Loss of NOTCH2 Creates a TRIM28-Dependent Vulnerability in Small Cell Lung Cancer [ChIP-seq]

Small cell lung cancer (SCLC) is a highly aggressive malignancy that lacks effective targeted therapies, in part due to frequent loss-of-function mutations in tumor suppressors and the absence of recurrent oncogenic drivers. Approximately 15% of SCLCs harbor inactivating mutations in NOTCH1 or NOTCH2, and most neuroendocrine-high SCLCs exhibit low NOTCH activity. Using CRISPR/Cas9 screening in primary cell lines derived from NOTCH1/2-isogenic SCLC genetically engineered mouse models, we identified TRIM28 as a synthetic lethal dependency in NOTCH2-inactivated SCLCs. Loss of TRIM28 in this context robustly induced expression of endogenous retroviruses, activated viral sensing pathways, and triggered a type I interferon response. Mechanistically, NOTCH2 inactivation increased reliance on TRIM28-mediated ERV silencing, creating a hyper-dependence on TRIM28 via the STING–MAVS–TBK1 axis. Notably, TRIM28 was essential for tumor growth only in the setting of NOTCH2 loss. These findings identify TRIM28 as a potential therapeutic target in NOTCH2-deficient or low-NOTCH2-expressing SCLC. Overall design: 1); ChIP-seq profiling of TRIM28-HA (using HA antibody) in human NCI-H1048 cells (NOTCH2-WT) overexpressing TRIM28-HA. 2); ChIP-seq profiling of TRIM28-HA (using HA antibody) in murine 1014 cells derived from the RPR2 genetically engineered mouse model, with TRIM28-dTAG-HA knock-in and either CRISPR-Cas9–mediated inactivation of NOTCH2 (NOTCH2-inactivated) or a non-targeting control (NOTCH2-WT). 3);ChIP-seq profiling of H3K27ac and H3K9me3 in murine 1014 TRIM28-dTAG-HA NOTCH2-isogenic cells (NOTCH2-WT or NOTCH2-inactivated) treated with 100 nM dTAG-V1 for 72 hours to degrade TRIM28 or with DMSO as a control.