201
|
Bhatia S, Kleinjan DA. Disruption of long-range gene regulation in human genetic disease: a kaleidoscope of general principles, diverse mechanisms and unique phenotypic consequences. Hum Genet 2014; 133:815-45. [DOI: 10.1007/s00439-014-1424-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Accepted: 01/18/2014] [Indexed: 01/05/2023]
|
202
|
|
203
|
Liu MH, Cheung E. Estrogen receptor-mediated long-range chromatin interactions and transcription in breast cancer. Mol Cell Endocrinol 2014; 382:624-632. [PMID: 24071518 DOI: 10.1016/j.mce.2013.09.019] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Revised: 09/17/2013] [Accepted: 09/17/2013] [Indexed: 12/15/2022]
Abstract
Estrogen induces the binding of ERα to thousands of locations in the breast cancer genome, preferring intergenic and distal regions rather than near the promoters of estrogen-regulated genes. With recent technological innovations in mapping and characterization of global chromatin organization, evidence now indicates ERα mediates long-range chromatin interactions to control gene transcription. The principles that govern how ERα communicates with their putative target genes via chromosomal interactions are also beginning to unravel. Herein, we summarize our current knowledge on the functional significance of chromatin looping in estrogen-mediated transcription. ERα collaborative factors and other players that contribute to define the genomic interactions in breast cancer cells will also be discussed. Defects in chromatin organization are emerging key players in diseases such as cancer, thus understanding how ERα-mediated chromatin looping affects genome organization will clarify the receptor's role in estrogen responsive pathways sensitive to defects in chromatin organization.
Collapse
Affiliation(s)
- Mei Hui Liu
- Food Science and Technology Programme, Department of Chemistry, National University of Singapore, Singapore 117543, Singapore; Cancer Biology and Pharmacology, Genome Institute of Singapore, A∗STAR (Agency for Science, Technology and Research), Singapore 138672, Singapore
| | - Edwin Cheung
- Cancer Biology and Pharmacology, Genome Institute of Singapore, A∗STAR (Agency for Science, Technology and Research), Singapore 138672, Singapore.
| |
Collapse
|
204
|
Regulation of MYC expression and differential JQ1 sensitivity in cancer cells. PLoS One 2014; 9:e87003. [PMID: 24466310 PMCID: PMC3900694 DOI: 10.1371/journal.pone.0087003] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Accepted: 12/16/2013] [Indexed: 11/19/2022] Open
Abstract
High level MYC expression is associated with almost all human cancers. JQ1, a chemical compound that inhibits MYC expression is therapeutically effective in preclinical animal models in midline carcinoma, and Burkitt's lymphoma (BL). Here we show that JQ1 does not inhibit MYC expression to a similar extent in all tumor cells. The BL cells showed a ∼90% decrease in MYC transcription upon treatment with JQ1, however, no corresponding reduction was seen in several non-BL cells. Molecularly, these differences appear due to requirements of Brd4, the most active version of the Positive Transcription Elongation Factor B (P-TEFb) within the Super Elongation Complex (SEC), and transcription factors such as Gdown1, and MED26 and also other unknown cell specific factors. Our study demonstrates that the regulation of high levels of MYC expression in different cancer cells is driven by unique regulatory mechanisms and that such exclusive regulatory signatures in each cancer cells could be employed for targeted therapeutics.
Collapse
|
205
|
Webster DE, Barajas B, Bussat RT, Yan KJ, Neela PH, Flockhart RJ, Kovalski J, Zehnder A, Khavari PA. Enhancer-targeted genome editing selectively blocks innate resistance to oncokinase inhibition. Genome Res 2014; 24:751-60. [PMID: 24443471 PMCID: PMC4009605 DOI: 10.1101/gr.166231.113] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Thousands of putative enhancers are characterized in the human genome, yet few have been shown to have a functional role in cancer progression. Inhibiting oncokinases, such as EGFR, ALK, ERBB2, and BRAF, is a mainstay of current cancer therapy but is hindered by innate drug resistance mediated by up-regulation of the HGF receptor, MET. The mechanisms mediating such genomic responses to targeted therapy are unknown. Here, we identify lineage-specific enhancers at the MET locus for multiple common tumor types, including a melanoma lineage-specific enhancer 63 kb downstream from the MET TSS. This enhancer displays inducible chromatin looping with the MET promoter to up-regulate MET expression upon BRAF inhibition. Epigenomic analysis demonstrated that the melanocyte-specific transcription factor, MITF, mediates this enhancer function. Targeted genomic deletion (<7 bp) of the MITF motif within the MET enhancer suppressed inducible chromatin looping and innate drug resistance, while maintaining MITF-dependent, inhibitor-induced melanoma cell differentiation. Epigenomic analysis can thus guide functional disruption of regulatory DNA to decouple pro- and anti-oncogenic functions of a dominant transcription factor and block innate resistance to oncokinase therapy.
Collapse
Affiliation(s)
- Dan E Webster
- The Veterans Affairs Palo Alto Healthcare System, Palo Alto, California 94304, USA; The Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California 94305, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
206
|
Mikropoulos C, Goh C, Leongamornlert D, Kote-Jarai Z, Eeles R. Translating genetic risk factors for prostate cancer to the clinic: 2013 and beyond. Future Oncol 2014; 10:1679-94. [PMID: 25145435 DOI: 10.2217/fon.14.72] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Prostate cancer (PrCa) is the most commonly diagnosed cancer in the male UK population, with over 40,000 new cases per year. PrCa has a complex, polygenic predisposition, due to rare variants such as BRCA and common variants such as single nucleotide polymorphisms (SNPs). With the introduction of genome-wide association studies, 78 susceptibility loci (SNPs) associated with PrCa risk have been identified. Genetic profiling could risk-stratify a population, leading to the discovery of a higher proportion of clinically significant disease and a reduction in the morbidity related to age-based prostate-specific antigen screening. Based on the combined risk of the 78 SNPs identified so far, the top 1% of the risk distribution has a 4.7-times higher risk of developing PrCa compared with the average of the general population.
Collapse
|
207
|
Eeles R, Goh C, Castro E, Bancroft E, Guy M, Al Olama AA, Easton D, Kote-Jarai Z. The genetic epidemiology of prostate cancer and its clinical implications. Nat Rev Urol 2014; 11:18-31. [PMID: 24296704 DOI: 10.1038/nrurol.2013.266] [Citation(s) in RCA: 178] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Worldwide, familial and epidemiological studies have generated considerable evidence of an inherited component to prostate cancer. Indeed, rare highly penetrant genetic mutations have been implicated. Genome-wide association studies (GWAS) have also identified 76 susceptibility loci associated with prostate cancer risk, which occur commonly but are of low penetrance. However, these mutations interact multiplicatively, which can result in substantially increased risk. Currently, approximately 30% of the familial risk is due to such variants. Evaluating the functional aspects of these variants would contribute to our understanding of prostate cancer aetiology and would enable population risk stratification for screening. Furthermore, understanding the genetic risks of prostate cancer might inform predictions of treatment responses and toxicities, with the goal of personalized therapy. However, risk modelling and clinical translational research are needed before we can translate risk profiles generated from these variants into use in the clinical setting for targeted screening and treatment.
Collapse
Affiliation(s)
- Rosalind Eeles
- Oncogenetics Team, Division of Cancer Genetics and Epidemiology, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, UK
| | - Chee Goh
- Oncogenetics Team, Division of Cancer Genetics and Epidemiology, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, UK
| | - Elena Castro
- Oncogenetics Team, Division of Cancer Genetics and Epidemiology, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, UK
| | - Elizabeth Bancroft
- Clinical Academic Cancer Genetics Unit, The Royal Marsden NHS Foundation Trust, Sutton, Surrey SM2 5PT, UK
| | - Michelle Guy
- Oncogenetics Team, Division of Cancer Genetics and Epidemiology, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, UK
| | - Ali Amin Al Olama
- Cancer Research UK Centre for Cancer Genetic Epidemiology, Strangeways Laboratory, University of Cambridge, Cambridge CB1 8RN, UK
| | - Douglas Easton
- Departments of Public Health & Primary Care and Oncology, Strangeways Laboratory, University of Cambridge, Cambridge CB1 8RN, UK
| | - Zsofia Kote-Jarai
- Oncogenetics Team, Division of Cancer Genetics and Epidemiology, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, UK
| |
Collapse
|
208
|
Zhao CX, Liu M, Wang JY, Xu Y, Wei D, Yang K, Yang Z. Association of 8 loci on chromosome 8q24 with prostate carcinoma risk in northern Chinese men. Asian Pac J Cancer Prev 2014; 14:6733-8. [PMID: 24377597 DOI: 10.7314/apjcp.2013.14.11.6733] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Multiple genetic studies have confirmed association of 8q24 variants with susceptibility to prostate cancer (PCa). As PCa risk SNPs may also influence disease outcome, we studied here eight 8q24 risk alleles, and evaluated their role in PCa clinical covariates in northern Chinese men. Blood samples and clinical information were collected from ethnically Chinese men from Northern China with histologically-confirmed PCa (n=289) and from age-matched normal controls (n=288). Eight 8q24 SNPs were genotyped by polymerase chain reaction- high-resolution melting analysis in 577 subjects. We examined the prevalence distribution of 8q24 risk alleles and analyzed the associations between the risk allele and PCa and clinical covariates to infer their impact on aggressive PCa. Three of the eight SNPs were associated with PCa risk in northern Chinese men, including rs16901966 (OR 1.31, 95% CI 1.01-1.70, p=0.042), rs1447295 (OR 1.47, 95% CI 1.09-1.98, p=0.011) and rs10090154 (OR 1.55, 95% CI 1.14-2.12, p=0.005). Haplotype analysis based association with the risk alleles revealed significant differences between cases and controls (OR 1.43, 95%CI 0.99-2.06, p=0.049). The risk alleles rs16901966, rs1447295 and rs10090154 were associated with age at diagnosis and tumor stage as compared with controls, while rs16901966 was associated with aggressive PCa (OR 1.43, 95% CI 1.01-2.03, p=0.042). The evidence for 8q24 SNPs with PCa risk in northern Chinese men showed rs16901966, rs1447295 and rs10090154 at 8q24 (region 1, region 2) to be strongly associated with PCa and clinical covariates. The three SNPs at 8q24 could be PCa susceptible genetic markers in northern Chinese men.
Collapse
Affiliation(s)
- Cheng-Xiao Zhao
- The Key Laboratory of Geriatrics, Beijing Hospital and Beijing Institute of Geriatrics, Chinese Ministry of Health, Beijing, China E-mail : ,
| | | | | | | | | | | | | |
Collapse
|
209
|
Schoeps A, Rudolph A, Seibold P, Dunning AM, Milne RL, Bojesen SE, Swerdlow A, Andrulis I, Brenner H, Behrens S, Orr N, Jones M, Ashworth A, Li J, Cramp H, Connley D, Czene K, Darabi H, Chanock SJ, Lissowska J, Figueroa JD, Knight J, Glendon G, Mulligan AM, Dumont M, Severi G, Baglietto L, Olson J, Vachon C, Purrington K, Moisse M, Neven P, Wildiers H, Spurdle A, Kosma VM, Kataja V, Hartikainen JM, Hamann U, Ko YD, Dieffenbach AK, Arndt V, Stegmaier C, Malats N, Arias Perez J, Benítez J, Flyger H, Nordestgaard BG, Truong T, Cordina-Duverger E, Menegaux F, Silva IDS, Fletcher O, Johnson N, Häberle L, Beckmann MW, Ekici AB, Braaf L, Atsma F, van den Broek AJ, Makalic E, Schmidt DF, Southey MC, Cox A, Simard J, Giles GG, Lambrechts D, Mannermaa A, Brauch H, Guénel P, Peto J, Fasching PA, Hopper J, Flesch-Janys D, Couch F, Chenevix-Trench G, Pharoah PDP, Garcia-Closas M, Schmidt MK, Hall P, Easton DF, Chang-Claude J. Identification of new genetic susceptibility loci for breast cancer through consideration of gene-environment interactions. Genet Epidemiol 2014; 38:84-93. [PMID: 24248812 PMCID: PMC3995140 DOI: 10.1002/gepi.21771] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Revised: 10/15/2013] [Accepted: 10/15/2013] [Indexed: 11/06/2022]
Abstract
Genes that alter disease risk only in combination with certain environmental exposures may not be detected in genetic association analysis. By using methods accounting for gene-environment (G × E) interaction, we aimed to identify novel genetic loci associated with breast cancer risk. Up to 34,475 cases and 34,786 controls of European ancestry from up to 23 studies in the Breast Cancer Association Consortium were included. Overall, 71,527 single nucleotide polymorphisms (SNPs), enriched for association with breast cancer, were tested for interaction with 10 environmental risk factors using three recently proposed hybrid methods and a joint test of association and interaction. Analyses were adjusted for age, study, population stratification, and confounding factors as applicable. Three SNPs in two independent loci showed statistically significant association: SNPs rs10483028 and rs2242714 in perfect linkage disequilibrium on chromosome 21 and rs12197388 in ARID1B on chromosome 6. While rs12197388 was identified using the joint test with parity and with age at menarche (P-values = 3 × 10(-07)), the variants on chromosome 21 q22.12, which showed interaction with adult body mass index (BMI) in 8,891 postmenopausal women, were identified by all methods applied. SNP rs10483028 was associated with breast cancer in women with a BMI below 25 kg/m(2) (OR = 1.26, 95% CI 1.15-1.38) but not in women with a BMI of 30 kg/m(2) or higher (OR = 0.89, 95% CI 0.72-1.11, P for interaction = 3.2 × 10(-05)). Our findings confirm comparable power of the recent methods for detecting G × E interaction and the utility of using G × E interaction analyses to identify new susceptibility loci.
