Literature DB >> 25371445

Association of prostate cancer risk variants with gene expression in normal and tumor tissue.

Kathryn L Penney1, Jennifer A Sinnott2, Svitlana Tyekucheva3, Travis Gerke4, Irene M Shui4, Peter Kraft5, Howard D Sesso6, Matthew L Freedman7, Massimo Loda8, Lorelei A Mucci9, Meir J Stampfer10.   

Abstract

BACKGROUND: Numerous germline genetic variants are associated with prostate cancer risk, but their biologic role is not well understood. One possibility is that these variants influence gene expression in prostate tissue. We therefore examined the association of prostate cancer risk variants with the expression of genes nearby and genome-wide.
METHODS: We generated mRNA expression data for 20,254 genes with the Affymetrix GeneChip Human Gene 1.0 ST microarray from normal prostate (N = 160) and prostate tumor (N = 264) tissue from participants of the Physicians' Health Study and Health Professionals Follow-up Study. With linear models, we tested the association of 39 risk variants with nearby genes and all genes, and the association of each variant with canonical pathways using a global test.
RESULTS: In addition to confirming previously reported associations, we detected several new significant (P < 0.05) associations of variants with the expression of nearby genes including C2orf43, ITGA6, MLPH, CHMP2B, BMPR1B, and MTL5. Genome-wide, five genes (MSMB, NUDT11, RBPMS2, NEFM, and KLHL33) were significantly associated after accounting for multiple comparisons for each SNP (P < 2.5 × 10(-6)). Many more genes had an FDR <10%, including SRD5A1 and PSCA, and we observed significant associations with pathways in tumor tissue.
CONCLUSIONS: The risk variants were associated with several genes, including promising prostate cancer candidates and lipid metabolism pathways, suggesting mechanisms for their impact on disease. These genes should be further explored in biologic and epidemiologic studies. IMPACT: Determining the biologic role of these variants can lead to improved understanding of prostate cancer etiology and identify new targets for chemoprevention. ©2014 American Association for Cancer Research.

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Year:  2014        PMID： 25371445      PMCID： PMC4294966          DOI： 10.1158/1055-9965.EPI-14-0694-T

Source DB:  PubMed          Journal:  Cancer Epidemiol Biomarkers Prev        ISSN： 1055-9965            Impact factor:   4.254


  34 in total

1.  Genetic and functional analyses implicate the NUDT11, HNF1B, and SLC22A3 genes in prostate cancer pathogenesis.

Authors:  Chiara Grisanzio; Lillian Werner; David Takeda; Bisola C Awoyemi; Mark M Pomerantz; Hiroki Yamada; Prasanna Sooriakumaran; Brian D Robinson; Robert Leung; Anna C Schinzel; Ian Mills; Helen Ross-Adams; David E Neal; Masahito Kido; Toshihiro Yamamoto; Gillian Petrozziello; Edward C Stack; Rosina Lis; Philip W Kantoff; Massimo Loda; Oliver Sartor; Shin Egawa; Ashutosh K Tewari; William C Hahn; Matthew L Freedman
Journal:  Proc Natl Acad Sci U S A       Date:  2012-06-22       Impact factor: 11.205

Review 2.  Cholesterol and prostate cancer.

Authors:  Kristine Pelton; Michael R Freeman; Keith R Solomon
Journal:  Curr Opin Pharmacol       Date:  2012-07-21       Impact factor: 5.547

3.  Genome-wide association study of prostate cancer identifies a second risk locus at 8q24.

Authors:  Meredith Yeager; Nick Orr; Richard B Hayes; Kevin B Jacobs; Peter Kraft; Sholom Wacholder; Mark J Minichiello; Paul Fearnhead; Kai Yu; Nilanjan Chatterjee; Zhaoming Wang; Robert Welch; Brian J Staats; Eugenia E Calle; Heather Spencer Feigelson; Michael J Thun; Carmen Rodriguez; Demetrius Albanes; Jarmo Virtamo; Stephanie Weinstein; Fredrick R Schumacher; Edward Giovannucci; Walter C Willett; Geraldine Cancel-Tassin; Olivier Cussenot; Antoine Valeri; Gerald L Andriole; Edward P Gelmann; Margaret Tucker; Daniela S Gerhard; Joseph F Fraumeni; Robert Hoover; David J Hunter; Stephen J Chanock; Gilles Thomas
Journal:  Nat Genet       Date:  2007-04-01       Impact factor: 38.330

4.  An expressed retrogene of the master embryonic stem cell gene POU5F1 is associated with prostate cancer susceptibility.

