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Yan H, Tian S, Kleinstern G, Wang Z, Lee JH, Boddicker NJ, Cerhan JR, Kay NE, Braggio E, Slager SL. Chronic lymphocytic leukemia (CLL) risk is mediated by multiple enhancer variants within CLL risk loci. Hum Mol Genet 2021; 29:2761-2774. [PMID: 32744316 DOI: 10.1093/hmg/ddaa165] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 07/02/2020] [Accepted: 07/25/2020] [Indexed: 12/12/2022] Open
Abstract
Chronic lymphocytic leukemia (CLL) is the most common adult leukemia in Western countries. It has a strong genetic basis, showing a ~ 8-fold increased risk of CLL in first-degree relatives. Genome-wide association studies (GWAS) have identified 41 risk variants across 41 loci. However, for a majority of the loci, the functional variants and the mechanisms underlying their causal roles remain undefined. Here, we examined the genetic and epigenetic features associated with 12 index variants, along with any correlated (r2 ≥ 0.5) variants, at the CLL risk loci located outside of gene promoters. Based on publicly available ChIP-seq and chromatin accessibility data as well as our own ChIP-seq data from CLL patients, we identified six candidate functional variants at six loci and at least two candidate functional variants at each of the remaining six loci. The functional variants are predominantly located within enhancers or super-enhancers, including bi-directionally transcribed enhancers, which are often restricted to immune cell types. Furthermore, we found that, at 78% of the functional variants, the alternative alleles altered the transcription factor binding motifs or histone modifications, indicating the involvement of these variants in the change of local chromatin state. Finally, the enhancers carrying functional variants physically interacted with genes enriched in the type I interferon signaling pathway, apoptosis, or TP53 network that are known to play key roles in CLL. These results support the regulatory roles for inherited noncoding variants in the pathogenesis of CLL.
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Affiliation(s)
- Huihuang Yan
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Shulan Tian
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Geffen Kleinstern
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Zhiquan Wang
- Division of Hematology, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Jeong-Heon Lee
- Division of Experimental Pathology and Laboratory Medicine, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
| | | | - James R Cerhan
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Neil E Kay
- Division of Hematology, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Esteban Braggio
- Division of Hematology/Oncology, Department of Medicine, Mayo Clinic, Scottsdale, AZ 85259, USA
| | - Susan L Slager
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
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2
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Wang L, Xia Y, Chen Y, Dai R, Qiu W, Meng Q, Kuney L, Chen C. Brain Banks Spur New Frontiers in Neuropsychiatric Research and Strategies for Analysis and Validation. GENOMICS, PROTEOMICS & BIOINFORMATICS 2019; 17:402-414. [PMID: 31811942 PMCID: PMC6943778 DOI: 10.1016/j.gpb.2019.02.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 02/13/2019] [Accepted: 03/01/2019] [Indexed: 12/27/2022]
Abstract
Neuropsychiatric disorders affect hundreds of millions of patients and families worldwide. To decode the molecular framework of these diseases, many studies use human postmortem brain samples. These studies reveal brain-specific genetic and epigenetic patterns via high-throughput sequencing technologies. Identifying best practices for the collection of postmortem brain samples, analyzing such large amounts of sequencing data, and interpreting these results are critical to advance neuropsychiatry. We provide an overview of human brain banks worldwide, including progress in China, highlighting some well-known projects using human postmortem brain samples to understand molecular regulation in both normal brains and those with neuropsychiatric disorders. Finally, we discuss future research strategies, as well as state-of-the-art statistical and experimental methods that are drawn upon brain bank resources to improve our understanding of the agents of neuropsychiatric disorders.
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Affiliation(s)
- Le Wang
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410078, China; Child Health Institute of New Jersey, Department of Neuroscience, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ 08901, USA
| | - Yan Xia
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410078, China; Psychiatry Department, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Yu Chen
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410078, China
| | - Rujia Dai
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410078, China; Psychiatry Department, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Wenying Qiu
- Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100101, China
| | - Qingtuan Meng
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410078, China; Affiliated Hospital of Guilin Medical University, Guilin 541000, China
| | - Liz Kuney
- Psychiatry Department, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Chao Chen
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410078, China; National Clinical Research Centre for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410000, China.
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3
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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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4
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Chen H, Kichaev G, Bien SA, MacDonald JW, Wang L, Bammler TK, Auer P, Pasaniuc B, Lindström S. Genetic associations of breast and prostate cancer are enriched for regulatory elements identified in disease-related tissues. Hum Genet 2019; 138:1091-1104. [PMID: 31230194 DOI: 10.1007/s00439-019-02041-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 06/17/2019] [Indexed: 01/01/2023]
Abstract
Although genome-wide association studies (GWAS) have identified hundreds of risk loci for breast and prostate cancer, only a few studies have characterized the GWAS association signals across functional genomic annotations with a particular focus on single nucleotide polymorphisms (SNPs) located in DNA regulatory elements. In this study, we investigated the enrichment pattern of GWAS signals for breast and prostate cancer in genomic functional regions located in normal tissue and cancer cell lines. We quantified the overall enrichment of SNPs with breast and prostate cancer association p values < 1 × 10-8 across regulatory categories. We then obtained annotations for DNaseI hypersensitive sites (DHS), typical enhancers, and super enhancers across multiple tissue types, to assess if significant GWAS signals were selectively enriched in annotations found in disease-related tissue. Finally, we quantified the enrichment of breast and prostate cancer SNP heritability in regulatory regions, and compared the enrichment pattern of SNP heritability with GWAS signals. DHS, typical enhancers, and super enhancers identified in the breast cancer cell line MCF-7 were observed with the highest enrichment of genome-wide significant variants for breast cancer. For prostate cancer, GWAS signals were mostly enriched in DHS and typical enhancers identified in the prostate cancer cell line LNCaP. With progressively stringent GWAS p value thresholds, an increasing trend of enrichment was observed for both diseases in DHS, typical enhancers, and super enhancers located in disease-related tissue. Results from heritability enrichment analysis supported the selective enrichment pattern of functional genomic regions in disease-related cell lines for both breast and prostate cancer. Our results suggest the importance of studying functional annotations identified in disease-related tissues when characterizing GWAS results, and further demonstrate the role of germline DNA regulatory elements from disease-related tissue in breast and prostate carcinogenesis.
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Affiliation(s)
- Hongjie Chen
- Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Gleb Kichaev
- Bioinformatics Interdepartmental Program, University of California Los Angeles, Los Angeles, CA, USA
| | - Stephanie A Bien
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - James W MacDonald
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA
| | - Lu Wang
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA
| | - Theo K Bammler
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA
| | - Paul Auer
- Zilber School of Public Health, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Bogdan Pasaniuc
- Bioinformatics Interdepartmental Program, University of California Los Angeles, Los Angeles, CA, USA.,Departments of Human Genetics, and Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Sara Lindström
- Department of Epidemiology, University of Washington, Seattle, WA, USA. .,Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
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Wang E, Zhao H, Zhao D, Li L, Du L. Functional Prediction of Chronic Kidney Disease Susceptibility Gene PRKAG2 by Comprehensively Bioinformatics Analysis. Front Genet 2018; 9:573. [PMID: 30559760 PMCID: PMC6287114 DOI: 10.3389/fgene.2018.00573] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Accepted: 11/08/2018] [Indexed: 02/01/2023] Open
Abstract
The genetic predisposition to chronic kidney disease (CKD) has been widely evaluated especially using the genome-wide association studies, which highlighted some novel genetic susceptibility variants in many genes, and estimated glomerular filtration rate to diagnose and stage CKD. Of these variants, rs7805747 in PRKAG2 was identified to be significantly associated with both serum creatinine and CKD with genome wide significance level. Until now, the potential mechanism by which rs7805747 affects CKD risk is still unclear. Here, we performed a functional analysis of rs7805747 variant using multiple bioinformatics software and databases. Using RegulomeDB and HaploReg (version 4.1), rs7805747 was predicated to locate in enhancer histone marks (Liver, Duodenum Mucosa, Fetal Intestine Large, Fetal Intestine Small, and Right Ventricle tissues). Using GWAS analysis in PhenoScanner, we showed that rs7805747 is not only associated with CKD, but also is significantly associated with other diseases or phenotypes. Using metabolite analysis in PhenoScanner, rs7805747 is identified to be significantly associated with not only the serum creatinine, but also with other 16 metabolites. Using eQTL analysis in PhenoScanner, rs7805747 is identified to be significantly associated with gene expression in multiple human tissues and multiple genes including PRKAG2. The gene expression analysis of PRKAG2 using 53 tissues from GTEx RNA-Seq of 8555 samples (570 donors) in GTEx showed that PRKAG2 had the highest median expression in Heart-Atrial Appendage. Using the gene expression profiles in human CKD, we further identified different expression of PRKAG2 gene in CKD cases compared with control samples. In summary, our findings provide new insight into the underlying susceptibility of PRKAG2 gene to CKD.
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Affiliation(s)
- Ermin Wang
- Department of Nephrology, The First Affiliated Hospital, Jinzhou Medical University, Jinzhou, China
| | - Hainan Zhao
- Department of Nephrology, The First Affiliated Hospital, Jinzhou Medical University, Jinzhou, China
| | - Deyan Zhao
- Department of Nephrology, The First Affiliated Hospital, Jinzhou Medical University, Jinzhou, China
| | - Lijing Li
- Department of Nephrology, The First Affiliated Hospital, Jinzhou Medical University, Jinzhou, China
| | - Limin Du
- Jinzhou Medical University, Jinzhou, China
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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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Hong MJ, Yoo SS, Choi JE, Kang HG, Do SK, Lee JH, Lee WK, Lee J, Lee SY, Cha SI, Kim CH, Lee EB, Cho S, Jheon S, Park JY. Functional intronic variant of SLC5A10 affects DRG2 expression and survival outcomes of early-stage non-small-cell lung cancer. Cancer Sci 2018; 109:3902-3909. [PMID: 30281872 PMCID: PMC6272084 DOI: 10.1111/cas.13814] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 09/11/2018] [Accepted: 09/18/2018] [Indexed: 01/10/2023] Open
Abstract
RegulomeDB is a new tool that can predict the regulatory function of genetic variants. We applied RegulomeDB in selecting putative functional variants and evaluated the relationship between these variants and survival outcomes of surgically resected non‐small‐cell lung cancer. Among the 244 variants studied, 14 were associated with overall survival (P < 0.05) in the discovery cohort and one variant (rs2257609 C>T) was replicated in the validation cohort. In the combined analysis, rs2257609 C>T was significantly associated with worse overall and disease‐free survival under a dominant model (P = 2 × 10−5 and P = 0.001, respectively). rs2257609 is located in the SLC5A10 intron, but RegulomeDB predicted that this variant affected DRG2, not SLC5A10 expression. The expression level of SLC5A10 was not different with the rs2257609 genotype. However, DRG2 expression was different according to the rs2257609 genotype (Ptrend = 0.03) and was significantly higher in tumor than in non‐malignant lung tissues (P = 1 × 10−5). Luciferase assay also showed higher promoter activity of DRG2 in samples with the rs2257609 T allele (P < 0.0001). rs2257609 C>T affected DRG2 expression and, thus, influenced the prognosis of early‐stage non‐small‐cell lung cancer. This study was approved by the Institutional Review Broad of Kyungpook National University of Hospital (Approval No. KNUMC 2014‐04‐210‐003).
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Affiliation(s)
- Mi Jeong Hong
- Department of Cell and Matrix Research Institute, School of Medicine, Kyungpook National University, Daegu, Korea
| | - Seung Soo Yoo
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Kyungpook National University Hospital, Deagu, Korea
| | - Jin Eun Choi
- Department of Cell and Matrix Research Institute, School of Medicine, Kyungpook National University, Daegu, Korea
| | - Hyo-Gyoung Kang
- Department of Cell and Matrix Research Institute, School of Medicine, Kyungpook National University, Daegu, Korea
| | - Sook Kyung Do
- Department of Biochemistry and Cell Biology, School of Medicine, Kyungpook National University, Daegu, Korea.,BK21 Plus KNU Biomedical Convergence Program, Department of Biomedical Science, Kyungpook National University, Daegu, Korea
| | - Jang Hyuck Lee
- Department of Biochemistry and Cell Biology, School of Medicine, Kyungpook National University, Daegu, Korea.,BK21 Plus KNU Biomedical Convergence Program, Department of Biomedical Science, Kyungpook National University, Daegu, Korea
| | - Won Kee Lee
- Biostatistics Center, School of Medicine, Kyungpook National University, Daegu, Korea
| | - Jaehee Lee
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Kyungpook National University Hospital, Deagu, Korea
| | - Shin Yup Lee
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Kyungpook National University Hospital, Deagu, Korea
| | - Seung Ick Cha
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Kyungpook National University Hospital, Deagu, Korea
| | - Chang Ho Kim
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Kyungpook National University Hospital, Deagu, Korea
| | - Eung Bae Lee
- Department of Thoracic Surgery, School of Medicine, Kyungpook National University, Daegu, Korea
| | - Sukki Cho
- Department of Thoracic and Cardiovascular Surgery, School of Medicine, Seoul National University, Seoul, Korea
| | - Sanghoon Jheon
- Department of Thoracic and Cardiovascular Surgery, School of Medicine, Seoul National University, Seoul, Korea
| | - Jae Yong Park
- Department of Cell and Matrix Research Institute, School of Medicine, Kyungpook National University, Daegu, Korea.,Department of Internal Medicine, School of Medicine, Kyungpook National University, Kyungpook National University Hospital, Deagu, Korea.,Department of Biochemistry and Cell Biology, School of Medicine, Kyungpook National University, Daegu, Korea.,BK21 Plus KNU Biomedical Convergence Program, Department of Biomedical Science, Kyungpook National University, Daegu, Korea
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8
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Guo Y, Perez AA, Hazelett DJ, Coetzee GA, Rhie SK, Farnham PJ. CRISPR-mediated deletion of prostate cancer risk-associated CTCF loop anchors identifies repressive chromatin loops. Genome Biol 2018; 19:160. [PMID: 30296942 PMCID: PMC6176514 DOI: 10.1186/s13059-018-1531-0] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 09/09/2018] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Recent genome-wide association studies (GWAS) have identified more than 100 loci associated with increased risk of prostate cancer, most of which are in non-coding regions of the genome. Understanding the function of these non-coding risk loci is critical to elucidate the genetic susceptibility to prostate cancer. RESULTS We generate genome-wide regulatory element maps and performed genome-wide chromosome confirmation capture assays (in situ Hi-C) in normal and tumorigenic prostate cells. Using this information, we annotate the regulatory potential of 2,181 fine-mapped prostate cancer risk-associated SNPs and predict a set of target genes that are regulated by prostate cancer risk-related H3K27Ac-mediated loops. We next identify prostate cancer risk-associated CTCF sites involved in long-range chromatin loops. We use CRISPR-mediated deletion to remove prostate cancer risk-associated CTCF anchor regions and the CTCF anchor regions looped to the prostate cancer risk-associated CTCF sites, and we observe up to 100-fold increases in expression of genes within the loops when the prostate cancer risk-associated CTCF anchor regions are deleted. CONCLUSIONS We identify GWAS risk loci involved in long-range loops that function to repress gene expression within chromatin loops. Our studies provide new insights into the genetic susceptibility to prostate cancer.
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Affiliation(s)
- 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 6503, Los Angeles, CA 90089-9601 USA
| | - Andrew A. Perez
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, 1450 Biggy Street, NRT 6503, Los Angeles, CA 90089-9601 USA
| | - Dennis J. Hazelett
- Department of Biomedical Sciences and the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048 USA
| | | | - 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 6503, Los Angeles, CA 90089-9601 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 6503, Los Angeles, CA 90089-9601 USA
- 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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9
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Yang C, Stueve TR, Yan C, Rhie SK, Mullen DJ, Luo J, Zhou B, Borok Z, Marconett CN, Offringa IA. Positional integration of lung adenocarcinoma susceptibility loci with primary human alveolar epithelial cell epigenomes. Epigenomics 2018; 10:1167-1187. [PMID: 30212242 DOI: 10.2217/epi-2018-0003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
AIM To identify functional lung adenocarcinoma (LUAD) risk SNPs. MATERIALS & METHODS Eighteen validated LUAD risk SNPs (p ≤ 5 × 10-8) and 930 SNPs in high linkage disequilibrium (r2 > 0.5) were integrated with epigenomic information from primary human alveolar epithelial cells. Enhancer-associated SNPs likely affecting transcription factor-binding sites were predicted. Three SNPs were functionally investigated using luciferase assays, expression quantitative trait loci and cancer-specific expression. RESULTS Forty-seven SNPs mapped to putative enhancers; 11 located to open chromatin. Of these, seven altered predicted transcription factor-binding motifs. Rs6942067 showed allele-specific luciferase expression and expression quantitative trait loci analysis indicates that it influences expression of DCBLD1, a gene that encodes an unknown membrane protein and is overexpressed in LUAD. CONCLUSION Integration of candidate LUAD risk SNPS with epigenomic marks from normal alveolar epithelium identified numerous candidate functional LUAD risk SNPs including rs6942067, which appears to affect DCBLD1 expression. Data deposition: Data are provided in GEO record GSE84273.
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Affiliation(s)
- Chenchen Yang
- Department of Surgery, University of Southern California, CA 90089, USA.,Department of Biochemistry & Molecular Medicine, University of Southern California, CA 90089, USA.,Norris Comprehensive Cancer Center, University of Southern California, CA 90089, USA
| | - Theresa Ryan Stueve
- Department of Surgery, University of Southern California, CA 90089, USA.,Department of Biochemistry & Molecular Medicine, University of Southern California, CA 90089, USA.,Norris Comprehensive Cancer Center, University of Southern California, CA 90089, USA.,Department of Preventive Medicine, University of Southern California, CA 90089, USA
| | - Chunli Yan
- Department of Surgery, University of Southern California, CA 90089, USA.,Department of Biochemistry & Molecular Medicine, University of Southern California, CA 90089, USA.,Norris Comprehensive Cancer Center, University of Southern California, CA 90089, USA
| | - Suhn K Rhie
- Department of Surgery, University of Southern California, CA 90089, USA.,Department of Biochemistry & Molecular Medicine, University of Southern California, CA 90089, USA.,Norris Comprehensive Cancer Center, University of Southern California, CA 90089, USA
| | - Daniel J Mullen
- Department of Surgery, University of Southern California, CA 90089, USA.,Department of Biochemistry & Molecular Medicine, University of Southern California, CA 90089, USA.,Norris Comprehensive Cancer Center, University of Southern California, CA 90089, USA
| | - Jiao Luo
- Department of Biochemistry & Molecular Medicine, University of Southern California, CA 90089, USA.,Department of Medicine, Division of Pulmonary & Critical Care & Sleep Medicine, University of Southern California, CA 90089, USA
| | - Beiyun Zhou
- Norris Comprehensive Cancer Center, University of Southern California, CA 90089, USA.,Department of Medicine, Division of Pulmonary & Critical Care & Sleep Medicine, University of Southern California, CA 90089, USA.,Hastings Center for Pulmonary Research, Keck School of Medicine, University of Southern California, CA 90089, USA
| | - Zea Borok
- Department of Biochemistry & Molecular Medicine, University of Southern California, CA 90089, USA.,Norris Comprehensive Cancer Center, University of Southern California, CA 90089, USA.,Department of Medicine, Division of Pulmonary & Critical Care & Sleep Medicine, University of Southern California, CA 90089, USA.,Hastings Center for Pulmonary Research, Keck School of Medicine, University of Southern California, CA 90089, USA
| | - Crystal N Marconett
- Department of Surgery, University of Southern California, CA 90089, USA.,Department of Biochemistry & Molecular Medicine, University of Southern California, CA 90089, USA.,Norris Comprehensive Cancer Center, University of Southern California, CA 90089, USA
| | - Ite A Offringa
- Department of Surgery, University of Southern California, CA 90089, USA.,Department of Biochemistry & Molecular Medicine, University of Southern California, CA 90089, USA.,Norris Comprehensive Cancer Center, University of Southern California, CA 90089, USA
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10
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Lin Y, Liu L, Sheng Y, Shen C, Zheng X, Zhou F, Yang S, Yin X, Zhang X. A catalog of potential putative functional variants in psoriasis genome-wide association regions. PLoS One 2018; 13:e0196635. [PMID: 29715312 PMCID: PMC5929547 DOI: 10.1371/journal.pone.0196635] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 04/15/2018] [Indexed: 01/20/2023] Open
Abstract
Psoriasis is a common inflammatory skin disease, with considerable genetic contribution. Genome-wide association studies have successfully identified a number of genomic regions for the risk of psoriasis. However, it is challenging to pinpoint the functional causal variants and then further decipher the genetic mechanisms underlying each region. In order to prioritize potential functional causal variants within psoriasis susceptibility regions, we integrated the genetic association findings and functional genomic data publicly available, i.e. histone modifications in relevant immune cells. We characterized a pervasive enrichment pattern of psoriasis variants in five core histone marks across immune cells/tissues. We discovered that genetic alleles within psoriasis association regions might influence gene expression levels through significantly affecting the binding affinities of 17 transcription factors. We established a catalog of 654 potential functional causal variants for psoriasis and suggested that they significantly overlapped with causal variants for autoimmune diseases. We identified potential causal variant rs79824801 overlay with the peaks of five histone marks in primary CD4+ T cells. Its alternative allele affected the binding affinity of transcription factor IKZF1. This study highlights the complex genetic architecture and complicated mechanisms for psoriasis. The findings will inform the functional experiment design for psoriasis.
