Abstract 1975: Genomic drivers of plasticity in transformed small cell lung cancer.

Abstract Background: An emerging mechanism of resistance to targeted therapies in lung cancer is the lineage switch from lung adenocarcinoma (LUAD) to a neuroendocrine (NE) histology, the most aggressive subtype being small cell lung cancer (SCLC). In EGFR-mutant tumors, concurrent TP53/RB1mutations are enriched in transformed tumors, but the mechanisms underlying transformation remain poorly defined. We present a single-cell atlas of transformed (T)-SCLC and identify genomic and transcriptional drivers of NE transformation. Methods: We curated a cohort of 97 T-SCLC, 777 de novo SCLC, and 10,140 LUAD patients from a single institution, with mutational profiling performed using MSK-IMPACT. A subset of 47 tumors from 24 patients with transformed or admixed LUAD-SCLC histology underwent 10x single-cell RNA sequencing compared to 10 EGFR/TP53/RB1-mutant LUAD (triple-mut), 17 de novo SCLC, and 4 normal lung samples, yielding ∼140,000 cells. Analysis was performed using scanpy, scVI, CellRank, Palantir, SPECTRA, and GSEApy. Results: Among stage IV patients, we observed worse median overall survival (OS) in EGFR-wt T-SCLC (9.70 mos) and de novo SCLC (10.22 mos) compared to EGFR-wt LUAD (19.33 mos) and EGFR-mut T-SCLC (27.58 mos). T-SCLC showed a higher mean mutational burden (12.4 mut/Mb) compared to LUAD (6.7 mut/Mb) and de novo SCLC (9.0 mut/Mb). TP53 and RB1 were the most common mutations in both T-SCLC and de novo SCLC. Only 38% of T-SCLC had EGFR mutations. Mutation enrichment differed by genotype. EGFR-mut tumors displayed higher rates of NFKB1, NKX2-1, FOXA1, CARD11, ELF3, RRAS2, and MDM4 mutations. EGFR-wt T-SCLC tumors were enriched in MYC, KRAS, KEAP1, CDKN2A, SF3B1, CCND1, and FGF3 mutations. PI3K/AKT pathway alterations were enriched across both EGFR-wt and EGFR-mut T-SCLC compared to de novo SCLC. Single-cell analysis revealed enrichment of MYC, PI3K/AKT, chromatin remodeling, and stemlike gene programs in T-SCLC, especially early in transformation. We identified a basal-like signature highly active in LUAD immediately prior to transformation that was previously unrecognized in patients. The basal-like signature persisted in T-SCLC samples that had the highest intratumoral heterogeneity. A subset of triple-mut LUAD also expressed the basal-like signature, indicating a potential ‘pre-transformation’ stage. We observed trajectories leading to alternative squamous and mesenchymal fates as well. Discussion: Our data show that NE transformation is shaped by interplay between genotype and underlying transcriptional rewiring. While EGFR-mut and EGFR-wt tumors display differential mutational patterns, they converge on PI3K/AKT activating mutations and a shared basal-like precursor state, which primes tumors for transformation to NE, squamous, and mesenchymal fates. Our study underscores the clinical need to better understand NE transformation and highlights potential therapeutic vulnerabilities. Citation Format: Swanand Rakhade, Mamie Wang, Lena Morrill Gavarró, Emmanuel Spanos, Alvaro Quintanal-Villalonga, Amin Sabet, Parvathy Manoj, Rishika Giri, Ronan Chaligné, Xinjun Wang, Helena A. Yu, Esther Redin, Dana Pe'er, Charles M. Rudin, Joseph Chan. Genomic drivers of plasticity in transformed small cell lung cancer abstract. In: Proceedings of the American Association for Cancer Research Annual Meeting 2026; Part 1 (Regular Abstracts); 2026 Apr 17-22; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2026;86(7 Suppl):Abstract nr 1975.