Collapse
Affiliation(s)
- Anja Schoeps
- Department of Cancer Epidemiology, German Cancer Research
Center (DKFZ), Heidelberg, Germany
- Institute of Public Health, University of Heidelberg,
Heidelberg, Germany
| | - Anja Rudolph
- Department of Cancer Epidemiology, German Cancer Research
Center (DKFZ), Heidelberg, Germany
| | - Petra Seibold
- Department of Cancer Epidemiology, German Cancer Research
Center (DKFZ), Heidelberg, Germany
| | - Alison M. Dunning
- Department of Oncology, University of Cambridge, Cambridge,
United Kingdom
| | - Roger L. Milne
- Genetic and Molecular Epidemiology Group, Spanish National
Cancer Research Centre (CNIO), Madrid, Spain
| | - Stig E. Bojesen
- Department of Clinical Biochemistry, Herlev Hospital,
Copenhagen University Hospital, Herlev, Denmark
- Copenhagen General Population Study, Herlev Hospital,
Copenhagen University Hospital, Herlev, Denmark
| | - Anthony Swerdlow
- Department of Genetics and Epidemiology, Institute of
Cancer Research, Sutton, United Kingdom
| | - Irene Andrulis
- Department of Molecular Genetics, Lunenfeld-Tanenbaum
Research Institute of Mount Sinai Hospital, Toronto, Canada
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research,
German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium, Heidelberg, Germany
| | - Sabine Behrens
- Department of Cancer Epidemiology, German Cancer Research
Center (DKFZ), Heidelberg, Germany
| | - Nicholas Orr
- Department of Breast Cancer Research, Institute of Cancer
Research, London, United Kingdom
| | - Michael Jones
- Copenhagen General Population Study, Herlev Hospital,
Copenhagen University Hospital, Herlev, Denmark
| | - Alan Ashworth
- Department of Human Genetics, Genome Institute of
Singapore, Singapore, Singapore
| | - Jingmei Li
- Department of Human Genetics, Genome Institute of
Singapore, Singapore, Singapore
| | - Helen Cramp
- Department of Oncology, Institute for Cancer Studies,
University of Sheffield, Sheffield, United Kingdom
| | - Dan Connley
- Department of Oncology, Institute for Cancer Studies,
University of Sheffield, Sheffield, United Kingdom
| | - Kamila Czene
- Department of Medical Epidemiology and Biostatistics,
Karolinska Institutet, Stockholm, Sweden
| | - Hatef Darabi
- Department of Medical Epidemiology and Biostatistics,
Karolinska Institutet, Stockholm, Sweden
| | - Stephen J. Chanock
- Division of Cancer Epidemiology and Genetics, National
Cancer Institute, Rockville, Maryland, United States of America
| | - Jolanta Lissowska
- Department of Cancer Epidemiology and Prevention, M.
Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw,
Poland
| | - Jonine D. Figueroa
- Division of Cancer Epidemiology and Genetics, National
Cancer Institute, Rockville, Maryland, United States of America
| | - Julia Knight
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai
Hospital, Toronto, Canada
- Prosserman Centre for Health Research, Toronto,
Canada
| | - Gord Glendon
- Prosserman Centre for Health Research, Toronto,
Canada
| | - Anna M. Mulligan
- Laboratory Medicine Program, University Health Network,
Toronto, Canada
| | - Martine Dumont
- Cancer Genomics Laboratory, Centre Hospitalier
Universitaire de Québec Research Center, Laval University, Québec,
Canada
- Department of Molecular Medicine, Faculty of Medicine,
Quebec, Canada
| | - Gianluca Severi
- Cancer Epidemiology Centre, Cancer Council Victoria,
Melbourne, Australia
| | - Laura Baglietto
- Cancer Epidemiology Centre, Cancer Council Victoria,
Melbourne, Australia
- Centre for Molecular, Environmental, Genetic, and
Analytic Epidemiology, University of Melbourne, Melbourne, Australia
| | - Janet Olson
- Department of Health Sciences Research, Mayo Clinic,
Minnesota, United States of America
| | - Celine Vachon
- Department of Health Sciences Research, Mayo Clinic,
Minnesota, United States of America
| | - Kristen Purrington
- Department of Health Sciences Research, Mayo Clinic,
Minnesota, United States of America
| | - Matthieu Moisse
- Vesalius Research Center (VRC), VIB, Flanders,
Belgium
- Laboratory of Translational Genetics, Department of
Oncology, University of Leuven, Leuven, Belgium
| | - Patrick Neven
- Department of Multidisciplinary Breast Cancer, University
Hospital Gasthuisberg, Leuven, Belgium
| | - Hans Wildiers
- Department of Multidisciplinary Breast Cancer, University
Hospital Gasthuisberg, Leuven, Belgium
| | - Amanda Spurdle
- Department of Molecular Cancer Epidemiology, Queensland
Institute of Medical Research, Brisbane Australia
| | | | - Vesa Kataja
- Pathology Department, University of Kuopio, Kuopio,
Finland
| | | | - Ute Hamann
- Division of Molecular Genetics of Breast Cancer, German
Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Yon-Dschun Ko
- Department of Internal Medicine, Evangelische Kliniken
Bonn GmbH, Johanniter Krankenhaus, Bonn, Germany
| | - Aida K. Dieffenbach
- Division of Clinical Epidemiology and Aging Research,
German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium, Heidelberg, Germany
| | - Volker Arndt
- Division of Clinical Epidemiology and Aging Research,
German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Núria Malats
- Genetic and Molecular Epidemiology Group, Spanish National
Cancer Research Centre (CNIO), Madrid, Spain
| | - JoséI. Arias Perez
- Servicio de Cirugía General y Especialidades,
Hospital Monte Naranco, Oviedo, Spain
| | - Javier Benítez
- Human Genetics Group, Spanish National Cancer Reserach
Centre (CNIO), Madrid, Spain
| | - Henrik Flyger
- Department of Breast Surgery, Herlev Hospital, Copenhagen
University Hospital, Herlev, Denmark
| | - Børge G. Nordestgaard
- Department of Clinical Biochemistry, Herlev Hospital,
Copenhagen University Hospital, Herlev, Denmark
- Copenhagen General Population Study, Herlev Hospital,
Copenhagen University Hospital, Herlev, Denmark
| | - Théresè Truong
- Unité Mixte de Recherche Scientifique (UMRS) 1018,
University Paris-Sud, Villejuif, France
- INSERM (National Institute of Health and Medical
Research), CESP (Center for Research in Epidemiology and Population Health), U1018,
Environmental Epidemiology of Cancer, Villejuif, France
| | - Emilie Cordina-Duverger
- Unité Mixte de Recherche Scientifique (UMRS) 1018,
University Paris-Sud, Villejuif, France
- INSERM (National Institute of Health and Medical
Research), CESP (Center for Research in Epidemiology and Population Health), U1018,
Environmental Epidemiology of Cancer, Villejuif, France
| | - Florence Menegaux
- Unité Mixte de Recherche Scientifique (UMRS) 1018,
University Paris-Sud, Villejuif, France
- INSERM (National Institute of Health and Medical
Research), CESP (Center for Research in Epidemiology and Population Health), U1018,
Environmental Epidemiology of Cancer, Villejuif, France
| | - Isabel dos Santos Silva
- Department of Non-Communicable Disease Epidemiology,
London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Olivia Fletcher
- Breakthrough Breast Cancer Research Centre, Institute of
Cancer Research, London, United Kingdom
| | - Nichola Johnson
- Breakthrough Breast Cancer Research Centre, Institute of
Cancer Research, London, United Kingdom
| | - Lothar Häberle
- Department of Gynecology and Obstetrics, University
Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen,
Germany
| | - Matthias W. Beckmann
- Department of Gynecology and Obstetrics, University
Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen,
Germany
| | - Arif B. Ekici
- Institute of Human Genetics, Friedrich-Alexander
University Erlangen-Nuremberg, Erlangen, Germany
| | - Linde Braaf
- Division of Molecular Pathology, Netherlands Cancer
Institute, Amsterdam, The Netherlands
- Division of Psychosocial Research and Epidemiology,
Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Femke Atsma
- Department of Donor Studies, Sanquin Nijmegen, Nijmegen,
The Netherlands
| | - Alexandra J. van den Broek
- Division of Psychosocial Research and Epidemiology,
Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Enes Makalic
- Department of Analytic Epidemiology, University of
Melbourne, Melbourne, Australia
| | - Daniel F. Schmidt
- Centre for Molecular, Environmental, Genetic, and
Analytic Epidemiology, University of Melbourne, Melbourne, Australia
| | | | - Angela Cox
- Department of Oncology, Institute for Cancer Studies,
University of Sheffield, Sheffield, United Kingdom
| | - Jacques Simard
- Cancer Genomics Laboratory, Centre Hospitalier
Universitaire de Québec Research Center, Laval University, Québec,
Canada
- Department of Molecular Medicine, Faculty of Medicine,
Quebec, Canada
| | - Graham G. Giles
- Cancer Epidemiology Centre, Cancer Council Victoria,
Melbourne, Australia
- Centre for Molecular, Environmental, Genetic, and
Analytic Epidemiology, University of Melbourne, Melbourne, Australia
| | - Diether Lambrechts
- Vesalius Research Center (VRC), VIB, Flanders,
Belgium
- Laboratory of Translational Genetics, Department of
Oncology, University of Leuven, Leuven, Belgium
| | - Arto Mannermaa
- Department of Pathology and Forensic Medicine, Kuopio
University Hospital, University of Kuopio, Kuopio, Finland
| | - Hiltrud Brauch
- Dr. Margarete Fischer-Bosch Institute of Clinical
Pharamcology, Stuttgart, Germany
| | - Pascal Guénel
- Unité Mixte de Recherche Scientifique (UMRS) 1018,
University Paris-Sud, Villejuif, France
- INSERM (National Institute of Health and Medical
Research), CESP (Center for Research in Epidemiology and Population Health), U1018,
Environmental Epidemiology of Cancer, Villejuif, France
| | - Julian Peto
- Department of Non-Communicable Disease Epidemiology,
London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Peter A. Fasching
- Department of Gynecology and Obstetrics, University
Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen,
Germany
- Department of Medicine, David Geffen School of Medicine,
University of California, Los Angeles, United States
| | - John Hopper
- Centre for Molecular, Environmental, Genetic, and
Analytic Epidemiology, University of Melbourne, Victoria, Australia
| | - 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
| | - Fergus Couch
- Department of Experimental Pathology, Mayo Clinic,
Rochester, Minnesota, United States of America
| | - Georgia Chenevix-Trench
- Department of Molecular Cancer Epidemiology, Queensland
Institute of Medical Research, Brisbane Australia
| | - Paul D. P. Pharoah
- Department of Oncology and Public Health and Primary
Care, University of Cambridge, Cambridge, United Kingdom
| | - Montserrat Garcia-Closas
- Division of Genetics and Epidemiology, Breakthrough
Breast Cancer Research Centre, Institute of Cancer Research, London, United
Kingdom
| | - Marjanka K. Schmidt
- Division of Molecular Pathology, Netherlands Cancer
Institute, Amsterdam, The Netherlands
- Division of Psychosocial Research and Epidemiology,
Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Per Hall
- Department of Medical Epidemiology and Biostatistics,
Karolinska Institutet, Stockholm, Sweden
| | - Douglas F. Easton
- Department of Public Health and Primary Care, University
of Cambridge, Cambridge, United Kingdom
| | - Jenny Chang-Claude
- Correspondence to: Jenny Chang-Claude, Department
of Cancer Epidemiology, German Cancer Research Center (DKFZ), Im Neuenheimer
Feld 581, 69120 Heidelberg, Germany.
| |
Collapse
|
210
|
Germline genetic variants associated with prostate cancer and potential relevance to clinical practice. Recent Results Cancer Res 2014; 202:9-26. [PMID: 24531773 DOI: 10.1007/978-3-642-45195-9_2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The inherited link of prostate cancer predisposition has been supported using data from early epidemiological studies, as well as from familial and twin studies. Early linkage analyses and candidate gene approaches to identify these variants yielded mixed results. Since then, multiple genetic variants associated with prostate cancer susceptibility have now been found from genome-wide association studies (GWAS). Their clinical utility, however, remains unknown. It is recognised that collaborative efforts are needed to ensure adequate sample sizes are available to definitively investigate the genetic-clinical interactions. These could have important implications for public health as well as individualised prostate cancer management strategies. With the costs of genotyping decreasing and direct-to-consumer testing already offered for these common variants, it is envisaged that a lot of attention will be focussed in this area. These results will enable more refined risk stratification which will be important for targeting screening and prevention to higher risk groups. Ascertaining their clinical role remains an important goal for the GWAS community with international consortia now established, pooling efforts and resources to move this field forward.