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Affiliation(s)
- Yan Lin
- Institute of Dermatology, Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, Anhui, China
- Department of Dermatology, The Fourth Affiliated Hospital, Anhui Medical University, Hefei, Anhui, China
- Key lab of Dermatology, Ministry of Education, Anhui Medical University and State Key lab of Dermatology Incubation, Hefei, Anhui, China
| | - Lu Liu
- Institute of Dermatology, Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, Anhui, China
- Key lab of Dermatology, Ministry of Education, Anhui Medical University and State Key lab of Dermatology Incubation, Hefei, Anhui, China
| | - Yujun Sheng
- Institute of Dermatology, Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, Anhui, China
- Key lab of Dermatology, Ministry of Education, Anhui Medical University and State Key lab of Dermatology Incubation, Hefei, Anhui, China
| | - Changbing Shen
- Department of Dermatology, China-Japan Friendship Hospital, Beijing, China
| | - Xiaodong Zheng
- Institute of Dermatology, Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, Anhui, China
- Key lab of Dermatology, Ministry of Education, Anhui Medical University and State Key lab of Dermatology Incubation, Hefei, Anhui, China
| | - Fusheng Zhou
- Institute of Dermatology, Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, Anhui, China
- Key lab of Dermatology, Ministry of Education, Anhui Medical University and State Key lab of Dermatology Incubation, Hefei, Anhui, China
| | - Sen Yang
- Institute of Dermatology, Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, Anhui, China
- Key lab of Dermatology, Ministry of Education, Anhui Medical University and State Key lab of Dermatology Incubation, Hefei, Anhui, China
| | - Xianyong Yin
- Institute of Dermatology, Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, Anhui, China
- Key lab of Dermatology, Ministry of Education, Anhui Medical University and State Key lab of Dermatology Incubation, Hefei, Anhui, China
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Xuejun Zhang
- Institute of Dermatology, Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, Anhui, China
- Key lab of Dermatology, Ministry of Education, Anhui Medical University and State Key lab of Dermatology Incubation, Hefei, Anhui, China
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11
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Hong Y, Sonneville R, Wang B, Scheidt V, Meier B, Woglar A, Demetriou S, Labib K, Jantsch V, Gartner A. LEM-3 is a midbody-tethered DNA nuclease that resolves chromatin bridges during late mitosis. Nat Commun 2018; 9:728. [PMID: 29463814 PMCID: PMC5820297 DOI: 10.1038/s41467-018-03135-w] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 01/22/2018] [Indexed: 12/18/2022] Open
Abstract
Faithful chromosome segregation and genome maintenance requires the removal of all DNA bridges that physically link chromosomes before cells divide. Using C. elegans embryos we show that the LEM-3/Ankle1 nuclease defines a previously undescribed genome integrity mechanism by processing DNA bridges right before cells divide. LEM-3 acts at the midbody, the structure where abscission occurs at the end of cytokinesis. LEM-3 localization depends on factors needed for midbody assembly, and LEM-3 accumulation is increased and prolonged when chromatin bridges are trapped at the cleavage plane. LEM-3 locally processes chromatin bridges that arise from incomplete DNA replication, unresolved recombination intermediates, or the perturbance of chromosome structure. Proper LEM-3 midbody localization and function is regulated by AIR-2/Aurora B kinase. Strikingly, LEM-3 acts cooperatively with the BRC-1/BRCA1 homologous recombination factor to promote genome integrity. These findings provide a molecular basis for the suspected role of the LEM-3 orthologue Ankle1 in human breast cancer.
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Affiliation(s)
- Ye Hong
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Remi Sonneville
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Bin Wang
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Viktor Scheidt
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Bettina Meier
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Alexander Woglar
- Department of Chromosome Biology, Max F. Perutz Laboratories, Vienna Biocenter, University of Vienna, Vienna, A-1030, Austria
- Departments of Developmental Biology and Genetics, Stanford University School of Medicine, Stanford, CA 94305-5329, USA
| | - Sarah Demetriou
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Karim Labib
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Verena Jantsch
- Department of Chromosome Biology, Max F. Perutz Laboratories, Vienna Biocenter, University of Vienna, Vienna, A-1030, Austria
| | - Anton Gartner
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK.
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12
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Guo L, Peng Y, Sun L, Han X, Xu J, Mao D. Ovarian cancer variant rs2072590 is associated with HOXD1 and HOXD3 gene expression. Oncotarget 2017; 8:103410-103414. [PMID: 29262571 PMCID: PMC5732737 DOI: 10.18632/oncotarget.21902] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 09/21/2017] [Indexed: 11/25/2022] Open
Abstract
Ovarian cancer (OC) is a common cancer in women and the leading cause of deaths from gynaecological malignancies in the world. In addition to the candidate gene approach to identify OC susceptibility genes, the genome-wide association study (GWAS) methods have reported new variants that are associated with OC risk. The minor allele of rs2072590 at 2q31 was associated with an increased OC risk, and was primarily significant for serous subtype. The OC risk-associated SNP rs2072590 lies in non-coding DNA downstream of HOXD3 and upstream of HOXD1, and it tags SNPs in the HOXD3 3′ UTR. We think that the non-coding rs2072590 variant may contribute to OC susceptibility by regulating the gene expression of HOXD1 and HOXD3. In order to investigate this association, we performed a bioinformatics analysis by a functional annotation of rs2072590 variant using RegulomeDB (version 1.1), HaploReg (version 4.1), and PhenoScanner (version 1.1). Using HaploReg, we identified 19 genetic variants tagged by rs2072590 variant with with r2 >= 0.8. Using RegulomeDB, we identified that three genetic variants are likely to affect TF binding + any motif + DNase Footprint + DNase peak. Other genetic variants are likely to affect TF binding + DNase peak. Using PhenoScanner (version 1.1), we identified that these 19 genetic variants could significantly regulate the expression of nearby genes, especially the HOXD1 and HOXD3 in human ovary tissue.
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Affiliation(s)
- Liyuan Guo
- Department of Gynecological Oncology, Cancer Hospital of Harbin Medical University, Harbin, China
| | - Yan Peng
- Disease Prevention Center, First Affiliated Hospital, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Lei Sun
- Department of Gynecology and Obstetrics, The Fourth Hospital of Harbin Medical University, Harbin, China
| | - Xia Han
- Shenzhen Hospital of Guangzhou University of Chinese Medicine, Shenzhen, China
| | - Juan Xu
- Shenzhen Hospital of Guangzhou University of Chinese Medicine, Shenzhen, China
| | - Dongwei Mao
- Shenzhen Hospital of Guangzhou University of Chinese Medicine, Shenzhen, China
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13
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Liu Y, Walavalkar NM, Dozmorov MG, Rich SS, Civelek M, Guertin MJ. Identification of breast cancer associated variants that modulate transcription factor binding. PLoS Genet 2017; 13:e1006761. [PMID: 28957321 PMCID: PMC5619690 DOI: 10.1371/journal.pgen.1006761] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 04/12/2017] [Indexed: 01/11/2023] Open
Abstract
Genome-wide association studies (GWAS) have discovered thousands loci associated with disease risk and quantitative traits, yet most of the variants responsible for risk remain uncharacterized. The majority of GWAS-identified loci are enriched for non-coding single-nucleotide polymorphisms (SNPs) and defining the molecular mechanism of risk is challenging. Many non-coding causal SNPs are hypothesized to alter transcription factor (TF) binding sites as the mechanism by which they affect organismal phenotypes. We employed an integrative genomics approach to identify candidate TF binding motifs that confer breast cancer-specific phenotypes identified by GWAS. We performed de novo motif analysis of regulatory elements, analyzed evolutionary conservation of identified motifs, and assayed TF footprinting data to identify sequence elements that recruit TFs and maintain chromatin landscape in breast cancer-relevant tissue and cell lines. We identified candidate causal SNPs that are predicted to alter TF binding within breast cancer-relevant regulatory regions that are in strong linkage disequilibrium with significantly associated GWAS SNPs. We confirm that the TFs bind with predicted allele-specific preferences using CTCF ChIP-seq data. We used The Cancer Genome Atlas breast cancer patient data to identify ANKLE1 and ZNF404 as the target genes of candidate TF binding site SNPs in the 19p13.11 and 19q13.31 GWAS-identified loci. These SNPs are associated with the expression of ZNF404 and ANKLE1 in breast tissue. This integrative analysis pipeline is a general framework to identify candidate causal variants within regulatory regions and TF binding sites that confer phenotypic variation and disease risk.
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Affiliation(s)
- Yunxian Liu
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia, United States of America
| | - Ninad M. Walavalkar
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia, United States of America
| | - Mikhail G. Dozmorov
- Department of Biostatistics, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Stephen S. Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, United States of America
| | - Mete Civelek
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, United States of America
- Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia, United Statess of America
| | - Michael J. Guertin
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia, United States of America
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, United States of America
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14
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Zhang Y. Epigenetic Combinatorial Patterns Predict Disease Variants. Front Genet 2017; 8:71. [PMID: 28611825 PMCID: PMC5447712 DOI: 10.3389/fgene.2017.00071] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 05/12/2017] [Indexed: 11/13/2022] Open
Abstract
Most genetic variants identified in genome-wide association studies are noncoding and are likely tagging nearby causal variants. It is a challenging task to pinpoint the precise locations of disease-causal variants and understand their functions in disease. A promising approach to improve fine mapping is to integrate the functional data currently available on hundreds of human tissues and cell types. Although there are several methods that use functional data to prioritize disease variants, they mainly use linear models, or equivalent naive likelihood-based models for prediction. Here, we investigate whether study of the combinatorial patterns of functional data across cell types can improve prediction accuracy for disease variants. Using functional annotation in 127 human cell types, we first introduce a Bayesian method to identify recurring cell-type-specificity partitions on the scale of the genome. We show that our de novo identification of epigenome partition patterns agrees well with known cell-type origins and that the associated functional elements are strongly enriched in disease variants. Using epigenetic cell-type specificity in addition to enrichment of functional elements, we further demonstrate that the power to predict disease variants can be greatly improved over that achievable with linear models. Our approach thus provides a new way to prioritize disease functional variants for testing.
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Affiliation(s)
- Yu Zhang
- Department of Statistics, Pennsylvania State UniversityUniversity Park, PA, United States
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15
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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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16
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Xiao X, Chang H, Li M. Molecular mechanisms underlying noncoding risk variations in psychiatric genetic studies. Mol Psychiatry 2017; 22:497-511. [PMID: 28044063 PMCID: PMC5378805 DOI: 10.1038/mp.2016.241] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Revised: 11/08/2016] [Accepted: 11/14/2016] [Indexed: 12/18/2022]
Abstract
Recent large-scale genetic approaches such as genome-wide association studies have allowed the identification of common genetic variations that contribute to risk architectures of psychiatric disorders. However, most of these susceptibility variants are located in noncoding genomic regions that usually span multiple genes. As a result, pinpointing the precise variant(s) and biological mechanisms accounting for the risk remains challenging. By reviewing recent progresses in genetics, functional genomics and neurobiology of psychiatric disorders, as well as gene expression analyses of brain tissues, here we propose a roadmap to characterize the roles of noncoding risk loci in the pathogenesis of psychiatric illnesses (that is, identifying the underlying molecular mechanisms explaining the genetic risk conferred by those genomic loci, and recognizing putative functional causative variants). This roadmap involves integration of transcriptomic data, epidemiological and bioinformatic methods, as well as in vitro and in vivo experimental approaches. These tools will promote the translation of genetic discoveries to physiological mechanisms, and ultimately guide the development of preventive, therapeutic and prognostic measures for psychiatric disorders.
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Affiliation(s)
- X Xiao
- Key Laboratory of Animal Models and Human Disease Mechanisms of The Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan, China
| | - H Chang
- Key Laboratory of Animal Models and Human Disease Mechanisms of The Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan, China
| | - M Li
- Key Laboratory of Animal Models and Human Disease Mechanisms of The Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan, China
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17
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Functional annotation of sixty-five type-2 diabetes risk SNPs and its application in risk prediction. Sci Rep 2017; 7:43709. [PMID: 28262806 PMCID: PMC5337961 DOI: 10.1038/srep43709] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 01/26/2017] [Indexed: 01/04/2023] Open
Abstract
Genome-wide association studies (GWAS) have identified more than sixty single nucleotide polymorphisms (SNPs) associated with increased risk for type 2 diabetes (T2D). However, the identification of causal risk SNPs for T2D pathogenesis was complicated by the factor that each risk SNP is a surrogate for the hundreds of SNPs, most of which reside in non-coding regions. Here we provide a comprehensive annotation of 65 known T2D related SNPs and inspect putative functional SNPs probably causing protein dysfunction, response element disruptions of known transcription factors related to T2D genes and regulatory response element disruption of four histone marks in pancreas and pancreas islet. In new identified risk SNPs, some of them were reported as T2D related SNPs in recent studies. Further, we found that accumulation of modest effects of single sites markedly enhanced the risk prediction based on 1989 T2D samples and 3000 healthy controls. The AROC value increased from 0.58 to 0.62 by only using genotype score when putative risk SNPs were added. Besides, the net reclassification improvement is 10.03% on the addition of new risk SNPs. Taken together, functional annotation could provide a list of prioritized potential risk SNPs for the further estimation on the T2D susceptibility of individuals.
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18
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Tinholt M, Sandset PM, Iversen N. Polymorphisms of the coagulation system and risk of cancer. Thromb Res 2017; 140 Suppl 1:S49-54. [PMID: 27067978 DOI: 10.1016/s0049-3848(16)30098-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Hypercoagulability is a frequently finding in patients with cancer, and is associated with an increased risk of venous thrombosis (VT). Cancer-associated VT is associated with poor prognosis and represents the leading non-cancer cause of death among these patients. Conversely, patients experiencing VT are at increased risk of subsequent cancer, suggesting an epidemiological bidirectional link between cancer and hemostasis, and indicating a role of the hemostatic system in cancer development. How the coagulation system relates to cancer etiology at the genetic level is largely unexplored. Data on the association of polymorphisms in genes involved in coagulation with cancer development is important to clarify the role of the coagulation system in cancer pathogenesis. Effects of coagulation-related gene polymorphisms on cancer risk may possibly be translated into novel treatment- and prevention strategies of cancer-associated thrombosis and the cancer itself. This article reviews the current knowledge of the relation between polymorphisms in genes involved in coagulation and cancer risk in solid tumors.
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Affiliation(s)
- Mari Tinholt
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Per Morten Sandset
- Department of Haematology, Oslo University Hospital, Oslo, Norway; Research Institute of Internal Medicine, Oslo University Hospital, Oslo, Norway; Institute of Clinical Medicine, University of Oslo, Oslo, Norway.
| | - Nina Iversen
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
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19
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SNP variants at the MAP3K1/SETD9 locus 5q11.2 associate with somatic PIK3CA variants in breast cancers. Eur J Hum Genet 2016; 25:384-387. [PMID: 28029147 DOI: 10.1038/ejhg.2016.179] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Revised: 10/12/2016] [Accepted: 11/22/2016] [Indexed: 02/01/2023] Open
Abstract
Genome-wide association studies have revealed many breast cancer (BC) risk-associated genetic variants that might functionally interact with other molecular determinants of BC. We analysed the association of 21 known risk-associated single-nucleotide variants (SNVs) with recurrent somatic variants in two cohorts of 77 and 754 oestrogen receptor α-positive BCs. Four SNVs located at 5q11.2 were found to be associated with the somatic PIK3CA variant status in the pilot cohort of 77 cases with odds ratio (OR) up to 6.5 indicating strong effects, and were selected for the validation phase. Two of these SNVs, rs252913 and rs331499, located in the MAP3K1/SETD9 gene boundary, were confirmed to be associated with somatic PIK3CA variants in the large cohort with OR 2.97 (1.17-7.75) and 1.76 (1.11-2.77), respectively, notably higher than their BC risk-associated values, both around 1.1. In the presence of the SNV or of somatic PIK3CA variants, cancers express significantly elevated levels of MAP3K1 and SETD9, with synergy of SNV and PIK3CA variants in MAP3K1 gene overexpression, consistent with a preferential PIK3CA-dependent regulation of the variant alleles.
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20
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Li M, Weinberger DR. RETRACTION: Illuminating the dark road from schizophrenia genetic associations to disease mechanisms. Natl Sci Rev 2016. [DOI: 10.1093/nsr/nww065] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Abstract
Recent large-scale genome-wide association studies (GWAS) have enabled the discovery of common genetic variations contributing to risk architectures of schizophrenia in human populations; however, the majority of GWAS-identified variants are located in large genomic regions spanning multiple genes, and recognizing the precise targets and mechanisms of these clinical associations is now the major challenge. Here, we review recent progress in schizophrenia genetics, functional genomics and related neuroscience research, and propose a functional pipeline to translate schizophrenia GWAS risk loci into disease biology and information for drug discovery. The pipeline includes identification of underlying molecular mechanisms using transcriptomic data in human brain, prioritization of putative functional causative variants by the integration of genetic epidemiological and bioinformatics methods as well as molecular approaches, and in vitro and in vivo experimental characterizations of the identified targeted species and causative variants to dissect the relevant disease biology. These approaches will accelerate progress from schizophrenia genetic studies to biological mechanisms and ultimately guide the development of prognostic, preventive and therapeutic measures.
