Abstract 7327: Investigating the cell-type specific regulation of IRF4 and its role in lung cancer via a lung cancer risk-associated pleiotropic variant
Authors: Kane Alexander , Yin Jinhu , Long Erping , Feng James , Gräwe Cathrin , Patel Harsh , Byun Jinyoung , Amos Christopher , Brown Kevin , Xia Jun , Vermeulen Michiel , Choi Jiyeon 
Published: March 2024

Although smoking is a main risk factor for lung cancer, genetic factors also contribute to the risk, as shown by over 50 genomic loci identified by genome-wide association studies (GWAS). A recent cross-ancestry lung cancer GWAS identified a common germline variant, rs12203592 (C/T), in chr6p25.3 as a new signal, and quantitative trait loci (eQTL) colocalization analysis using lung and blood tissues (GTEx v8) identified IRF4 as a likely target of rs12203592. rs12203592 has previously been linked with diverse traits, including pigmentation phenotypes, smoking cessation, lymphoblastic leukemia, melanoma, and other skin cancers. rs12203592 also appears to have varied allelic effects in different cell types. Namely, the lung cancer risk-associated T allele is correlated with higher IRF4 expression in lung tissue and blood cells (GTEx v8) but lower expression in primary melanocytes (n = 106; Zhang et al). Since previous studies established the melanocyte-specific allelic function of this SNP through lineage-specific transcription factors (TFs), we hypothesized that cell-type-specific TFs mediate the observed allelic effect in different tissue/cell types and further contribute to the unique role of IRF4 in lung tumorigenesis. To identify these potential cell-type-specific regulators, we performed mass spectrometry using the nuclear extracts from three cell lines representing lung, blood, and melanocyte lineage. The results nominated the NF-kB and ZEB protein families as the most prominent T-specific binders in the A549 lung cancer cell line, which was validated by electromobility shift assays. Consistent with these findings, tissue-based SNP-gene interaction analysis demonstrated that the mRNA levels of NF-kB and ZEB family members (4 of 7 genes) were correlated with IRF4 expression with a significant interaction with rs12203592 in GTEx lung tissue (P &lt; 0.017), where the correlation is mainly observed with the T allele. Notably, the SNP interaction was less pronounced in whole blood or melanocytes, and the correlation of these TFs and IRF4 expression was mainly observed with the C allele in melanocytes. To begin to establish the roles of these TFs and IRF4 in lung tumorigenesis and given that IRF4 was shown to promote endogenous DNA damage and proliferation of lung-lineage cell lines, we will investigate the roles of NF-kB and ZEB in IRF4 regulation in these contexts using knockdown and overexpression of these TFs. To further investigate lung cancer-specific IRF4 function, we will identify potential targets of IRF4 among lung cancer-associated functional variants established through our previous studies. This data will help elucidate the context-specific roles of IRF4 in lung cancer development and provide clues to gene regulation in a pleiotropic GWAS locus.

Citation Format: Alexander Kane, Jinhu Yin, Erping Long, James Feng, Cathrin Gräwe, Harsh Patel, Jinyoung Byun, Christopher Amos, Kevin Brown, Jun Xia, Michiel Vermeulen, Jiyeon Choi. Investigating the cell-type specific regulation of IRF4 and its role in lung cancer via a lung cancer risk-associated pleiotropic variant [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 7327.