi M, Piccolo S. Genome-wide association between YAP/TAZ/TEAD and AP-1 at enhancers drives oncogenic growth. Nat Cell Biol 2015; 17:1218-27. [PMID: 26258633 PMCID: PMC6186417 DOI: 10.1038/ncb3216] [Citation(s) in RCA: 776] [Impact Index Per Article: 86.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Accepted: 07/02/2015] [Indexed: 12/14/2022]
Abstract
YAP/TAZ are nuclear effectors of the Hippo pathway regulating organ growth and tumorigenesis. Yet, their function as transcriptional regulators remains underinvestigated. By ChIP-seq analyses in breast cancer cells, we discovered that the YAP/TAZ transcriptional response is pervasively mediated by a dual element: TEAD factors, through which YAP/TAZ bind to DNA, co-occupying chromatin with activator protein-1 (AP-1, dimer of JUN and FOS proteins) at composite cis-regulatory elements harbouring both TEAD and AP-1 motifs. YAP/TAZ/TEAD and AP-1 form a complex that synergistically activates target genes directly involved in the control of S-phase entry and mitosis. This control occurs almost exclusively from distal enhancers that contact target promoters through chromatin looping. YAP/TAZ-induced oncogenic growth is strongly enhanced by gain of AP-1 and severely blunted by its loss. Conversely, AP-1-promoted skin tumorigenesis is prevented in YAP/TAZ conditional knockout mice. This work highlights a new layer of signalling integration, feeding on YAP/TAZ function at the chromatin level.
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Affiliation(s)
- Francesca Zanconato
- Department of Molecular Medicine, University of Padua School of Medicine, viale Colombo 3, 35126 Padua, Italy
| | - Mattia Forcato
- Center for Genome Research, Department of Biomedical Sciences, University of Modena and Reggio Emilia, via G. Campi 287, 41100 Modena, Italy
| | - Giusy Battilana
- Department of Molecular Medicine, University of Padua School of Medicine, viale Colombo 3, 35126 Padua, Italy
| | - Luca Azzolin
- Department of Molecular Medicine, University of Padua School of Medicine, viale Colombo 3, 35126 Padua, Italy
| | - Erika Quaranta
- Department of Molecular Medicine, University of Padua School of Medicine, viale Colombo 3, 35126 Padua, Italy
| | - Beatrice Bodega
- Genome Biology Unit, Istituto Nazionale di Genetica Molecolare (INGM) 'Romeo and Enrica Invernizzi', via Francesco Sforza 35, Milan 20126, Italy
| | - Antonio Rosato
- Department of Surgery, Oncology and Gastroenterology, University of Padua School of Medicine, Via Gattamelata 64, 35126 Padua, Italy
- Istituto Oncologico Veneto IRCCS, Via Gattamelata 64, 35126 Padua, Italy
| | - Silvio Bicciato
- Center for Genome Research, Department of Biomedical Sciences, University of Modena and Reggio Emilia, via G. Campi 287, 41100 Modena, Italy
| | - Michelangelo Cordenonsi
- Department of Molecular Medicine, University of Padua School of Medicine, viale Colombo 3, 35126 Padua, Italy
| | - Stefano Piccolo
- Department of Molecular Medicine, University of Padua School of Medicine, viale Colombo 3, 35126 Padua, Italy
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35
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Kazemian M, Ren M, Lin JX, Liao W, Spolski R, Leonard WJ. Comprehensive assembly of novel transcripts from unmapped human RNA-Seq data and their association with cancer. Mol Syst Biol 2015; 11:826. [PMID: 26253570 PMCID: PMC4562499 DOI: 10.15252/msb.156172] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Crucial parts of the genome including genes encoding microRNAs and noncoding RNAs went unnoticed for years, and even now, despite extensive annotation and assembly of the human genome, RNA-sequencing continues to yield millions of unmappable and thus uncharacterized reads. Here, we examined > 300 billion reads from 536 normal donors and 1,873 patients encompassing 21 cancer types, identified ∼300 million such uncharacterized reads, and using a distinctive approach de novo assembled 2,550 novel human transcripts, which mainly represent long noncoding RNAs. Of these, 230 exhibited relatively specific expression or non-expression in certain cancer types, making them potential markers for those cancers, whereas 183 exhibited tissue specificity. Moreover, we used lentiviral-mediated expression of three selected transcripts that had higher expression in normal than in cancer patients and found that each inhibited the growth of HepG2 cells. Our analysis provides a comprehensive and unbiased resource of unmapped human transcripts and reveals their associations with specific cancers, providing potentially important new genes for therapeutic targeting.