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Affiliation(s)
- Ming Li
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Kunming 650223, China
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, 21205, USA
| | - Daniel R Weinberger
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, 21205, USA
- Department of Psychiatry, Johns Hopkins University School of Medicine, Baltimore, 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, 21205, USA
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, 21205, USA
- McKusick Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, 21205, USA
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21
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Stueve TR, Marconett CN, Zhou B, Borok Z, Laird-Offringa IA. The importance of detailed epigenomic profiling of different cell types within organs. Epigenomics 2016; 8:817-29. [PMID: 27305639 PMCID: PMC5066118 DOI: 10.2217/epi-2016-0005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The human body consists of hundreds of kinds of cells specified from a single genome overlaid with cell type-specific epigenetic information. Comprehensively profiling the body's distinct epigenetic landscapes will allow researchers to verify cell types used in regenerative medicine and to determine the epigenetic effects of disease, environmental exposures and genetic variation. Key marks/factors that should be investigated include regions of nucleosome-free DNA accessible to regulatory factors, histone marks defining active enhancers and promoters, DNA methylation levels, regulatory RNAs, and factors controlling the three-dimensional conformation of the genome. Here we use the lung to illustrate the importance of investigating an organ's purified cell epigenomes, and outline the challenges and promise of realizing a comprehensive catalog of primary cell epigenomes.
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Affiliation(s)
- Theresa Ryan Stueve
- Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA.,Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA.,Department of Biochemistry & Molecular Biology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Crystal N Marconett
- Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA.,Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Beiyun Zhou
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA.,Division of Pulmonary & Critical Care Medicine, Department of Medicine, Will Rogers Institute Pulmonary Research Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Zea Borok
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA.,Department of Biochemistry & Molecular Biology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA.,Division of Pulmonary & Critical Care Medicine, Department of Medicine, Will Rogers Institute Pulmonary Research Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Ite A Laird-Offringa
- Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA.,Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA.,Department of Biochemistry & Molecular Biology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
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22
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Hazelett DJ, Conti DV, Han Y, Al Olama AA, Easton D, Eeles RA, Kote-Jarai Z, Haiman CA, Coetzee GA. Reducing GWAS Complexity. Cell Cycle 2016; 15:22-4. [PMID: 26771711 PMCID: PMC4825730 DOI: 10.1080/15384101.2015.1120928] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 11/12/2015] [Indexed: 10/22/2022] Open
Abstract
Genome-wide association studies (GWAS) have revealed numerous genomic 'hits' associated with complex phenotypes. In most cases these hits, along with surrogate genetic variation as measure by numerous single nucleotide polymorphisms (SNPs) that are in linkage disequilibrium, are not in coding genes making assignment of functionality or causality intractable. Here we propose that fine-mapping along with the matching of risk SNPs at chromatin biofeatures lessen this complexity by reducing the number of candidate functional/causal SNPs. For example, we show here that only on average 2 SNPs per prostate cancer risk locus are likely candidates for functionality/causality; we further propose that this manageable number should be taken forward in mechanistic studies. The candidate SNPs can be looked up for each prostate cancer risk region in 2 recent publications in 2015 (1,2) from our groups.
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Affiliation(s)
- Dennis J. Hazelett
- Bioinformatics and Computational Biology Research Center, Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - David V. Conti
- Departments of Preventive Medicine and Urology, USC/Norris Cancer Center, USA
| | - Ying Han
- Departments of Preventive Medicine and Urology, USC/Norris Cancer Center, USA
| | - Ali Amin Al Olama
- Division of Genetics & Epidemiology, Centre of Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
| | - Doug Easton
- Division of Genetics & Epidemiology, Centre of Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
| | - Rosalind A. Eeles
- The Institute of Cancer Research & Royal Marsden NHS Foundation Trust, London, UK
| | - Zsofia Kote-Jarai
- The Institute of Cancer Research & Royal Marsden NHS Foundation Trust, London, UK
| | | | - Gerhard A. Coetzee
- Departments of Preventive Medicine and Urology, USC/Norris Cancer Center, USA
- The Institute of Cancer Research & Royal Marsden NHS Foundation Trust, London, UK
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23
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Warburton A, Miyajima F, Shazadi K, Crossley J, Johnson MR, Marson AG, Baker GA, Quinn JP, Sills GJ. NRSF and BDNF polymorphisms as biomarkers of cognitive dysfunction in adults with newly diagnosed epilepsy. Epilepsy Behav 2016; 54:117-27. [PMID: 26708060 PMCID: PMC4732989 DOI: 10.1016/j.yebeh.2015.11.013] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Revised: 11/09/2015] [Accepted: 11/14/2015] [Indexed: 12/31/2022]
Abstract
Cognitive dysfunction is a common comorbidity in people with epilepsy, but its causes remain unclear. It may be related to the etiology of the disorder, the consequences of seizures, or the effects of antiepileptic drug treatment. Genetics may also play a contributory role. We investigated the influence of variants in the genes encoding neuron-restrictive silencer factor (NRSF) and brain-derived neurotrophic factor (BDNF), proteins previously associated with cognition and epilepsy, on cognitive function in people with newly diagnosed epilepsy. A total of 82 patients who had previously undergone detailed neuropsychological assessment were genotyped for single nucleotide polymorphisms (SNPs) across the NRSF and BDNF genes. Putatively functional SNPs were included in a genetic association analysis with specific cognitive domains, including memory, psychomotor speed, and information processing. Cross-sectional and longitudinal designs were used to explore genetic influences on baseline cognition at diagnosis and change from baseline over the first year since diagnosis, respectively. We found a statistically significant association between genotypic variation and memory function at both baseline (NRSF: rs1105434, rs2227902 and BDNF: rs1491850, rs2030324, rs11030094) and in our longitudinal analysis (NRSF: rs2227902 and BDNF: rs12273363). Psychomotor speed was also associated with genotype (NRSF rs3796529) in the longitudinal assessment. In line with our previous work on general cognitive function in the healthy aging population, we observed an additive interaction between risk alleles for the NRSF rs2227902 (G) and BDNF rs6265 (A) polymorphisms which was again consistent with a significantly greater decline in delayed recall over the first year since diagnosis. These findings support a role for the NRSF-BDNF pathway in the modulation of cognitive function in patients with newly diagnosed epilepsy.
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Affiliation(s)
- Alix Warburton
- Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, University of Liverpool, Liverpool L69 3GL, UK
| | - Fabio Miyajima
- Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, University of Liverpool, Liverpool L69 3GL, UK
| | - Kanvel Shazadi
- Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, University of Liverpool, Liverpool L69 3GL, UK
| | - Joanne Crossley
- Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, University of Liverpool, Liverpool L69 3GL, UK
| | | | - Anthony G Marson
- Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, University of Liverpool, Liverpool L69 3GL, UK
| | - Gus A Baker
- Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, University of Liverpool, Liverpool L69 3GL, UK
| | - John P Quinn
- Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, University of Liverpool, Liverpool L69 3GL, UK
| | - Graeme J Sills
- Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, University of Liverpool, Liverpool L69 3GL, UK.
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24
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Lei J, Rudolph A, Moysich KB, Behrens S, Goode EL, Bolla MK, Dennis J, Dunning AM, Easton DF, Wang Q, Benitez J, Hopper JL, Southey MC, Schmidt MK, Broeks A, Fasching PA, Haeberle L, Peto J, Dos-Santos-Silva I, Sawyer EJ, Tomlinson I, Burwinkel B, Marmé F, Guénel P, Truong T, Bojesen SE, Flyger H, Nielsen SF, Nordestgaard BG, González-Neira A, Menéndez P, Anton-Culver H, Neuhausen SL, Brenner H, Arndt V, Meindl A, Schmutzler RK, Brauch H, Hamann U, Nevanlinna H, Fagerholm R, Dörk T, Bogdanova NV, Mannermaa A, Hartikainen JM, Van Dijck L, Smeets A, Flesch-Janys D, Eilber U, Radice P, Peterlongo P, Couch FJ, Hallberg E, Giles GG, Milne RL, Haiman CA, Schumacher F, Simard J, Goldberg MS, Kristensen V, Borresen-Dale AL, Zheng W, Beeghly-Fadiel A, Winqvist R, Grip M, Andrulis IL, Glendon G, García-Closas M, Figueroa J, Czene K, Brand JS, Darabi H, Eriksson M, Hall P, Li J, Cox A, Cross SS, Pharoah PDP, Shah M, Kabisch M, Torres D, Jakubowska A, Lubinski J, Ademuyiwa F, Ambrosone CB, Swerdlow A, Jones M, Chang-Claude J. Genetic variation in the immunosuppression pathway genes and breast cancer susceptibility: a pooled analysis of 42,510 cases and 40,577 controls from the Breast Cancer Association Consortium. Hum Genet 2016; 135:137-54. [PMID: 26621531 PMCID: PMC4698282 DOI: 10.1007/s00439-015-1616-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 11/13/2015] [Indexed: 12/11/2022]
Abstract
Immunosuppression plays a pivotal role in assisting tumors to evade immune destruction and promoting tumor development. We hypothesized that genetic variation in the immunosuppression pathway genes may be implicated in breast cancer tumorigenesis. We included 42,510 female breast cancer cases and 40,577 controls of European ancestry from 37 studies in the Breast Cancer Association Consortium (2015) with available genotype data for 3595 single nucleotide polymorphisms (SNPs) in 133 candidate genes. Associations between genotyped SNPs and overall breast cancer risk, and secondarily according to estrogen receptor (ER) status, were assessed using multiple logistic regression models. Gene-level associations were assessed based on principal component analysis. Gene expression analyses were conducted using RNA sequencing level 3 data from The Cancer Genome Atlas for 989 breast tumor samples and 113 matched normal tissue samples. SNP rs1905339 (A>G) in the STAT3 region was associated with an increased breast cancer risk (per allele odds ratio 1.05, 95 % confidence interval 1.03-1.08; p value = 1.4 × 10(-6)). The association did not differ significantly by ER status. On the gene level, in addition to TGFBR2 and CCND1, IL5 and GM-CSF showed the strongest associations with overall breast cancer risk (p value = 1.0 × 10(-3) and 7.0 × 10(-3), respectively). Furthermore, STAT3 and IL5 but not GM-CSF were differentially expressed between breast tumor tissue and normal tissue (p value = 2.5 × 10(-3), 4.5 × 10(-4) and 0.63, respectively). Our data provide evidence that the immunosuppression pathway genes STAT3, IL5, and GM-CSF may be novel susceptibility loci for breast cancer in women of European ancestry.
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Affiliation(s)
- Jieping Lei
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 581, 69120, Heidelberg, Germany
| | - Anja Rudolph
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 581, 69120, Heidelberg, Germany
| | - Kirsten B Moysich
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Sabine Behrens
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 581, 69120, Heidelberg, Germany
| | - Ellen L Goode
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Manjeet K Bolla
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Joe Dennis
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - 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
| | - Qin Wang
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Javier Benitez
- Human Cancer Genetics Program, Spanish National Cancer Research Centre, Madrid, Spain
- Centro de Investigación en Red de Enfermedades Raras, Valencia, Spain
| | - John L Hopper
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Australia
| | - Melissa C Southey
- Department of Pathology, The University of Melbourne, Melbourne, Australia
| | - Marjanka K Schmidt
- Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
| | - Annegien Broeks
- Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
| | - Peter A Fasching
- Department of Gynaecology and Obstetrics, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Comprehensive Cancer Center Erlangen-EMN, Erlangen, Germany
- David Geffen School of Medicine, Department of Medicine Division of Hematology and Oncology, University of California at Los Angeles, Los Angeles, CA, USA
| | - Lothar Haeberle
- Department of Gynaecology and Obstetrics, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Comprehensive Cancer Center Erlangen-EMN, Erlangen, Germany
| | - Julian Peto
- Department of Non-Communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
| | - Isabel Dos-Santos-Silva
- Department of Non-Communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
| | - Elinor J Sawyer
- Research Oncology, Guy's Hospital, King's College London, London, UK
| | - Ian Tomlinson
- Wellcome Trust Centre for Human Genetics and Oxford NIHR Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Barbara Burwinkel
- Department of Obstetrics and Gynecology, University of Heidelberg, Heidelberg, Germany
- Molecular Epidemiology Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Frederik Marmé
- Department of Obstetrics and Gynecology, University of Heidelberg, Heidelberg, Germany
- National Center for Tumor Diseases, University of Heidelberg, Heidelberg, Germany
| | - Pascal Guénel
- Environmental Epidemiology of Cancer, Center for Research in Epidemiology and Population Health, INSERM, Villejuif, France
- University Paris-Sud, Villejuif, France
| | - Thérèse Truong
- Environmental Epidemiology of Cancer, Center for Research in Epidemiology and Population Health, INSERM, Villejuif, France
- University Paris-Sud, Villejuif, France
| | - Stig E Bojesen
- Copenhagen General Population Study, Herlev Hospital, Copenhagen University Hospital, Herlev, Denmark
- Department of Clinical Biochemistry, Herlev Hospital, Copenhagen University Hospital, Herlev, Denmark
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Henrik Flyger
- Department of Breast Surgery, Herlev Hospital, Copenhagen University Hospital, Herlev, Denmark
| | - Sune F Nielsen
- Department of Clinical Biochemistry, Herlev Hospital, Copenhagen University Hospital, Herlev, Denmark
| | - Børge G Nordestgaard
- Department of Clinical Biochemistry, Herlev Hospital, Copenhagen University Hospital, Herlev, Denmark
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Anna González-Neira
- Human Cancer Genetics Program, Spanish National Cancer Research Centre, Madrid, Spain
| | | | - Hoda Anton-Culver
- Department of Epidemiology, University of California Irvine, Irvine, CA, USA
| | | | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Division of Preventive Oncology, National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Volker Arndt
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Alfons Meindl
- Division of Gynaecology and Obstetrics, Technische Universität München, Munich, Germany
| | - Rita K Schmutzler
- Center for Hereditary Breast and Ovarian Cancer, University Hospital of Cologne, Cologne, Germany
- Center for Integrated Oncology (CIO), University Hospital of Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Hiltrud Brauch
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology Stuttgart, Stuttgart, Germany
- University of Tübingen, Tübingen, Germany
| | - Ute Hamann
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Heli Nevanlinna
- Department of Obstetrics and Gynecology, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - Rainer Fagerholm
- Department of Obstetrics and Gynecology, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - Thilo Dörk
- Gynaecology Research Unit, Hannover Medical School, Hannover, Germany
| | - Natalia V Bogdanova
- Department of Radiation Oncology, Hannover Medical School, Hannover, Germany
| | - Arto Mannermaa
- Cancer Center, Kuopio University Hospital, Kuopio, Finland
- Institute of Clinical Medicine, Pathology and Forensic Medicine, University of Eastern Finland, Kuopio, Finland
- Imaging Center, Department of Clinical Pathology, Kuopio University Hospital, Kuopio, Finland
| | - Jaana M Hartikainen
- Cancer Center, Kuopio University Hospital, Kuopio, Finland
- Institute of Clinical Medicine, Pathology and Forensic Medicine, University of Eastern Finland, Kuopio, Finland
- Imaging Center, Department of Clinical Pathology, Kuopio University Hospital, Kuopio, Finland
| | - Laurien Van Dijck
- VIB Vesalius Research Center, Department of Oncology, University of Leuven, Leuven, Belgium
| | - Ann Smeets
- Multidisciplinary Breast Center, University Hospitals Leuven, University of Leuven, Leuven, Belgium
| | - Dieter Flesch-Janys
- Institute for Medical Biometrics and Epidemiology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Department of Cancer Epidemiology, Clinical Cancer Registry, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Ursula Eilber
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 581, 69120, Heidelberg, Germany
| | - Paolo Radice
- Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Preventive and Predictive Medicine, Fondazione IRCCS (Istituto Di Ricovero e Cura a Carattere Scientifico) Istituto Nazionale dei Tumori (INT), Milan, Italy
| | - Paolo Peterlongo
- IFOM, Fondazione Istituto FIRC (Italian Foundation of Cancer Research) di Oncologia Molecolare, Milan, Italy
| | - Fergus J Couch
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Emily Hallberg
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Graham G Giles
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Australia
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Australia
| | - Roger L Milne
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Australia
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Australia
| | - Christopher A Haiman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Fredrick Schumacher
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Jacques Simard
- Genomics Center, Centre Hospitalier Universitaire de Québec Research Center, Laval University, Québec City, Canada
| | - Mark S Goldberg
- Department of Medicine, McGill University, Montreal, Canada
- Division of Clinical Epidemiology, Royal Victoria Hospital, McGill University, Montreal, Canada
| | - Vessela Kristensen
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Oslo, Norway
- K.G. Jebsen Center for Breast Cancer Research, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Department of Clinical Molecular Biology, Oslo University Hospital, University of Oslo, Oslo, Norway
| | - Anne-Lise Borresen-Dale
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Oslo, Norway
- K.G. Jebsen Center for Breast Cancer Research, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Alicia Beeghly-Fadiel
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Robert Winqvist
- Laboratory of Cancer Genetics and Tumor Biology, Department of Clinical Chemistry and Biocenter Oulu, University of Oulu, Oulu, Finland
- Central Finland Hospital District, Jyväskylä Central Hospital, Jyväskylä, Finland
| | - Mervi Grip
- Department of Surgery, Oulu University Hospital, University of Oulu, Oulu, Finland
| | - Irene L Andrulis
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Gord Glendon
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, Canada
| | - Montserrat García-Closas
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Jonine Figueroa
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Kamila Czene
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Judith S Brand
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Hatef Darabi
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Mikael Eriksson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Per Hall
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Jingmei Li
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Angela Cox
- Sheffield Cancer Research Centre, Department of Oncology, University of Sheffield, Sheffield, UK
| | - Simon S Cross
- Academic Unit of Pathology, Department of Neuroscience, University of Sheffield, Sheffield, UK
| | - Paul D P Pharoah
- 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
| | - Mitul Shah
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Maria Kabisch
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Diana Torres
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Institute of Human Genetics, Pontificia Universidad Javeriana, Bogota, Colombia
| | - Anna Jakubowska
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Jan Lubinski
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | | | | | - Anthony Swerdlow
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
- Division of Breast Cancer Research, Institute of Cancer Research, London, UK
| | - Michael Jones
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 581, 69120, Heidelberg, Germany.
- University Cancer Center Hamburg (UCCH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
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25
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Caswell JL, Camarda R, Zhou AY, Huntsman S, Hu D, Brenner SE, Zaitlen N, Goga A, Ziv E. Multiple breast cancer risk variants are associated with differential transcript isoform expression in tumors. Hum Mol Genet 2015; 24:7421-31. [PMID: 26472073 PMCID: PMC4664170 DOI: 10.1093/hmg/ddv432] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Accepted: 10/09/2015] [Indexed: 12/18/2022] Open
Abstract
Genome-wide association studies have identified over 70 single-nucleotide polymorphisms (SNPs) associated with breast cancer. A subset of these SNPs are associated with quantitative expression of nearby genes, but the functional effects of the majority remain unknown. We hypothesized that some risk SNPs may regulate alternative splicing. Using RNA-sequencing data from breast tumors and germline genotypes from The Cancer Genome Atlas, we tested the association between each risk SNP genotype and exon-, exon–exon junction- or transcript-specific expression of nearby genes. Six SNPs were associated with differential transcript expression of seven nearby genes at FDR < 0.05 (BABAM1, DCLRE1B/PHTF1, PEX14, RAD51L1, SRGAP2D and STXBP4). We next developed a Bayesian approach to evaluate, for each SNP, the overlap between the signal of association with breast cancer and the signal of association with alternative splicing. At one locus (SRGAP2D), this method eliminated the possibility that the breast cancer risk and the alternate splicing event were due to the same causal SNP. Lastly, at two loci, we identified the likely causal SNP for the alternative splicing event, and at one, functionally validated the effect of that SNP on alternative splicing using a minigene reporter assay. Our results suggest that the regulation of differential transcript isoform expression is the functional mechanism of some breast cancer risk SNPs and that we can use these associations to identify causal SNPs, target genes and the specific transcripts that may mediate breast cancer risk.
