High-throughput characterization of functional variants highlights heterogeneity and polygenicity underlying lung cancer susceptibility
Erping Long 1, Harsh Patel 2, Alyxandra
Golden 2, Michelle Antony 2, Jinhu Yin 2, Karen Funderburk 2, James Feng 2, Lei
Song 2, Jason W Hoskins 2, Laufey T Amundadottir 2, Rayjean J Hung 3,
Christopher I Amos 4, Jianxin Shi 2, Nathaniel Rothman 2, Qing Lan 2;
International Lung Cancer Consortium; Jiyeon Choi 5
Am J Hum Genet. 2024 Jun
17:S0002-9297(24)00184-8. doi: 10.1016/j.ajhg.2024.05.021.
PMID: 38906146
Abstract
Genome-wide association studies (GWASs)
have identified numerous lung cancer risk-associated loci. However, decoding
molecular mechanisms of these associations is challenging since most of these
genetic variants are non-protein-coding with unknown function. Here, we
implemented massively parallel reporter assays (MPRAs) to simultaneously
measure the allelic transcriptional activity of risk-associated variants. We
tested 2,245 variants at 42 loci from 3 recent GWASs in East Asian and European
populations in the context of two major lung cancer histological types and
exposure to benzo(a)pyrene. This MPRA approach identified one or more variants
(median 11 variants) with significant effects on transcriptional activity at
88% of GWAS loci. Multimodal integration of lung-specific epigenomic data
demonstrated that 63% of the loci harbored multiple potentially functional
variants in linkage disequilibrium. While 22% of the significant variants
showed allelic effects in both A549 (adenocarcinoma) and H520 (squamous cell
carcinoma) cell lines, a subset of the functional variants displayed a
significant cell-type interaction. Transcription factor analyses nominated
potential regulators of the functional variants, including those with
cell-type-specific expression and those predicted to bind multiple potentially
functional variants across the GWAS loci. Linking functional variants to target
genes based on four complementary approaches identified candidate
susceptibility genes, including those affecting lung cancer cell growth. CRISPR
interference of the top functional variant at 20q13.33 validated
variant-to-gene connections, including RTEL1, SOX18, and ARFRP1. Our data
provide a comprehensive functional analysis of lung cancer GWAS loci and help
elucidate the molecular basis of heterogeneity and polygenicity underlying lung
cancer susceptibility.