8085 Background: Histological transformation of EGFR mutant lung cancer adenocarcinoma (LUAD) to small-cell lung cancer (SCLC) is a well-known resistance mechanism and has been found in about 14% resistant cases. This phenomenon is associated with extremely poor prognosis and limited therapeutic options. This underscores the need to identify the biological mechanisms triggering lineage plasticity in EGFR+ LUADs. We and others have shown that several genomic and epigenetic alterations play a central role in the activation of small cell like neuroendocrine (NE) states. However, the impact of these changes on the immune microenvironment and vice versa is not understood, limiting the identification of novel immunotherapy approaches in this setting. Methods: We describe the evolution of the tumor microenvironment (TME) during SCLC transformation by comparing tissues from de novo LUAD ( n = 10), de novo SCLC ( n = 15), and transformed SCLC (n =12) including 11 cases with EGFR -mutant LUAD/SCLC mixed histology and 1 pre-transformed LUAD. Additionally, we used de novo lung squamous cancer (LUSC, n = 11), and transformed LUSC (n = 11) including 8 mixed LUSC/LUAD histology and 3 post-transformed samples to inform the LUSC transformation program as a comparator. All samples were analyzed by RNA sequencing, DNA methylation, and whole-exome sequencing. Spatial proteomics (ORION, n = 4) and transcriptomics (XENIUM, n = 6) were performed on pre- and post-transformed paired samples from EGFR+ patients. Results: Differential gene expression and pathway analysis highlight the upregulation of G2M, E2F, and MYC targets during both SCLC and LUSC transformation, occurring at an earlier stage for SCLC compared to LUSC. Conversely, a more pronounced and broader and earlier downregulation of immune pathways was detected during SCLC, compared to LUSC, transformation. Analysis of the epigenetic regulators potentially driving these signaling changes pointed to EZH2 as master regulators of SCLC transformation, while the LUSC program was mainly driven by the TP63 and FOXA1 transcription factors. Spatial proteomics and transcriptomics highlighted a decrease in immune-related programs with an increased proportion of immune suppressive subsets and NE features in SCLC-transformed samples compared to baseline specimens. Sub-clustering analysis showed a higher percentage of pro-tumoral macrophages and exhausted T-cells in transformed samples. Conclusions: Our results suggest that a broader transcriptional reprogramming is associated with the transition from LUAD to SCLC than from LUAD to LUSC. The TF profile associated with SCLC histological transformation negatively regulates immune pathways leading to profound remodeling of the immune compartment and a cold TME that supports the aggressive phenotype of transformed tumors.
Gobbini et al. (Thu,) studied this question.