Collapse
|
211
|
Su WH, Yao Shugart Y, Chang KP, Tsang NM, Tse KP, Chang YS. How genome-wide SNP-SNP interactions relate to nasopharyngeal carcinoma susceptibility. PLoS One 2013; 8:e83034. [PMID: 24376627 PMCID: PMC3871583 DOI: 10.1371/journal.pone.0083034] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Accepted: 10/29/2013] [Indexed: 11/18/2022] Open
Abstract
This study is the first to use genome-wide association study (GWAS) data to evaluate the multidimensional genetic architecture underlying nasopharyngeal cancer. Since analysis of data from GWAS confirms a close and consistent association between elevated risk for nasopharyngeal carcinoma (NPC) and major histocompatibility complex class 1 genes, our goal here was to explore lesser effects of gene-gene interactions. We conducted an exhaustive genome-wide analysis of GWAS data of NPC, revealing two-locus interactions occurring between single nucleotide polymorphisms (SNPs), and identified a number of suggestive interaction loci which were missed by traditional GWAS analyses. Although none of the interaction pairs we identified passed the genome-wide Bonferroni-adjusted threshold for significance, using independent GWAS data from the same population (Stage 2), we selected 66 SNP pairs in 39 clusters with P<0.01. We identified that in several chromosome regions, multiple suggestive interactions group to form a block-like signal, effectively reducing the rate of false discovery. The strongest cluster of interactions involved the CREB5 gene and a SNP rs1607979 on chromosome 17q22 (P = 9.86×10(-11)) which also show trans-expression quantitative loci (eQTL) association in Chinese population. We then detected a complicated cis-interaction pattern around the NPC-associated HLA-B locus, which is immediately adjacent to copy-number variations implicated in male susceptibility for NPC. While it remains to be seen exactly how and to what degree SNP-SNP interactions such as these affect susceptibility for nasopharyngeal cancer, future research on these questions holds great promise for increasing our understanding of this disease's genetic etiology, and possibly also that of other gene-related cancers.
Collapse
Affiliation(s)
- Wen-Hui Su
- Department of Biomedical Sciences, Chang Gung University, Taoyuan, Taiwan
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Chang Gung Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
| | - Yin Yao Shugart
- Genomic Research Branch, Division of Neuroscience and Behavioral Sciences, National Institute of Mental Health, NIH, Bethesda, Maryland, United States of America
- Department of Gastroenterology, Johns Hopkins Medical School, Baltimore, Maryland, United States of America
| | - Kai-Ping Chang
- Department of Otolaryngology - Head and Neck Surgery, Chang Gung Memorial Hospital at Lin-Kou, Taoyuan, Taiwan
| | - Ngan-Ming Tsang
- Department of Radiation Oncology, Chang Gung Memorial Hospital at Lin-Kou, Taoyuan, Taiwan
| | - Ka-Po Tse
- Chang Gung Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
| | - Yu-Sun Chang
- Chang Gung Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
| |
Collapse
|
212
|
Genome-wide association studies of cancer predisposition. Mol Oncol 2013. [DOI: 10.1017/cbo9781139046947.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
|
213
|
From GWAS to function: genetic variation in sodium channel gene enhancer influences electrical patterning. Trends Cardiovasc Med 2013; 24:99-104. [PMID: 24360055 DOI: 10.1016/j.tcm.2013.09.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Revised: 08/29/2013] [Accepted: 08/30/2013] [Indexed: 12/19/2022]
Abstract
The electrical activity of the heart depends on the correct interplay between key transcription factors and cis-regulatory elements, which together regulate the proper heterogeneous expression of genes encoding for ion channels and other proteins. Genome-wide association studies of ECG parameters implicated genetic variants in the genes for these factors and ion channels modulating conduction and depolarization. Here, we review recent insights into the regulation of localized expression of ion channel genes and the mechanism by which a single-nucleotide polymorphism (SNP) associated with alterations in cardiac conduction patterns in humans affects the transcriptional regulation of the sodium channel genes, SCN5A and SCN10A. The identification of regulatory elements of electrical activity genes helps to explain the impact of genetic variants in non-coding regulatory DNA sequences on regulation of cardiac conduction and the predisposition for cardiac arrhythmias.
Collapse
|
214
|
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: 555] [Impact Index Per Article: 50.5] [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.
Collapse
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.
| | | | | | | |
Collapse
|
215
|
Hnisz D, Abraham BJ, Lee TI, Lau A, Saint-André V, Sigova AA, Hoke H, Young RA. Super-enhancers in the control of cell identity and disease. Cell 2013; 155:934-47. [PMID: 24119843 PMCID: PMC3841062 DOI: 10.1016/j.cell.2013.09.053] [Citation(s) in RCA: 2454] [Impact Index Per Article: 223.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Revised: 09/27/2013] [Accepted: 09/30/2013] [Indexed: 02/07/2023]
Abstract
Super-enhancers are large clusters of transcriptional enhancers that drive expression of genes that define cell identity. Improved understanding of the roles that super-enhancers play in biology would be afforded by knowing the constellation of factors that constitute these domains and by identifying super-enhancers across the spectrum of human cell types. We describe here the population of transcription factors, cofactors, chromatin regulators, and transcription apparatus occupying super-enhancers in embryonic stem cells and evidence that super-enhancers are highly transcribed. We produce a catalog of super-enhancers in a broad range of human cell types and find that super-enhancers associate with genes that control and define the biology of these cells. Interestingly, disease-associated variation is especially enriched in the super-enhancers of disease-relevant cell types. Furthermore, we find that cancer cells generate super-enhancers at oncogenes and other genes important in tumor pathogenesis. Thus, super-enhancers play key roles in human cell identity in health and in disease.
Collapse
Affiliation(s)
- Denes Hnisz
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142
| | - Brian J. Abraham
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142
| | - Tong Ihn Lee
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142
| | - Ashley Lau
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139
| | - Violaine Saint-André
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142
| | - Alla A. Sigova
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142
| | - Heather Hoke
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139
| | - Richard A. Young
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139
| |
Collapse
|
216
|
Ghoussaini M, Pharoah PDP, Easton DF. Inherited genetic susceptibility to breast cancer: the beginning of the end or the end of the beginning? THE AMERICAN JOURNAL OF PATHOLOGY 2013; 183:1038-1051. [PMID: 23973388 DOI: 10.1016/j.ajpath.2013.07.003] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2013] [Revised: 06/24/2013] [Accepted: 07/22/2013] [Indexed: 02/06/2023]
Abstract
Genome-wide association studies have identified 72 loci associated with breast cancer susceptibility. Seventeen of these are known to predispose to other cancers. High-penetrance susceptibility loci for breast cancer usually result from coding alterations, principally in genes involved in DNA repair, whereas almost all of the associations identified through genome-wide association studies are found in noncoding regions of the genome and are likely to involve regulation of genes in multiple pathways. However, the genes underlying most associations are not yet known. In this review, we summarize the findings from genome-wide association studies in breast cancer and describe the genes and mechanisms that are likely to be involved in the tumorigenesis process. We also discuss approaches to fine-scale mapping of susceptibility regions used to identify the likely causal variant(s) underlying the associations, a major challenge in genetic epidemiology. Finally, we discuss the potential impact of such findings on personalized medicine and future avenues for screening, prediction, and prevention programs.
Collapse
Affiliation(s)
- Maya Ghoussaini
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, United Kingdom.
| | - Paul D P Pharoah
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, United Kingdom; Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, United Kingdom
| | - Douglas F Easton
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, United Kingdom
| |
Collapse
|
217
|
Yang B, Thyagarajan B, Gross MD, Fedirko V, Goodman M, Bostick RM. No evidence that associations of incident, sporadic colorectal adenoma with its major modifiable risk factors differ by chromosome 8q24 region rs6983267 genotype. Mol Carcinog 2013; 53 Suppl 1:E193-200. [PMID: 24115145 DOI: 10.1002/mc.22086] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2013] [Revised: 08/15/2013] [Accepted: 08/20/2013] [Indexed: 12/15/2022]
Abstract
A single nucleotide polymorphism (SNP), rs6983267, in the chromosome 8q24 region, has been associated with higher risk for colorectal neoplasms, but its relation to carcinogenic mechanisms is unclear. To investigate whether associations of colorectal adenoma with its major modifiable risk factors differ according to rs6983267 genotype, we performed a pooled analysis of the White participants (n = 401 cases, 518 controls) from three colonoscopy-based, case-control studies of incident, sporadic colorectal adenoma conducted between 1991 and 2002. There was a statistically significant direct association of rs6983267 with colorectal adenoma that was consistent with those in previous reports. We found no clear indications that rs6983267 impacts the association of colorectal adenomas with the following risk factors: physical activity, body mass index (BMI), nonsteroidal anti-inflammatory drug (NSAID) use, tobacco or alcohol use, hormone replacement therapy among women, blood 25-OH-vitamin D3 levels, oxidative balance, or total energy, calcium, red meat, vegetable and fruit, and folate intakes. These findings, together with previously reported null results on 8q24-environment interactions for colorectal cancer, suggest that associations of colorectal adenoma with its major modifiable risk factors may not differ according to chromosome 8q24 region rs6983267 genotype.
Collapse
Affiliation(s)
- Baiyu Yang
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, Georgia
| | | | | | | | | | | |
Collapse
|
218
|
McClellan MJ, Wood CD, Ojeniyi O, Cooper TJ, Kanhere A, Arvey A, Webb HM, Palermo RD, Harth-Hertle ML, Kempkes B, Jenner RG, West MJ. Modulation of enhancer looping and differential gene targeting by Epstein-Barr virus transcription factors directs cellular reprogramming. PLoS Pathog 2013; 9:e1003636. [PMID: 24068937 PMCID: PMC3771879 DOI: 10.1371/journal.ppat.1003636] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2013] [Accepted: 08/03/2013] [Indexed: 12/28/2022] Open
Abstract
Epstein-Barr virus (EBV) epigenetically reprogrammes B-lymphocytes to drive immortalization and facilitate viral persistence. Host-cell transcription is perturbed principally through the actions of EBV EBNA 2, 3A, 3B and 3C, with cellular genes deregulated by specific combinations of these EBNAs through unknown mechanisms. Comparing human genome binding by these viral transcription factors, we discovered that 25% of binding sites were shared by EBNA 2 and the EBNA 3s and were located predominantly in enhancers. Moreover, 80% of potential EBNA 3A, 3B or 3C target genes were also targeted by EBNA 2, implicating extensive interplay between EBNA 2 and 3 proteins in cellular reprogramming. Investigating shared enhancer sites neighbouring two new targets (WEE1 and CTBP2) we discovered that EBNA 3 proteins repress transcription by modulating enhancer-promoter loop formation to establish repressive chromatin hubs or prevent assembly of active hubs. Re-ChIP analysis revealed that EBNA 2 and 3 proteins do not bind simultaneously at shared sites but compete for binding thereby modulating enhancer-promoter interactions. At an EBNA 3-only intergenic enhancer site between ADAM28 and ADAMDEC1 EBNA 3C was also able to independently direct epigenetic repression of both genes through enhancer-promoter looping. Significantly, studying shared or unique EBNA 3 binding sites at WEE1, CTBP2, ITGAL (LFA-1 alpha chain), BCL2L11 (Bim) and the ADAMs, we also discovered that different sets of EBNA 3 proteins bind regulatory elements in a gene and cell-type specific manner. Binding profiles correlated with the effects of individual EBNA 3 proteins on the expression of these genes, providing a molecular basis for the targeting of different sets of cellular genes by the EBNA 3s. Our results therefore highlight the influence of the genomic and cellular context in determining the specificity of gene deregulation by EBV and provide a paradigm for host-cell reprogramming through modulation of enhancer-promoter interactions by viral transcription factors. Epstein-Barr virus (EBV) is associated with numerous cancers. The ability of the virus to infect B-cells and convert them from short-lived into immortal cells is the key to its cancer-promoting properties. A small number of EBV transcription factors are required for immortalization and act in concert to drive cell growth by deregulating the expression of cellular genes through largely unknown mechanisms. We have demonstrated that four of these key transcription factors function cooperatively by targeting common genes via long-range enhancer elements and modulating their looping interactions with gene promoters. Specifically we show that gene repression by the EBV EBNA 3 family of proteins can be mediated through the modulation of enhancer-promoter looping. Our results also reveal that different subsets of EBNA 3 proteins are bound at different genes and that this differential binding can vary in lymphoma cells compared to cells immortalized in culture, indicating that cell-background-specific gene regulation may be important in lymphoma development. Our results demonstrate how cellular genes can be deregulated by an oncogenic virus through modulation of enhancer-promoter looping with the specificity of binding by viral transcription factors controlling cellular reprogramming in a gene and cell-type specific manner.
