Abstract 1923: A tract of homozygosity analysis reveals methylation-driven <i>CSMD1</i> expression in non-small cell lung cancers

Abstract INTRODUCTION: The genetic and epigenetic alterations associated with smoking remain incompletely defined in Non-Small Cell Lung Cancer (NSCLC) carcinogenesis. This study investigates methylation-driven gene expression differences by smoking behaviors in lung adenocarcinoma (LUAD) and squamous cell carcinoma (LUSC) using the Tracts of Homozygosity (TOH) approach. METHODS: Genetic, epigenetic, and environmental factors were examined to identify potential methylation-driven genes in NSCLC by subtype and smoking status. The analysis incorporated data from a genome-wide association study (GWAS), the Cancer Genome Atlas Program (TCGA), including methylation arrays/RNA-Seq, and clinical information among European Americans. A TOH block is defined as a string of SNP genotypes that harbor both common and rare variants. Multivariable logistic regression models were used to identify significant genes that also overlapped significant TOH clusters and contained differentially methylated regions (DMRs). A refined analysis was performed to assess methylation status at the probe level for all differentially expressed genes in the overlapping TOH regions and DMRs. Further, the multivariable Cox proportional hazards regression model was used to evaluate the association between gene expression levels and mortality risk. RESULTS: Analysis of differentially expressed genes in TOH regions and DMRs showed hypermethylation at a CpG promoter site (cg08383399) upstream of CSMD1 in smokers with LUAD and negatively correlated with CSMD1 expression (r=-0.18; p=0.004). LUAD smokers with high CSMD1 expression showed better survival probability than those with low CSMD1 expression, especially among those with &amp;gt; 30 pack-years of smoking history (Hazard Ratio: 0.57; 95% Confidence Interval: 0.32, 0.99). In addition, we identified several genes related to smoking-induced inflammation from the list of differentially expressed genes overlapping DMRs and differentially methylated probes in TOH regions. CONCLUSION: The TOH approach identified smoking-associated methylation patterns linked to differentially expressed genes in NSCLC by subtypes. These findings contribute to the identification of smoking-induced biomarkers for NSCLC facilitating personalized screening and suggesting intervention strategies to reduce smoking-related risks. Citation Format: Jing Jin, Yasir Rahmatallah, Horacio Gomez-Acevedo, Yong-Moon Mark Park, David W. Ussery, Mohammed S. Orloff. A tract of homozygosity analysis reveals methylation-driven CSMD1 expression in non-small cell lung cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 1923.