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Affiliation(s)
- Majid Kazemian
- Laboratory of Molecular Immunology and the Immunology Center, National Heart, Lung, and Blood Institute National Institutes of Health, Bethesda, MD, USA
| | - Min Ren
- Laboratory of Molecular Immunology and the Immunology Center, National Heart, Lung, and Blood Institute National Institutes of Health, Bethesda, MD, USA
| | - Jian-Xin Lin
- Laboratory of Molecular Immunology and the Immunology Center, National Heart, Lung, and Blood Institute National Institutes of Health, Bethesda, MD, USA
| | - Wei Liao
- Laboratory of Molecular Immunology and the Immunology Center, National Heart, Lung, and Blood Institute National Institutes of Health, Bethesda, MD, USA
| | - Rosanne Spolski
- Laboratory of Molecular Immunology and the Immunology Center, National Heart, Lung, and Blood Institute National Institutes of Health, Bethesda, MD, USA
| | - Warren J Leonard
- Laboratory of Molecular Immunology and the Immunology Center, National Heart, Lung, and Blood Institute National Institutes of Health, Bethesda, MD, USA
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Coetzee SG, Shen HC, Hazelett DJ, Lawrenson K, Kuchenbaecker K, Tyrer J, Rhie SK, Levanon K, Karst A, Drapkin R, Ramus SJ, Couch FJ, Offit K, Chenevix-Trench G, Monteiro ANA, Antoniou A, Freedman M, Coetzee GA, Pharoah PDP, Noushmehr H, Gayther SA. Cell-type-specific enrichment of risk-associated regulatory elements at ovarian cancer susceptibility loci. Hum Mol Genet 2015; 24:3595-607. [PMID: 25804953 PMCID: PMC4459387 DOI: 10.1093/hmg/ddv101] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 03/16/2015] [Indexed: 02/07/2023] Open
Abstract
Understanding the regulatory landscape of the human genome is a central question in complex trait genetics. Most single-nucleotide polymorphisms (SNPs) associated with cancer risk lie in non-protein-coding regions, implicating regulatory DNA elements as functional targets of susceptibility variants. Here, we describe genome-wide annotation of regions of open chromatin and histone modification in fallopian tube and ovarian surface epithelial cells (FTSECs, OSECs), the debated cellular origins of high-grade serous ovarian cancers (HGSOCs) and in endometriosis epithelial cells (EECs), the likely precursor of clear cell ovarian carcinomas (CCOCs). The regulatory architecture of these cell types was compared with normal human mammary epithelial cells and LNCaP prostate cancer cells. We observed similar positional patterns of global enhancer signatures across the three different ovarian cancer precursor cell types, and evidence of tissue-specific regulatory signatures compared to non-gynecological cell types. We found significant enrichment for risk-associated SNPs intersecting regulatory biofeatures at 17 known HGSOC susceptibility loci in FTSECs (P = 3.8 × 10(-30)), OSECs (P = 2.4 × 10(-23)) and HMECs (P = 6.7 × 10(-15)) but not for EECs (P = 0.45) or LNCaP cells (P = 0.88). Hierarchical clustering of risk SNPs conditioned on the six different cell types indicates FTSECs and OSECs are highly related (96% of samples using multi-scale bootstrapping) suggesting both cell types may be precursors of HGSOC. These data represent the first description of regulatory catalogues of normal precursor cells for different ovarian cancer subtypes, and provide unique insights into the tissue specific regulatory variation with respect to the likely functional targets of germline genetic susceptibility variants for ovarian cancer.
