Transcriptome-wide association study reveals candidate causal genes for lung cancer

Research output: Contribution to journalArticle

Abstract

We have recently completed the largest GWAS on lung cancer including 29,266 cases and 56,450 controls of European descent. The goal of our study has been to integrate the complete GWAS results with a large-scale expression quantitative trait loci (eQTL) mapping study in human lung tissues (n = 1,038) to identify candidate causal genes for lung cancer. We performed transcriptome-wide association study (TWAS) for lung cancer overall, by histology (adenocarcinoma, squamous cell carcinoma and small cell lung cancer) and smoking subgroups (never- and ever-smokers). We performed replication analysis using lung data from the Genotype-Tissue Expression (GTEx) project. DNA damage assays were performed in human lung fibroblasts for selected TWAS genes. As expected, the main TWAS signal for all histological subtypes and ever-smokers was on chromosome 15q25. The gene most strongly associated with lung cancer at this locus using the TWAS approach was IREB2 (pTWAS = 1.09E−99), where lower predicted expression increased lung cancer risk. A new lung adenocarcinoma susceptibility locus was revealed on 9p13.3 and associated with higher predicted expression of AQP3 (pTWAS = 3.72E−6). Among the 45 previously described lung cancer GWAS loci, we mapped candidate target gene for 17 of them. The association AQP3-adenocarcinoma on 9p13.3 was replicated using GTEx (pTWAS = 6.55E−5). Consistent with the effect of risk alleles on gene expression levels, IREB2 knockdown and AQP3 overproduction promote endogenous DNA damage. These findings indicate genes whose expression in lung tissue directly influences lung cancer risk.

Details

Authors
  • Yohan Bossé
  • Zhonglin Li
  • Jun Xia
  • Venkata Manem
  • Robert Carreras-Torres
  • Aurélie Gabriel
  • Nathalie Gaudreault
  • Demetrius Albanes
  • Melinda C. Aldrich
  • Angeline Andrew
  • Susanne Arnold
  • Heike Bickeböller
  • Stig E. Bojesen
  • Paul Brennan
  • Neil Caporaso
  • Chu Chen
  • David C. Christiani
  • John K. Field
  • Gary Goodman
  • Kjell Grankvist
  • Richard Houlston
  • Mattias Johansson
  • Mikael Johansson
  • Lambertus A. Kiemeney
  • Stephen Lam
  • Maria T. Landi
  • Philip Lazarus
  • Loic Le Marchand
  • Geoffrey Liu
  • Gadi Rennert
  • Angela Risch
  • Susan M. Rosenberg
  • Matthew B. Schabath
  • Sanjay Shete
  • Zhuoyi Song
  • Victoria L. Stevens
  • Adonina Tardon
  • H. Erich Wichmann
  • Penella Woll
  • Shan Zienolddiny
  • Ma'en Obeidat
  • Wim Timens
  • Rayjean J. Hung
  • Philippe Joubert
  • Christopher I. Amos
  • James D. McKay
Organisations
External organisations
  • Institut universitaire de cardiologie et de pneumologie de Québec
  • Laval University
  • Baylor College of Medicine
  • International Agency for Research on Cancer, World Health Organization
  • Dartmouth-Hitchcock Medical Center
  • University Medical Center Göttingen
  • Copenhagen University Hospital
  • Fred Hutchinson Cancer Research Center
  • Harvard University
  • University of Liverpool
  • Swedish Medical Center
  • Umeå University
  • Institute of Cancer Research London
  • Radboud University Medical Center
  • British Columbia Cancer Agency
  • Washington State University
  • University of Hawaii Cancer Center
  • Princess Margaret Hospital University of Toronto
  • University of Salzburg
  • H. Lee Moffitt Cancer Center & Research Institute
  • University of Texas
  • American Cancer Society
  • University of Oviedo
  • Helmholtz Zentrum München
  • University of Sheffield
  • National Institute of Occupational Health, Norway
  • University of British Columbia
  • University Medical Center Groningen
  • Sinai Health System
  • Vanderbilt University Medical Center
  • University of Kentucky
  • National Cancer Institute, NCI
  • Carmel Medical Center
  • St. Paul’s Hospital
Research areas and keywords

Subject classification (UKÄ) – MANDATORY

  • Medical Genetics
  • Cancer and Oncology

Keywords

  • GWAS, lung cancer, lung eQTL, transcriptome-wide association study
Original languageEnglish
Pages (from-to)1862-1878
Number of pages17
JournalInternational Journal of Cancer
Volume146
Issue number7
Early online date2019 Nov 6
Publication statusE-pub ahead of print - 2019 Nov 6
Publication categoryResearch
Peer-reviewedYes