Collapse
Affiliation(s)
- Michael J. McClellan
- School of Life Sciences, John Maynard-Smith Building, University of Sussex, Falmer, Brighton, United Kingdom
| | - C. David Wood
- School of Life Sciences, John Maynard-Smith Building, University of Sussex, Falmer, Brighton, United Kingdom
| | - Opeoluwa Ojeniyi
- School of Life Sciences, John Maynard-Smith Building, University of Sussex, Falmer, Brighton, United Kingdom
| | - Tim J. Cooper
- School of Life Sciences, John Maynard-Smith Building, University of Sussex, Falmer, Brighton, United Kingdom
| | - Aditi Kanhere
- MRC Centre for Medical Molecular Virology, Division of Infection and Immunity, Paul O'Gorman Building, University College London, London, United Kingdom
| | - Aaron Arvey
- Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
| | - Helen M. Webb
- School of Life Sciences, John Maynard-Smith Building, University of Sussex, Falmer, Brighton, United Kingdom
| | - Richard D. Palermo
- School of Life Sciences, John Maynard-Smith Building, University of Sussex, Falmer, Brighton, United Kingdom
| | - Marie L. Harth-Hertle
- Department of Gene Vectors, Helmholtz Center Munich, German Research Center for Environmental Health, Munich, Germany
| | - Bettina Kempkes
- Department of Gene Vectors, Helmholtz Center Munich, German Research Center for Environmental Health, Munich, Germany
| | - Richard G. Jenner
- MRC Centre for Medical Molecular Virology, Division of Infection and Immunity, Paul O'Gorman Building, University College London, London, United Kingdom
| | - Michelle J. West
- School of Life Sciences, John Maynard-Smith Building, University of Sussex, Falmer, Brighton, United Kingdom
- * E-mail:
| |
Collapse
|
219
|
Adey A, Burton JN, Kitzman JO, Hiatt JB, Lewis AP, Martin BK, Qiu R, Lee C, Shendure J. The haplotype-resolved genome and epigenome of the aneuploid HeLa cancer cell line. Nature 2013; 500:207-11. [PMID: 23925245 PMCID: PMC3740412 DOI: 10.1038/nature12064] [Citation(s) in RCA: 249] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2012] [Accepted: 03/11/2013] [Indexed: 12/18/2022]
Abstract
The HeLa cell line was established in 1951 from cervical cancer cells taken from a patient, Henrietta Lacks, marking the first successful attempt to continually culture human-derived cells in vitro1. HeLa’s robust growth and unrestricted distribution resulted in its broad adoption – both intentionally and through widespread cross-contamination2 – and for the past sixty years it has served a role analogous to that of a model organism3. Its cumulative impact is illustrated by the fact that HeLa is named in >74,000 or ~0.3% of PubMed abstracts. The genomic architecture of HeLa remains largely unexplored beyond its karyotype4, in part because like many cancers, its extensive aneuploidy renders such analyses challenging. We performed haplotype-resolved whole genome sequencing5 of the HeLa CCL-2 strain, discovering point and indel variation, mapping copy-number and loss of heterozygosity (LOH), and phasing variants across full chromosome arms. We further investigated variation and copy-number profiles for HeLa S3 and eight additional strains. Surprisingly, HeLa is relatively stable with respect to point variation, accumulating few new mutations since early passaging. Haplotype resolution facilitated reconstruction of an amplified, highly rearranged region at chromosome 8q24.21 at which the HPV-18 viral genome integrated as the likely initial event underlying tumorigenesis. We combined these maps with RNA-Seq6 and ENCODE Project7 datasets to phase the HeLa epigenome, revealing strong, haplotype-specific activation of the proto-oncogene MYC by the integrated HPV-18 genome ~500 kilobases upstream, and permitting global analyses of the relationship between gene dosage and expression. These data provide an extensively phased, high-quality reference genome for past and future experiments relying on HeLa, and demonstrate the value of haplotype resolution for characterizing cancer genomes and epigenomes.
Collapse
Affiliation(s)
- Andrew Adey
- Department of Genome Sciences, University of Washington, Seattle, Washington 98115, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
220
|
Brown JR. Inherited susceptibility to chronic lymphocytic leukemia: evidence and prospects for the future. Ther Adv Hematol 2013; 4:298-308. [PMID: 23926461 PMCID: PMC3734903 DOI: 10.1177/2040620713495639] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Chronic lymphocytic leukemia (CLL) is the most common leukemia in the United States and one of the most heritable cancers. A family history of the disease is perhaps the best defined risk factor, and approximately 15-20% of CLL patients have a family member with CLL or a related lymphoproliferative disorder. Much effort has been devoted to trying to elucidate the mechanisms underlying this genetic risk. Familial CLL appears to be clinically and biologically similar to sporadic CLL, and most if not all CLL appears to be preceded by monoclonal B-cell lymphocytosis (MBL), which does appear to occur at higher frequency in relatives in families with CLL. Neither linkage studies nor candidate gene association studies have proven particularly informative in CLL, but genomewide association studies have identified multiple low-risk variants that together explain about 16% of the familial risk of CLL. Studies of individual families have identified higher-risk single nucleotide polymorphisms or copy number variants associated with disease risk in those families. Current efforts to identify additional risk loci are focused on applying next-generation sequencing to the germline of informative CLL families as well as individuals with sporadic CLL.
Collapse
Affiliation(s)
- Jennifer R Brown
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
| |
Collapse
|
221
|
Sur I, Tuupanen S, Whitington T, Aaltonen LA, Taipale J. Lessons from functional analysis of genome-wide association studies. Cancer Res 2013; 73:4180-4. [PMID: 23832660 DOI: 10.1158/0008-5472.can-13-0789] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Most cancer-associated single-nucleotide polymorphisms (SNP) identified using genome-wide association studies are located outside of protein-coding regions, and their significance and mode of action have been a source of continuing debate. One proposed mechanism of action of the SNPs is that they would affect the activity of enhancer elements regulating critical target genes. In this review, we summarize recent results that substantiate this model. These studies have identified a cancer-specific enhancer element at the 8q24 gene desert that controls the expression of the MYC oncogene. We further discuss implications of the observed difference between normal growth control and cancer for drug development, and the inherent features of genome-wide association studies that may specifically lead to identification of disease-specific regulatory elements.
Collapse
Affiliation(s)
- Inderpreet Sur
- Department of Biosciences and Nutrition, SciLife Center, Karolinska Institutet, Clinical Research Center, Karolinska University Hospital, Stockholm, Sweden
| | | | | | | | | |
Collapse
|
222
|
Yang B, Thyagarajan B, Gross MD, Goodman M, Sun YV, Bostick RM. Genetic variants at chromosome 8q24, colorectal epithelial cell proliferation, and risk for incident, sporadic colorectal adenomas. Mol Carcinog 2013; 53 Suppl 1:E187-92. [PMID: 23776012 DOI: 10.1002/mc.22047] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2013] [Revised: 04/24/2013] [Accepted: 05/03/2013] [Indexed: 01/02/2023]
Abstract
Three polymorphic sites at chromosome 8q24 (rs7837328, rs10808555, rs6983267) have been associated with risk for colorectal adenomas. It was also previously reported that the single nucleotide polymorphism (SNP) rs6983267 may enhance Wnt signaling, which regulates cell proliferation. To investigate associations between the 8q24 variants and colorectal epithelial cell proliferation in the normal-appearing colorectal mucosa, as well as with colorectal adenoma, we analyzed data from a previously conducted pilot, colonoscopy-based case-control study of incident, sporadic colorectal adenoma (n = 90 cases, 132 controls). Proliferation was measured in biopsies of the normal-appearing mucosa of the rectum, sigmoid colon, and cecum using immunohistochemistry for proliferating cell nuclear antigen (PCNA). The direct associations of each SNP with colorectal adenoma were consistent with those in previous reports. For all three SNPs, proliferation tended to be higher among those homozygous for the risk alleles compared to those heterozygous or homozygous for the nonrisk alleles combined; among the controls, proliferation was 32.1% higher (P = 0.23) for those with the rs10808555 GG genotype, 16.4% higher (P = 0.16) for those with the rs7837328 AA genotype, and 6.5% higher (P = 0.52) for those with the rs6983267 GG genotype. These preliminary findings, which are consistent with previously reported direct associations between genetic variants at chromosome 8q24 and risk for colorectal adenoma, suggest that the genetic variants may also be associated with higher levels of colorectal epithelial cell proliferation, thus providing support for further investigation of the hypothesis that 8q24 variants may increase risk via enhanced Wnt signaling.
Collapse
Affiliation(s)
- Baiyu Yang
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, Georgia
| | | | | | | | | | | |
Collapse
|
223
|
Dudek AM, Grotenhuis AJ, Vermeulen SH, Kiemeney LALM, Verhaegh GW. Urinary bladder cancer susceptibility markers. What do we know about functional mechanisms? Int J Mol Sci 2013; 14:12346-66. [PMID: 23752272 PMCID: PMC3709789 DOI: 10.3390/ijms140612346] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Revised: 05/23/2013] [Accepted: 05/30/2013] [Indexed: 12/24/2022] Open
Abstract
Genome-wide association studies (GWAS) have been successful in the identification of the several urinary bladder cancer (UBC) susceptibility loci, pointing towards novel genes involved in tumor development. Despite that, functional characterization of the identified variants remains challenging, as they mostly map to poorly understood, non-coding regions. Recently, two of the UBC risk variants (PSCA and UGT1A) were confirmed to have functional consequences. They were shown to modify bladder cancer risk by influencing gene expression in an allele-specific manner. Although the role of the other UBC risk variants is unknown, it can be hypothesized-based on studies from different cancer types-that they influence cancer susceptibility by alterations in regulatory networks. The insight into UBC heritability gained through GWAS and further functional studies can impact on cancer prevention and screening, as well as on the development of new biomarkers and future personalized therapies.
Collapse
Affiliation(s)
- Aleksandra M. Dudek
- Department of Urology, Radboud University Medical Centre, Geert Grooteplein 16, Nijmegen 6525 GA, The Netherlands; E-Mails: (L.A.L.M.K.); (G.W.V.)
- Department for Health Evidence, Radboud University Medical Centre, Geert Grooteplein 21, Nijmegen 6525 EZ, The Netherlands; E-Mails: (A.J.G.); (S.H.V.)
- Nijmegen Centre for Molecular Life Sciences, Geert Grooteplein 28, Nijmegen 6525 GA, The Netherlands
| | - Anne J. Grotenhuis
- Department for Health Evidence, Radboud University Medical Centre, Geert Grooteplein 21, Nijmegen 6525 EZ, The Netherlands; E-Mails: (A.J.G.); (S.H.V.)
- Nijmegen Centre for Evidence Based Practice, Geert Grooteplein 21, Nijmegen 6525 GA, The Netherlands
| | - Sita H. Vermeulen
- Department for Health Evidence, Radboud University Medical Centre, Geert Grooteplein 21, Nijmegen 6525 EZ, The Netherlands; E-Mails: (A.J.G.); (S.H.V.)
- Nijmegen Centre for Evidence Based Practice, Geert Grooteplein 21, Nijmegen 6525 GA, The Netherlands
| | - Lambertus A. L. M. Kiemeney
- Department of Urology, Radboud University Medical Centre, Geert Grooteplein 16, Nijmegen 6525 GA, The Netherlands; E-Mails: (L.A.L.M.K.); (G.W.V.)
- Department for Health Evidence, Radboud University Medical Centre, Geert Grooteplein 21, Nijmegen 6525 EZ, The Netherlands; E-Mails: (A.J.G.); (S.H.V.)
- Nijmegen Centre for Evidence Based Practice, Geert Grooteplein 21, Nijmegen 6525 GA, The Netherlands
| | - Gerald W. Verhaegh
- Department of Urology, Radboud University Medical Centre, Geert Grooteplein 16, Nijmegen 6525 GA, The Netherlands; E-Mails: (L.A.L.M.K.); (G.W.V.)
- Nijmegen Centre for Molecular Life Sciences, Geert Grooteplein 28, Nijmegen 6525 GA, The Netherlands
| |
Collapse
|
224
|
Abstract
Systematic studies of the cancer genome have exploded in recent years. These studies have revealed scores of new cancer genes, including many in processes not previously known to be causal targets in cancer. The genes affect cell signaling, chromatin, and epigenomic regulation; RNA splicing; protein homeostasis; metabolism; and lineage maturation. Still, cancer genomics is in its infancy. Much work remains to complete the mutational catalog in primary tumors and across the natural history of cancer, to connect recurrent genomic alterations to altered pathways and acquired cellular vulnerabilities, and to use this information to guide the development and application of therapies.
Collapse
Affiliation(s)
- Levi A Garraway
- Department of Medical Oncology and Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | | |
Collapse
|
225
|
The genomic landscape of prostate cancer. Int J Mol Sci 2013; 14:10822-51. [PMID: 23708091 PMCID: PMC3709705 DOI: 10.3390/ijms140610822] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2013] [Revised: 05/06/2013] [Accepted: 05/09/2013] [Indexed: 12/12/2022] Open
Abstract
By the age of 80, approximately 80% of men will manifest some cancerous cells within their prostate, indicating that prostate cancer constitutes a major health burden. While this disease is clinically insignificant in most men, it can become lethal in others. The most challenging task for clinicians is developing a patient-tailored treatment in the knowledge that this disease is highly heterogeneous and that relatively little adequate prognostic tools are available to distinguish aggressive from indolent disease. Next-generation sequencing allows a description of the cancer at an unprecedented level of detail and at different levels, going from whole genome or exome sequencing to transcriptome analysis and methylation-specific immunoprecipitation, followed by sequencing. Integration of all these data is leading to a better understanding of the initiation, progression and metastatic processes of prostate cancer. Ultimately, these insights will result in a better and more personalized treatment of patients suffering from prostate cancer. The present review summarizes current knowledge on copy number changes, gene fusions, single nucleotide mutations and polymorphisms, methylation, microRNAs and long non-coding RNAs obtained from high-throughput studies.