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Affiliation(s)
- Jennifer L Caswell
- Department of Medicine, Institute for Human Genetics, Helen Diller Family Comprehensive Cancer Center and, Department of Medicine, Division of Medical Oncology, Stanford University, Stanford, CA, USA and
| | - Roman Camarda
- Department of Medicine, Helen Diller Family Comprehensive Cancer Center and, Department of Cell and Tissue Biology, University of California, San Francisco, CA, USA
| | - Alicia Y Zhou
- Department of Medicine, Helen Diller Family Comprehensive Cancer Center and, Department of Cell and Tissue Biology, University of California, San Francisco, CA, USA
| | - Scott Huntsman
- Department of Medicine, Institute for Human Genetics, Helen Diller Family Comprehensive Cancer Center and
| | - Donglei Hu
- Department of Medicine, Institute for Human Genetics, Helen Diller Family Comprehensive Cancer Center and
| | - Steven E Brenner
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Noah Zaitlen
- Department of Medicine, Institute for Human Genetics
| | - Andrei Goga
- Department of Medicine, Helen Diller Family Comprehensive Cancer Center and, Department of Cell and Tissue Biology, University of California, San Francisco, CA, USA
| | - Elad Ziv
- Department of Medicine, Institute for Human Genetics, Helen Diller Family Comprehensive Cancer Center and
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Machiela MJ, Ho BM, Fisher VA, Hua X, Chanock SJ. Limited evidence that cancer susceptibility regions are preferential targets for somatic mutation. Genome Biol 2015; 16:193. [PMID: 26374197 PMCID: PMC4571124 DOI: 10.1186/s13059-015-0755-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 08/19/2015] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Genome wide-association studies have successfully identified several hundred independent loci harboring common cancer susceptibility alleles that are distinct from the more than 110 cancer predisposition genes. The latter are generally characterized by disruptive mutations in coding genes that have been established as 'drivers' of cancer in large somatic sequencing studies. We set out to determine whether, similarly, common cancer susceptibility loci map to genes that have altered frequencies of mutation. RESULTS In our analysis of the intervals defined by the cancer susceptibility markers, we observed that cancer susceptibility regions have gene mutation frequencies comparable to background mutation frequencies. Restricting analyses to genes that have been determined to be pleiotropic across cancer types, genes affected by expression quantitative trait loci, or functional genes indicates that most cancer susceptibility genes classified into these subgroups do not display mutation frequencies that deviate from those expected. We observed limited evidence that cancer susceptibility regions that harbor common alleles with small estimated effect sizes are preferential targets for altered somatic mutation frequencies. CONCLUSIONS Our findings suggest a complex interplay between germline susceptibility and somatic mutation, underscoring the cumulative effect of common variants on redundant pathways as opposed to driver genes. Complex biological pathways and networks likely link these genetic features of carcinogenesis, particularly as they relate to distinct polygenic models for each cancer type.
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Affiliation(s)
- Mitchell J Machiela
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, 9609 Medical Center Drive, Bethesda, MD, 20892, USA.
| | - Brian M Ho
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, 9609 Medical Center Drive, Bethesda, MD, 20892, USA.
| | - Victoria A Fisher
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, 9609 Medical Center Drive, Bethesda, MD, 20892, USA.
| | - Xing Hua
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, 9609 Medical Center Drive, Bethesda, MD, 20892, USA.
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, 9609 Medical Center Drive, Bethesda, MD, 20892, USA.
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27
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Blanco I, Kuchenbaecker K, Cuadras D, Wang X, Barrowdale D, de Garibay GR, Librado P, Sánchez-Gracia A, Rozas J, Bonifaci N, McGuffog L, Pankratz VS, Islam A, Mateo F, Berenguer A, Petit A, Català I, Brunet J, Feliubadaló L, Tornero E, Benítez J, Osorio A, Cajal TRY, Nevanlinna H, Aittomäki K, Arun BK, Toland AE, Karlan BY, Walsh C, Lester J, Greene MH, Mai PL, Nussbaum RL, Andrulis IL, Domchek SM, Nathanson KL, Rebbeck TR, Barkardottir RB, Jakubowska A, Lubinski J, Durda K, Jaworska-Bieniek K, Claes K, Van Maerken T, Díez O, Hansen TV, Jønson L, Gerdes AM, Ejlertsen B, de la Hoya M, Caldés T, Dunning AM, Oliver C, Fineberg E, Cook M, Peock S, McCann E, Murray A, Jacobs C, Pichert G, Lalloo F, Chu C, Dorkins H, Paterson J, Ong KR, Teixeira MR, Hogervorst FBL, van der Hout AH, Seynaeve C, van der Luijt RB, Ligtenberg MJL, Devilee P, Wijnen JT, Rookus MA, Meijers-Heijboer HEJ, Blok MJ, van den Ouweland AMW, Aalfs CM, Rodriguez GC, Phillips KAA, Piedmonte M, Nerenstone SR, Bae-Jump VL, O'Malley DM, Ratner ES, Schmutzler RK, Wappenschmidt B, Rhiem K, Engel C, Meindl A, Ditsch N, Arnold N, Plendl HJ, Niederacher D, Sutter C, Wang-Gohrke S, Steinemann D, Preisler-Adams S, Kast K, Varon-Mateeva R, Gehrig A, Bojesen A, Pedersen IS, Sunde L, Jensen UB, Thomassen M, Kruse TA, Foretova L, Peterlongo P, Bernard L, Peissel B, Scuvera G, Manoukian S, Radice P, Ottini L, Montagna M, Agata S, Maugard C, Simard J, Soucy P, Berger A, Fink-Retter A, Singer CF, Rappaport C, Geschwantler-Kaulich D, Tea MK, Pfeiler G, John EM, Miron A, Neuhausen SL, Terry MB, Chung WK, Daly MB, Goldgar DE, Janavicius R, Dorfling CM, van Rensburg EJ, Fostira F, Konstantopoulou I, Garber J, Godwin AK, Olah E, Narod SA, Rennert G, Paluch SS, Laitman Y, Friedman E, Liljegren A, Rantala J, Stenmark-Askmalm M, Loman N, Imyanitov EN, Hamann U, Spurdle AB, Healey S, Weitzel JN, Herzog J, Margileth D, Gorrini C, Esteller M, Gómez A, Sayols S, Vidal E, Heyn H, Stoppa-Lyonnet D, Léoné M, Barjhoux L, Fassy-Colcombet M, de Pauw A, Lasset C, Ferrer SF, Castera L, Berthet P, Cornelis F, Bignon YJ, Damiola F, Mazoyer S, Sinilnikova OM, Maxwell CA, Vijai J, Robson M, Kauff N, Corines MJ, Villano D, Cunningham J, Lee A, Lindor N, Lázaro C, Easton DF, Offit K, Chenevix-Trench G, Couch FJ, Antoniou AC, Pujana MA. Assessing associations between the AURKA-HMMR-TPX2-TUBG1 functional module and breast cancer risk in BRCA1/2 mutation carriers. PLoS One 2015; 10:e0120020. [PMID: 25830658 PMCID: PMC4382299 DOI: 10.1371/journal.pone.0120020] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Accepted: 01/22/2015] [Indexed: 12/30/2022] Open
Abstract
While interplay between BRCA1 and AURKA-RHAMM-TPX2-TUBG1 regulates mammary epithelial polarization, common genetic variation in HMMR (gene product RHAMM) may be associated with risk of breast cancer in BRCA1 mutation carriers. Following on these observations, we further assessed the link between the AURKA-HMMR-TPX2-TUBG1 functional module and risk of breast cancer in BRCA1 or BRCA2 mutation carriers. Forty-one single nucleotide polymorphisms (SNPs) were genotyped in 15,252 BRCA1 and 8,211 BRCA2 mutation carriers and subsequently analyzed using a retrospective likelihood approach. The association of HMMR rs299290 with breast cancer risk in BRCA1 mutation carriers was confirmed: per-allele hazard ratio (HR) = 1.10, 95% confidence interval (CI) 1.04-1.15, p = 1.9 x 10(-4) (false discovery rate (FDR)-adjusted p = 0.043). Variation in CSTF1, located next to AURKA, was also found to be associated with breast cancer risk in BRCA2 mutation carriers: rs2426618 per-allele HR = 1.10, 95% CI 1.03-1.16, p = 0.005 (FDR-adjusted p = 0.045). Assessment of pairwise interactions provided suggestions (FDR-adjusted pinteraction values > 0.05) for deviations from the multiplicative model for rs299290 and CSTF1 rs6064391, and rs299290 and TUBG1 rs11649877 in both BRCA1 and BRCA2 mutation carriers. Following these suggestions, the expression of HMMR and AURKA or TUBG1 in sporadic breast tumors was found to potentially interact, influencing patients' survival. Together, the results of this study support the hypothesis of a causative link between altered function of AURKA-HMMR-TPX2-TUBG1 and breast carcinogenesis in BRCA1/2 mutation carriers.
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Affiliation(s)
- Ignacio Blanco
- Hereditary Cancer Program, Catalan Institute of Oncology (ICO), Bellvitge Institute for Biomedical Research (IDIBELL), L’Hospitalet del Llobregat, Catalonia, Spain
| | - Karoline Kuchenbaecker
- Epidemiological Study of Familial Breast Cancer (EMBRACE), Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Strangeways Research Laboratory, Cambridge, United Kingdom
| | - Daniel Cuadras
- Statistics Unit, Bellvitge Institute for Biomedical Research (IDIBELL), L’Hospitalet del Llobregat, Catalonia, Spain
| | - Xianshu Wang
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, United States of America
| | - Daniel Barrowdale
- Epidemiological Study of Familial Breast Cancer (EMBRACE), Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Strangeways Research Laboratory, Cambridge, United Kingdom
| | - Gorka Ruiz de Garibay
- Breast Cancer and Systems Biology Unit, Catalan Institute of Oncology (ICO), Bellvitge Institute for Biomedical Research (IDIBELL), L’Hospitalet del Llobregat, Catalonia, Spain
| | - Pablo Librado
- Department of Genetics and Biodiversity Research Institute (IRBio), University of Barcelona, Barcelona, Catalonia, Spain
| | - Alejandro Sánchez-Gracia
- Department of Genetics and Biodiversity Research Institute (IRBio), University of Barcelona, Barcelona, Catalonia, Spain
| | - Julio Rozas
- Department of Genetics and Biodiversity Research Institute (IRBio), University of Barcelona, Barcelona, Catalonia, Spain
| | - Núria Bonifaci
- Breast Cancer and Systems Biology Unit, Catalan Institute of Oncology (ICO), Bellvitge Institute for Biomedical Research (IDIBELL), L’Hospitalet del Llobregat, Catalonia, Spain
| | - Lesley McGuffog
- Epidemiological Study of Familial Breast Cancer (EMBRACE), Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Strangeways Research Laboratory, Cambridge, United Kingdom
| | - Vernon S. Pankratz
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Abul Islam
- Department of Genetic Engineering and Biotechnology, University of Dhaka, Dhaka, Bangladesh
| | - Francesca Mateo
- Breast Cancer and Systems Biology Unit, Catalan Institute of Oncology (ICO), Bellvitge Institute for Biomedical Research (IDIBELL), L’Hospitalet del Llobregat, Catalonia, Spain
| | - Antoni Berenguer
- Statistics Unit, Bellvitge Institute for Biomedical Research (IDIBELL), L’Hospitalet del Llobregat, Catalonia, Spain
| | - Anna Petit
- Department of Pathology, University Hospital of Bellvitge, Bellvitge Institute for Biomedical Research (IDIBELL), L’Hospitalet del Llobregat, Catalonia, Spain
| | - Isabel Català
- Department of Pathology, University Hospital of Bellvitge, Bellvitge Institute for Biomedical Research (IDIBELL), L’Hospitalet del Llobregat, Catalonia, Spain
| | - Joan Brunet
- Hereditary Cancer Program, Catalan Institute of Oncology (ICO), Girona Biomedical Research Institute (IDIBGI), Hospital Josep Trueta, Girona, Catalonia, Spain
| | - Lidia Feliubadaló
- Hereditary Cancer Program, Catalan Institute of Oncology (ICO), Bellvitge Institute for Biomedical Research (IDIBELL), L’Hospitalet del Llobregat, Catalonia, Spain
| | - Eva Tornero
- Hereditary Cancer Program, Catalan Institute of Oncology (ICO), Bellvitge Institute for Biomedical Research (IDIBELL), L’Hospitalet del Llobregat, Catalonia, Spain
| | - Javier Benítez
- Human Genetics Group, Spanish National Cancer Centre (CNIO), and Biomedical Network on Rare Diseases, Madrid, Spain
| | - Ana Osorio
- Human Genetics Group, Spanish National Cancer Centre (CNIO), and Biomedical Network on Rare Diseases, Madrid, Spain
| | - Teresa Ramón y Cajal
- Oncology Service, Hospital de la Santa Creu i Sant Pau, Barcelona, Catalonia, Spain
| | - Heli Nevanlinna
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland
| | - Kristiina Aittomäki
- Department of Clinical Genetics, Helsinki University Central Hospital, Helsinki, Finland
| | - Banu K. Arun
- Division of Cancer Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Amanda E. Toland
- Division of Human Cancer Genetics, Departments of Internal Medicine and Molecular Virology, Immunology and Medical Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, United States of America
| | - Beth Y. Karlan
- Women's Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
| | - Christine Walsh
- Women's Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
| | - Jenny Lester
- Women's Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
| | - Mark H. Greene
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Maryland, Rockville, United States of America
| | - Phuong L. Mai
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Maryland, Rockville, United States of America
| | - Robert L. Nussbaum
- Department of Medicine and Genetics, University of California San Francisco, San Francisco, California, United States of America
| | - Irene L. Andrulis
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, and Departments of Molecular Genetics and Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Susan M. Domchek
- Abramson Cancer Center and Department of Medicine, The University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Katherine L. Nathanson
- Abramson Cancer Center and Department of Medicine, The University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Timothy R. Rebbeck
- Abramson Cancer Center and Center for Clinical Epidemiology and Biostatistics, The University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Rosa B. Barkardottir
- Department of Pathology, Landspitali University Hospital and BMC, Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Anna Jakubowska
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Jan Lubinski
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Katarzyna Durda
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | | | - Kathleen Claes
- Center for Medical Genetics, Ghent University, Ghent, Belgium
| | - Tom Van Maerken
- Center for Medical Genetics, Ghent University, Ghent, Belgium
| | - Orland Díez
- Oncogenetics Group, Vall d’Hebron Institute of Oncology (VHIO), Vall d’Hebron Research Institute (VHIR) and Universitat Autònoma de Barcelona, Barcelona, Catalonia, Spain
| | - Thomas V. Hansen
- Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Lars Jønson
- Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Anne-Marie Gerdes
- Department of Clinical Genetics, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Bent Ejlertsen
- Department of Oncology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Miguel de la Hoya
- Molecular Oncology Laboratory, Hospital Clínico San Carlos, San Carlos Research Institute (IdISSC), Madrid, Spain
| | - Trinidad Caldés
- Molecular Oncology Laboratory, Hospital Clínico San Carlos, San Carlos Research Institute (IdISSC), Madrid, Spain
| | - Alison M. Dunning
- Epidemiological Study of Familial Breast Cancer (EMBRACE), Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Strangeways Research Laboratory, Cambridge, United Kingdom
| | - Clare Oliver
- Epidemiological Study of Familial Breast Cancer (EMBRACE), Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Strangeways Research Laboratory, Cambridge, United Kingdom
| | - Elena Fineberg
- Epidemiological Study of Familial Breast Cancer (EMBRACE), Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Strangeways Research Laboratory, Cambridge, United Kingdom
| | - Margaret Cook
- Epidemiological Study of Familial Breast Cancer (EMBRACE), Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Strangeways Research Laboratory, Cambridge, United Kingdom
| | - Susan Peock
- Epidemiological Study of Familial Breast Cancer (EMBRACE), Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Strangeways Research Laboratory, Cambridge, United Kingdom
| | - Emma McCann
- All Wales Medical Genetics Service, Glan Clwyd Hospital, Rhyl, United Kingdom
| | - Alex Murray
- All Wales Medical Genetics Services, Singleton Hospital, Swansea, United Kingdom
| | - Chris Jacobs
- Clinical Genetics, Guy’s and St. Thomas’ National Health Service (NHS) Foundation Trust, London, United Kingdom
| | - Gabriella Pichert
- Clinical Genetics, Guy’s and St. Thomas’ National Health Service (NHS) Foundation Trust, London, United Kingdom
| | - Fiona Lalloo
- Genetic Medicine, Manchester Academic Health Sciences Centre, Central Manchester University Hospitals National Health Service (NHS) Foundation Trust, Manchester, United Kingdom
| | - Carol Chu
- Yorkshire Regional Genetics Service, Leeds, United Kingdom
| | - Huw Dorkins
- North West Thames Regional Genetics Service, Kennedy-Galton Centre, Harrow, United Kingdom
| | - Joan Paterson
- Department of Clinical Genetics, East Anglian Regional Genetics Service, Addenbrookes Hospital, Cambridge, United Kingdom
| | - Kai-Ren Ong
- West Midlands Regional Genetics Service, Birmingham Women’s Hospital Healthcare National Health Service (NHS) Trust, Edgbaston, Birmingham, United Kingdom
| | - Manuel R. Teixeira
- Department of Genetics, Portuguese Oncology Institute, and Biomedical Sciences Institute (ICBAS), Porto University, Porto, Portugal
| | - Teixeira
- Hereditary Breast and Ovarian Cancer Research Group Netherlands (HEBON), Netherlands Cancer Institute (NKI), Amsterdam, The Netherlands
| | | | - Annemarie H. van der Hout
- Department of Genetics, University Medical Centre Groningen, University of Groningen, Groningen, Netherlands
| | - Caroline Seynaeve
- Department of Medical Oncology, Family Cancer Clinic, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Rob B. van der Luijt
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Marjolijn J. L. Ligtenberg
- Department of Human Genetics and Department of Pathology, Radboud university medical center, Nijmegen, The Netherlands
| | - Peter Devilee
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Juul T. Wijnen
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Matti A. Rookus
- Department of Epidemiology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | | | - Marinus J. Blok
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
| | | | - Cora M. Aalfs
- Department of Clinical Genetics, Academic Medical Center, Amsterdam, The Netherlands
| | - Gustavo C. Rodriguez
- Division of Gynecologic Oncology, NorthShore University HealthSystem, University of Chicago, Chicago, Illinois, United States of America
| | - Kelly-Anne A. Phillips