Authors:  Joan P Breyer; Daniel C Dorset; Travis A Clark; Kevin M Bradley; Tiina A Wahlfors; Kate M McReynolds; William H Maynard; Sam S Chang; Michael S Cookson; Joseph A Smith; Johanna Schleutker; William D Dupont; Jeffrey R Smith
Journal:  Am J Hum Genet       Date:  2014-02-27       Impact factor: 11.025

5.  Analysis of the 10q11 cancer risk locus implicates MSMB and NCOA4 in human prostate tumorigenesis.

Authors:  Mark M Pomerantz; Yashaswi Shrestha; Richard J Flavin; Meredith M Regan; Kathryn L Penney; Lorelei A Mucci; Meir J Stampfer; David J Hunter; Stephen J Chanock; Eric J Schafer; Jennifer A Chan; Josep Tabernero; José Baselga; Andrea L Richardson; Massimo Loda; William K Oh; Philip W Kantoff; William C Hahn; Matthew L Freedman
Journal:  PLoS Genet       Date:  2010-11-11       Impact factor: 5.917

Review 6.  The fat side of prostate cancer.

Authors:  Giorgia Zadra; Cornelia Photopoulos; Massimo Loda
Journal:  Biochim Biophys Acta       Date:  2013-04-02

7.  Identification, replication, and functional fine-mapping of expression quantitative trait loci in primary human liver tissue.

Authors:  Federico Innocenti; Gregory M Cooper; Ian B Stanaway; Eric R Gamazon; Joshua D Smith; Snezana Mirkov; Jacqueline Ramirez; Wanqing Liu; Yvonne S Lin; Cliona Moloney; Shelly Force Aldred; Nathan D Trinklein; Erin Schuetz; Deborah A Nickerson; Ken E Thummel; Mark J Rieder; Allan E Rettie; Mark J Ratain; Nancy J Cox; Christopher D Brown
Journal:  PLoS Genet       Date:  2011-05-26       Impact factor: 5.917

8.  Identification of a new prostate cancer susceptibility locus on chromosome 8q24.

Authors:  Meredith Yeager; Nilanjan Chatterjee; Julia Ciampa; Kevin B Jacobs; Jesus Gonzalez-Bosquet; Richard B Hayes; Peter Kraft; Sholom Wacholder; Nick Orr; Sonja Berndt; Kai Yu; Amy Hutchinson; Zhaoming Wang; Laufey Amundadottir; Heather Spencer Feigelson; Michael J Thun; W Ryan Diver; Demetrius Albanes; Jarmo Virtamo; Stephanie Weinstein; Fredrick R Schumacher; Geraldine Cancel-Tassin; Olivier Cussenot; Antoine Valeri; Gerald L Andriole; E David Crawford; Christopher A Haiman; Brian Henderson; Laurence Kolonel; Loic Le Marchand; Afshan Siddiq; Elio Riboli; Timothy J Key; Rudolf Kaaks; William Isaacs; Sarah Isaacs; Kathleen E Wiley; Henrik Gronberg; Fredrik Wiklund; Pär Stattin; Jianfeng Xu; S Lilly Zheng; Jielin Sun; Lars J Vatten; Kristian Hveem; Merethe Kumle; Margaret Tucker; Daniela S Gerhard; Robert N Hoover; Joseph F Fraumeni; David J Hunter; Gilles Thomas; Stephen J Chanock
Journal:  Nat Genet       Date:  2009-09-20       Impact factor: 38.330