Collapse
|
226
|
Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data. Nat Rev Genet 2013; 14:390-403. [PMID: 23657480 DOI: 10.1038/nrg3454] [Citation(s) in RCA: 751] [Impact Index Per Article: 68.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
How DNA is organized in three dimensions inside the cell nucleus and how this affects the ways in which cells access, read and interpret genetic information are among the longest standing questions in cell biology. Using newly developed molecular, genomic and computational approaches based on the chromosome conformation capture technology (such as 3C, 4C, 5C and Hi-C), the spatial organization of genomes is being explored at unprecedented resolution. Interpreting the increasingly large chromatin interaction data sets is now posing novel challenges. Here we describe several types of statistical and computational approaches that have recently been developed to analyse chromatin interaction data.
Collapse
|
227
|
Rada-Iglesias A, Prescott SL, Wysocka J. Human genetic variation within neural crest enhancers: molecular and phenotypic implications. Philos Trans R Soc Lond B Biol Sci 2013; 368:20120360. [PMID: 23650634 DOI: 10.1098/rstb.2012.0360] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Developmental gene expression programmes are coordinated by the specialized distal cis-regulatory elements called enhancers, which integrate lineage- and signalling-dependent inputs to guide morphogenesis. In previous work, we characterized the genome-wide repertoire of active enhancers in human neural crest cells (hNCC), an embryonic cell population with critical roles in craniofacial development. We showed that in hNCC, co-occupancy of a master regulator TFAP2A with nuclear receptors NR2F1 and NR2F2 correlates with the presence of permissive enhancer chromatin states. Here, we take advantage of pre-existing human genetic variation to further explore potential cooperation between TFAP2A and NR2F1/F2. We demonstrate that isolated single nucleotide polymorphisms affecting NR2F1/F2-binding sites within hNCC enhancers can alter TFAP2A occupancy and overall chromatin features at the same enhancer allele. We propose that a similar strategy can be used to elucidate other cooperative relationships between transcription factors involved in developmental transitions. Using the neural crest and its major contribution to human craniofacial phenotypes as a paradigm, we discuss how genetic variation might modulate the molecular properties and activity of enhancers, and ultimately impact human phenotypic diversity.
Collapse
Affiliation(s)
- Alvaro Rada-Iglesias
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | | | | |
Collapse
|
228
|
Andreassen KE, Kristiansen W, Karlsson R, Aschim EL, Dahl O, Fosså SD, Adami HO, Wiklund F, Haugen TB, Grotmol T. Genetic variation in AKT1, PTEN and the 8q24 locus, and the risk of testicular germ cell tumor. Hum Reprod 2013; 28:1995-2002. [PMID: 23639623 DOI: 10.1093/humrep/det127] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
STUDY QUESTION Is there an association between testicular germ cell tumor (TGCT) and genetic polymorphisms in AKT1, PTEN and the 8q24 locus? SUMMARY ANSWER Our findings suggest that genetic variation in PTEN may influence the risk of TGCT. WHAT IS KNOWN ALREADY There is strong evidence that genetic variation influences the risk of TGCT. The oncogene, AKT1, the tumor suppressor gene, PTEN and the chromosome 8q24 locus play important roles in cancer development in general. STUDY DESIGN, SIZE, DURATION We have conducted a population-based Norwegian-Swedish case-parent study, based on cases diagnosed in 1990-2008, including 831 triads (TGCT case and both parents), 474 dyads (TGCT case and one parent) and 712 singletons (only the TGCT case). In addition we expanded the study to include 3922 unrelated male controls from the TwinGene project. PARTICIPANTS/MATERIALS, SETTING, METHODS We genotyped 26 single nucleotide polymorphisms (SNPs) in AKT1, PTEN and the 8q24 locus. First, triads and dyads were included in a likelihood-based association test. To increase the statistical power, case singletons and controls from the TwinGene project were included in a single test for association. We examined if the allelic effect on TGCT risk differed by histological subgroup, country of origin or parent of origin. Odds ratios (ORs) and 95% confidence intervals (CI) were calculated with Bonferroni correction (P bonf) for multiple testing. MAIN RESULTS AND THE ROLE OF CHANCE In the case-parent analyses, none of the 26 SNPs were significantly associated with TGCT. Of the 23 SNPs investigated in the combined study, one SNP in PTEN (rs11202586) remained associated with TGCT risk after adjusting for multiple testing (OR = 1.16, 95% CI = 1.06-1.28, P bonf = 0.040). We found no difference in risk according to histological subgroup, parent of origin or between countries. LIMITATIONS, REASONS FOR CAUTION Our study is strengthened by the population-based design and large sample size, which gives high power to detect risk alleles. The reported association was not highly significant, and although it was based on an a priori hypothesis of this tumor suppressor gene being implicated in the etiology of TGCT, replication studies, as well as functional studies of this polymorphism, are warranted. WIDER IMPLICATIONS OF THE FINDINGS We report, to our knowledge, a novel association between TGCT and a marker in the tumor suppressor gene PTEN. Previous studies have linked PTEN to TGCT etiology, and there is also a link between PTEN and KITLG, which contains TGCT susceptibility loci revealed through recent genome-wide studies.
Collapse
Affiliation(s)
- K E Andreassen
- Department of Oncology, Oslo University Hospital, P.O. Box 4950, Nydalen, Oslo NO-0434, Norway. kristine.engen.andreassen@ous
| | | | | | | | | | | | | | | | | | | |
Collapse
|
229
|
George J, Alsop K, Etemadmoghadam D, Hondow H, Mikeska T, Dobrovic A, deFazio A, Smyth GK, Levine DA, Mitchell G, Bowtell DD. Nonequivalent gene expression and copy number alterations in high-grade serous ovarian cancers with BRCA1 and BRCA2 mutations. Clin Cancer Res 2013; 19:3474-84. [PMID: 23633455 DOI: 10.1158/1078-0432.ccr-13-0066] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE High-grade serous carcinoma (HGSC) accounts for the majority of epithelial ovarian cancer deaths. Genomic and functional data suggest that approximately half of unselected HGSC have disruption of the BRCA pathway and defects in homologous recombination repair (HRR). Pathway disruption is regarded as imparting a BRCAness phenotype. We explored the molecular changes in HGSC arising in association with specific BRCA1/BRCA2 somatic or germline mutations and in those with BRCA1 DNA promoter methylation. EXPERIMENTAL DESIGN We describe gene expression and copy number analysis of two large cohorts of HGSC in which both germline and somatic inactivation of HRR has been measured. RESULTS BRCA1 disruptions were associated with the C2 (immunoreactive) molecular subtype of HGSC, characterized by intense intratumoral T-cell infiltration. We derived and validated a predictor of BRCA1 mutation or methylation status, but could not distinguish BRCA2 from wild-type tumors. DNA copy number analysis showed that cases with BRCA1 mutation were significantly associated with amplification both at 8q24 (frequencies: BRCA1 tumors 50%, BRCA2 tumors 32%, and wild-type tumors 9%) and regions of the X-chromosome specifically dysregulated in basal-like breast cancer (BLBC; BRCA1 62%, BRCA2 34%, and wild-type 35%). Tumors associated with BRCA1/BRCA2 mutations shared a negative association with amplification at 19p13 (BRCA1 0%, BRCA2 3%, and wild-type 20%) and 19q12 (BRCA1 6%, BRCA2 3%, and wild-type 29%). CONCLUSION The molecular differences between tumors associated with BRCA1 compared with BRCA2 mutations are in accord with emerging clinical and pathologic data and support a growing appreciation of the relationship between HGSC and BLBC.
Collapse
Affiliation(s)
- Joshy George
- Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
230
|
Matullo G, Guarrera S, Betti M, Fiorito G, Ferrante D, Voglino F, Cadby G, Di Gaetano C, Rosa F, Russo A, Hirvonen A, Casalone E, Tunesi S, Padoan M, Giordano M, Aspesi A, Casadio C, Ardissone F, Ruffini E, Betta PG, Libener R, Guaschino R, Piccolini E, Neri M, Musk AWB, de Klerk NH, Hui J, Beilby J, James AL, Creaney J, Robinson BW, Mukherjee S, Palmer LJ, Mirabelli D, Ugolini D, Bonassi S, Magnani C, Dianzani I. Genetic variants associated with increased risk of malignant pleural mesothelioma: a genome-wide association study. PLoS One 2013; 8:e61253. [PMID: 23626673 PMCID: PMC3634031 DOI: 10.1371/journal.pone.0061253] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Accepted: 03/06/2013] [Indexed: 12/19/2022] Open
Abstract
Asbestos exposure is the main risk factor for malignant pleural mesothelioma (MPM), a rare aggressive tumor. Nevertheless, only 5-17% of those exposed to asbestos develop MPM, suggesting the involvement of other environmental and genetic risk factors. To identify the genetic risk factors that may contribute to the development of MPM, we conducted a genome-wide association study (GWAS; 370,000 genotyped SNPs, 5 million imputed SNPs) in Italy, among 407 MPM cases and 389 controls with a complete history of asbestos exposure. A replication study was also undertaken and included 428 MPM cases and 1269 controls from Australia. Although no single marker reached the genome-wide significance threshold, several associations were supported by haplotype-, chromosomal region-, gene- and gene-ontology process-based analyses. Most of these SNPs were located in regions reported to harbor aberrant alterations in mesothelioma (SLC7A14, THRB, CEBP350, ADAMTS2, ETV1, PVT1 and MMP14 genes), causing at most a 2-3-fold increase in MPM risk. The Australian replication study showed significant associations in five of these chromosomal regions (3q26.2, 4q32.1, 7p22.2, 14q11.2, 15q14). Multivariate analysis suggested an independent contribution of 10 genetic variants, with an Area Under the ROC Curve (AUC) of 0.76 when only exposure and covariates were included in the model, and of 0.86 when the genetic component was also included, with a substantial increase of asbestos exposure risk estimation (odds ratio, OR: 45.28, 95% confidence interval, CI: 21.52-95.28). These results showed that genetic risk factors may play an additional role in the development of MPM, and that these should be taken into account to better estimate individual MPM risk in individuals who have been exposed to asbestos.
