Abstract 3532: Post-GWAS in lung cancer: From transcriptome-wide association to the DNA damageome by Integrative functional screens
Authors: Xia Jun , Song Zhuoyi , Amos Chris 
Published: September 2020

We recently finished the largest transcriptome-wide association study (TWAS) analysis of the lung cancer genome-wide association studies (GWAS)-nominated loci, which revealed 18 new candidate causal genes for lung cancer. The recent discovery of the DNA damageome proteins (DDPs) predicts that many GWAS/TWAS genes are driving cancer by DNA damage-promoting mechanisms. Here, we have screened all 18 candidates and validated the DDP activities for at least five of these genes. We also developed a series of single-cell assays to profile cancer-relevant properties and assign their cancer-driving roles to genome instability. Last, we have demonstrated a reactive oxygen species (ROS)-dependent role of AQP3 overproduction-induced DNA damage, a pan-cancer mechanism.

Methods: We measured endogenous DNA damage levels for all TWAS-nominated candidates using high-throughput single cell-based flow cytometric assays. Additional high-throughput single-cell assays were developed to quantify reactive oxygen species, replication fork stalling, and other DNA-related cancer properties, which allowed us to rapidly harvest functional information.

Results: We screened 18 lung cancer TWAS-nominated genes for DNA damage in a lung cell line, and five showed increased DNA damage, including recently confirmed AQP3 overproduction, IREB2 knockdown, newly identified RNASET2 overproduction, TRIM38 knockdown, and JAML knockdown cells. None of these genes has been previously reported to be associated with DNA damage, prioritizing these lung cancer genes for further genome-destabilizing mechanistic studies. AQP3 overproduction promotes DNA damage in a variety of cell lines with different tissues of origin, including lung, kidney, and colon, supporting the hypothesis that DNA damage induced by AQP3 overproduction is universal. Moreover, we have shown that AQP3 overproduction causes high ROS at a level higher than 2mM H2O2 treatment, and ROS quencher N-acetyl-l-cysteine (NAC) can reduce AQP3 overproduction-induced DNA damage, supporting the conclusion that AQP3 overproduction induces ROS-dependent DNA damage. Furthermore, additional functional dissections revealed a high replication fork-stalling phenotype for a previously uncharacterized lung cancer risk protein, KIAA0930, providing the first-ever functional annotation of this uncharacterized protein.

Conclusions: We established a high-throughput functional validation platform that measures endogenous DNA damage and other cancer genome-related properties for lung cancer susceptibility genes. More importantly, the strategy for predicting DNA damageome genes and the functional validation platform are transferable to other cancers.

Citation Format: Jun Xia, Zhuoyi Song, Chris Amos. Post-GWAS in lung cancer: From transcriptome-wide association to the DNA damageome by Integrative functional screens [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 3532.