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Affiliation(s)
- Simon G Coetzee
- Department of Genetics - Ribeirão Preto Medical School, University of São Paulo, Avenida Bandeirantes 3900, Monte Alegre, Ribeirão Preto-SP CEP: 14049-900, Brazil, Center for Cell Based Therapy, Rua Tenente Catão Roxo, 2501, Monte Alegre, Ribeirão Preto, SP, CEP: 14051-140, Brazil
| | - Howard C Shen
- Department of Preventive Medicine, Keck School of Medicine and
| | - Dennis J Hazelett
- Department of Preventive Medicine, Keck School of Medicine and, Department of Urology, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, CA, USA
| | - Kate Lawrenson
- Department of Preventive Medicine, Keck School of Medicine and
| | - Karoline Kuchenbaecker
- Department of Oncology, Department of Public Health and Primary Care, University of Cambridge, Strangeways Research Laboratory, Cambridge, UK
| | - Jonathan Tyrer
- Department of Oncology, Department of Public Health and Primary Care, University of Cambridge, Strangeways Research Laboratory, Cambridge, UK
| | - Suhn K Rhie
- Department of Preventive Medicine, Keck School of Medicine and, Department of Urology, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, CA, USA
| | - Keren Levanon
- Sheba Cancer Research Center, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Alison Karst
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, USA
| | - Ronny Drapkin
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Susan J Ramus
- Department of Preventive Medicine, Keck School of Medicine and
| | - Fergus J Couch
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Kenneth Offit
- Clinical Genetics Service, Cancer Biology and Genetics Program, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Georgia Chenevix-Trench
- Department of Genetics and Computational Biology, Queensland Institute of Medical Research, Brisbane, Australia
| | - Alvaro N A Monteiro
- Cancer Epidemiology Program, Division of Population Sciences, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Antonis Antoniou
- Department of Oncology, Department of Public Health and Primary Care, University of Cambridge, Strangeways Research Laboratory, Cambridge, UK
| | - Matthew Freedman
- Department of Medical Oncology, The Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA and
| | - Gerhard A Coetzee
- Department of Preventive Medicine, Keck School of Medicine and, Department of Urology, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, CA, USA
| | - Paul D P Pharoah
- Department of Oncology, Department of Public Health and Primary Care, University of Cambridge, Strangeways Research Laboratory, Cambridge, UK
| | - Houtan Noushmehr
- Department of Genetics - Ribeirão Preto Medical School, University of São Paulo, Avenida Bandeirantes 3900, Monte Alegre, Ribeirão Preto-SP CEP: 14049-900, Brazil, Center for Cell Based Therapy, Rua Tenente Catão Roxo, 2501, Monte Alegre, Ribeirão Preto, SP, CEP: 14051-140, Brazil, Center for Integrative Systems Biology - CISBi, NAP/USP, Rua Catão Roxo, 2501, Monte Alegre, Ribeirão Preto, SP CEP: 14051-140, Brazil
| | - Simon A Gayther
- Department of Preventive Medicine, Keck School of Medicine and,
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Reschen ME, Gaulton KJ, Lin D, Soilleux EJ, Morris AJ, Smyth SS, O'Callaghan CA. Lipid-induced epigenomic changes in human macrophages identify a coronary artery disease-associated variant that regulates PPAP2B Expression through Altered C/EBP-beta binding. PLoS Genet 2015; 11:e1005061. [PMID: 25835000 PMCID: PMC4383549 DOI: 10.1371/journal.pgen.1005061] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Accepted: 02/09/2015] [Indexed: 01/17/2023] Open
Abstract
Genome-wide association studies (GWAS) have identified over 40 loci that affect risk of coronary artery disease (CAD) and the causal mechanisms at the majority of loci are unknown. Recent studies have suggested that many causal GWAS variants influence disease through altered transcriptional regulation in disease-relevant cell types. We explored changes in transcriptional regulation during a key pathophysiological event in CAD, the environmental lipid-induced transformation of macrophages to lipid-laden foam cells. We used a combination of open chromatin mapping with formaldehyde-assisted isolation of regulatory elements (FAIRE-seq) and enhancer and transcription factor mapping using chromatin immuno-precipitation (ChIP-seq) in primary human macrophages before and after exposure to atherogenic oxidized low-density lipoprotein (oxLDL), with resultant foam cell formation. OxLDL-induced foam cell formation was associated with changes in a subset of open chromatin and active enhancer sites that strongly correlated with expression changes of nearby genes. OxLDL-regulated enhancers were enriched for several transcription factors including C/EBP-beta, which has no previously documented role in foam cell formation. OxLDL exposure up-regulated C/EBP-beta expression and increased genomic binding events, most prominently around genes involved in inflammatory response pathways. Variants at CAD-associated loci were significantly