Collapse
Affiliation(s)
- Giuseppe Matullo
- Human Genetics Foundation, HuGeF, Turin, Italy
- Department of Medical Sciences, University of Turin, Turin, Italy
| | | | - Marta Betti
- Laboratory of Genetic Pathology, Department Health Sciences, University of Piemonte Orientale, Novara, Italy
| | | | - Daniela Ferrante
- CPO-Piemonte and Unit of Medical Statistics and Epidemiology, Department Translational Medicine, University of Piemonte Orientale, Novara, Italy
| | | | - Gemma Cadby
- Genetic Epidemiology and Biostatistics Platform, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Prosserman Centre for Health Research, Samuel Lunenfeld Research Institute, Toronto, Ontario, Canada
- Centre for Genetic Epidemiology and Biostatistics, University of Western Australia, Nedlands, Western Australia, Australia
| | - Cornelia Di Gaetano
- Human Genetics Foundation, HuGeF, Turin, Italy
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Fabio Rosa
- Human Genetics Foundation, HuGeF, Turin, Italy
| | - Alessia Russo
- Human Genetics Foundation, HuGeF, Turin, Italy
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Ari Hirvonen
- Centre of Expertise for Health and Work Ability, Finnish Institute of Occupational Health, Helsinki, Finland
| | - Elisabetta Casalone
- Laboratory of Genetic Pathology, Department Health Sciences, University of Piemonte Orientale, Novara, Italy
| | - Sara Tunesi
- CPO-Piemonte and Unit of Medical Statistics and Epidemiology, Department Translational Medicine, University of Piemonte Orientale, Novara, Italy
| | - Marina Padoan
- CPO-Piemonte and Unit of Medical Statistics and Epidemiology, Department Translational Medicine, University of Piemonte Orientale, Novara, Italy
| | - Mara Giordano
- Laboratory of Genetics, Department Health Sciences, University of Piemonte Orientale, Novara, Italy
| | - Anna Aspesi
- Laboratory of Genetic Pathology, Department Health Sciences, University of Piemonte Orientale, Novara, Italy
| | - Caterina Casadio
- Thoracic Surgery Unit, University of Piemonte Orientale, Novara, Italy
| | - Francesco Ardissone
- Chest Surgery, Department of Clinical and Biological Sciences, University of Turin, Orbassano, Italy
| | - Enrico Ruffini
- Thoracic Surgery Unit, University of Turin, Turin, Italy
| | - Pier Giacomo Betta
- Pathology Unit, Azienda Ospedaliera Nazionale SS, Antonio e Biagio e Cesare Arrigo, Alessandria, Italy
| | - Roberta Libener
- Pathology Unit, Azienda Ospedaliera Nazionale SS, Antonio e Biagio e Cesare Arrigo, Alessandria, Italy
| | - Roberto Guaschino
- Transfusion Centre, Azienda Ospedaliera Nazionale SS, Antonio e Biagio e Cesare Arrigo, Alessandria, Italy
| | - Ezio Piccolini
- Pneumology Unit, Santo Spirito Hospital, Casale Monferrato, Italy
| | - Monica Neri
- Unit of Clinical and Molecular Epidemiology IRCCS San Raffaele Pisana, Rome, Italy
| | - Arthur W. B. Musk
- Department of Respiratory Medicine, Sir Charles Gairdner Hospital, Nedlands, Western Australia, Australia
- National Centre for Asbestos Related Disease, School of Medicine and Pharmacology, University of Western Australia, Nedlands, Western Australia, Australia
| | - Nicholas H. de Klerk
- Centre for Child Health Research, The University of Western Australia, Nedlands, Western Australia, Australia
| | - Jennie Hui
- National Centre for Asbestos Related Disease, School of Medicine and Pharmacology, University of Western Australia, Nedlands, Western Australia, Australia
- PathWest Laboratory Medicine WA, Nedlands, Western Australia, Australia
| | - John Beilby
- National Centre for Asbestos Related Disease, School of Medicine and Pharmacology, University of Western Australia, Nedlands, Western Australia, Australia
- PathWest Laboratory Medicine WA, Nedlands, Western Australia, Australia
| | - Alan L. James
- Department of Respiratory Medicine, Sir Charles Gairdner Hospital, Nedlands, Western Australia, Australia
- National Centre for Asbestos Related Disease, School of Medicine and Pharmacology, University of Western Australia, Nedlands, Western Australia, Australia
| | - Jenette Creaney
- Department of Respiratory Medicine, Sir Charles Gairdner Hospital, Nedlands, Western Australia, Australia
- National Centre for Asbestos Related Disease, School of Medicine and Pharmacology, University of Western Australia, Nedlands, Western Australia, Australia
| | - Bruce W. Robinson
- Department of Respiratory Medicine, Sir Charles Gairdner Hospital, Nedlands, Western Australia, Australia
- National Centre for Asbestos Related Disease, School of Medicine and Pharmacology, University of Western Australia, Nedlands, Western Australia, Australia
| | - Sutapa Mukherjee
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
- Women's College Research Institute and Women's College Hospital, Toronto, Ontario, Canada
| | - Lyle J. Palmer
- Genetic Epidemiology and Biostatistics Platform, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Prosserman Centre for Health Research, Samuel Lunenfeld Research Institute, Toronto, Ontario, Canada
| | - Dario Mirabelli
- Unit of Cancer Epidemiology, CPO-Piemonte and University of Turin, Turin, Italy
- Interdepartmental Center for Studies on Asbestos and other Toxic Particulates “G. Scansetti”, University of Turin, Turin, Italy
| | - Donatella Ugolini
- Department of Internal Medicine, University of Genoa and IRCSS AOU San Martino-IST-Istituto Nazionale per la Ricerca sul Cancro, Genoa, Italy
| | - Stefano Bonassi
- Unit of Clinical and Molecular Epidemiology IRCCS San Raffaele Pisana, Rome, Italy
| | - Corrado Magnani
- CPO-Piemonte and Unit of Medical Statistics and Epidemiology, Department Translational Medicine, University of Piemonte Orientale, Novara, Italy
- Interdepartmental Center for Studies on Asbestos and other Toxic Particulates “G. Scansetti”, University of Turin, Turin, Italy
| | - Irma Dianzani
- Laboratory of Genetic Pathology, Department Health Sciences, University of Piemonte Orientale, Novara, Italy
- Interdepartmental Center for Studies on Asbestos and other Toxic Particulates “G. Scansetti”, University of Turin, Turin, Italy
| |
Collapse
|
231
|
Abstract
Prostate cancer (PCa) is one of the most common malignancies in the world with over 890 000 cases and over 258 000 deaths worldwide each year. Nearly all mortalities from PCa are due to metastatic disease, typically through tumors that evolve to be hormone-refractory or castrate-resistant. Despite intensive epidemiological study, there are few known environmental risk factors, and age and family history are the major determinants. However, there is extreme heterogeneity in PCa incidence worldwide, suggesting that major determining factors have not been described. Genome-wide association studies have been performed and a considerable number of significant, but low-risk loci have been identified. In addition, several groups have analyzed PCa by determination of genomic copy number, fusion gene generation and targeted resequencing of candidate genes, as well as exome and whole genome sequencing. These initial studies have examined both primary and metastatic tumors as well as murine xenografts and identified somatic alterations in TP53 and other potential driver genes, and the disturbance of androgen response and cell cycle pathways. It is hoped that continued characterization of risk factors as well as gene mutation and misregulation in tumors will aid in understanding, diagnosing and better treating PCa.
Collapse
Affiliation(s)
- Michael Dean
- Cancer and Inflammation Program, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA.
| | | |
Collapse
|
232
|
Koutros S, Berndt SI, Hughes Barry K, Andreotti G, Hoppin JA, Sandler DP, Yeager M, Burdett LA, Yuenger J, Alavanja MCR, Beane Freeman LE. Genetic susceptibility loci, pesticide exposure and prostate cancer risk. PLoS One 2013; 8:e58195. [PMID: 23593118 PMCID: PMC3617165 DOI: 10.1371/journal.pone.0058195] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2012] [Accepted: 02/03/2013] [Indexed: 12/22/2022] Open
Abstract
Uncovering SNP (single nucleotide polymorphisms)-environment interactions can generate new hypotheses about the function of poorly characterized genetic variants and environmental factors, like pesticides. We evaluated SNP-environment interactions between 30 confirmed prostate cancer susceptibility loci and 45 pesticides and prostate cancer risk in 776 cases and 1,444 controls in the Agricultural Health Study. We used unconditional logistic regression to estimate odds ratios (ORs) and 95% confidence intervals (CIs). Multiplicative SNP-pesticide interactions were calculated using a likelihood ratio test. After correction for multiple tests using the False Discovery Rate method, two interactions remained noteworthy. Among men carrying two T alleles at rs2710647 in EH domain binding protein 1 (EHBP1) SNP, the risk of prostate cancer in those with high malathion use was 3.43 times those with no use (95% CI: 1.44–8.15) (P-interaction = 0.003). Among men carrying two A alleles at rs7679673 in TET2, the risk of prostate cancer associated with high aldrin use was 3.67 times those with no use (95% CI: 1.43, 9.41) (P-interaction = 0.006). In contrast, associations were null for other genotypes. Although additional studies are needed and the exact mechanisms are unknown, this study suggests known genetic susceptibility loci may modify the risk between pesticide use and prostate cancer.
Collapse
Affiliation(s)
- Stella Koutros
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland, United States of America.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
233
|
Michailidou K, Hall P, Gonzalez-Neira A, Ghoussaini M, Dennis J, Milne RL, Schmidt MK, Chang-Claude J, Bojesen SE, Bolla MK, Wang Q, Dicks E, Lee A, Turnbull C, Rahman N, Fletcher O, Peto J, Gibson L, Dos Santos Silva I, Nevanlinna H, Muranen TA, Aittomäki K, Blomqvist C, Czene K, Irwanto A, Liu J, Waisfisz Q, Meijers-Heijboer H, Adank M, van der Luijt RB, Hein R, Dahmen N, Beckman L, Meindl A, Schmutzler RK, Müller-Myhsok B, Lichtner P, Hopper JL, Southey MC, Makalic E, Schmidt DF, Uitterlinden AG, Hofman A, Hunter DJ, Chanock SJ, Vincent D, Bacot F, Tessier DC, Canisius S, Wessels LFA, Haiman CA, Shah M, Luben R, Brown J, Luccarini C, Schoof N, Humphreys K, Li J, Nordestgaard BG, Nielsen SF, Flyger H, Couch FJ, Wang X, Vachon C, Stevens KN, Lambrechts D, Moisse M, Paridaens R, Christiaens MR, Rudolph A, Nickels S, Flesch-Janys D, Johnson N, Aitken Z, Aaltonen K, Heikkinen T, Broeks A, Veer LJV, van der Schoot CE, Guénel P, Truong T, Laurent-Puig P, Menegaux F, Marme F, Schneeweiss A, Sohn C, Burwinkel B, Zamora MP, Perez JIA, Pita G, Alonso MR, Cox A, Brock IW, Cross SS, Reed MWR, Sawyer EJ, Tomlinson I, Kerin MJ, Miller N, Henderson BE, Schumacher F, Le Marchand L, Andrulis IL, Knight JA, Glendon G, Mulligan AM, Lindblom A, Margolin S, Hooning MJ, Hollestelle A, van den Ouweland AMW, Jager A, Bui QM, Stone J, Dite GS, Apicella C, Tsimiklis H, Giles GG, Severi G, Baglietto L, Fasching PA, Haeberle L, Ekici AB, Beckmann MW, Brenner H, Müller H, Arndt V, Stegmaier C, Swerdlow A, Ashworth A, Orr N, Jones M, Figueroa J, Lissowska J, Brinton L, Goldberg MS, Labrèche F, Dumont M, Winqvist R, Pylkäs K, Jukkola-Vuorinen A, Grip M, Brauch H, Hamann U, Brüning T, Radice P, Peterlongo P, Manoukian S, Bonanni B, Devilee P, Tollenaar RAEM, Seynaeve C, van Asperen CJ, Jakubowska A, Lubinski J, Jaworska K, Durda K, Mannermaa A, Kataja V, Kosma VM, Hartikainen JM, Bogdanova NV, Antonenkova NN, Dörk T, Kristensen VN, Anton-Culver H, Slager S, Toland AE, Edge S, Fostira F, Kang D, Yoo KY, Noh DY, Matsuo K, Ito H, Iwata H, Sueta A, Wu AH, Tseng CC, Van Den Berg D, Stram DO, Shu XO, Lu W, Gao YT, Cai H, Teo SH, Yip CH, Phuah SY, Cornes BK, Hartman M, Miao H, Lim WY, Sng JH, Muir K, Lophatananon A, Stewart-Brown S, Siriwanarangsan P, Shen CY, Hsiung CN, Wu PE, Ding SL, Sangrajrang S, Gaborieau V, Brennan P, McKay J, Blot WJ, Signorello LB, Cai Q, Zheng W, Deming-Halverson S, Shrubsole M, Long J, Simard J, Garcia-Closas M, Pharoah PDP, Chenevix-Trench G, Dunning AM, Benitez J, Easton DF. Large-scale genotyping identifies 41 new loci associated with breast cancer risk. Nat Genet 2013; 45:353-61, 361e1-2. [PMID: 23535729 PMCID: PMC3771688 DOI: 10.1038/ng.2563] [Citation(s) in RCA: 843] [Impact Index Per Article: 76.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2012] [Accepted: 01/30/2013] [Indexed: 12/14/2022]
Abstract
Breast cancer is the most common cancer among women. Common variants at 27 loci have been identified as associated with susceptibility to breast cancer, and these account for ∼9% of the familial risk of the disease. We report here a meta-analysis of 9 genome-wide association studies, including 10,052 breast cancer cases and 12,575 controls of European ancestry, from which we selected 29,807 SNPs for further genotyping. These SNPs were genotyped in 45,290 cases and 41,880 controls of European ancestry from 41 studies in the Breast Cancer Association Consortium (BCAC). The SNPs were genotyped as part of a collaborative genotyping experiment involving four consortia (Collaborative Oncological Gene-environment Study, COGS) and used a custom Illumina iSelect genotyping array, iCOGS, comprising more than 200,000 SNPs. We identified SNPs at 41 new breast cancer susceptibility loci at genome-wide significance (P < 5 × 10(-8)). Further analyses suggest that more than 1,000 additional loci are involved in breast cancer susceptibility.
Collapse
Affiliation(s)
- Kyriaki Michailidou
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
234
|
Li Q, Seo JH, Stranger B, McKenna A, Pe'er I, Laframboise T, Brown M, Tyekucheva S, Freedman ML. Integrative eQTL-based analyses reveal the biology of breast cancer risk loci. Cell 2013; 152:633-41. [PMID: 23374354 DOI: 10.1016/j.cell.2012.12.034] [Citation(s) in RCA: 251] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2012] [Revised: 10/20/2012] [Accepted: 12/20/2012] [Indexed: 01/16/2023]
Abstract
Germline determinants of gene expression in tumors are infrequently studied due to the complexity of transcript regulation caused by somatically acquired alterations. We performed expression quantitative trait locus (eQTL)-based analyses using the multi-level information provided in The Cancer Genome Atlas (TCGA). Of the factors we measured, cis-acting eQTLs accounted for 1.2% of the total variation of tumor gene expression, while somatic copy-number alteration and CpG methylation accounted for 7.3% and 3.3%, respectively. eQTL analyses of 15 previously reported breast cancer risk loci resulted in the discovery of three variants that are significantly associated with transcript levels (false discovery rate [FDR] < 0.1). Our trans-based analysis identified an additional three risk loci to act through ESR1, MYC, and KLF4. These findings provide a more comprehensive picture of gene expression determinants in breast cancer as well as insights into the underlying biology of breast cancer risk loci.
Collapse
Affiliation(s)
- Qiyuan Li
- Department of Medical Oncology, The Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
235
|
Krijger PHL, de Laat W. Identical cells with different 3D genomes; cause and consequences? Curr Opin Genet Dev 2013; 23:191-6. [PMID: 23415810 DOI: 10.1016/j.gde.2012.12.010] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Accepted: 12/20/2012] [Indexed: 10/27/2022]
Abstract
The mammalian genome is folded into topological domains, chromosomal units that probably serve to spatially accommodate enhancer-promoter interactions and control gene expression levels across cell populations. Longer-range contacts beyond topological domains are also formed, but only in subpopulations of cells. We propose a model (dog-on-a-lead model) to understand the principles behind and consequences of cell-specific remote DNA contacts and speculate that cell-specific genome topologies can cause variegated gene expression among otherwise identical cells.
