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

Yohan Bossé1,2, Zhonglin Li1, Jun Xia3

  • 1Institut universitaire de cardiologie et de pneumologie de Québec, Université Laval, Quebec City, Canada.

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|November 8, 2019
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Summary

This study identifies key genes, IREB2 and AQP3, influencing lung cancer risk by linking genetic variations to gene expression. Lower IREB2 expression and higher AQP3 expression increase lung cancer susceptibility.

Keywords:
GWASlung cancerlung eQTLtranscriptome-wide association study

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Area of Science:

  • Genomics
  • Cancer Research
  • Molecular Biology

Background:

  • Genome-Wide Association Studies (GWAS) have identified numerous genetic loci associated with lung cancer risk.
  • Integrating GWAS with expression quantitative trait loci (eQTL) data can help identify causal genes underlying these associations.

Purpose of the Study:

  • To identify candidate causal genes for lung cancer by integrating GWAS results with large-scale eQTL mapping.
  • To perform transcriptome-wide association studies (TWAS) for lung cancer across different subtypes and smoking behaviors.

Main Methods:

  • Conducted the largest GWAS on lung cancer to date (29,266 cases, 56,450 controls).
  • Performed TWAS integrating GWAS data with lung tissue eQTL data (n=1,038).
  • Utilized Genotype-Tissue Expression (GTEx) data for replication and performed DNA damage assays.

Main Results:

  • Identified a strong TWAS signal for IREB2 on chromosome 15q25, where lower predicted expression increases lung cancer risk.
  • Discovered a novel lung adenocarcinoma locus on 9p13.3 associated with AQP3, where higher predicted expression increases risk.
  • Mapped candidate target genes for 17 of 45 previously described lung cancer GWAS loci; AQP3-adenocarcinoma association was replicated.

Conclusions:

  • Gene expression levels in lung tissue directly influence lung cancer risk.
  • IREB2 and AQP3 are identified as key candidate causal genes for lung cancer.
  • Functional assays showed that altered expression of IREB2 and AQP3 impacts DNA damage, supporting their role in lung carcinogenesis.