Small cell lung cancer (SCLC) typically displays a “cold” tumor microenvironment with a paucity of immune infiltrate. Neuroendocrine SCLC cells also profoundly repress MHC-I expression, rendering them vulnerable to NK cell-mediated cytotoxicity. Here, we confirm that neuroendocrine SCLC cells are sensitive to NK cell-mediated attack, yet the quantitative spatial profiling of the SCLC immune microenvironment in patient samples reveals that effector immune cells, including NK cells, are excluded from MHC-Ilow/neg SCLC regions. To study this biology, we develop dynamic single-cell RNA sequencing of microphysiological immune tumor environments (DynaMITE-seq) and integrate findings with spatial transcriptomics in patient tissue, unveiling the microvasculature as a major checkpoint restricting NK cell extravasation/recruitment. We demonstrate that the activation of vascular Stimulator of Interferon Genes (STING) signaling restores NK cell infiltration and killing of neuroendocrine SCLC, suggesting a strategy to overcome this key SCLC immunologic barrier and prime therapeutic response to DLL3-targeted CAR-NK cell therapy.

Although small cell lung cancer (SCLC) comprises transcription factor (TF)-defined molecular subtypes (ASCL1, NEUROD1, POU2F3), the extent to which these subtypes predict response to clinically effective therapy in patients-and whether therapy can select for subtype switching-remains unknown. The recent approval of the DLL3×CD3 bispecific T-cell engager tarlatamab represents one of the first meaningful advances in relapsed small cell lung cancer (SCLC) in decades, yet responses remain heterogeneous and resistance is inevitable. Here, we inferred SCLC gene expression from circulating chromatin in prospectively collected patient plasma (46 patients; 167 samples), 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-subtype tumors, whereas NEUROD1-subtype tumors exhibited inferior responses and POU2F3-subtype tumors were uniformly resistant, consistent with DLL3 being a direct ASCL1 transcriptional target and most highly expressed in ASCL1-positive tumors. Strikingly, one mode of acquired resistance revealed therapeutic selection for a NEUROD1-high state with concomitant DLL3 downregulation. Other resistant tumors exhibited enrichment of regulatory and exhausted T-cell programs, highlighting tarlatamab's dual-targeting mechanism of action. Together, these results reveal that tarlatamab exerts selective pressure against ASCL1-driven lineages, facilitating resistance through loss of an antigen intrinsically linked to that state. These findings underscore 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 from patient plasma with functional mouse modeling to uncover clinical and biological mechanisms of response and resistance to cell-surface-targeted therapies.