- Division of Cancer Medicine, Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia
| | - Marion Piedmonte
- Gynecologic Oncology Group Statistical and Data Center, Roswell Park Cancer Institute, Buffalo, New York, United States of America
| | - Stacy R. Nerenstone
- Central Connecticut Cancer Consortium, Hartford Hospital/Helen and Harry Gray Cancer Center, Hartford, Connecticut, United States of America
| | - Victoria L. Bae-Jump
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - David M. O'Malley
- Division of Gynecologic Oncology, Ohio State University, Columbus Cancer Council, Hilliard, Ohio, United States of America
| | - Elena S. Ratner
- Division of Gynecologic Oncology, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Rita K. Schmutzler
- Centre of Familial Breast and Ovarian Cancer and Centre for Integrated Oncology (CIO), University Hospital of Cologne, Cologne, Germany
| | - Barbara Wappenschmidt
- Centre of Familial Breast and Ovarian Cancer and Centre for Integrated Oncology (CIO), University Hospital of Cologne, Cologne, Germany
| | - Kerstin Rhiem
- Centre of Familial Breast and Ovarian Cancer and Centre for Integrated Oncology (CIO), University Hospital of Cologne, Cologne, Germany
| | - Christoph Engel
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
| | - Alfons Meindl
- Department of Gynecology and Obstetrics, Division of Tumor Genetics, Klinikum Rechts der Isar, Technical University Munich, Munich, Germany
| | - Nina Ditsch
- Department of Gynecology and Obstetrics, Ludwig-Maximilian University Munich, Munich, Germany
| | - Norbert Arnold
- Department of Gynecology and Obstetrics, Christian-Albrechts-University of Kiel University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Hansjoerg J. Plendl
- Institute of Human Genetics, Christian-Albrechts-University of Kiel University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Dieter Niederacher
- Department of Gynecology and Obstetrics, University Hospital Düsseldorf, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
| | - Christian Sutter
- Institute of Human Genetics, Department of Human Genetics, University Hospital Heidelberg, Heidelberg, Germany
| | - Shan Wang-Gohrke
- Department of Gynecology and Obstetrics, University Hospital Ulm, Ulm, Germany
| | - Doris Steinemann
- Institute of Cell and Molecular Pathology, Hannover Medical School, Hannover, Germany
| | | | - Karin Kast
- Department of Gynecology and Obstetrics, University Hospital Carl Gustav Carus, Technical University Dresden, Dresden, Germany
| | | | - Andrea Gehrig
- Centre of Familial Breast and Ovarian Cancer, Department of Medical Genetics, Institute of Human Genetics, University Würzburg, Würzburg, Germany
| | - Anders Bojesen
- Department of Clinical Genetics, Vejle Hospital, Vejle, Denmark
| | - Inge Sokilde Pedersen
- Section of Molecular Diagnostics, Department of Biochemistry, Aalborg University Hospital, Aalborg, Denmark
| | - Lone Sunde
- Department of Clinical Genetics, Aarhus University Hospital, Aarhus, Denmark
| | - Uffe Birk Jensen
- Department of Clinical Genetics, Aarhus University Hospital, Aarhus, Denmark
| | - Mads Thomassen
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | - Torben A. Kruse
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | - Lenka Foretova
- Department of Cancer Epidemiology and Genetics, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Paolo Peterlongo
- Fondazione Istituto di Oncologia Molecolare (IFOM), Fondazione Italiana per la Ricerca sul Cancro (FIRC), Milan, Italy
| | - Loris Bernard
- Department of Experimental Oncology, Istituto Europeo di Oncologia (IEO), Cogentech Cancer Genetic Test Laboratory, Milan, Italy
| | - Bernard Peissel
- Unit of Medical Genetics, Department of Preventive and Predictive Medicine, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Fondazione Istituto Nazionale Tumori (INT), Milan, Italy
| | - Giulietta Scuvera
- Unit of Medical Genetics, Department of Preventive and Predictive Medicine, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Fondazione Istituto Nazionale Tumori (INT), Milan, Italy
| | - Siranoush Manoukian
- Unit of Medical Genetics, Department of Preventive and Predictive Medicine, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Fondazione Istituto Nazionale Tumori (INT), Milan, Italy
| | - Paolo Radice
- Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Preventive and Predictive Medicine, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Fondazione Istituto Nazionale Tumori (INT), Milan, Italy
| | - Laura Ottini
- Department of Molecular Medicine, "Sapienza" University, Rome, Italy
| | - Marco Montagna
- Immunology and Molecular Oncology Unit, Istituto Oncologico Veneto (IOV), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Padua, Italy
| | - Simona Agata
- Immunology and Molecular Oncology Unit, Istituto Oncologico Veneto (IOV), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Padua, Italy
| | - Christine Maugard
- Laboratoire de Diagnostic Génétique et Service d'Onco-Hématologie, Hopitaux Universitaire de Strasbourg, Centre Hospitalier Régional Universitaire (CHRU) Nouvel Hôpital Civil, Strasbourg, France
| | - Jacques Simard
- Cancer Genomics Laboratory, Centre Hospitalier Universitaire de Québec Research Center and Laval University, Quebec City, Canada
| | - Penny Soucy
- Cancer Genomics Laboratory, Centre Hospitalier Universitaire de Québec Research Center and Laval University, Quebec City, Canada
| | - Andreas Berger
- Department of Gynecology and Obstetrics, and Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Anneliese Fink-Retter
- Department of Gynecology and Obstetrics, and Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Christian F. Singer
- Department of Gynecology and Obstetrics, and Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Christine Rappaport
- Department of Gynecology and Obstetrics, and Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Daphne Geschwantler-Kaulich
- Department of Gynecology and Obstetrics, and Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Muy-Kheng Tea
- Department of Gynecology and Obstetrics, and Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Georg Pfeiler
- Department of Gynecology and Obstetrics, and Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - BCFR
- Breast Cancer Family Registry (BCFR), Cancer Prevention Institute of California, Fremont, California, United States of America
| | - Esther M. John
- Department of Epidemiology, Cancer Prevention Institute of California, Fremont, California, United States of America
| | - Alex Miron
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - Susan L. Neuhausen
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, California, United States of America
| | - Mary Beth Terry
- Department of Epidemiology, Columbia University, New York, New York, United States of America
| | - Wendy K. Chung
- Departments of Pediatrics and Medicine, Columbia University Medical Center, New York, New York, United States of America
| | - Mary B. Daly
- Department of Clinical Genetics, Fox Chase Cancer Center, Philadelphia, Pennsylvania, United States of America
| | - David E. Goldgar
- Department of Dermatology, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | - Ramunas Janavicius
- Vilnius University Hospital Santariskiu Clinics, Hematology, Oncology and Transfusion Medicine Center, Department of Molecular and Regenerative Medicine, State Research Centre Institute for Innovative medicine, Vilnius, Lithuania
| | - Cecilia M. Dorfling
- Cancer Genetics Laboratory, Department of Genetics, University of Pretoria, Arcadia, South Africa
| | | | - Florentia Fostira
- Molecular Diagnostics Laboratory, Institute of Radioisotopes and Radiodiagnostic Products (IRRP), National Centre for Scientific Research Demokritos, Athens, Greece
| | - Irene Konstantopoulou
- Molecular Diagnostics Laboratory, Institute of Radioisotopes and Radiodiagnostic Products (IRRP), National Centre for Scientific Research Demokritos, Athens, Greece
| | - Judy Garber
- Center for Cancer Genetics and Prevention, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Andrew K. Godwin
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, Kansas, United States of America
| | - Edith Olah
- Department of Molecular Genetics, National Institute of Oncology, Budapest, Hungary
| | - Steven A. Narod
- Women's College Research Institute, University of Toronto, Toronto, Canada
| | - 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, Israel
| | | | - Yael Laitman
- The Susanne Levy Gertner Oncogenetics Unit, Institute of Human Genetics, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Eitan Friedman
- The Susanne Levy Gertner Oncogenetics Unit, Institute of Human Genetics, Chaim Sheba Medical Center, Ramat Gan, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv, Israel
| | - SWE-BRCA
- Swedish BRCA1 and BRCA2 Study (SWE-BRCA), Stockholm, Sweden
| | - Annelie Liljegren
- Department of Oncology, Karolinska University Hospital, Stockholm, Sweden
| | - Johanna Rantala
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Marie Stenmark-Askmalm
- Division of Clinical Genetics, Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Niklas Loman
- Department of Oncology, Lund University Hospital, Lund, Sweden
| | | | - Ute Hamann
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - kConFab Investigators
- Kathleen Cuningham Consortium for Research into Familial Breast Cancer (kConFab), Peter MacCallum Cancer Center, Melbourne, Australia
| | - Amanda B. Spurdle
- Queensland Institute of Medical Research (QIMR) Berghofer Medical Research Institute, Brisbane, Australia
| | - Sue Healey
- Queensland Institute of Medical Research (QIMR) Berghofer Medical Research Institute, Brisbane, Australia
| | - Jeffrey N. Weitzel
- Clinical Cancer Genetics, City of Hope, Duarte, California, United States of America
| | - Josef Herzog
- Clinical Cancer Genetics, City of Hope, Duarte, California, United States of America
| | - David Margileth
- St. Joseph Hospital of Orange, Care of City of Hope Clinical Cancer Genetics Community Research Network, Duarte, California, United States of America
| | - Chiara Gorrini
- The Campbell Family Institute for Breast Cancer Research, Ontario Cancer Institute, University Health Network, Toronto, Canada
| | - Manel Esteller
- Cancer Epigenetics and Biology Program (PEBC), IDIBELL, L’Hospitalet del Llobregat, Catalonia, Spain
- Department of Physiological Sciences II, School of Medicine, University of Barcelona, L’Hospitalet del Llobregat, Catalonia, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Catalonia, Spain
| | - Antonio Gómez
- Cancer Epigenetics and Biology Program (PEBC), IDIBELL, L’Hospitalet del Llobregat, Catalonia, Spain
| | - Sergi Sayols
- Cancer Epigenetics and Biology Program (PEBC), IDIBELL, L’Hospitalet del Llobregat, Catalonia, Spain
| | - Enrique Vidal
- Cancer Epigenetics and Biology Program (PEBC), IDIBELL, L’Hospitalet del Llobregat, Catalonia, Spain
| | - Holger Heyn
- Cancer Epigenetics and Biology Program (PEBC), IDIBELL, L’Hospitalet del Llobregat, Catalonia, Spain
| | - GEMO
- Groupe Genetique et Cancer (GEMO), National Cancer Genetics Network, French Federation of Comprehensive Cancer Centers (UNICANCER), Paris, France
| | - Dominique Stoppa-Lyonnet
- Department of Tumour Biology, Institut Curie, Paris, France
- Institut National de la Santé et de la Recherche Médicale (INSERM) U830, Institut Curie, Paris, France
- Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Melanie Léoné
- Unité Mixte de Génétique Constitutionnelle des Cancers Fréquents, Hospices Civils de Lyon–Centre Léon Bérard, Lyon, France
| | - Laure Barjhoux
- Institut National de la Santé et de la Recherche Médicale (INSERM) U1052, Centre National de la Recherche Scientifique (CNRS) UMR5286, Université Lyon 1, Centre de Recherche en Cancérologie de Lyon, Lyon, France
| | | | | | - Christine Lasset
- Université Lyon 1, Centre National de la Recherche Scientifique (CNRS) UMR5558, and Unité de Prévention et d’Epidémiologie Génétique, Centre Léon Bérard, Lyon, France
| | - Sandra Fert Ferrer
- Laboratoire de Génétique Chromosomique, Hôtel Dieu Centre Hospitalier, Chambéry, France
| | | | | | - François Cornelis
- Genetic Unit, Avicenne Hospital, Assitance Publique-Hôpitaux de Paris, Paris, Sud-Francilien Hospital, Evry-Corbeil, and University Hospital, Clermont-Ferrand, France
| | - Yves-Jean Bignon
- Département d'Oncogénétique, Centre Jean Perrin, Université de Clermont-Ferrand, Clermont-Ferrand, France
| | - Francesca Damiola
- Institut National de la Santé et de la Recherche Médicale (INSERM) U1052, Centre National de la Recherche Scientifique (CNRS) UMR5286, Université Lyon 1, Centre de Recherche en Cancérologie de Lyon, Lyon, France
| | - Sylvie Mazoyer
- Institut National de la Santé et de la Recherche Médicale (INSERM) U1052, Centre National de la Recherche Scientifique (CNRS) UMR5286, Université Lyon 1, Centre de Recherche en Cancérologie de Lyon, Lyon, France
| | - Olga M. Sinilnikova
- Unité Mixte de Génétique Constitutionnelle des Cancers Fréquents, Hospices Civils de Lyon–Centre Léon Bérard, Lyon, France
- Institut National de la Santé et de la Recherche Médicale (INSERM) U1052, Centre National de la Recherche Scientifique (CNRS) UMR5286, Université Lyon 1, Centre de Recherche en Cancérologie de Lyon, Lyon, France
| | - Christopher A. Maxwell
- Department of Pediatrics, Child and Family Research Institute, University of British Columbia, Vancouver, Canada
| | - Joseph Vijai
- Clinical Genetics Research Laboratory, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
| | - Mark Robson
- Clinical Genetics Research Laboratory, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
| | - Noah Kauff
- Clinical Genetics Research Laboratory, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
| | - Marina J. Corines
- Clinical Genetics Research Laboratory, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
| | - Danylko Villano
- Clinical Genetics Research Laboratory, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
| | - Julie Cunningham
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, United States of America
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Adam Lee
- Department of Oncology, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Noralane Lindor
- Center for Individualized Medicine, Mayo Clinic, Scottsdale, Arizona, United States of America
| | - Conxi Lázaro
- Hereditary Cancer Program, Catalan Institute of Oncology (ICO), Bellvitge Institute for Biomedical Research (IDIBELL), L’Hospitalet del Llobregat, Catalonia, Spain
| | - Douglas F. Easton
- Epidemiological Study of Familial Breast Cancer (EMBRACE), Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Strangeways Research Laboratory, Cambridge, United Kingdom
| | - Kenneth Offit
- Clinical Genetics Research Laboratory, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
| | - Georgia Chenevix-Trench
- Queensland Institute of Medical Research (QIMR) Berghofer Medical Research Institute, Brisbane, Australia
| | - Fergus J. Couch
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, United States of America
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Antonis C. Antoniou
- Epidemiological Study of Familial Breast Cancer (EMBRACE), Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Strangeways Research Laboratory, Cambridge, United Kingdom
| | - Miguel Angel Pujana
- Breast Cancer and Systems Biology Unit, Catalan Institute of Oncology (ICO), Bellvitge Institute for Biomedical Research (IDIBELL), L’Hospitalet del Llobregat, Catalonia, Spain
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Rudolph A, Milne RL, Truong T, Knight JA, Seibold P, Flesch-Janys D, Behrens S, Eilber U, Bolla MK, Wang Q, Dennis J, Dunning AM, Shah M, Munday HR, Darabi H, Eriksson M, Brand JS, Olson J, Vachon CM, Hallberg E, Castelao JE, Carracedo A, Torres M, Li J, Humphreys K, Cordina-Duverger E, Menegaux F, Flyger H, Nordestgaard BG, Nielsen SF, Yesilyurt BT, Floris G, Leunen K, Engelhardt EG, Broeks A, Rutgers EJ, Glendon G, Mulligan AM, Cross S, Reed M, Gonzalez-Neira A, Perez JIA, Provenzano E, Apicella C, Southey MC, Spurdle A, Investigators KC, Group AOCS, Häberle L, Beckmann MW, Ekici AB, Dieffenbach AK, Arndt V, Stegmaier C, McLean C, Baglietto L, Chanock SJ, Lissowska J, Sherman ME, Brüning T, Hamann U, Ko YD, Orr N, Schoemaker M, Ashworth A, Kosma VM, Kataja V, Hartikainen JM, Mannermaa A, Swerdlow A, Giles GG, Brenner H, Fasching PA, Chenevix-Trench G, Hopper J, Benítez J, Cox A, Andrulis IL, Lambrechts D, Gago-Dominguez M, Couch F, Czene K, Bojesen SE, Easton DF, Schmidt MK, Guénel P, Hall P, Pharoah PDP, Garcia-Closas M, Chang-Claude J. Investigation of gene-environment interactions between 47 newly identified breast cancer susceptibility loci and environmental risk factors. Int J Cancer 2015; 136:E685-96. [PMID: 25227710 PMCID: PMC4289418 DOI: 10.1002/ijc.29188] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Revised: 06/04/2014] [Accepted: 06/06/2014] [Indexed: 12/21/2022]
Abstract
A large genotyping project within the Breast Cancer Association Consortium (BCAC) recently identified 41 associations between single nucleotide polymorphisms (SNPs) and overall breast cancer (BC) risk. We investigated whether the effects of these 41 SNPs, as well as six SNPs associated with estrogen receptor (ER) negative BC risk are modified by 13 environmental risk factors for BC. Data from 22 studies participating in BCAC were pooled, comprising up to 26,633 cases and 30,119 controls. Interactions between SNPs and environmental factors were evaluated using an empirical Bayes-type shrinkage estimator. Six SNPs showed interactions with associated p-values (pint ) <1.1 × 10(-3) . None of the observed interactions was significant after accounting for multiple testing. The Bayesian False Discovery Probability was used to rank the findings, which indicated three interactions as being noteworthy at 1% prior probability of interaction. SNP rs6828523 was associated with increased ER-negative BC risk in women ≥170 cm (OR = 1.22, p = 0.017), but inversely associated with ER-negative BC risk in women <160 cm (OR = 0.83, p = 0.039, pint = 1.9 × 10(-4) ). The inverse association between rs4808801 and overall BC risk was stronger for women who had had four or more pregnancies (OR = 0.85, p = 2.0 × 10(-4) ), and absent in women who had had just one (OR = 0.96, p = 0.19, pint = 6.1 × 10(-4) ). SNP rs11242675 was inversely associated with overall BC risk in never/former smokers (OR = 0.93, p = 2.8 × 10(-5) ), but no association was observed in current smokers (OR = 1.07, p = 0.14, pint = 3.4 × 10(-4) ). In conclusion, recently identified BC susceptibility loci are not strongly modified by established risk factors and the observed potential interactions require confirmation in independent studies.
