Loss of NOTCH2 Creates a TRIM28-Dependent Vulnerability in Small Cell Lung Cancer [bulk_murine_RNA_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. Bulk RNA-seq profiling of 1). Neuroendocrine suspension and non-neuroendocrine adherent NOTCH-WT (K93) and NOTCH2-Mutant (K60) SCLC cell lines derived from RPR2 genetically engineered mouse model and genetic inactivation of TRIM28 with two sgRNA and non-targeting control using CRISPR-Cas9. 2). SCLC cell line 1014 cells derived from RPR2 genetically engineered mouse model with TRIM28-dTAG-HA knock-in and genetic inactivation of NOTCH2 with two sgRNA and non-targeting control using CRISPR-Cas9 and treated with 100 nM dTAG-V1 for 72 hours to degrade TRIM28 or with DMSO as a control.