and specifically enriched in the subset of chromatin sites altered by oxLDL exposure, including rs72664324 in an oxLDL-induced enhancer at the PPAP2B locus. OxLDL increased C/EBP beta binding to this site and C/EBP beta binding and enhancer activity were stronger with the protective A allele of rs72664324. In addition, expression of the PPAP2B protein product LPP3 was present in foam cells in human atherosclerotic plaques and oxLDL exposure up-regulated LPP3 in macrophages resulting in increased degradation of pro-inflammatory mediators. Our results demonstrate a genetic mechanism contributing to CAD risk at the PPAP2B locus and highlight the value of studying epigenetic changes in disease processes involving pathogenic environmental stimuli. Coronary artery disease is a complex disease where over 40 genomic loci contributing to genetic risk have been identified. However, identifying the precise variants, genomic elements and genes that mediate this risk at each locus has proved challenging. We hypothesized that some genetic risk variants may influence a key step in development of coronary artery disease, which occurs when macrophages encounter environmentally-derived lipid. These cells take up lipid and accumulate in atherosclerotic plaques in the walls of blood vessels where they contribute to the inflammatory atherosclerotic disease process. Therefore, we studied the effects of this lipid exposure on the genomic activity of these cells. Environmental lipid exposure triggered changes in transcriptional regulation and gene expression. Variants at coronary artery disease risk loci were enriched for genomic regions altered by lipid exposure. We studied one such risk variant rs72664324 in detail and found that it altered binding of the C/EBP-beta transcription factor and altered expression of the PPAP2B gene. PPAP2B encodes an enzyme that degrades pro-inflammatory substances. Our study demonstrates a hitherto unknown genetic mechanism underlying atherosclerotic heart disease and demonstrates the value of studying changes in transcriptional regulation in key disease processes involving environmental influences.
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Affiliation(s)
- Michael E. Reschen
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Kyle J. Gaulton
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Da Lin
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Elizabeth J. Soilleux
- Nuffield Department of Clinical Laboratory Sciences, University of Oxford and Department of Cellular Pathology, John Radcliffe Hospital, Oxford, United Kingdom
| | - Andrew J. Morris
- Division of Cardiovascular Medicine, The Gill Heart Institute, University of Kentucky, Lexington, Kentucky, United States of America
- Department of Veterans Affairs Medical Center, Lexington, Kentucky, United States of America
| | - Susan S. Smyth
- Division of Cardiovascular Medicine, The Gill Heart Institute, University of Kentucky, Lexington, Kentucky, United States of America
- Department of Veterans Affairs Medical Center, Lexington, Kentucky, United States of America
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Chopra M, Bohlander SK. Disturbing the histone code in leukemia: translocations and mutations affecting histone methyl transferases. Cancer Genet 2014; 208:192-205. [PMID: 25592767 DOI: 10.1016/j.cancergen.2014.10.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Revised: 10/01/2014] [Accepted: 10/14/2014] [Indexed: 10/24/2022]
Abstract
Leukemia is characterized by increased numbers of blasts originating from transformed early hematopoietic stem and progenitor cells. Genetic alterations are widely recognized as the main drivers of oncogenic transformation. Of considerable interest are mutations affecting the writers of epigenetic marks. In this review, we focus on histone methyltransferases--enzymes that catalyze the methylation of lysine residues in core histones. Histone methylation is a tightly controlled mechanism that is responsible for both activating as well as repressing gene expression in a site-specific manner, depending on which lysine residue is methylated. Histone methyltransferases, including MLL1, DOT1L, EZH2, and SETD2 are recurrently deregulated in human leukemia, either directly by gene mutations or balanced translocations, or indirectly as components of protein complexes that are disturbed in leukemia due to alterations of the other components in these complexes. Several small molecule inhibitors of histone methyltransferases are currently being clinically evaluated for their therapeutic potential in human leukemia. These drugs reverse some of the adverse effects of aberrant histone methylation, and can induce differentiation and cell death in leukemic blasts.
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Affiliation(s)
- Martin Chopra
- Department of Molecular Medicine and Pathology, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand
| | - Stefan K Bohlander
- Department of Molecular Medicine and Pathology, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand.
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