Comprehensive DNA repair landscape analysis reveals novel small cell lung cancer biology

Abstract Background: Small cell lung cancer (SCLC) is the most lethal form of lung cancer. The five-year overall survival rate for SCLC patients is only ~7%, a statistic that has not improved for decades. Compared to non-small cell lung cancers, SCLCs highly express DNA repair proteins. Despite this acknowledgement, a comprehensive analysis of the DNA repair machinery within SCLC has not been completed. This study was performed to study the SCLC DNA repair landscape. Methods: We applied a novel DNA repair analysis method to IMPOWER133 (n = 271) and MD Anderson GEMINI (n = 85) clinical SCLC datasets. This single-sample weighted expression (ssWE) method uses transcriptomic data to assess regulation of ten single-strand break repair, double-strand break repair, translesion synthesis, and damage sensing pathways within individual tumors. Importantly, this method considers all pathway effectors and applies a scaling factor to capture effector essentiality to repair completion. Unsupervised k-means clustering was used to group samples following ssWE analysis. Chi-square tests were used to test for significant enrichment patterns between DNA repair and established SCLC transcription factor (TF) subtypes assignments. Results: Unsupervised clustering demonstrated that IMPOWER133 and GEMINI SCLCs were robustly split into three clusters as defined by their DNA repair phenotypes (DNA Damage Response (DDR) High, Intermediate, Low). We found that expression of DNA damage responsive transcription factors (E2F1, MYBL2, FOXM1) and the intra-S and G2/M checkpoint machinery significantly increased across DDR clusters (High>Intermediate>Low). Also, we found that SCLC TF subtypes showed statistically significant enrichment patterns across DDR clusters (IMPOWER133, MDACC Χ2 p<0.001). Most notably, inflamed SCLC (SCLC-I) were significantly under-represented in the DDR High cluster. Given this, we hypothesized that DDR Low tumors exhibited a more “inflamed” phenotype. To test this hypothesis, we isolated ASCL1+ SCLC (SCLC-A) tumors, which are considered “immune cold” compared to other subtypes, stratified them by their DDR status, and analyzed expression patterns of key immune genes. Strikingly, we found that splitting treatment naïve SCLC-A tumors by their DDR status identified tumors that appeared more “inflamed” (DDR Low). DDR Low SCLC-A showed increased expression of MHC Class I and inflammatory cytokine genes. Conversely, DDR High SCLC-A tumors exhibited an immune evasive profile. Conclusions: We provide the first evidence that SCLCs exhibit a spectrum of DNA repair machinery and cell cycle checkpoint pathway expression within TF subtypes. Additionally, we find that DDR status may be a key determinant of “inflamed” biology in treatment naïve SCLC-A—the predominant form of SCLC—independent of the SCLC-I subtype. Moving forward, our results have important implications for SCLC treatment and clinical trial design. Citation Format: Benjamin B. Morris, Barzin Nabet, David Shames, Simon Heeke, Carl M. Gay, Jing Wang, Jianjun Zhang, John V. Heymach, Lauren A. Byers. Comprehensive DNA repair landscape analysis reveals novel small cell lung cancer biology [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6115.