Tumor NLRP3 Amplification Promotes Immunotherapy Resistance by Inhibiting STAT1 Signaling and Suppressing MHC Class I Expression

Immunotherapy resistance remains a significant challenge in immuno-oncology and predictive biomarkers are needed to guide combination immunotherapy selection for the individual patient. Using transcriptional signature analysis as well as accessible tissue and plasma-based assays, we show that elevated tumor-intrinsic NOD-, LRR-, and pyrin domain-containing protein 3 (NLRP3) signaling activity correlates with checkpoint inhibitor resistance in several independent cohorts of stage III/IV melanoma and gastroesophageal (GE) adenocarcinoma patients. In situ hybridization studies demonstrate that tumor NLRP3 copy-number gain is observed in immunotherapy resistant melanomas and GE adenocarcinomas harboring enhanced NLRP3 signaling activity. Spatial transcriptomic analysis of GE adenocarcinomas reveals that NLRP3 signaling activity inversely correlates with NOD-, LRR-, and CARD-containing 5 (NLRC5) and major histocompatibility (MHC) class I-associated gene expression. Indeed, pre-clinical models of melanoma and GE adenocarcinoma demonstrate that Nlrp3 amplification suppresses NLRC5-mediated MHC class I upregulation, while pharmacologic NLRP3 inhibition augments tumor MHC class I surface levels. Upon activation, mechanistic studies reveal that NLRP3 binds to and inhibits STAT1 dimerization, nuclear translocation, and NLRC5 transcription. Consistent with these findings, inhibiting the NLRP3 inflammasome augments tumor STAT1-NLRC5 signaling, MHC class I surface expression, and overcomes anti-PD-1 resistance in an orthotopic model of microsatellite stable chromosomal instability (CIN) gastric adenocarcinoma. This work reveals a fundamental link between cellular stress and tumor-mediated immune evasion. In addition, these findings indicate that the tumor NLRP3 inflammasome signaling pathway merits further clinical study as a therapeutic target and a source of companion biomarkers for overcoming checkpoint inhibitor resistance in cancer patients.