Additional datasets, to be included in the next update of LCMAGDB

PCA of reprocessed Mouse430_2 microarray data

Current collection of LCAMGDB datasets

Ascl1 expression across reprocessed RNA-seq datasets

Abstract Lung cancer histological transformation from lung adenocarcinoma (LUAD) to small cell lung cancer (SCLC) can occur as a resistance mechanism to targeted therapies, particularly in EGFR-mutant LUADs with concurrent RB1 and TP53 mutations. SCLC transformation has a poor prognosis and there are no targeted therapies to block SCLC transformation. Increased PRC2 complex expression is correlated with SCLC transformation, but it is unknown whether PRC2 complex is functionally necessary for SCLC transformation. In this study, we investigated the functional role of EED, a scaffolding component of the PRC2 complex, in SCLC tumorigenesis and in LUAD to SCLC transformation utilizing two state-of-the-art CRISPR-based, autochthonous immunocompetent genetically engineered mouse models (GEMMs) with comprehensive genomic, transcriptomic, and epigenomic analyses. In a de novo SCLC GEMM, we show that loss of EED hinders SCLC development and selects for the formation of LUAD through a NEUROD1-positive intermediate cell state. Mechanistically, EED loss de-represses bivalent genes co-marked by H3K27me3 and H3K4me3, including LUAD oncogenic RAS, PI3K, and MAPK pathway genes, to promote transformation to LUAD. Consistently, these same signaling pathway genes are bivalently marked and silenced in human SCLC patient-derived xenografts, indicating a conserved PRC2-mediated mechanism to repress LUAD oncogenic signaling to maintain the SCLC neuroendocrine identity. In a novel CRISPR-based EGFR-mutant LUAD GEMM with RB1/TP53 loss, we found EED is necessary for LUAD to SCLC transformation and metastatic progression following EGFR withdrawal. Altogether, these findings identify the PRC2 complex as an epigenetic regulator that maintains the SCLC neuroendocrine identity and highlights EED inhibition as a potential therapeutic approach to prevent SCLC transformation in high-risk LUAD. Citation Format: Yixiang Li, Yasmin N. Laimon, Hyeonseo Cho, Marina Vivero, Gabriel R. De Oliveira, Andrew Delcea, Varunika Savla, Yuting Chen, Yavuz Durmaz, Xintao Qiu, Shweta Kukreja, Rong Li, Talal El Zarif, Wesley S. Lu, McKayla Van Orden, Jacob E Berchuck, Roderick Bronson, Shuqiang Li, Hongbin Ji, Katerina A. Politi, Matthew L. Freedman, Henry Long, Sabina Signoretti, Matthew Gilbert Oser. EED drives the small cell lung cancer neuroendocrine phenotype in lung cancer histological 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 3528.

Dotplot of Ezh2 expression across various samples profiled by the Mouse430_2 microarray platform

User interface of the GEMMs table in the LCAMGDB web application

Identification of data redundancy by hierarchical clustering

Sample table, providing sample characteristics

Depositor communications, describing input from data depositors

Custom sample filtering and selection

Top 100 frequent genetic mutations in realworld lung cancer patients

Small cell lung cancer (SCLC) comprises molecular subtypes, among which POU2F3-driven SCLC (SCLC-P) lacks effective targeted therapies. Because POU2F3 is a lineage-defining transcription factor that remains largely undruggable, defining mechanisms that maintain its protein stability may reveal therapeutic vulnerabilities. Using CRISPR-Cas9 screening and deubiquitinase (DUB) inhibitor profiling, we identified USP2 as a dominant DUB stabilizing POU2F3. Mechanistically, USP2 interacts with and removes K48-linked ubiquitin chains, thereby preventing proteasomal degradation, while K251 and K348 serve as major ubiquitination sites. USP28 also deubiquitinates POU2F3 but exerts relatively weaker effects. Pharmacological inhibition of USP2-associated DUB activity with MS102 increased POU2F3 ubiquitination, accelerated its degradation, and selectively suppressed SCLC-P growth in vitro and in vivo. Re-expression of POU2F3 or a ubiquitination-resistant POU2F3 mutant partially rescued these effects. Together, these findings establish USP2 as a critical proteostatic regulator of POU2F3 and support targeting lineage-specific proteostatic mechanisms as a therapeutic strategy for SCLC-P.

Lung cancer histological subtypes include lung adenocarcinoma (LUAD) and small cell lung cancer (SCLC). Although usually distinct, rare combined LUAD/SCLC tumors occur, and LUAD can transform into SCLC as a mechanism of resistance to targeted therapies, particularly in EGFR -Mutant LUADs with RB1/TP53 inactivation. Although PRC2 complex expression increases during this transformation, its functional role remains unclear. Using CRISPR-based autochthonous immunocompetent GEMMs, we found that inactivation of EED, the core PRC2 scaffolding subunit, impaired SCLC tumorigenesis and promoted LUAD histological identity likely through a NEUROD1-positive intermediate state. Mechanistically, EED loss derepressed bivalent genes co-marked by H3K27me3 and H3K4me3, including LUAD oncogenic RAS, PI3K, and MAPK pathway genes and NEUROD1. These same LUAD oncogenic signaling genes were bivalently repressed in human SCLC patient-derived xenografts, suggesting a conserved PRC2-dependent mechanism that represses LUAD oncogenic signaling and thereby supports the SCLC neuroendocrine identity. In a complementary EGFR -Mutant LUAD GEMM with Rb1 and Trp53 inactivation, EED inactivation at tumor initiation prevented the emergence of SCLC histology after EGFR oncogene withdrawal and redirected recurrent tumors toward mucinous LUAD states with reduced spontaneous metastasis. These findings identify PRC2/EED as a regulator of SCLC neuroendocrine identity and nominate pharmacologic EED inhibition for future investigation in therapy-associated LUAD-to-SCLC transformation.