Collapse
Affiliation(s)
- Peter H L Krijger
- Hubrecht Institute-KNAW & University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Urecht, The Netherlands
| | | |
Collapse
|
236
|
Analysis of genetic aberrations on chromosomal region 8q21–24 identifies E2F5 as an oncogene with copy number gain in prostate cancer. Med Oncol 2013; 30:465. [DOI: 10.1007/s12032-013-0465-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2012] [Accepted: 01/09/2013] [Indexed: 10/27/2022]
|
237
|
Shin H, Liu T, Duan X, Zhang Y, Liu XS. Computational methodology for ChIP-seq analysis. QUANTITATIVE BIOLOGY 2013; 1:54-70. [PMID: 25741452 DOI: 10.1007/s40484-013-0006-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Chromatin immunoprecipitation coupled with massive parallel sequencing (ChIP-seq) is a powerful technology to identify the genome-wide locations of DNA binding proteins such as transcription factors or modified histones. As more and more experimental laboratories are adopting ChIP-seq to unravel the transcriptional and epigenetic regulatory mechanisms, computational analyses of ChIP-seq also become increasingly comprehensive and sophisticated. In this article, we review current computational methodology for ChIP-seq analysis, recommend useful algorithms and workflows, and introduce quality control measures at different analytical steps. We also discuss how ChIP-seq could be integrated with other types of genomic assays, such as gene expression profiling and genome-wide association studies, to provide a more comprehensive view of gene regulatory mechanisms in important physiological and pathological processes.
Collapse
Affiliation(s)
- Hyunjin Shin
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute/Harvard School of Public Health, Boston, MA 02115, USA
| | - Tao Liu
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute/Harvard School of Public Health, Boston, MA 02115, USA
| | - Xikun Duan
- Department of Bioinformatics, School of Life Science and Technology, Tongji University, Shanghai 200092, China
| | - Yong Zhang
- Department of Bioinformatics, School of Life Science and Technology, Tongji University, Shanghai 200092, China
| | - X Shirley Liu
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute/Harvard School of Public Health, Boston, MA 02115, USA
| |
Collapse
|
238
|
Ney JT, Juhasz-Boess I, Gruenhage F, Graeber S, Bohle RM, Pfreundschuh M, Solomayer EF, Assmann G. Genetic polymorphism of the OPG gene associated with breast cancer. BMC Cancer 2013; 13:40. [PMID: 23369128 PMCID: PMC3563620 DOI: 10.1186/1471-2407-13-40] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Accepted: 01/22/2013] [Indexed: 12/20/2022] Open
Abstract
Background The receptor activator of NF-κB (RANK), its ligand (RANKL) and osteoprotegerin (OPG) have been reported to play a role in the pathophysiological bone turnover and in the pathogenesis of breast cancer. Based on this we investigated the role of single nucleotide polymorphisms (SNPs) within RANK, RANKL and OPG and their possible association to breast cancer risk. Methods Genomic DNA was obtained from Caucasian participants consisting of 307 female breast cancer patients and 396 gender-matched healthy controls. We studied seven SNPs in the genes of OPG (rs3102735, rs2073618), RANK (rs1805034, rs35211496) and RANKL (rs9533156, rs2277438, rs1054016) using TaqMan genotyping assays. Statistical analyses were performed using the χ2-tests for 2 x 2 and 2 x 3 tables. Results The allelic frequencies (OR: 1.508 CI: 1.127-2.018, p=0.006) and the genotype distribution (p=0.019) of the OPG SNP rs3102735 differed significantly between breast cancer patients and healthy controls. The minor allele C and the corresponding homo- and heterozygous genotypes are more common in breast cancer patients (minor allele C: 18.4% vs. 13.0%; genotype CC: 3.3% vs. 1.3%; genotype CT: 30.3% vs. 23.5%). No significantly changed risk was detected in the other investigated SNPs. Additional analysis showed significant differences when comparing patients with invasive vs. non-invasive tumors (OPG rs2073618) as well as in terms of tumor localization (RANK rs35211496) and body mass index (RANKL rs9533156 and rs1054016). Conclusions This is the first study reporting a significant association of the SNP rs3102735 (OPG) with the susceptibility to develop breast cancer in the Caucasian population.
Collapse
Affiliation(s)
- Jasmin Teresa Ney
- Gynecology, Obstetrics and Reproductive Medicine, University Medical School of Saarland, 66421, Homburg/Saar, Saarland, Germany.
| | | | | | | | | | | | | | | |
Collapse
|
239
|
Dai G, Guo Z, Yang X, Yu B, Li L. Association of 8q24 rs13281615A > G polymorphism with breast cancer risk: evidence from 40,762 cases and 50,380 controls. Mol Biol Rep 2013; 40:4065-73. [PMID: 23292077 DOI: 10.1007/s11033-012-2484-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Accepted: 12/21/2012] [Indexed: 01/15/2023]
Abstract
The association between a single nucleotide polymorphism rs13281615A > G located in the 8q24 and breast cancer risk is still controversial and ambiguous. Hence, we performed a more convincing and precise estimation of the relationship between 8q24 and breast cancer by meta-analyzing the currently available evidence from literature. PubMed, Ovid, Medline, and Web of Science databases were searched. A total of 10 publications containing 11 studies including 40,762 cases and 50,380 controls were identified. Crude odds ratio with 95 % confidence interval was used to assess the strength of association. We observed that the 8q24 rs13281615A > G polymorphism was significantly correlated with breast cancer risk when all studies were pooled into the meta analysis. In the stratified analysis by ethnicity, significantly increased risks were also found among Caucasians for all genetic models. For mixed ethnicities, significantly increased risks were found for all genetic models except for the allele contrast model. However, no significantly increased risk was found among Africans for all genetic models. Interestingly, when stratified by BRCA1 mutation carriers status, significantly decreased breast cancer risk was found for allele contrast model. But significantly increased breast cancer risk was found in the BRCA2 mutation carriers for all genetic models except for the recessive model. There was no evidence for significant association between 8q24 rs13281615A > G polymorphism and breast cancer risk in BRCA1 and BRCA2 positive cohort in all comparable models. In conclusion, this meta-analysis suggests that the 8q24 rs13281615A > G polymorphism is a low-penetrant risk factor for developing breast cancer but may not be in Africans.
Collapse
Affiliation(s)
- Guiping Dai
- Oncology Institute, The Fourth Affiliated Hospital of Soochow University, Wuxi, 214062, China
| | | | | | | | | |
Collapse
|
240
|
Koutros S, Beane Freeman LE, Lubin JH, Heltshe SL, Andreotti G, Barry KH, DellaValle CT, Hoppin JA, Sandler DP, Lynch CF, Blair A, Alavanja MCR. Risk of total and aggressive prostate cancer and pesticide use in the Agricultural Health Study. Am J Epidemiol 2013; 177:59-74. [PMID: 23171882 DOI: 10.1093/aje/kws225] [Citation(s) in RCA: 124] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Because pesticides may operate through different mechanisms, the authors studied the risk of prostate cancer associated with specific pesticides in the Agricultural Health Study (1993-2007). With 1,962 incident cases, including 919 aggressive prostate cancers among 54,412 applicators, this is the largest study to date. Rate ratios and 95% confidence intervals were calculated by using Poisson regression to evaluate lifetime use of 48 pesticides and prostate cancer incidence. Three organophosphate insecticides were significantly associated with aggressive prostate cancer: fonofos (rate ratio (RR) for the highest quartile of exposure (Q4) vs. nonexposed = 1.63, 95% confidence interval (CI): 1.22, 2.17; P(trend) < 0.001); malathion (RR for Q4 vs. nonexposed = 1.43, 95% CI: 1.08, 1.88; P(trend) = 0.04); and terbufos (RR for Q4 vs. nonexposed = 1.29, 95% CI: 1.02, 1.64; P(trend) = 0.03). The organochlorine insecticide aldrin was also associated with increased risk of aggressive prostate cancer (RR for Q4 vs. nonexposed = 1.49, 95% CI: 1.03, 2.18; P(trend) = 0.02). This analysis has overcome several limitations of previous studies with the inclusion of a large number of cases with relevant exposure and detailed information on use of specific pesticides at 2 points in time. Furthermore, this is the first time specific pesticides are implicated as risk factors for aggressive prostate cancer.
Collapse
Affiliation(s)
- Stella Koutros
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, 6120 Executive Boulevard, EPS 8115, MSC 7240, Rockville, MD 20852, USA.
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
241
|
Sandhu KS, Li G, Poh HM, Quek YLK, Sia YY, Peh SQ, Mulawadi FH, Lim J, Sikic M, Menghi F, Thalamuthu A, Sung WK, Ruan X, Fullwood MJ, Liu E, Csermely P, Ruan Y. Large-scale functional organization of long-range chromatin interaction networks. Cell Rep 2012; 2:1207-19. [PMID: 23103170 PMCID: PMC4181841 DOI: 10.1016/j.celrep.2012.09.022] [Citation(s) in RCA: 90] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2012] [Revised: 07/31/2012] [Accepted: 09/24/2012] [Indexed: 11/27/2022] Open
Abstract
Chromatin interactions play important roles in transcription regulation. To better understand the underlying evolutionary and functional constraints of these interactions, we implemented a systems approach to examine RNA polymerase-II-associated chromatin interactions in human cells. We found that 40% of the total genomic elements involved in chromatin interactions converged to a giant, scale-free-like, hierarchical network organized into chromatin communities. The communities were enriched in specific functions and were syntenic through evolution. Disease-associated SNPs from genome-wide association studies were enriched among the nodes with fewer interactions, implying their selection against deleterious interactions by limiting the total number of interactions, a model that we further reconciled using somatic and germline cancer mutation data. The hubs lacked disease-associated SNPs, constituted a nonrandomly interconnected core of key cellular functions, and exhibited lethality in mouse mutants, supporting an evolutionary selection that favored the nonrandom spatial clustering of the least-evolving key genomic domains against random genetic or transcriptional errors in the genome. Altogether, our analyses reveal a systems-level evolutionary framework that shapes functionally compartmentalized and error-tolerant transcriptional regulation of human genome in three dimensions.
Collapse
Affiliation(s)
- Kuljeet Singh Sandhu
- Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Knowledge City, Sector 81, Mohali 140306, India
| | - Guoliang Li
- Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672
| | - Huay Mei Poh
- Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672
| | - Yu Ling Kelly Quek
- Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St. Lucia 4072, Australia
| | - Yee Yen Sia
- Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672
| | - Su Qin Peh
- Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672
| | | | - Joanne Lim
- Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672
| | - Mile Sikic
- Bioinformatics Institute, 30 Biopolis Street, Singapore 138671
- Faculty of Electrical Engineering and Computing, University of Zagreb, Unska 3, HR 10000 Zagreb, Croatia
| | - Francesca Menghi
- Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672
| | | | - Wing Kin Sung
- Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672
- School of Computing, National University of Singapore, Singapore 117417
| | - Xiaoan Ruan
- Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672
| | - Melissa Jane Fullwood
- Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672
- A*STAR-Duke-NUS Neuroscience Research Partnership, 8 College Road, Singapore 169857
| | - Edison Liu
- Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - Peter Csermely
- Department of Medical Chemistry, School of Medicine, Semmelweis University, Tuzolto Street 37-47, Budapest 1094, Hungary
| | - Yijun Ruan
- Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| |
Collapse
|
242
|
Willard SS, Koochekpour S. Regulators of gene expression as biomarkers for prostate cancer. Am J Cancer Res 2012; 2:620-657. [PMID: 23226612 PMCID: PMC3512182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2012] [Accepted: 10/09/2012] [Indexed: 06/01/2023] Open
Abstract
Recent technological advancements in gene expression analysis have led to the discovery of a promising new group of prostate cancer (PCa) biomarkers that have the potential to influence diagnosis and the prediction of disease severity. The accumulation of deleterious changes in gene expression is a fundamental mechanism of prostate carcinogenesis. Aberrant gene expression can arise from changes in epigenetic regulation or mutation in the genome affecting either key regulatory elements or gene sequences themselves. At the epigenetic level, a myriad of abnormal histone modifications and changes in DNA methylation are found in PCa patients. In addition, many mutations in the genome have been associated with higher PCa risk. Finally, over- or underexpression of key genes involved in cell cycle regulation, apoptosis, cell adhesion and regulation of transcription has been observed. An interesting group of biomarkers are emerging from these studies which may prove more predictive than the standard prostate specific antigen (PSA) serum test. In this review, we discuss recent results in the field of gene expression analysis in PCa including the most promising biomarkers in the areas of epigenetics, genomics and the transcriptome, some of which are currently under investigation as clinical tests for early detection and better prognostic prediction of PCa.
Collapse
Affiliation(s)
- Stacey S Willard
- Departments of Cancer Genetics and Urology, Center for Genetics and Pharmacology, Roswell Park Cancer Institute Elm and Carlton Streets, Buffalo, NY, USA
| | | |
Collapse
|
243
|
Abstract
The discovery of numerous noncoding RNA (ncRNA) transcripts in species from yeast to mammals has dramatically altered our understanding of cell biology, especially the biology of diseases such as cancer. In humans, the identification of abundant long ncRNA (lncRNA) >200 bp has catalyzed their characterization as critical components of cancer biology. Recently, roles for lncRNAs as drivers of tumor suppressive and oncogenic functions have appeared in prevalent cancer types, such as breast and prostate cancer. In this review, we highlight the emerging impact of ncRNAs in cancer research, with a particular focus on the mechanisms and functions of lncRNAs.