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Affiliation(s)
- Anja Rudolph
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Roger L. Milne
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Australia
- Centre for Epidemiology & Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Australia
| | - Thérèse Truong
- Inserm (National Institute of Health and Medical Research), CESP (Center for Research in Epidemiology and Population Health), U1018, Environmental Epidemiology of Cancer, Villejuif, France
- Unité Mixte de Recherche Scientifique (UMRS) 1018, University Paris-Sud, Villejuif, France
| | - Julia A. Knight
- Prosserman Centre for Health Research, Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, Ontario, Canada
- Division of Epidemiology, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Petra Seibold
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Dieter Flesch-Janys
- Department of Cancer Epidemiology/Clinical Cancer Registry, University Clinic Hamburg-Eppendorf, Hamburg, Germany
- Institute for Medical Biometrics and Epidemiology, University Clinic Hamburg-Eppendorf, Hamburg, Germany
| | - Sabine Behrens
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ursula Eilber
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Manjeet K. Bolla
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Qin Wang
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Joe Dennis
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Alison M. Dunning
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Mitul Shah
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Hannah R. Munday
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Hatef Darabi
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Mikael Eriksson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Judith S. Brand
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Janet Olson
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Celine M. Vachon
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Emily Hallberg
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - J. Esteban Castelao
- Oncology and Genetics Unit, Biomedical Research Institute of Vigo (IBIV), Complejo Hospitalario Universitario de Vigo, Servicio Galego de Saude (SERGAS), Vigo, Spain
| | - Angel Carracedo
- Genomic Medicine Group, Galician Foundation of Genomic Medicine, Servicio Galego de Saude (SERGAS), Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela, Spain
- National Genotyping Center - Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), University of Santiago de Compostela, Spain
- Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, KSA
| | - Maria Torres
- National Genotyping Center - Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), University of Santiago de Compostela, Spain
| | - Jingmei Li
- Human Genetics Division, Genome Institute of Singapore, Singapore, Singapore
| | - Keith Humphreys
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Emilie Cordina-Duverger
- Inserm (National Institute of Health and Medical Research), CESP (Center for Research in Epidemiology and Population Health), U1018, Environmental Epidemiology of Cancer, Villejuif, France
- Unité Mixte de Recherche Scientifique (UMRS) 1018, University Paris-Sud, Villejuif, France
| | - Florence Menegaux
- Inserm (National Institute of Health and Medical Research), CESP (Center for Research in Epidemiology and Population Health), U1018, Environmental Epidemiology of Cancer, Villejuif, France
- Unité Mixte de Recherche Scientifique (UMRS) 1018, University Paris-Sud, Villejuif, France
| | - Henrik Flyger
- Department of Breast Surgery, Herlev Hospital, Copenhagen University Hospital, Copenhagen, Denmark
| | - Børge G. Nordestgaard
- Copenhagen General Population Study, Herlev Hospital, Copenhagen University Hospital, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Biochemistry, Herlev Hospital, Copenhagen University Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Sune F. Nielsen
- Copenhagen General Population Study, Herlev Hospital, Copenhagen University Hospital, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Biochemistry, Herlev Hospital, Copenhagen University Hospital, University of Copenhagen, Copenhagen, Denmark
| | | | - Giuseppe Floris
- Multidisciplinary Breast Center, University Hospital Gasthuisberg, Leuven, Belgium
| | - Karin Leunen
- Multidisciplinary Breast Center, University Hospital Gasthuisberg, Leuven, Belgium
| | - Ellen G. Engelhardt
- Division of Psychosocial Research and Epidemiology, Netherlands Cancer Institute, Antoni van Leeuwenhoek hospital, Amsterdam, The Netherlands
| | - Annegien Broeks
- Division of Molecular Pathology, Netherlands Cancer Institute, Antoni van Leeuwenhoek hospital, Amsterdam, The Netherlands
| | - Emiel J. Rutgers
- Department of Surgery, Netherlands Cancer Institute, Antoni van Leeuwenhoek hospital, Amsterdam, The Netherlands
| | - Gord Glendon
- Ontario Cancer Genetics Network, Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Anna Marie Mulligan
- Laboratory Medicine Program, University Health Network, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Simon Cross
- Academic Unit of Pathology, Department of Neuroscience, University of Sheffield, UK
| | - Malcolm Reed
- Sheffield Cancer Research Centre, Department of Oncology, University of Sheffield, Sheffield, UK
| | - Anna Gonzalez-Neira
- Human Genotyping Unit-CEGEN, Human Cancer Genetics Program, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | | | - Elena Provenzano
- Cancer Research UK Cambridge Institute, Cambridge, UK
- Cambridge Breast Unit, Addenbrooke’s Hospital, Cambridge University Hospital NHS Foundation Trust and NIHR Cambridge Biomedical Research Centre, Cambridge, UK
| | - Carmel Apicella
- Centre for Molecular, Environmental, Genetic and Analytic Epidemiology, University of Melbourne, Melbourne, Australia
| | | | - Amanda Spurdle
- Department of Genetics, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | | | - AOCS Group
- QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Lothar Häberle
- Department of Gynecology and Obstetrics, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Comprehensive Cancer Center Erlangen-EMN, Erlangen, Germany
| | - Matthias W. Beckmann
- Department of Gynecology and Obstetrics, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Comprehensive Cancer Center Erlangen-EMN, Erlangen, Germany
| | - Arif B. Ekici
- Institute of Human Genetics, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Comprehensive Cancer Center Erlangen-EMN, Erlangen, Germany
| | - Aida Karina Dieffenbach
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Volker Arndt
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Catriona McLean
- Anatomical Pathology, The Alfred Hospital, Melbourne, Australia
| | - Laura Baglietto
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Australia
- Centre for Epidemiology & Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Australia
| | - Stephen J. Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Jolanta Lissowska
- Department of Cancer Epidemiology and Prevention, M. Sklodowska-Curie Memorial Cancer Center & Institute of Oncology, Warsaw, Poland
| | - Mark E. Sherman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
- Division of Cancer Prevention, National Cancer Institute, Bethesda, Maryland, USA
| | - Thomas Brüning
- Institute for Prevention and Occupational Medicine of the German Social Accident Insurance, Institute of the Ruhr University Bochum (IPA), Bochum, Germany
| | - Ute Hamann
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Yon-Dschun Ko
- Department of Internal Medicine, Evangelische Kliniken Bonn gGmbH, Johanniter Krankenhaus, Bonn, Germany
| | - Nick Orr
- Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, UK
| | - Minouk Schoemaker
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, Surrey, UK
| | - Alan Ashworth
- Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, UK
| | - Veli-Matti Kosma
- School of Medicine, Institute of Clinical Medicine, Pathology and Forensic Medicine and Cancer Center of Eastern Finland, University of Eastern Finland, Kuopio, Finland
- Imaging Center, Department of Clinical Pathology, Kuopio University Hospital, Kuopio, Finland
| | - Vesa Kataja
- School of Medicine, Institute of Clinical Medicine, Oncology and Cancer Center of Eastern Finland, University of Eastern Finland, Kuopio, Finland
- Cancer Center, Kuopio University Hospital, Kuopio, Finland
- Jyväskylä Central Hospital, Jyväskylä, Finland
| | - Jaana M. Hartikainen
- School of Medicine, Institute of Clinical Medicine, Pathology and Forensic Medicine and Cancer Center of Eastern Finland, University of Eastern Finland, Kuopio, Finland
- Imaging Center, Department of Clinical Pathology, Kuopio University Hospital, Kuopio, Finland
| | - Arto Mannermaa
- School of Medicine, Institute of Clinical Medicine, Pathology and Forensic Medicine and Cancer Center of Eastern Finland, University of Eastern Finland, Kuopio, Finland
- Imaging Center, Department of Clinical Pathology, Kuopio University Hospital, Kuopio, Finland
| | - Anthony Swerdlow
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, Surrey, UK
- Division of Breast Cancer Research, Institute of Cancer Research, Sutton, Surrey, UK
| | - GENICA-Network
- The GENICA Network: Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, and University of Tübingen, Germany; Department of Internal Medicine, Evangelische Kliniken Bonn gGmbH, Johanniter Krankenhaus, Bonn, Germany, Institute of Pathology, University of Bonn, Germany, Molecular Genetics of Breast Cancer, Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany, and Institute for Prevention and Occupational Medicine of the German Social Accident Insurance, Institute of the Ruhr University Bochum (IPA), Bochum, Germany; Institute of Occupational Medicine and Maritime Medicine, University Medical Center Hamburg-Eppendorf, Germany
| | - Graham G. Giles
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Australia
- Centre for Epidemiology & Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Australia
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Peter A. Fasching
- Department of Gynecology and Obstetrics, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Comprehensive Cancer Center Erlangen-EMN, Erlangen, Germany
- David Geffen School of Medicine, Department of Medicine Division of Hematology and Oncology, University of California at Los Angeles, CA, USA
| | | | - John Hopper
- Centre for Molecular, Environmental, Genetic and Analytic Epidemiology, University of Melbourne, Melbourne, Australia
| | - Javier Benítez
- Human Genetics Group, Human Cancer Genetics Program, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Angela Cox
- Sheffield Cancer Research Centre, Department of Oncology, University of Sheffield, Sheffield, UK
| | - Irene L. Andrulis
- Ontario Cancer Genetics Network, Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | | | - Manuela Gago-Dominguez
- Genomic Medicine Group, Galician Foundation of Genomic Medicine, Servicio Galego de Saude (SERGAS), Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela, Spain
| | - Fergus Couch
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Kamila Czene
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Stig E. Bojesen
- Copenhagen General Population Study, Herlev Hospital, Copenhagen University Hospital, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Biochemistry, Herlev Hospital, Copenhagen University Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Doug 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
| | - Marjanka K. Schmidt
- Netherlands Cancer Institute, Antoni van Leeuwenhoek hospital, Amsterdam, The Netherlands
| | - Pascal Guénel
- Inserm (National Institute of Health and Medical Research), CESP (Center for Research in Epidemiology and Population Health), U1018, Environmental Epidemiology of Cancer, Villejuif, France
- Unité Mixte de Recherche Scientifique (UMRS) 1018, University Paris-Sud, Villejuif, France
| | - Per Hall
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Paul D. P. Pharoah
- 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
| | - Montserrat Garcia-Closas
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, Surrey, UK
- Breakthrough Breast Cancer Research Centre, Division of Breast Cancer Research, The Institute of Cancer Research, London, UK
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
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Purrington KS, Slettedahl S, Bolla MK, Michailidou K, Czene K, Nevanlinna H, Bojesen SE, Andrulis IL, Cox A, Hall P, Carpenter J, Yannoukakos D, Haiman CA, Fasching PA, Mannermaa A, Winqvist R, Brenner H, Lindblom A, Chenevix-Trench G, Benitez J, Swerdlow A, Kristensen V, Guénel P, Meindl A, Darabi H, Eriksson M, Fagerholm R, Aittomäki K, Blomqvist C, Nordestgaard BG, Nielsen SF, Flyger H, Wang X, Olswold C, Olson JE, Mulligan AM, Knight JA, Tchatchou S, Reed MWR, Cross SS, Liu J, Li J, Humphreys K, Clarke C, Scott R, Fostira F, Fountzilas G, Konstantopoulou I, Henderson BE, Schumacher F, Le Marchand L, Ekici AB, Hartmann A, Beckmann MW, Hartikainen JM, Kosma VM, Kataja V, Jukkola-Vuorinen A, Pylkäs K, Kauppila S, Dieffenbach AK, Stegmaier C, Arndt V, Margolin S, Balleine R, Arias Perez JI, Pilar Zamora M, Menéndez P, Ashworth A, Jones M, Orr N, Arveux P, Kerbrat P, Truong T, Bugert P, Toland AE, Ambrosone CB, Labrèche F, Goldberg MS, Dumont M, Ziogas A, Lee E, Dite GS, Apicella C, Southey MC, Long J, Shrubsole M, Deming-Halverson S, Ficarazzi F, Barile M, Peterlongo P, Durda K, Jaworska-Bieniek K, Tollenaar RAEM, Seynaeve C, Brüning T, Ko YD, Van Deurzen CHM, Martens JWM, Kriege M, Figueroa JD, Chanock SJ, Lissowska J, Tomlinson I, Kerin MJ, Miller N, Schneeweiss A, Tapper WJ, Gerty SM, Durcan L, Mclean C, Milne RL, Baglietto L, dos Santos Silva I, Fletcher O, Johnson N, Van'T Veer LJ, Cornelissen S, Försti A, Torres D, Rüdiger T, Rudolph A, Flesch-Janys D, Nickels S, Weltens C, Floris G, Moisse M, Dennis J, Wang Q, Dunning AM, Shah M, Brown J, Simard J, Anton-Culver H, Neuhausen SL, Hopper JL, Bogdanova N, Dörk T, Zheng W, Radice P, Jakubowska A, Lubinski J, Devillee P, Brauch H, Hooning M, García-Closas M, Sawyer E, Burwinkel B, Marmee F, Eccles DM, Giles GG, Peto J, Schmidt M, Broeks A, Hamann U, Chang-Claude J, Lambrechts D, Pharoah PDP, Easton D, Pankratz VS, Slager S, Vachon CM, Couch FJ. Genetic variation in mitotic regulatory pathway genes is associated with breast tumor grade. Hum Mol Genet 2014; 23:6034-46. [PMID: 24927736 PMCID: PMC4204763 DOI: 10.1093/hmg/ddu300] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Revised: 05/20/2014] [Accepted: 06/10/2014] [Indexed: 01/01/2023] Open
Abstract
Mitotic index is an important component of histologic grade and has an etiologic role in breast tumorigenesis. Several small candidate gene studies have reported associations between variation in mitotic genes and breast cancer risk. We measured associations between 2156 single nucleotide polymorphisms (SNPs) from 194 mitotic genes and breast cancer risk, overall and by histologic grade, in the Breast Cancer Association Consortium (BCAC) iCOGS study (n = 39 067 cases; n = 42 106 controls). SNPs in TACC2 [rs17550038: odds ratio (OR) = 1.24, 95% confidence interval (CI) 1.16-1.33, P = 4.2 × 10(-10)) and EIF3H (rs799890: OR = 1.07, 95% CI 1.04-1.11, P = 8.7 × 10(-6)) were significantly associated with risk of low-grade breast cancer. The TACC2 signal was retained (rs17550038: OR = 1.15, 95% CI 1.07-1.23, P = 7.9 × 10(-5)) after adjustment for breast cancer risk SNPs in the nearby FGFR2 gene, suggesting that TACC2 is a novel, independent genome-wide significant genetic risk locus for low-grade breast cancer. While no SNPs were individually associated with high-grade disease, a pathway-level gene set analysis showed that variation across the 194 mitotic genes was associated with high-grade breast cancer risk (P = 2.1 × 10(-3)). These observations will provide insight into the contribution of mitotic defects to histological grade and the etiology of breast cancer.
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Affiliation(s)
- Kristen S Purrington
- Department of Health Sciences Research, Department of Oncology, Wayne State University School of Medicine and Karmanos Cancer Institute, Detroit, USA
| | | | - Manjeet K Bolla
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care
| | - Kyriaki Michailidou
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care
| | - Kamila Czene
- Department of Medical Epidemiology and Biostatistics
| | | | - Stig E Bojesen
- Copenhagen General Population Study, Department of Clinical Biochemistry, Herlev Hospital, Copenhagen University Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Irene L Andrulis
- Ontario Cancer Genetics Network, Department of Molecular Genetics
| | - Angela Cox
- CRUK/YCR Sheffield Cancer Research Centre, Department of Oncology
| | - Per Hall
- Department of Medical Epidemiology and Biostatistics
| | | | - Drakoulis Yannoukakos
- Molecular Diagnostics Laboratory INRASTES, National Centre for Scientific Research 'Demokritos', Athens, Greece
| | - Christopher A Haiman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, USA
| | - Peter A Fasching
- University Breast Center Franconia, Department of Gynecology and Obstetrics, David Geffen School of Medicine, Department of Medicine Division of Hematology and Oncology, University of California at Los Angeles, Los Angeles, USA
| | - Arto Mannermaa
- School of Medicine, Institute of Clinical Medicine, Oncology, Cancer Center of Eastern Finland, University of Eastern Finland, Kuopio, Finland, Imaging Center, Department of Clinical Pathology
| | - Robert Winqvist
- Laboratory of Cancer Genetics and Tumor Biology, Department of Clinical Chemistry and Biocenter Oulu, University of Oulu, Oulu University Hospital/NordLab Oulu, Oulu, Finland
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Consortium (DKTK), Heidelberg, Germany
| | | | | | - Javier Benitez
- Human Genetics Group, Human Cancer Genetics Program, Spanish National Cancer Research Centre (CNIO), Madrid, Spain, Centro de Investigación en Red de Enfermedades Raras (CIBERER), Valencia, Spain
| | - Anthony Swerdlow
- Division of Genetics and Epidemiology, Division of Breast Cancer Research, Institute of Cancer Research, Sutton, UK
| | - Vessela Kristensen
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital, Radiumhospitalet, Oslo, Norway, Faculty of Medicine (Faculty Division Ahus), University of Oslo (UiO), Oslo, Norway
| | - Pascal Guénel
- Inserm (National Institute of Health and Medical Research), CESP (Center for Research in Epidemiology and Population Health), U1018, Environmental Epidemiology of Cancer, Villejuif, France, University Paris-Sud, UMRS 1018, Villejuif, France
| | - Alfons Meindl
- Division of Gynaecology and Obstetrics, Technische Universität München, Munich, Germany
| | - Hatef Darabi
- Department of Medical Epidemiology and Biostatistics
| | | | - Rainer Fagerholm
- Department of Obstetrics and Gynecology, Oncology and Clinical Genetics
| | | | - Carl Blomqvist
- Department of Oncology, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland
| | - Børge G Nordestgaard
- Department of Clinical Biochemistry, Herlev Hospital, Copenhagen University Hospital, University of Copenhagen, Copenhagen, Denmark
| | | | - Henrik Flyger
- Department of Breast Surgery, Herlev Hospital, Copenhagen University Hospital, Copenhagen, Denmark
| | - Xianshu Wang
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, USA
| | | | | | - Anna Marie Mulligan
- Department of Laboratory Medicine and Pathobiology, Laboratory Medicine Program, University Health Network, Toronto, Canada
| | - Julia A Knight
- Prosserman Centre for Health Research, Division of Epidemiology, Dalla Lana School of Public Health, University of Toronto, Toronto, Canada
| | - Sandrine Tchatchou
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, Canada
| | - Malcolm W R Reed
- CRUK/YCR Sheffield Cancer Research Centre, Department of Oncology
| | - Simon S Cross
- Academic Unit of Pathology, Department of Neuroscience, University of Sheffield, Sheffield, UK
| | - Jianjun Liu
- Human Genetics Division, Genome Institute of Singapore, Singapore, Singapore
| | - Jingmei Li
- Human Genetics Division, Genome Institute of Singapore, Singapore, Singapore
| | | | - Christine Clarke
- Westmead Institute for Cancer Research, Sydney Medical School Westmead, University of Sydney at the Westmead Millennium Institute, Westmead, Australia
| | - Rodney Scott
- Division of Genetics, Hunter Area Pathology Service and University of Newcastle, Newcastle, Australia
| | - Florentia Fostira
- Molecular Diagnostics Laboratory INRASTES, National Centre for Scientific Research 'Demokritos', Athens, Greece
| | - George Fountzilas
- Department of Medical Oncology, "Papageorgiou" Hospital, Aristotle University of Thessaloniki School of Medicine, Thessaloniki, Greece
| | - Irene Konstantopoulou
- Molecular Diagnostics Laboratory INRASTES, National Centre for Scientific Research 'Demokritos', Athens, Greece
| | - Brian E Henderson
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, USA
| | - Fredrick Schumacher
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, USA
| | - Loic Le Marchand
- Epidemiology Program, Cancer Research Center, University of Hawaii, Honolulu, USA
| | | | - Arndt Hartmann
- Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Comprehensive Cancer Center Erlangen-EMN, Erlangen, Germany
| | | | - Jaana M Hartikainen
- School of Medicine, Institute of Clinical Medicine, Oncology, Cancer Center of Eastern Finland, University of Eastern Finland, Kuopio, Finland, Imaging Center, Department of Clinical Pathology
| | - Veli-Matti Kosma
- School of Medicine, Institute of Clinical Medicine, Oncology, Cancer Center of Eastern Finland, University of Eastern Finland, Kuopio, Finland, Imaging Center, Department of Clinical Pathology
| | - Vesa Kataja
- School of Medicine, Institute of Clinical Medicine, Oncology, Cancer Center of Eastern Finland, University of Eastern Finland, Kuopio, Finland, Cancer Center, Kuopio University Hospital, Kuopio, Finland
| | | | - Katri Pylkäs
- Laboratory of Cancer Genetics and Tumor Biology, Department of Clinical Chemistry and Biocenter Oulu, University of Oulu, Oulu University Hospital/NordLab Oulu, Oulu, Finland
| | - Saila Kauppila
- Department of Pathology, Oulu University Hospital, University of Oulu, Oulu, Finland
| | - Aida Karina Dieffenbach
- Division of Clinical Epidemiology and Aging Research, German Cancer Consortium (DKTK), Heidelberg, Germany
| | | | - Volker Arndt
- Division of Clinical Epidemiology and Aging Research
| | - Sara Margolin
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Rosemary Balleine
- Westmead Millenium Institute for Medical Research, Sydney, Australia
| | | | - M Pilar Zamora
- Servicio de Oncología Médica, Hospital Universitario La Paz, Madrid, Spain
| | | | - Alan Ashworth
- Breakthrough Breast Cancer Research Centre and Division of Breast Cancer Research
| | | | - Nick Orr
