Transcription Factor Subtype Governs Response and Resistance to DLL3-Directed T-Cell Engagement in Small Cell Lung Cancer [scRNA-seq]

Here, we profiled cell-free circulating chromatin from prospectively collected patient plasma (46 patients; 167 samples) and applied APEX to infer tumor gene expression at single-gene resolution, enabling interrogation of response and acquired resistance to tarlatamab. Parallel development of the first immunocompetent syngeneic mouse model to study tarlatamab response and resistance enabled functional validation. Across species, findings converged on a central principle: TF subtype governs both initial response and acquired resistance. Therapeutic response was significantly associated with ASCL1⁺ tumors, whereas NEUROD1⁺ tumors exhibited inferior responses and POU2F3⁺ tumors were uniformly resistant, consistent with DLL3 being a direct ASCL1 transcriptional target and most highly expressed in ASCL1⁺ tumors. Strikingly, one mode of acquired resistance converged on therapeutic selection for a NEUROD1-high state with concomitant DLL3 downregulation. Some tumors also exhibited enrichment of regulatory and exhausted T-cell programs underscoring tarlatamab’s dual-targeting mechanism of action. Together, these results reveal that under tarlatamab pressure, tumors select against ASCL1-driven cell states, driving resistance to an antigen intrinsically linked to ASCL1 activity. These findings establish the clinical relevance of TF-defined molecular subtypes in human SCLC. More broadly, they highlight the power of integrating longitudinal in vivo plasma transcriptional profiling in patients with functional mouse modeling to uncover clinical and biological mechanisms of response and resistance to cell-surface-targeted therapies.