Abstract 2734: Exploring epigenetic control of immunogenicity in small cell lung cancer through multi-omics analyses

Abstract Background: Small Cell Lung Cancer (SCLC) is an aggressive neuroendocrine malignancy characterized by epigenetic dysregulation. EZH2, a key component of the Polycomb Repressive Complex 2 (PRC2), is overexpressed in SCLC and correlates with poor prognosis. Recent studies show that EZH2 inhibition enhances SCLC cell immunogenicity, though the underlying mechanisms remain unclear. Aim: This study investigates how EZH2 function alters the epigenetic landscape in SCLC using an integrated multi-omics approach. In SCLC cell lines treated with EZH1/2 dual inhibitor valemetostat, we examine changes in chromatin accessibility (ATAC-seq), three-dimensional chromatin organization (micro-C profile), and gene expression (RNA-seq). Key Findings: Gene set enrichment analysis of RNA-seq data revealed upregulation of genes involved in antigen processing, presentation, and inflammatory response pathways following EZH1/2 dual inhibition in SCLC cell line H146. ATAC-seq analysis showed increased chromatin accessibility of genes with increased expression, primarily in distal regulatory regions. Crucially, we addressed the limitation of ATAC-seq in providing only one-dimensional accessibility information by performing Micro-C profiling. This approach confirmed that EZH1/2 dual inhibition led to the formation of neo-loops between accessible promoters and their enhancers. Specifically, we observed gained loops leading to increased HLA-B and HLA-C expression with valemetostat treatment. Validating these findings at the transcriptional and protein levels, qRT-PCR and flow cytometry analyses confirmed increased surface expression of pan-HLA molecules following valemetostat treatment. Functional inhibition of EZH1/2 was confirmed by Western blot analyses showing decreased H3K27me3 levels. These results collectively demonstrate that EZH1/2 controls gene expression in SCLC by establishing long-range interactions between promoter and enhancer elements through modulation of chromatin accessibility, ultimately impacting the expression of key immunogenic factors. Conclusion: Our integrative multi-omics approach reveals a comprehensive model of EZH1/2 contribution to SCLC pathogenesis, highlighting its role in chromatin reorganization and gene expression regulation. Future work will focus on identifying additional therapeutically relevant genes within the EZH1/2-regulated network for potential intervention strategies. Citation Format: Sana Parveen, Ramesh Adhinaveni, Meijun Du, Neshatul Haque, Tianxiang Liu, Kun Fang, Raul Urrutia, Victor X. Jin, Hui-Zi Chen. Exploring epigenetic control of immunogenicity in small cell lung cancer through multi-omics analyses [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 2734.