- Breakthrough Breast Cancer Research Centre and Division of Breast Cancer Research
| | - Patrick Arveux
- Center Georges-Francois Leclerc, Registry of Gynecologic Tumors, Dijon, France
| | - Pierre Kerbrat
- Centre Eugène Marquis, Department of Medical Oncology, Rennes, France
| | - Thérèse Truong
- Inserm (National Institute of Health and Medical Research), CESP (Center for Research in Epidemiology and Population Health), U1018, Environmental Epidemiology of Cancer, Villejuif, France, University Paris-Sud, UMRS 1018, Villejuif, France
| | - Peter Bugert
- German Red Cross Blood Service of Baden-Württemberg-Hessen, Mannheim, Germany, Medical Faculty Mannheim, Institute of Transfusion Medicine and Immunology, Heidelberg University, Heidelberg, Germany
| | - Amanda E Toland
- Department of Molecular Virology, Immunology and Medical Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, USA
| | | | - France Labrèche
- Department of Environmental & Occupational Health and of Social & Preventive Medicine, School of Public Health, Université de Montréal, Montreal, Canada
| | - Mark S Goldberg
- Department of Medicine, McGill University, Montreal, Canada, Division of Clinical Epidemiology, McGill University Health Centre, Royal Victoria Hospital, Montreal, Canada
| | - Martine Dumont
- Cancer Genomics Laboratory, Centre Hospitalier Universitaire de Québec Research Center and Laval University, Quebec City, Canada
| | - Argyrios Ziogas
- Department of Epidemiology, University of California Irvine, Irvine, USA
| | - Eunjung Lee
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, USA
| | - Gillian S Dite
- Centre for Molecular, Environmental, Genetic and Analytic Epidemiology, Melbourne School of Population Health
| | - Carmel Apicella
- Centre for Molecular, Environmental, Genetic and Analytic Epidemiology, Melbourne School of Population Health
| | | | - Jirong Long
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, USA
| | - Martha Shrubsole
- Department of Molecular Virology, Immunology and Medical Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, USA
| | - Sandra Deming-Halverson
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, USA
| | - Filomena Ficarazzi
- Cogentech Cancer Genetic Test Laboratory, Milan, Italy, IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, Milan, Italy
| | - Monica Barile
- Division of Cancer Prevention and Genetics, Istituto Europeo di Oncologia (IEO), Milan, Italy
| | - Paolo Peterlongo
- IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, Milan, Italy
| | - Katarzyna Durda
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | | | | | - Caroline Seynaeve
- Family Cancer Clinic, Department of Medical Oncology, Erasmus MC-Daniel den Hoed Cancer Centrer, Rotterdam, The Netherlands
| | - Thomas Brüning
- Institute for Prevention and Occupational Medicine of the German Social Accident Insurance (IPA), Bochum, Germany
| | - Yon-Dschun Ko
- Department of Internal Medicine, Evangelische Kliniken Bonn gGmbH, Johanniter Krankenhaus, Bonn, Germany
| | | | - John W M Martens
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Mieke Kriege
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Jonine D Figueroa
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, USA
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, USA
| | - Jolanta Lissowska
- Department of Cancer Epidemiology and Prevention, M. Sklodowska-Curie Memorial Cancer Center & Institute of Oncology, Warsaw, Poland
| | - Ian Tomlinson
- Wellcome Trust Centre for Human Genetics and Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Michael J Kerin
- Clinical Science Institute, University Hospital Galway, Galway, Ireland
| | - Nicola Miller
- Clinical Science Institute, University Hospital Galway, Galway, Ireland
| | - Andreas Schneeweiss
- Department of Obstetrics and Gynecology, National Center for Tumor Diseases, University of Heidelberg, Heidelberg, Germany
| | | | - Susan M Gerty
- Faculty of Medicine, University of Southampton, Southampton, UK
| | - Lorraine Durcan
- Faculty of Medicine, University of Southampton, Southampton, UK
| | - Catriona Mclean
- Anatomical Pathology, The Alfred Hospital, Melbourne, Australia
| | - Roger L Milne
- Centre for Molecular, Environmental, Genetic, and Analytic Epidemiology, The University of Melbourne, Melbourne, Australia, Cancer Epidemiology Centre, The Cancer Council Victoria, Melbourne, Australia
| | - Laura Baglietto
- Centre for Molecular, Environmental, Genetic, and Analytic Epidemiology, The University of Melbourne, Melbourne, Australia, Cancer Epidemiology Centre, The Cancer Council Victoria, Melbourne, Australia
| | - Isabel dos Santos Silva
- Non-communicable Disease Epidemiology Department, London School of Hygiene and Tropical Medicine, London, UK
| | - Olivia Fletcher
- Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, UK
| | - Nichola Johnson
- Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, UK
| | - Laura J Van'T Veer
- Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
| | - Sten Cornelissen
- Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
| | - Asta Försti
- Division of Molecular Genetic Epidemiology, Center for Primary Health Care Research, University of Lund, Malmö, Sweden
| | - Diana Torres
- Molecular Genetics of Breast Cancer, Institute of Human Genetics, Pontificia University Javeriana, Bogota, Colombia
| | - Thomas Rüdiger
- Institute of Pathology, Städtisches Klinikum Karlsruhe, Karlsruhe, Germany
| | | | - Dieter Flesch-Janys
- Department of Cancer Epidemiology/Clinical Cancer Registry and Institute for Medical Biometrics and Epidemiology, University Clinic Hamburg-Eppendorf, Hamburg, Germany
| | | | | | | | - Matthieu Moisse
- Laboratory for Translational Genetics, Department of Oncology, University of Leuven, Leuven, Belgium, Vesalius Research Center (VRC), VIB, Leuven, Belgium
| | - Joe Dennis
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care
| | - Qin Wang
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care
| | - Alison M Dunning
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Mitul Shah
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Judith Brown
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care
| | - Jacques Simard
- Cancer Genomics Laboratory, Centre Hospitalier Universitaire de Québec Research Center and Laval University, Quebec City, Canada
| | - Hoda Anton-Culver
- Department of Epidemiology, University of California Irvine, Irvine, USA
| | | | - John L Hopper
- Centre for Molecular, Environmental, Genetic and Analytic Epidemiology, Melbourne School of Population Health
| | | | - Thilo Dörk
- Department of Obstetrics and Gynaecology, Hannover Medical School, Hannover, Germany
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, USA
| | - Paolo Radice
- Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori (INT), Milan, Italy and
| | - Anna Jakubowska
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Jan Lubinski
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Peter Devillee
- Department of Human Genetics & Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Hiltrud Brauch
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany, University of Tübingen, Tübingen, Germany
| | - Maartje Hooning
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | | | - Elinor Sawyer
- Division of Cancer Studies, Kings College London, Guy's Hospital, London, UK
| | - Barbara Burwinkel
- Department of Obstetrics and Gynecology, Molecular Epidemiology Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Frederick Marmee
- Department of Obstetrics and Gynecology, National Center for Tumor Diseases, University of Heidelberg, Heidelberg, Germany
| | - Diana M Eccles
- Faculty of Medicine, University of Southampton, Southampton, UK
| | - Graham G Giles
- Centre for Molecular, Environmental, Genetic, and Analytic Epidemiology, The University of Melbourne, Melbourne, Australia, Cancer Epidemiology Centre, The Cancer Council Victoria, Melbourne, Australia
| | - Julian Peto
- Non-communicable Disease Epidemiology Department, London School of Hygiene and Tropical Medicine, London, UK
| | - Marjanka Schmidt
- Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
| | - Annegien Broeks
- Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
| | | | | | - Diether Lambrechts
- Laboratory for Translational Genetics, Department of Oncology, University of Leuven, Leuven, Belgium, Vesalius Research Center (VRC), VIB, Leuven, Belgium
| | - Paul D P Pharoah
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Douglas Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | | | | | | | - Fergus J Couch
- Department of Health Sciences Research, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, USA,
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Abstract
Gene enhancer elements are noncoding segments of DNA that play a central role in regulating transcriptional programs that control development, cell identity, and evolutionary processes. Recent studies have shown that noncoding single nucleotide polymorphisms (SNPs) that have been associated with risk for numerous common diseases through genome-wide association studies frequently lie in cell-type-specific enhancer elements. These enhancer variants probably influence transcriptional output, thereby offering a mechanistic basis to explain their association with risk for many common diseases. This review focuses on the identification and interpretation of disease-susceptibility variants that influence enhancer function. We discuss strategies for prioritizing the study of functional enhancer SNPs over those likely to be benign, review experimental and computational approaches to identifying the gene targets of enhancer variants, and highlight efforts to quantify the impact of enhancer variants on target transcript levels and cellular phenotypes. These studies are beginning to provide insights into the mechanistic basis of many common diseases, as well as into how we might translate this knowledge for improved disease diagnosis, prevention and treatments. Finally, we highlight five major challenges often associated with interpreting enhancer variants, and discuss recent technical advances that may help to surmount these challenges.
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Affiliation(s)
- Olivia Corradin
- />Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44122 USA
| | - Peter C Scacheri
- />Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44122 USA
- />Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH 44106 USA
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Primiani CT, Ryan VH, Rao JS, Cam MC, Ahn K, Modi HR, Rapoport SI. Coordinated gene expression of neuroinflammatory and cell signaling markers in dorsolateral prefrontal cortex during human brain development and aging. PLoS One 2014; 9:e110972. [PMID: 25329999 PMCID: PMC4203852 DOI: 10.1371/journal.pone.0110972] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Accepted: 09/17/2014] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Age changes in expression of inflammatory, synaptic, and neurotrophic genes are not well characterized during human brain development and senescence. Knowing these changes may elucidate structural, metabolic, and functional brain processes over the lifespan, as well vulnerability to neurodevelopmental or neurodegenerative diseases. HYPOTHESIS Expression levels of inflammatory, synaptic, and neurotrophic genes in the human brain are coordinated over the lifespan and underlie changes in phenotypic networks or cascades. METHODS We used a large-scale microarray dataset from human prefrontal cortex, BrainCloud, to quantify age changes over the lifespan, divided into Development (0 to 21 years, 87 brains) and Aging (22 to 78 years, 144 brains) intervals, in transcription levels of 39 genes. RESULTS Gene expression levels followed different trajectories over the lifespan. Many changes were intercorrelated within three similar groups or clusters of genes during both Development and Aging, despite different roles of the gene products in the two intervals. During Development, changes were related to reported neuronal loss, dendritic growth and pruning, and microglial events; TLR4, IL1R1, NFKB1, MOBP, PLA2G4A, and PTGS2 expression increased in the first years of life, while expression of synaptic genes GAP43 and DBN1 decreased, before reaching plateaus. During Aging, expression was upregulated for potentially pro-inflammatory genes such as NFKB1, TRAF6, TLR4, IL1R1, TSPO, and GFAP, but downregulated for neurotrophic and synaptic integrity genes such as BDNF, NGF, PDGFA, SYN, and DBN1. CONCLUSIONS Coordinated changes in gene transcription cascades underlie changes in synaptic, neurotrophic, and inflammatory phenotypic networks during brain Development and Aging. Early postnatal expression changes relate to neuronal, glial, and myelin growth and synaptic pruning events, while late Aging is associated with pro-inflammatory and synaptic loss changes. Thus, comparable transcriptional regulatory networks that operate throughout the lifespan underlie different phenotypic processes during Aging compared to Development.
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Affiliation(s)
- Christopher T. Primiani
- Brain Physiology and Metabolism Section, Laboratory of Neurosciences, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail:
| | - Veronica H. Ryan
- Brain Physiology and Metabolism Section, Laboratory of Neurosciences, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Jagadeesh S. Rao
- Brain Physiology and Metabolism Section, Laboratory of Neurosciences, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Margaret C. Cam
- Office of Science and Technology Resources, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Kwangmi Ahn
- Child Psychiatry Branch, National Institute of Mental Health, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Hiren R. Modi
- Brain Physiology and Metabolism Section, Laboratory of Neurosciences, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Stanley I. Rapoport
- Brain Physiology and Metabolism Section, Laboratory of Neurosciences, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, United States of America
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Chen CY, Chang IS, Hsiung CA, Wasserman WW. On the identification of potential regulatory variants within genome wide association candidate SNP sets. BMC Med Genomics 2014; 7:34. [PMID: 24920305 PMCID: PMC4066296 DOI: 10.1186/1755-8794-7-34] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Accepted: 06/02/2014] [Indexed: 12/04/2022] Open
Abstract
BACKGROUND Genome wide association studies (GWAS) are a population-scale approach to the identification of segments of the genome in which genetic variations may contribute to disease risk. Current methods focus on the discovery of single nucleotide polymorphisms (SNPs) associated with disease traits. As there are many SNPs within identified risk loci, and the majority of these are situated within non-coding regions, a key challenge is to identify and prioritize variants affecting regulatory sequences that are likely to contribute to the phenotype assessed. METHODS We focused investigation on SNPs within lung and breast cancer GWAS loci that reached genome-wide significance for potential roles in gene regulation with a specific focus on SNPs likely to disrupt transcription factor binding sites. Within risk loci, the regulatory potential of sub-regions was classified using relevant open chromatin and epigenetic high throughput sequencing data sets from the ENCODE project in available cancer and normal cell lines. Furthermore, transcription factor affinity altering variants were predicted by comparison of position weight matrix scores between disease and reference alleles. Lastly, ChIP-seq data of transcription associated factors and topological domains were included as binding evidence and potential gene target inference. RESULTS The sets of SNPs, including both the disease-associated markers and those in high linkage disequilibrium with them, were significantly over-represented in regulatory sequences of cancer and/or normal cells; however, over-representation was generally not restricted to disease-relevant tissue specific regions. The calculated regulatory potential, allelic binding affinity scores and ChIP-seq binding evidence were the three criteria used to prioritize candidates. Fitting all three criteria, we highlighted breast cancer susceptibility SNPs and a borderline lung cancer relevant SNP located in cancer-specific enhancers overlapping multiple distinct transcription associated factor ChIP-seq binding sites. CONCLUSION Incorporating high throughput sequencing epigenetic and transcription factor data sets from both cancer and normal cells into cancer genetic studies reveals potential functional SNPs and informs subsequent characterization efforts.
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Affiliation(s)
- Chih-yu Chen
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
- Graduate Program in Bioinformatics, University of British Columbia, Vancouver, British Columbia, Canada
| | - I-Shou Chang
- National Institute of Cancer Research, National Health Research Institutes, Zhunan, Taiwan
| | - Chao A Hsiung
- Division of Biostatistics and Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Taiwan
| | - Wyeth W Wasserman
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
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Rhie SK, Hazelett DJ, Coetzee SG, Yan C, Noushmehr H, Coetzee GA. Nucleosome positioning and histone modifications define relationships between regulatory elements and nearby gene expression in breast epithelial cells. BMC Genomics 2014; 15:331. [PMID: 24885402 PMCID: PMC4035062 DOI: 10.1186/1471-2164-15-331] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Accepted: 04/24/2014] [Indexed: 02/03/2023] Open
Abstract
Background The precise nature of how cell type specific chromatin structures at enhancer sites affect gene expression is largely unknown. Here we identified cell type specific enhancers coupled with gene expression in two different types of breast epithelial cells, HMEC (normal breast epithelial cells) and MDAMB231 (triple negative breast cancer cell line). Results Enhancers were defined by modified neighboring histones [using chromatin immunoprecipitation followed by sequencing (ChIP-seq)] and nucleosome depletion [using formaldehyde-assisted isolation of regulatory elements followed by sequencing (FAIRE-seq)]. Histone modifications at enhancers were related to the expression levels of nearby genes up to 750 kb away. These expression levels were correlated with enhancer status (poised or active), defined by surrounding histone marks. Furthermore, about fifty percent of poised and active enhancers contained nucleosome-depleted regions. We also identified response element motifs enriched at these enhancer sites that revealed key transcription factors (e.g. TP63) likely involved in regulating breast epithelial enhancer-mediated gene expression. By utilizing expression data, potential target genes of more than 600 active enhancers were identified. These genes were involved in proteolysis, epidermis development, cell adhesion, mitosis, cell cycle, and DNA replication. Conclusions These findings facilitate the understanding of epigenetic regulation specifically, such as the relationships between regulatory elements and gene expression and generally, how breast epithelial cellular phenotypes are determined by cell type specific enhancers. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-331) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | - Gerhard A Coetzee
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA.
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Purrington KS, Slager S, Eccles D, Yannoukakos D, Fasching PA, Miron P, Carpenter J, Chang-Claude J, Martin NG, Montgomery GW, Kristensen V, Anton-Culver H, Goodfellow P, Tapper WJ, Rafiq S, Gerty SM, Durcan L, Konstantopoulou I, Fostira F, Vratimos A, Apostolou P, Konstanta I, Kotoula V, Lakis S, Dimopoulos MA, Skarlos D, Pectasides D, Fountzilas G, Beckmann MW, Hein A, Ruebner M, Ekici AB, Hartmann A, Schulz-Wendtland R, Renner SP, Janni W, Rack B, Scholz C, Neugebauer J, Andergassen U, Lux MP, Haeberle L, Clarke C, Pathmanathan N, Rudolph A, Flesch-Janys D, Nickels S, Olson JE, Ingle JN, Olswold C, Slettedahl S, Eckel-Passow JE, Anderson S, Visscher DW, Cafourek VL, Sicotte H, Prodduturi N, Weiderpass E, Bernstein L, Ziogas A, Ivanovich J, Giles GG, Baglietto L, Southey M, Kosma VM, Fischer HP, Reed MW, Cross SS, Deming-Halverson S, Shrubsole M, Cai Q, Shu XO, Daly M, Weaver J, Ross E, Klemp J, Sharma P, Torres D, Rüdiger T, Wölfing H, Ulmer HU, Försti A, Khoury T, Kumar S, Pilarski R, Shapiro CL, Greco D, Heikkilä P, Aittomäki K, Blomqvist C, Irwanto A, Liu J, Pankratz VS, Wang X, Severi G, Mannermaa A, Easton D, Hall P, Brauch H, Cox A, Zheng W, Godwin AK, Hamann U, Ambrosone C, Toland AE, Nevanlinna H, Vachon CM, Couch FJ. Genome-wide association study identifies 25 known breast cancer susceptibility loci as risk factors for triple-negative breast cancer. Carcinogenesis 2014; 35:1012-9. [PMID: 24325915 PMCID: PMC4004200 DOI: 10.1093/carcin/bgt404] [Citation(s) in RCA: 114] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Revised: 11/04/2013] [Accepted: 11/27/2013] [Indexed: 11/14/2022] Open
Abstract
Triple-negative (TN) breast cancer is an aggressive subtype of breast cancer associated with a unique set of epidemiologic and genetic risk factors. We conducted a two-stage genome-wide association study of TN breast cancer (stage 1: 1529 TN cases, 3399 controls; stage 2: 2148 cases, 1309 controls) to identify loci that influence TN breast cancer risk. Variants in the 19p13.1 and PTHLH loci showed genome-wide significant associations (P < 5 × 10(-) (8)) in stage 1 and 2 combined. Results also suggested a substantial enrichment of significantly associated variants among the single nucleotide polymorphisms (SNPs) analyzed in stage 2. Variants from 25 of 74 known breast cancer susceptibility loci were also associated with risk of TN breast cancer (P < 0.05). Associations with TN breast cancer were confirmed for 10 loci (LGR6, MDM4, CASP8, 2q35, 2p24.1, TERT-rs10069690, ESR1, TOX3, 19p13.1, RALY), and we identified associations with TN breast cancer for 15 additional breast cancer loci (P < 0.05: PEX14, 2q24.1, 2q31.1, ADAM29, EBF1, TCF7L2, 11q13.1, 11q24.3, 12p13.1, PTHLH, NTN4, 12q24, BRCA2, RAD51L1-rs2588809, MKL1). Further, two SNPs independent of previously reported signals in ESR1 [rs12525163 odds ratio (OR) = 1.15, P = 4.9 × 10(-) (4)] and 19p13.1 (rs1864112 OR = 0.84, P = 1.8 × 10(-) (9)) were associated with TN breast cancer. A polygenic risk score (PRS) for TN breast cancer based on known breast cancer risk variants showed a 4-fold difference in risk between the highest and lowest PRS quintiles (OR = 4.03, 95% confidence interval 3.46-4.70, P = 4.8 × 10(-) (69)). This translates to an absolute risk for TN breast cancer ranging from 0.8% to 3.4%, suggesting that genetic variation may be used for TN breast cancer risk prediction.