9.  Identification of 23 new prostate cancer susceptibility loci using the iCOGS custom genotyping array.

Authors:  Rosalind A Eeles; Ali Amin Al Olama; Sara Benlloch; Edward J Saunders; Daniel A Leongamornlert; Malgorzata Tymrakiewicz; Maya Ghoussaini; Craig Luccarini; Joe Dennis; Sarah Jugurnauth-Little; Tokhir Dadaev; David E Neal; Freddie C Hamdy; Jenny L Donovan; Ken Muir; Graham G Giles; Gianluca Severi; Fredrik Wiklund; Henrik Gronberg; Christopher A Haiman; Fredrick Schumacher; Brian E Henderson; Loic Le Marchand; Sara Lindstrom; Peter Kraft; David J Hunter; Susan Gapstur; Stephen J Chanock; Sonja I Berndt; Demetrius Albanes; Gerald Andriole; Johanna Schleutker; Maren Weischer; Federico Canzian; Elio Riboli; Tim J Key; Ruth C Travis; Daniele Campa; Sue A Ingles; Esther M John; Richard B Hayes; Paul D P Pharoah; Nora Pashayan; Kay-Tee Khaw; Janet L Stanford; Elaine A Ostrander; Lisa B Signorello; Stephen N Thibodeau; Dan Schaid; Christiane Maier; Walther Vogel; Adam S Kibel; Cezary Cybulski; Jan Lubinski; Lisa Cannon-Albright; Hermann Brenner; Jong Y Park; Radka Kaneva; Jyotsna Batra; Amanda B Spurdle; Judith A Clements; Manuel R Teixeira; Ed Dicks; Andrew Lee; Alison M Dunning; Caroline Baynes; Don Conroy; Melanie J Maranian; Shahana Ahmed; Koveela Govindasami; Michelle Guy; Rosemary A Wilkinson; Emma J Sawyer; Angela Morgan; David P Dearnaley; Alan Horwich; Robert A Huddart; Vincent S Khoo; Christopher C Parker; Nicholas J Van As; Christopher J Woodhouse; Alan Thompson; Tim Dudderidge; Chris Ogden; Colin S Cooper; Artitaya Lophatananon; Angela Cox; Melissa C Southey; John L Hopper; Dallas R English; Markus Aly; Jan Adolfsson; Jiangfeng Xu; Siqun L Zheng; Meredith Yeager; Rudolf Kaaks; W Ryan Diver; Mia M Gaudet; Mariana C Stern; Roman Corral; Amit D Joshi; Ahva Shahabi; Tiina Wahlfors; Teuvo L J Tammela; Anssi Auvinen; Jarmo Virtamo; Peter Klarskov; Børge G Nordestgaard; M Andreas Røder; Sune F Nielsen; Stig E Bojesen; Afshan Siddiq; Liesel M Fitzgerald; Suzanne Kolb; Erika M Kwon; Danielle M Karyadi; William J Blot; Wei Zheng; Qiuyin Cai; Shannon K McDonnell; Antje E Rinckleb; Bettina Drake; Graham Colditz; Dominika Wokolorczyk; Robert A Stephenson; Craig Teerlink; Heiko Muller; Dietrich Rothenbacher; Thomas A Sellers; Hui-Yi Lin; Chavdar Slavov; Vanio Mitev; Felicity Lose; Srilakshmi Srinivasan; Sofia Maia; Paula Paulo; Ethan Lange; Kathleen A Cooney; Antonis C Antoniou; Daniel Vincent; François Bacot; Daniel C Tessier; Zsofia Kote-Jarai; Douglas F Easton
Journal:  Nat Genet       Date:  2013-04       Impact factor: 38.330

10.  Comprehensive functional annotation of 77 prostate cancer risk loci.

Authors:  Dennis J Hazelett; Suhn Kyong Rhie; Malaina Gaddis; Chunli Yan; Daniel L Lakeland; Simon G Coetzee; Brian E Henderson; Houtan Noushmehr; Wendy Cozen; Zsofia Kote-Jarai; Rosalind A Eeles; Douglas F Easton; Christopher A Haiman; Wange Lu; Peggy J Farnham; Gerhard A Coetzee
Journal:  PLoS Genet       Date:  2014-01-30       Impact factor: 5.917
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  58 in total

1.  Molecular differences in transition zone and peripheral zone prostate tumors.

Authors:  Jennifer A Sinnott; Jennifer R Rider; Jessica Carlsson; Travis Gerke; Svitlana Tyekucheva; Kathryn L Penney; Howard D Sesso; Massimo Loda; Katja Fall; Meir J Stampfer; Lorelei A Mucci; Yudi Pawitan; Sven-Olof Andersson; Ove Andrén
Journal:  Carcinogenesis       Date:  2015-04-13       Impact factor: 4.944

2.  Identification of Novel Susceptibility Loci and Genes for Prostate Cancer Risk: A Transcriptome-Wide Association Study in Over 140,000 European Descendants.

Authors:  Lang Wu; Jifeng Wang; Qiuyin Cai; Taylor B Cavazos; Nima C Emami; Jirong Long; Xiao-Ou Shu; Yingchang Lu; Xingyi Guo; Joshua A Bauer; Bogdan Pasaniuc; Kathryn L Penney; Matthew L Freedman; Zsofia Kote-Jarai; John S Witte; Christopher A Haiman; Rosalind A Eeles; Wei Zheng
Journal:  Cancer Res       Date:  2019-05-17       Impact factor: 12.701

3.  Gene expression profiling of prostate tissue identifies chromatin regulation as a potential link between obesity and lethal prostate cancer.