Small cell lung cancer (SCLC) transformation is an incompletely characterized mechanism of resistance to epidermal growth factor receptor tyrosine kinase inhibitors (EGFR-TKIs) in EGFR-mutant cancers, limiting development of optimal treatment approaches. Through single-cell RNA sequencing of malignant pleural effusions from patients who underwent SCLC transformation, we identified heterogeneity and diversity, including distinct neuroendocrine (NE) and mesenchymal non-NE cancer cell subsets, which were maintained in patient-derived cell lines. We demonstrate that EZH2 regulates EGFR expression in NE cells where EGFR expression is silenced at baseline. Although neither epigenetic derepression nor exogenous overexpression of mutant EGFR sensitized the cells to EGFR inhibition, non-NE cells exhibited selective sensitivity to MEK inhibitors. Combined MEK inhibitor and chemotherapy effectively inhibited growth of both NE and non-NE cells in vitro and in vivo. Our findings demonstrate that EGFR-mutant SCLC is composed of mixed cell states with distinct therapeutic vulnerabilities and offer a therapeutic strategy to target tumor heterogeneity in highly plastic and treatment-resistant malignancies such as transformed SCLC.

Dataset table, summarizing input datasets for LCMAGDB

Abstract TEA/TEF-domain [TEAD] inhibitors are being evaluated in clinical trials for cancers with alterations in the Hippo pathway including mesothelioma. We recently developed and showcased the potency of TEAD palmitoylation inhibitors MYF-03-69 and MYF-03-176 in mesothelioma cell lines. However, TEAD inhibition results in cell cycle arrest in cell line models with Hippo pathway alterations without inducing cell death, potentially limiting their long-term clinical efficacy. Using a genome-wide CRISPR/Cas9 screen, we identified EZH2 as a critical modulator of the cellular response to TEAD inhibition. Compared to single agent treatments, EZH2i/TEADi robustly triggered apoptosis and suppressed the growth of Hippo-mutated cells in vitro and in vivo. Mechanistically, EZH2i/TEADi-treated cells exhibited heightened activation of tumor-intrinsic innate immune signaling which resulted in DNA damage and subsequent apoptosis. Taken together, we propose this novel combinatorial strategy as a potential approach to enhancing the anti-tumor efficacy of single agent TEAD targeting therapies in Hippo pathway altered tumors. Citation Format: Antja-Voy Hartley, Mustafa Al-Dulaimi, Navin R. Mahadevan, Pinar Eser, William W. Feng, Tran Thai, Jeanelle A. Tsai, Caitlyn Weston, Nicholas Tourtillot, Matthew Booker, Joseph Kulesza, Zhaorong Li, Elizabeth Cohen, Sean Lenahan, Choudhury Fabliha Yusuf, Abeba Teshager, Prafulla C. Gokhale, Shweta Kukreja, Sonsoles Liria Veiga, Rong Li, Xintao Qiu, Henry W. Long, Michael Y. Tolstorukov, Matthew G. Oser, Nathanael S. Gray, David A. Barbie, Pasi A. Janne. Co-targeting EZH2 and TEAD elicits apoptosis through tumor-intrinsic innate immune signaling in Hippo pathway-mutated cancers [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 1850.