211P Transcriptional and epigenetic landscape of neuroendocrine transformation during emergence of resistance to targeted therapies in EGFR mutant lung adenocarcinoma

Histological transformation from lung adenocarcinoma (LUAD) to small cell carcinoma (SCLC) is a signature example of lineage plasticity (LP) and the primary mechanism of acquired resistance in up to 15% of EGFR-mutant LUADs. It is a dynamic process controlled by transcriptional and epigenetic dysregulation. We determine the transcriptional and epigenetic regulators of LP and their interplay with tumor microenvironment. Multi-omic profiling (whole exome sequencing, bulk and single-cell RNA sequencing, methylation array, and immunohistochemistry) comparing pre-transformation (pre-T) LUAD and post-transformation (post-T) SCLC clinical samples. Upregulation of neuroendocrine markers (SYP, SYN1, INSM1), Notch inhibition (DLL3, HES6), chromatin remodeling (EZH2), and AKT signaling; and downregulation of immune genes, including neutrophil degranulation, cytokine signaling, T cell immunity was seen in post-T SCLCs. Differential methylation of transcription factor (TF) binding motifs revealed hypomethylation of key master regulators of neuroendocrine differentiation (ASCL1, NEUROD1) and demethylation of TFs involved in WNT signaling and stemness in the post-T SCLCs. Single-cell analysis and multiplex-ion beam imagining confirmed suppression of immune modulators and Notch signaling and intra- and intertumoral heterogeneity in post-T SCLCs. We also observed overexpressed TFs SOX2 and ELF3 in pre-T vs classical LUADs, and PHOX2B and ELF3 in post-T vs de novo SCLC. Finally, inhibition of therapeutic targets like epigenetic modifier, EZH2, and PI3K/AKT caused significant tumor regression, re-sensitized the EGFR mutant LUAD PDXs to osimertinib and significantly delayed transformation, highlighting their role as therapeutic targets. Deciphering the complex interplay between transcriptomic and epigenomic drivers and the immune microenvironment is essential to designing therapeutic interventions to prevent or reverse LP. In this study, we highlight key transcriptional and epigenetic regulators of LP in lung cancer, show suppression of the immune response, and propose therapeutic approaches for patient benefit.