Collapse
Affiliation(s)
- John R Prensner
- Michigan Center for Translational Pathology, Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | | |
Collapse
|
244
|
McEwan MV, Eccles MR, Horsfield JA. Cohesin is required for activation of MYC by estradiol. PLoS One 2012; 7:e49160. [PMID: 23145106 PMCID: PMC3493498 DOI: 10.1371/journal.pone.0049160] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2012] [Accepted: 10/09/2012] [Indexed: 12/13/2022] Open
Abstract
Cohesin is best known as a multi-subunit protein complex that holds together replicated sister chromatids from S phase until G2. Cohesin also has an important role in the regulation of gene expression. We previously demonstrated that the cohesin complex positively regulates expression of the oncogene MYC. Cell proliferation driven by MYC contributes to many cancers, including breast cancer. The MYC oncogene is estrogen-responsive and a transcriptional target of estrogen receptor alpha (ERα). Estrogen-induced cohesin binding sites coincide with ERα binding at the MYC locus, raising the possibility that cohesin and ERα combine actions to regulate MYC transcription. The objective of this study was to investigate a putative role for cohesin in estrogen induction of MYC expression. We found that siRNA-targeted depletion of a cohesin subunit, RAD21, decreased MYC expression in ER-positive (MCF7 and T47D) and ER-negative (MDA-MB-231) breast cancer cell lines. In addition, RAD21 depletion blocked estradiol-mediated activation of MYC in ER-positive cell lines, and decreased ERα binding to estrogen response elements (EREs) upstream of MYC, without affecting total ERα levels. Treatment of MCF7 cells with estradiol caused enrichment of RAD21 binding at upstream enhancers and at the P2 promoter of MYC. Enriched binding at all sites, except the P2 promoter, was dependent on ERα. Since RAD21 depletion did not affect transcription driven by an exogenous reporter construct containing a naked ERE, chromatin-based mechanisms are likely to be involved in cohesin-dependent MYC transcription. This study demonstrates that ERα activation of MYC can be modulated by cohesin. Together, these results demonstrate a novel role for cohesin in estrogen-mediated regulation of MYC and the first evidence that cohesin plays a role in ERα binding.
Collapse
Affiliation(s)
- Miranda V. McEwan
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Michael R. Eccles
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Julia A. Horsfield
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| |
Collapse
|
245
|
Sur IK, Hallikas O, Vähärautio A, Yan J, Turunen M, Enge M, Taipale M, Karhu A, Aaltonen LA, Taipale J. Mice lacking a Myc enhancer that includes human SNP rs6983267 are resistant to intestinal tumors. Science 2012; 338:1360-3. [PMID: 23118011 DOI: 10.1126/science.1228606] [Citation(s) in RCA: 190] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Multiple cancer-associated single-nucleotide polymorphisms (SNPs) have been mapped to conserved sequences within a 500-kilobase region upstream of the MYC oncogene on human chromosome 8q24. These SNPs may affect cancer development through altered regulation of MYC expression, but this hypothesis has been difficult to confirm. We generated mice deficient in Myc-335, a putative MYC regulatory element that contains rs6983267, a SNP accounting for more human cancer-related morbidity than any other genetic variant or mutation. In Myc-335 null mice, Myc transcripts were expressed in the intestinal crypts in a pattern similar to that in wild-type mice but at modestly reduced levels. The mutant mice displayed no overt phenotype but were markedly resistant to intestinal tumorigenesis induced by the APCmin mutation. These results establish that a cancer-associated SNP identified in human genome-wide association studies has a functional effect in vivo.
Collapse
Affiliation(s)
- Inderpreet Kaur Sur
- Science for Life Center, Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | | | | | | | | | | | | | | | | | | |
Collapse
|
246
|
Betts JA, French JD, Brown MA, Edwards SL. Long-range transcriptional regulation of breast cancer genes. Genes Chromosomes Cancer 2012; 52:113-25. [PMID: 23077082 DOI: 10.1002/gcc.22020] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2012] [Revised: 09/19/2012] [Accepted: 09/19/2012] [Indexed: 12/11/2022] Open
Abstract
Breast cancer is a major health problem and understanding the genetic basis of this disease is crucial for predicting risk and developing effective targeted therapeutics. Several breast cancer predisposing genes have been identified, but mutations in the coding regions of these genes only accounts for a small proportion of risk. Research now suggests that combinations of multiple non-coding changes in breast cancer susceptibility genes, which cause moderate alterations in gene expression, will be responsible for the remaining inherited risk. These non-coding changes will include variants in proximal and distal transcriptional and post-transcriptional regulatory elements and may affect the levels and function of trans-acting factors, including proteins and RNAs, which act on these elements. Somatic changes in such elements and factors have also been associated with breast cancer progression. With the recent advent of techniques allowing the detection of long-range DNA interactions spanning the human genome, it has become increasingly clear that long-range regulatory elements constitute an important mechanism for gene regulation. Recent studies have identified several such elements that are important for regulating genes involved in breast cancer, raising the possibility that defects in these sequences may contribute to breast cancer predisposition and progression. In this review, we discuss the emerging functions of cis-regulatory elements and a subset of trans-acting factors in breast tumorigenesis. We also discuss some recent progress in our understanding of how dysregulation in these transcriptional components may contribute to breast cancer, and the potential implications for molecular diagnosis, prognosis prediction, and the treatment of this disease.
Collapse
Affiliation(s)
- Joshua A Betts
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Queensland, Australia
| | | | | | | |
Collapse
|
247
|
Palstra RJ, Grosveld F. Transcription factor binding at enhancers: shaping a genomic regulatory landscape in flux. Front Genet 2012; 3:195. [PMID: 23060900 PMCID: PMC3460357 DOI: 10.3389/fgene.2012.00195] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2012] [Accepted: 09/12/2012] [Indexed: 12/26/2022] Open
Abstract
The mammalian genome is packed tightly in the nucleus of the cell. This packing is primarily facilitated by histone proteins and results in an ordered organization of the genome in chromosome territories that can be roughly divided in heterochromatic and euchromatic domains. On top of this organization several distinct gene regulatory elements on the same chromosome or other chromosomes are thought to dynamically communicate via chromatin looping. Advances in genome-wide technologies have revealed the existence of a plethora of these regulatory elements in various eukaryotic genomes. These regulatory elements are defined by particular in vitro assays as promoters, enhancers, insulators, and boundary elements. However, recent studies indicate that the in vivo distinction between these elements is often less strict. Regulatory elements are bound by a mixture of common and lineage-specific transcription factors which mediate the long-range interactions between these elements. Inappropriate modulation of the binding of these transcription factors can alter the interactions between regulatory elements, which in turn leads to aberrant gene expression with disease as an ultimate consequence. Here we discuss the bi-modal behavior of regulatory elements that act in cis (with a focus on enhancers), how their activity is modulated by transcription factor binding and the effect this has on gene regulation.
Collapse
Affiliation(s)
- Robert-Jan Palstra
- Department of Cell Biology, Erasmus MC University Medical Center Rotterdam, Netherlands
| | | |
Collapse
|
248
|
El-Kasti MM, Wells T, Carter DA. A novel long-range enhancer regulates postnatal expression of Zeb2: implications for Mowat-Wilson syndrome phenotypes. Hum Mol Genet 2012; 21:5429-42. [PMID: 23001561 DOI: 10.1093/hmg/dds389] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The zinc-finger, E-box-binding homeobox-2 (Zeb2) gene encodes a SMAD-interacting transcription factor that has diverse roles in development and disease. Mutations at the hZeb2 locus cause Mowat-Wilson syndrome (MWS), a genetic disorder that is associated with mental retardation and other, case- and sex-dependent clinical features. Recent studies have detailed microRNA-mediated control of Zeb2, but little is known about the genomic context of this gene or of enhancer sequences that may direct its diverse functions. Here, we describe a novel transgenic rodent model in which Zeb2 regulatory sequence has been disrupted, resulting in a postnatal developmental phenotype that is autosomal dominant. The phenotype exhibits a genotype-by-sex interaction and manifests primarily as an acute attenuation of postnatal kidney development in males. Other aspects of embryonic and neonatal development, including neuronal, are unaffected. The transgene insertion site is associated with a 12 kb deletion, 1.2 Mb upstream of Zeb2, within a 4.1 Mb gene desert. A conserved sequence, derived from the deleted region, enhanced Zeb2 promoter activity in transcription assays. Tissue and temporal restriction of this enhancer activity may involve postnatal changes in proteins that bind this sequence. A control human/mouse VISTA enhancer (62 kb upstream of Zeb2) also up-regulated the Zeb2 promoter, providing evidence of a string of conserved distal enhancers. The phenotype arising from deletion of one copy of the extreme long-range enhancer indicates a critical role for this enhancer at one developmental stage. Haploinsufficiency of Zeb2 in this developmental context reflects inheritance of MWS and may underlie some sex-dependent, non-neural characteristics of this human inherited disorder.
Collapse
Affiliation(s)
- Muna M El-Kasti
- Nuffield Department of Obstetrics and Gynaecology, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | | | | |
Collapse
|
249
|
Naumova N, Smith EM, Zhan Y, Dekker J. Analysis of long-range chromatin interactions using Chromosome Conformation Capture. Methods 2012; 58:192-203. [PMID: 22903059 DOI: 10.1016/j.ymeth.2012.07.022] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2012] [Accepted: 07/18/2012] [Indexed: 10/28/2022] Open
Abstract
Chromosome Conformation Capture, or 3C, is a pioneering method for investigating the three-dimensional structure of chromatin. 3C is used to analyze long-range looping interactions between any pair of selected genomic loci. Most 3C studies focus on defined genomic regions of interest that can be up to several hundred Kb in size. The method has become widely adopted and has been modified to increase throughput to allow unbiased genome-wide analysis. These large-scale adaptations are presented in other articles in this issue of Methods. Here we describe the 3C procedure in detail, including the appropriate use of the technology, the experimental set-up, an optimized protocol and troubleshooting guide, and considerations for data analysis. The protocol described here contains previously unpublished improvements, which save time and reduce labor. We pay special attention to primer design, appropriate controls and data analysis. We include notes and discussion based on our extensive experience to help researchers understand the principles of 3C-based techniques and to avoid common pitfalls and mistakes. This paper represents a complete resource and detailed guide for anyone who desires to perform 3C.
Collapse
Affiliation(s)
- Natalia Naumova
- Programs in Systems Biology and Gene Function and Expression, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA 01605-0103, USA
| | | | | | | |
Collapse
|
250
|
Thean LF, Li HH, Teo YY, Koh WP, Yuan JM, Teoh ML, Koh PK, Tang CL, Cheah PY. Association of Caucasian-identified variants with colorectal cancer risk in Singapore Chinese. PLoS One 2012; 7:e42407. [PMID: 22879968 PMCID: PMC3411754 DOI: 10.1371/journal.pone.0042407] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2012] [Accepted: 07/04/2012] [Indexed: 01/09/2023] Open
Abstract
Background Genome-wide association studies (GWAS) in Caucasians have identified fourteen index single nucleotide polymorphisms (iSNPs) that influence colorectal cancer (CRC) risk. Methods We investigated the role of eleven iSNPs or surrogate SNPs (sSNPs), in high linkage disequilibrium (LD, r2≥0.8) and within 100 kb vicinity of iSNPs, in 2,000 age- and gender-matched Singapore Chinese (SCH) cases and controls. Results Only iSNP rs6983267 at 8q24.21 and sSNPs rs6695584, rs11986063, rs3087967, rs2059254, and rs7226855 at 1q41, 8q23.3, 11q23.1, 16q22.1 and 18q21.1 respectively showed evidence of association with CRC risk, with odds ratios (OR) ranging from 1.13 to 1.40. sSNP rs827401 at 10p14 was associated with rectal cancer risk (OR = 0.74, 95% CI 0.63–0.88) but not disease prognosis (OR = 0.91, 95% CI 0.69–1.20). Interestingly, sSNP rs3087967 at 11q23.1 was associated with CRC risk in men (OR = 1.34, 95% CI 1.14–1.58) but not women (OR = 1.07, 95% CI: 0.88–1.29), suggesting a gender-specific role. Half of the Caucasian-identified variants, including the recently fine-mapped BMP pathway loci, BMP4, GREM1, BMP2 and LAMA 5, did not show any evidence for association with CRC in SCH (OR ∼1; p-value >0.1). Comparing the results of this study with that of the Northern and Hong Kong Chinese, only variants at chromosomes 8q24.21, 10p14, 11q23.1 and 18q21.1 were replicated in at least two out of the three Chinese studies. Conclusions The contrasting results between Caucasians and Chinese could be due to different LD patterns and allelic frequencies or genetic heterogeneity. The results suggest that additional common variants contributing to CRC predisposition remained to be identified.
Collapse
Affiliation(s)
- Lai Fun Thean
- Department of Colorectal Surgery, Singapore General Hospital, Singapore
| | - Hui Hua Li
- Department of Clinical Research, Singapore General Hospital, Singapore, Singapore
| | - Yik Ying Teo
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
| | - Woon-Puay Koh
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
| | - Jian-Min Yuan
- University of Pittsburgh Cancer Institute, and Department of Epidemiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Mei Lin Teoh
- Health Screening Unit, Singapore General Hospital, Singapore Singapore
| | - Poh Koon Koh
- Department of Colorectal Surgery, Singapore General Hospital, Singapore
| | - Choong Leong Tang
- Department of Colorectal Surgery, Singapore General Hospital, Singapore
| | - Peh Yean Cheah
- Department of Colorectal Surgery, Singapore General Hospital, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
- Duke-National University of Singapore, Graduate Medical School, National University of Singapore, Singapore
- * E-mail:
| |
Collapse
|