Abstract 1167: Single-cell transcriptomic profiling of SCLC transformation reveals increased intratumoral diversity of variant and non-neuroendocrine subtypes

Abstract Lineage plasticity is the ability for a cell to change its phenotypic state under evolutionary pressure. This process mediates acquired resistance to EGFR-targeted therapies in lung adenocarcinoma (LUAD), through transformation to small cell lung cancer (SCLC), an aggressive cancer type of neuroendocrine (NE) histology. This transformed SCLC has worse clinical outcomes than either its LUAD or de novo SCLC counterparts, with less than one-year overall survival following transformation. Classical SCLC itself can display plasticity through interconversion between classical, variant, and non-NE transcriptional subtypes, with non-classical subtypes displaying increased metastasis and chemoresistance. It is poorly understood what factors drive SCLC transformation or subtype switching. Prior studies poorly model intratumoral heterogeneity because they profile tumors in bulk, which only estimates the average phenotype. However, SCLC transformation often results in admixed LUAD/SCLC tumors. We sought to capture the full intratumoral heterogeneity of SCLC transformation and identify potential molecular determinants of plasticity by applying single-cell RNA sequencing (scRNA-seq) to 41 tumors and patient-derived xenografts from 22 patients with transformed or combined LUAD/NE histology, with matched targeted DNA sequencing and 17 de novo SCLC tumors, 10 LUAD tumors with concurrent EGFR/RB1/TP53 mutations, and 4 tumor-adjacent normal lung samples for comparison. Of 234,322 single transcriptomes assessed, we found 89,113 NE cancer cells and 18,197 LUAD cancer cells. We confirmed that NE and LUAD components within the same tumor shared clonal mutations and common ancestry. Compared to de novo, transformed SCLC harbored greater phenotypic diversity across patients (p < 1 × 10−10), driven largely by enrichment of variant and non-NE subtypes (p < 0.02), including NEUROD1, POU2F3, and YAP1-high subtypes, the latter of which was completely absent in de novo. Within each tumor, transformed SCLC displayed higher intratumoral subtype diversity than de novo SCLC (likelihood ratio p < 0.025). After adjusting for SCLC subtype, differential expression and pathway analysis demonstrated that transformed SCLC is a distinct phenotype from de novo and shares features of the ancestral clone that include residual EGFR and NSCLC gene signatures, as well as pathways in neuronal stemness, MYC targets, AKT/MTOR signaling, JAK/STAT inflammation, and chromatin remodeling. In sum, we find increased intratumoral phenotypic diversity in transformed SCLC, including variant and non-NE subtypes, that may explain worse clinical outcomes. We show that transformed SCLC is a distinct phenotype from de novo, marked by pathways that may offer new potential drug targets to constrain plasticity, with the goal of restoring original sensitivity to targeted therapies. Citation Format: Joseph Minhow Chan, Alvaro Quintanal-Villalonga, Amin Sabet, Parvathy Manoj, Ojasvi Chaudhary, Tianhao Xu, Ignas Masilionis, Jacklynn Egger, Noor Sohail, Jaeyoung Chun, Tal Nawy, Linas Mazutis, Triparna Sen, Ronan Chaligne, Helena Yu, Dana Pe'er, Charles Rudin. Single-cell transcriptomic profiling of SCLC transformation reveals increased intratumoral diversity of variant and non-neuroendocrine subtypes [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1167.