Abstract 4058: CUT&amp;RUN reveals E2F7 as a key transcriptional regulator of oncogenic functions in neuroendocrine small cell lung cancer
Authors: Meijun Du, Jessica Schmeling, Angela Mathison, Victor Jin, Hui-Zi Chen
Journal: Cancer Research (2025)

Abstract Small cell lung cancer (SCLC) is a molecularly heterogeneous disease, classified into neuroendocrine (NE) and non-neuroendocrine (non-NE) subtypes. The NE subtypes, including ASCL1 and NEUROD1, account for approximately 80% of SCLC cases. E2F7, a non-canonical E2F transcription factor family member, regulates cell cycle progression, and its dysfunction has been linked to cancers. A recent study identified E2F7 as a cofactor of ASCL1, enhancing its neurogenic activity. However, the role of E2F7 in SCLC subtypes is not yet clearly defined. The objective of this study is to profile both common and subtype specific E2F7 target genes and pathways that contribute to pathogenesis and may serve as targets for therapeutic intervention. To identify E2F7 targets in NE SCLC subtypes, we performed CUT&amp;RUN (Cleavage Under Targets &amp; Release Using Nuclease) in ASCL1 (DMS79, H146) and NEUROD1 (H82, H446) cell lines. Two antibodies against E2F7 and one against histone H3K4me3, marks of active gene promoters, were used in each cell line, with IgG as a negative control. Total 32 CUT&amp;RUN next generation sequencing libraries (NGS) were generated and sequenced. NGS data was analyzed with a custom bioinformatics pipeline, using SEACR for peak calling and ChIPseeker for annotation. The identified E2F7 targets were then correlated with RNA-seq data from the CCLE database. In both ASCL1 and NEUROD1 cell lines, ∼95% of E2F7-bound peaks were within 1 kilobase (kb) of gene promoters, most co-localizing with H3K4me3 peaks. Combining peaks from two E2F7 antibodies, we identified 872 E2F7 target genes in H146 (ASCL1) cell line, 818 in DMS79 (ASCL1) and 754 in H446 (NEUROD1). Fewer E2F7 peaks were called for H82 (NEUROD1) due to higher background. These targets included common and subtype-specific genes. Notably, E2F1 (regulator of G1/S transition) and EZH2 (mediator of the repressive H3K27me3 mark) were common targets, while DLL3 (target of multiple therapeutics in clinical development for SCLC) was ASCL1-specific, and CD82, a cell surface glycoprotein involved in cancer cell signaling, was NEUROD1-specific.Pathway analysis of E2F7-bound genes in ASCL1 and NEUROD1 cell lines revealed several shared pathways: cell cycle, spliceosome, ATP-dependent chromatin remodeling, and the Polycomb repressive complex. ASCL1-specific pathway was related to endocytosis, while NEUROD1 was linked to the HIF-1 signaling pathway. Correlation of E2F7 target genes with RNA-seq data revealed distinct gene expression patterns, specific to both the cell line and the subtype. These results offer new insights into E2F7-mediated transcriptional regulation in SCLC subtypes, providing a foundation for targeted therapeutic strategies. Our results support E2F7 as a master transcriptional regulator in SCLC and an important therapeutic target. Further analysis is needed to extend these findings to other subtypes, including POU2F3 and YAP1 Citation Format: Meijun Du, Jessica Schmeling, Angela Mathison, Victor Jin, Hui-Zi Chen. CUT&amp;RUN reveals E2F7 as a key transcriptional regulator of oncogenic functions in neuroendocrine small cell lung cancer [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 4058.