Abstract 4061: Single cell transcriptomic analysis of T-SCLC patients identifies PHOX2B as a factor in NE transformation

Abstract Lung neuroendocrine (NE) transformation is a molecular process by which non-small cell lung cancers (NSCLCs) transdifferentiate into small-cell lung cancer (SCLC). This transition involves coordinated histological and molecular reprogramming. NE transformation is frequently observed in EGFR-mutant LUAD, occurring in up to 15% of patients treated with EGFR targeted therapies. Whereas LUAD is typically driven by activating oncogenic mutations that hyperactivate the MAPK signaling, SCLC is defined by near-universal inactivation of the tumor suppressor genes TP53 and RB1. Although concurrent loss of TP53 and RB1 appears to be a prerequisite for NE transformation, this genetic background alone is insufficient to induce the phenotypic switch. In this project, we aim to identify molecular drivers that promote NE transformation in TP53/RB1-deficient LUAD tumors.We conducted single cell transcriptomic profiling on a cohort of 47 tumors and patient-derived xenografts (PDXs) from 24 patients with transformed or combined NE histology. Our analysis identified high levels of PHOX2B in transformed SCLC (T-SCLC) cases versus non-transformed SCLC and LUAD. PHOX2B is a neural crest transcription factor (TF) and acts a known oncogenic driver in neuroblastoma. In two EGFR-mutant LUAD cell lines with concurrent inactivation of TP53 and RB1, we found that PHOX2B overexpression induced upregulation of NE markers such as SYP. Furthermore, we observed a pronounced decrease in EGFR signaling along with MAPK (ERK) and YAP activity. ChIP-seq analysis revealed PHOX2B binding to the EGFR promoter, suggesting that PHOX2B may act as a transcriptional repressor of EGFR. Despite these changes, PHOX2B overexpression did not drive full morphologic NE transformation in vitro or in vivo. Moreover, PHOX2B knockout in de novo as well as T-SCLC cell lines did not substantially reduce NE marker expression. Our research uncovers a previously unidentified role for PHOX2B in NE differentiation. They suggest that PHOX2B likely primes cells for transformation by shutting down EGFR signaling, which may represent a necessary but insufficient factor for NE transformation. Future work will investigate the molecular mechanism by which PHOX2B contributes to NE differentiation and cooperates with other factors to drive plasticity. Citation Format: Amin Sabet, Meng Wang, Swanand Rakhade, Alvaro Quintanal-Villalonga, Esther Redin, Charles M. Rudin, Joseph Chan. Single cell transcriptomic analysis of T-SCLC patients identifies PHOX2B as a factor in NE transformation 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 4061.