Authors:  Ericka M Ebot; Travis Gerke; David P Labbé; Jennifer A Sinnott; Giorgia Zadra; Jennifer R Rider; Svitlana Tyekucheva; Kathryn M Wilson; Rachel S Kelly; Irene M Shui; Massimo Loda; Philip W Kantoff; Stephen Finn; Matthew G Vander Heiden; Myles Brown; Edward L Giovannucci; Lorelei A Mucci
Journal:  Cancer       Date:  2017-07-12       Impact factor: 6.860

4.  epiTAD: a web application for visualizing chromosome conformation capture data in the context of genetic epidemiology.

Authors:  Jordan H Creed; Garrick Aden-Buie; Alvaro N Monteiro; Travis A Gerke
Journal:  Bioinformatics       Date:  2019-11-01       Impact factor: 6.937

5.  A large multiethnic genome-wide association study of prostate cancer identifies novel risk variants and substantial ethnic differences.

Authors:  Thomas J Hoffmann; Stephen K Van Den Eeden; Lori C Sakoda; Eric Jorgenson; Laurel A Habel; Rebecca E Graff; Michael N Passarelli; Clinton L Cario; Nima C Emami; Chun R Chao; Nirupa R Ghai; Jun Shan; Dilrini K Ranatunga; Charles P Quesenberry; David Aaronson; Joseph Presti; Zhaoming Wang; Sonja I Berndt; Stephen J Chanock; Shannon K McDonnell; Amy J French; Daniel J Schaid; Stephen N Thibodeau; Qiyuan Li; Matthew L Freedman; Kathryn L Penney; Lorelei A Mucci; Christopher A Haiman; Brian E Henderson; Daniela Seminara; Mark N Kvale; Pui-Yan Kwok; Catherine Schaefer; Neil Risch; John S Witte
Journal:  Cancer Discov       Date:  2015-06-01       Impact factor: 39.397

6.  MYC Overexpression at the Protein and mRNA Level and Cancer Outcomes among Men Treated with Radical Prostatectomy for Prostate Cancer.

Authors:  Andreas Pettersson; Travis Gerke; Kathryn L Penney; Rosina T Lis; Edward C Stack; Nelma Pértega-Gomes; Giorgia Zadra; Svitlana Tyekucheva; Edward L Giovannucci; Lorelei A Mucci; Massimo Loda
Journal:  Cancer Epidemiol Biomarkers Prev       Date:  2017-11-15       Impact factor: 4.254

7.  Prostate cancer risk SNP rs10993994 is a trans-eQTL for SNHG11 mediated through MSMB.

Authors:  Mesude Bicak; Xing Wang; Xiaoni Gao; Xing Xu; Riina-Minna Väänänen; Pekka Taimen; Hans Lilja; Kim Pettersson; Robert J Klein
Journal:  Hum Mol Genet       Date:  2020-06-27       Impact factor: 6.150

8.  Prognostic Utility of a New mRNA Expression Signature of Gleason Score.

Authors:  Jennifer A Sinnott; Sam F Peisch; Svitlana Tyekucheva; Travis Gerke; Rosina Lis; Jennifer R Rider; Michelangelo Fiorentino; Meir J Stampfer; Lorelei A Mucci; Massimo Loda; Kathryn L Penney
Journal:  Clin Cancer Res       Date:  2016-09-23       Impact factor: 12.531

9.  Gene regulatory mechanisms underpinning prostate cancer susceptibility.

Authors:  Thomas Whitington; Ping Gao; Wei Song; Helen Ross-Adams; Alastair D Lamb; Yuehong Yang; Ilaria Svezia; Daniel Klevebring; Ian G Mills; Robert Karlsson; Silvia Halim; Mark J Dunning; Lars Egevad; Anne Y Warren; David E Neal; Henrik Grönberg; Johan Lindberg; Gong-Hong Wei; Fredrik Wiklund
Journal:  Nat Genet       Date:  2016-03-07       Impact factor: 38.330

10.  Low Expression of the Androgen-Induced Tumor Suppressor Gene PLZF and Lethal Prostate Cancer.

Authors:  Lorelei A Mucci; Philip W Kantoff; Konrad H Stopsack; Travis Gerke; Svitlana Tyekucheva; Ying Z Mazzu; Gwo-Shu Mary Lee; Goutam Chakraborty; Wassim Abida
Journal:  Cancer Epidemiol Biomarkers Prev       Date:  2019-01-02       Impact factor: 4.254
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