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Affiliation(s)
| | - Susan Slager
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Diana Eccles
- Faculty of Medicine, University of Southampton SO17 1BJ, Southampton, UK
| | - Drakoulis Yannoukakos
- Molecular Diagnostics Laboratory INRASTES, National Centre for Scientific Research “Demokritos”, Athens 153 10, Greece
| | - Peter A. Fasching
- Department of Medicine, Division of Hematology/Oncology, University of California at Los Angeles, David Geffen School of Medicine, Los Angeles, CA 90095, USA
- Department of Gynecology and Obstetrics, University Breast Center Franconia, University Hospital Erlangen; Friedrich-Alexander University Erlangen-Nuremberg, Erlangen D-91012, Germany
| | - Penelope Miron
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Jane Carpenter
- Australian Breast Cancer Tissue Bank, University of Sydney at the Westmead Millennium Institute, Westmead, New South Wales, NSW 2145 Australia
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Nicholas G. Martin
- QIMR GWAS Collective, Queensland Institute of Medical Research, Brisbane, Queensland, QLD 4006 Australia
| | - Grant W. Montgomery
- QIMR GWAS Collective, Queensland Institute of Medical Research, Brisbane, Queensland, QLD 4006 Australia
| | - Vessela Kristensen
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital, Radiumhospitalet, Oslo 0316, Norway
- Faculty of Medicine (Faculty Division Ahus), Universitetet i Oslo, Oslo 0316, Norway
| | - Hoda Anton-Culver
- Department of Epidemiology, University of California–Irvine, Irvine, CA 92697, USA
| | - Paul Goodfellow
- Washington University School of Medicine, Barnes-Jewish Hospital and Siteman Cancer Center, St Louis, MO 63110, USA
| | - William J. Tapper
- Faculty of Medicine, University of Southampton SO17 1BJ, Southampton, UK
| | - Sajjad Rafiq
- Faculty of Medicine, University of Southampton SO17 1BJ, Southampton, UK
| | - Susan M. Gerty
- Faculty of Medicine, University of Southampton SO17 1BJ, Southampton, UK
| | - Lorraine Durcan
- Faculty of Medicine, University of Southampton SO17 1BJ, Southampton, UK
| | - Irene Konstantopoulou
- Molecular Diagnostics Laboratory INRASTES, National Centre for Scientific Research “Demokritos”, Athens 153 10, Greece
| | - Florentia Fostira
- Molecular Diagnostics Laboratory INRASTES, National Centre for Scientific Research “Demokritos”, Athens 153 10, Greece
| | - Athanassios Vratimos
- Molecular Diagnostics Laboratory INRASTES, National Centre for Scientific Research “Demokritos”, Athens 153 10, Greece
| | - Paraskevi Apostolou
- Molecular Diagnostics Laboratory INRASTES, National Centre for Scientific Research “Demokritos”, Athens 153 10, Greece
| | - Irene Konstanta
- Molecular Diagnostics Laboratory INRASTES, National Centre for Scientific Research “Demokritos”, Athens 153 10, Greece
| | | | - Sotiris Lakis
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research, Aristotle University of Thessaloniki School of Medicine, Thessaloniki 54124, Greece
| | - Meletios A. Dimopoulos
- Department of Clinical Therapeutics, “Alexandra” Hospital, University of Athens School of Medicine, Athens 115 27, Greece
| | - Dimosthenis Skarlos
- Second Department of Medical Oncology, “Metropolitan” Hospital, Athens 151 25, Greece
| | - Dimitrios Pectasides
- Second Department of Internal Medicine, Oncology Section, “Hippokration” Hospital, University of Athens School of Medicine, Athens 115 27, Greece
| | - George Fountzilas
- Department of Medical Oncology, “Papageorgiou” Hospital, Aristotle University of Thessaloniki School of Medicine, Thessaloniki 54124, Greece
| | - Matthias W. Beckmann
- Department of Gynecology and Obstetrics, University Breast Center Franconia, University Hospital Erlangen; Friedrich-Alexander University Erlangen-Nuremberg, Erlangen D-91012, Germany
| | - Alexander Hein
- Department of Gynecology and Obstetrics, University Breast Center Franconia, University Hospital Erlangen; Friedrich-Alexander University Erlangen-Nuremberg, Erlangen D-91012, Germany
| | - Matthias Ruebner
- Department of Gynecology and Obstetrics, University Breast Center Franconia, University Hospital Erlangen; Friedrich-Alexander University Erlangen-Nuremberg, Erlangen D-91012, Germany
| | | | | | - Ruediger Schulz-Wendtland
- Institute of Diagnostic Radiology, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen D-91012, Germany
| | - Stefan P. Renner
- Department of Gynecology and Obstetrics, University Breast Center Franconia, University Hospital Erlangen; Friedrich-Alexander University Erlangen-Nuremberg, Erlangen D-91012, Germany
| | - Wolfgang Janni
- Department of Gynecology and Obstetrics, University Hospital Ulm, Ulm 89069, Germany
| | - Brigitte Rack
- Department of Gynecology and Obstetrics, University Hospital Ludwig Maximilians University, Campus Innenstadt, Munich 80539, Germany
| | - Christoph Scholz
- Department of Gynecology and Obstetrics, University Hospital Ulm, Ulm 89069, Germany
| | - Julia Neugebauer
- Department of Gynecology and Obstetrics, University Hospital Ludwig Maximilians University, Campus Innenstadt, Munich 80539, Germany
| | - Ulrich Andergassen
- Department of Gynecology and Obstetrics, University Hospital Ludwig Maximilians University, Campus Innenstadt, Munich 80539, Germany
| | - Michael P. Lux
- Department of Gynecology and Obstetrics, University Breast Center Franconia, University Hospital Erlangen; Friedrich-Alexander University Erlangen-Nuremberg, Erlangen D-91012, Germany
| | - Lothar Haeberle
- Department of Gynecology and Obstetrics, University Breast Center Franconia, University Hospital Erlangen; Friedrich-Alexander University Erlangen-Nuremberg, Erlangen D-91012, Germany
| | - Christine Clarke
- Westmead Institute for Cancer Research, Sydney Medical School Westmead, University of Sydney at the Westmead Millennium Institute, Westmead, New South Wales NSW 2145, Australia
| | - Nirmala Pathmanathan
- Westmead Breast Cancer Institute, Westmead Hospital, Westmead, New South Wales NSW 2145, Australia
| | - Anja Rudolph
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Dieter Flesch-Janys
- Institute for Medical Biometrics and Epidemiology, University Clinic Hamburg-Eppendorf, Hamburg 20246, Germany
| | - Stefan Nickels
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Janet E. Olson
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| | | | - Curtis Olswold
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Seth Slettedahl
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| | | | - S.Keith Anderson
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Daniel W. Visscher
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
| | | | - Hugues Sicotte
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Naresh Prodduturi
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Elisabete Weiderpass
- Department of Community Medicine, University of Tromsø, Tromsø 9019, Norway
- Folkhälsan Research Cancer Centre, Helsinki 00250, Finland
- Cancer Registry of Norway, Oslo N-0304, Norway
| | - Leslie Bernstein
- Department of Population Sciences, Division of Cancer Etiology, Beckman Research Institute, City of Hope, Duarte 91010, USA
| | - Argyrios Ziogas
- Department of Epidemiology, University of California–Irvine, Irvine, CA 92697, USA
| | - Jennifer Ivanovich
- Washington University School of Medicine, Barnes-Jewish Hospital and Siteman Cancer Center, St Louis, MO 63110, USA
| | - Graham G. Giles
- Cancer Epidemiology Centre, The Cancer Council Victoria, Melbourne, Victoria VIC 3053, Australia
| | - Laura Baglietto
- Cancer Epidemiology Centre, The Cancer Council Victoria, Melbourne, Victoria VIC 3053, Australia
| | - Melissa Southey
- Department of Pathology, The University of Melbourne, Melbourne, Victoria VIC 3053, Australia
| | - Veli-Matti Kosma
- School of Medicine, Institute of Clinical Medicine, Pathology and Forensic Medicine; Biocenter Kuopio, Cancer Center of Eastern Finland, and Imaging Center, Department of Clinical Pathology, Kuopio University Hospital, University of Eastern Finland, Kuopio 80130, Finland
| | - Hans-Peter Fischer
- Department of Pathology, Medical Faculty University Bonn, Bonn 53127, Germany
| | - The GENICA Network
- Dr Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart and University of Tuebingen, Tuebingen 72074, Germany, 72074
- Department of Internal Medicine, Evangelische Kliniken Bonn gGmbH, Johanniter Krankenhaus, Bonn 53127, Germany
- Institute for Occupational Medicine and Maritime Medicine, University Medical Center Hamburg-Eppendorf, Hamburg 20246, Germany
- Institute for Prevention and Occupational Medicine of the German Social Accident Insurance, Institute of the Ruhr University Bochum (IPA), Bochum D-44789, Germany
- Institute of Pathology, Medical Faculty of the University of Bonn, Bonn 53127, Germany
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Malcom W.R. Reed
- Department of Oncology, Cancer Research UK/Yorkshire Cancer Research Sheffield Cancer Research Centre and
| | - Simon S. Cross
- Department of Neuroscience, University of Sheffield, Sheffield S10 2TN, UK
| | - Sandra Deming-Halverson
- Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Division of Epidemiology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Martha Shrubsole
- Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Division of Epidemiology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Qiuyin Cai
- Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Division of Epidemiology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Xiao-Ou Shu
- Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Division of Epidemiology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Mary Daly
- Department of Clinical Genetics, Fox Chase Cancer Center, Philadelphia, PA 19111-2497, USA
| | - JoEllen Weaver
- PennMed Biobank, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
| | - Eric Ross
- Department of Biostatistics and Bioinformatics, Fox Chase Cancer Center, Philadelphia, PA 19111-2497, USA
| | - Jennifer Klemp
- Department of Oncology/Hematology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Priyanka Sharma
- Department of Oncology/Hematology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Diana Torres
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
- Institute of Human Genetics, Pontificia University Javeriana, Bogota D.C. 11001000, Colombia
| | - Thomas Rüdiger
- Institute of Pathology, Städtisches Klinikum Karlsruhe, Karlsruhe 76133, Germany
| | - Heidrun Wölfing
- Institute of Pathology, Städtisches Klinikum Karlsruhe, Karlsruhe 76133, Germany
| | - Hans-Ulrich Ulmer
- Frauenklinik der Stadtklinik Baden-Baden, Baden-Baden 76530, Germany
| | - Asta Försti
- Center for Primary Health Care Research, University of Lund, Malmö 223 63, Sweden
- Division of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | | | - Shicha Kumar
- Department of Surgical Oncology, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
| | - Robert Pilarski
- Department of Internal Medicine, Division of Human Genetics and
| | - Charles L. Shapiro
- Department of Internal Medicine, Division of Medical Oncology, Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA
| | | | | | | | - Carl Blomqvist
- Department of Oncology, Helsinki University Central Hospital, Helsinki 00014, Finland
| | - Astrid Irwanto
- Human Genetics Division, Genome Institute of Singapore, Singapore 138672 Singapore
| | - Jianjun Liu
- Human Genetics Division, Genome Institute of Singapore, Singapore 138672 Singapore
| | | | - Xianshu Wang
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
| | - Gianluca Severi
- Cancer Epidemiology Centre, The Cancer Council Victoria, Melbourne, Victoria VIC 3053, Australia
| | - Arto Mannermaa
- School of Medicine, Institute of Clinical Medicine, Pathology and Forensic Medicine; Biocenter Kuopio, Cancer Center of Eastern Finland, and Imaging Center, Department of Clinical Pathology, Kuopio University Hospital, University of Eastern Finland, Kuopio 80130, Finland
| | - Douglas Easton
- Department of Public Health and Primary Care, Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge CB2 1TN, UK
| | - Per Hall
- Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm 171 77, Sweden
| | - Hiltrud Brauch
- Dr Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart and University of Tuebingen, Tuebingen 72074, Germany, 72074
| | - Angela Cox
- Department of Oncology, Cancer Research UK/Yorkshire Cancer Research Sheffield Cancer Research Centre and
| | - Wei Zheng
- Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Division of Epidemiology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Andrew K. Godwin
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Ute Hamann
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Christine Ambrosone
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
| | - Amanda Ewart Toland
- Departments of Internal Medicine and Molecular Virology, Immunology and Medical Genetics, Division of Human Cancer Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA
| | | | - Celine M. Vachon
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Fergus J. Couch
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
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Hazelett DJ, Rhie SK, Gaddis M, Yan C, Lakeland DL, Coetzee SG, Henderson BE, Noushmehr H, Cozen W, Kote-Jarai Z, Eeles RA, Easton DF, Haiman CA, Lu W, Farnham PJ, Coetzee GA. Comprehensive functional annotation of 77 prostate cancer risk loci. PLoS Genet 2014; 10:e1004102. [PMID: 24497837 PMCID: PMC3907334 DOI: 10.1371/journal.pgen.1004102] [Citation(s) in RCA: 146] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Accepted: 11/14/2013] [Indexed: 11/19/2022] Open
Abstract
Genome-wide association studies (GWAS) have revolutionized the field of cancer genetics, but the causal links between increased genetic risk and onset/progression of disease processes remain to be identified. Here we report the first step in such an endeavor for prostate cancer. We provide a comprehensive annotation of the 77 known risk loci, based upon highly correlated variants in biologically relevant chromatin annotations--we identified 727 such potentially functional SNPs. We also provide a detailed account of possible protein disruption, microRNA target sequence disruption and regulatory response element disruption of all correlated SNPs at r(2) ≥ 0.88%. 88% of the 727 SNPs fall within putative enhancers, and many alter critical residues in the response elements of transcription factors known to be involved in prostate biology. We define as risk enhancers those regions with enhancer chromatin biofeatures in prostate-derived cell lines with prostate-cancer correlated SNPs. To aid the identification of these enhancers, we performed genomewide ChIP-seq for H3K27-acetylation, a mark of actively engaged enhancers, as well as the transcription factor TCF7L2. We analyzed in depth three variants in risk enhancers, two of which show significantly altered androgen sensitivity in LNCaP cells. This includes rs4907792, that is in linkage disequilibrium (r(2) = 0.91) with an eQTL for NUDT11 (on the X chromosome) in prostate tissue, and rs10486567, the index SNP in intron 3 of the JAZF1 gene on chromosome 7. Rs4907792 is within a critical residue of a strong consensus androgen response element that is interrupted in the protective allele, resulting in a 56% decrease in its androgen sensitivity, whereas rs10486567 affects both NKX3-1 and FOXA-AR motifs where the risk allele results in a 39% increase in basal activity and a 28% fold-increase in androgen stimulated enhancer activity. Identification of such enhancer variants and their potential target genes represents a preliminary step in connecting risk to disease process.
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Affiliation(s)
- Dennis J. Hazelett
- Departments of Urology and Preventive Medicine, Norris Cancer Center, University of Southern California Keck School of Medicine, Los Angeles, California, United States of America
| | - Suhn Kyong Rhie
- Departments of Urology and Preventive Medicine, Norris Cancer Center, University of Southern California Keck School of Medicine, Los Angeles, California, United States of America
| | - Malaina Gaddis
- Department of Biochemistry and Molecular Biology, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Chunli Yan
- Departments of Urology and Preventive Medicine, Norris Cancer Center, University of Southern California Keck School of Medicine, Los Angeles, California, United States of America
| | - Daniel L. Lakeland
- Sonny Astani Department of Civil and Environmental Engineering, University of Southern California, Los Angeles, California, United States of America
| | - Simon G. Coetzee
- Department of Genetics, University of São Paulo, Ribeirão Preto, Brazil
| | - Ellipse/GAME-ON consortium
- Department of Preventive Medicine, Norris Cancer Center, University of Southern California Keck School of Medicine, Los Angeles, California, United States of America
| | | | - Brian E. Henderson
- Department of Preventive Medicine, Norris Cancer Center, University of Southern California Keck School of Medicine, Los Angeles, California, United States of America
| | - Houtan Noushmehr
- Department of Genetics, University of São Paulo, Ribeirão Preto, Brazil
| | - Wendy Cozen
- USC Keck School of Medicine, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California, United States of America
| | | | - Rosalind A. Eeles
- The Institute of Cancer Research, Sutton, United Kingdom
- Royal Marsden National Health Service (NHS) Foundation Trust, London and Sutton, United Kingdom
| | - Douglas F. Easton
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, United Kingdom
| | - Christopher A. Haiman
- Department of Preventive Medicine, Norris Cancer Center, University of Southern California Keck School of Medicine, Los Angeles, California, United States of America
| | - Wange Lu
- Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Department of Biochemistry and Molecular Biology, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Peggy J. Farnham
- Department of Biochemistry and Molecular Biology, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Gerhard A. Coetzee
- Departments of Urology and Preventive Medicine, Norris Cancer Center, University of Southern California Keck School of Medicine, Los Angeles, California, United States of America
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37
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Edwards SL, Beesley J, French JD, Dunning AM. Beyond GWASs: illuminating the dark road from association to function. Am J Hum Genet 2013; 93:779-97. [PMID: 24210251 PMCID: PMC3824120 DOI: 10.1016/j.ajhg.2013.10.012] [Citation(s) in RCA: 544] [Impact Index Per Article: 49.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Indexed: 12/15/2022] Open
Abstract
Genome-wide association studies (GWASs) have enabled the discovery of common genetic variation contributing to normal and pathological traits and clinical drug responses, but recognizing the precise targets of these associations is now the major challenge. Here, we review recent approaches to the functional follow-up of GWAS loci, including fine mapping of GWAS signal(s), prioritization of putative functional SNPs by the integration of genetic epidemiological and bioinformatic methods, and in vitro and in vivo experimental verification of predicted molecular mechanisms for identifying the targeted genes. The majority of GWAS-identified variants fall in noncoding regions of the genome. Therefore, this review focuses on strategies for assessing likely mechanisms affected by noncoding variants; such mechanisms include transcriptional regulation, noncoding RNA function, and epigenetic regulation. These approaches have already accelerated progress from genetic studies to biological knowledge and might ultimately guide the development of prognostic, preventive, and therapeutic measures.
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Affiliation(s)
- Stacey L Edwards
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4029, Australia; School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland 4072, Australia.
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