A Tracts of Homozygosity Approach Identifies Methylation-Regulated CSMD1 Expression Targets in Non-Small Cell Lung Cancers Related to Smoking Behavior

Background: Tobacco smoking drives complex genetic and epigenetic changes in non-small cell lung cancer (NSCLC), but the interplay between these alterations remains incompletely understood. This study investigates methylation-driven gene expression changes associated with smoking in lung adenocarcinoma (LUAD) and squamous cell carcinoma (LUSC), with a focus on identifying prognostic biomarkers and gaining etiologic insights using a Tracts of Homozygosity (TOH)-based framework. Methods: We integrated genome-wide SNP data, methylation array profiles, RNA-Seq, and clinical information from European-American patients in The Cancer Genome Atlas (TCGA). Differentially expressed genes were identified within overlapping TOH regions and differentially methylated regions (DMRs) by smoking status. Associations with overall survival were assessed using multivariable Cox proportional hazards models. Results: Genes involved in smoking-related inflammation, oxidative stress, and immune regulation were enriched within TOH regions harboring DMRs. In LUAD, we identified higher methylation at CpG site cg08383399 upstream of CSMD1, which was inversely correlated with gene expression (r = –0.18; p = 0.004). Additional inflammation-related genes (C8orf34, C2, FBN2, SLC44A4, CHD13, INMT, NRG1) within TOH-DMR regions showed subtype-specific expression patterns linked to smoking exposure, supporting their potential as prognostic biomarkers and providing insights into the disease etiology. Conclusions: This integrative analysis highlights TOH-associated epigenetic dysregulation in smoking-related NSCLC and identifies candidate prognostic biomarkers. Impact: These findings offer new insights into the molecular mechanisms underlying smoking-induced lung carcinogenesis and progression.