Determinants of resistance to nivolumab (nivo) monotherapy investigated through genomic and transcriptomic analysis of renal cell carcinoma (RCC) tumors from the HCRN GU16-260 study.

4524 Background: Nivo monotherapy demonstrated anti-tumor activity in treatment-naïve RCC in Part A of HCRN GU16-260 across all IMDC groups and in multiple histologies. Patient tumor samples were collected to characterize the tumor-immune microenvironmental determinants of effective anti-tumor immunity with nivo. Methods: Whole exome sequencing (WES) was performed on formalin-fixed, paraffin-embedded tissue collected within one year prior to nivo. For single-cell RNA-sequencing (scRNA-seq), eligible patients (pts) with any RCC histology underwent tumor biopsy prior to and/or at resistance to nivo monotherapy. Gene expression signatures discovered through scRNA-seq were used to interrogate previously published bulk transcriptomic data of nivo in the treatment-refractory setting. Results: WES analysis (n = 96 tumors) identified recurrent focal amplifications within chromosome 11q13 (amp11q13), which was observed in 6 of 18 (33.3%) of tumors from pts with progressive disease (PD) compared to 0 of 20 (0%) of tumors from pts with complete or partial response (CR/PR; p = 0.005). amp11q13 was associated with worse progression free survival (PFS; p = 0.008) and overall survival (OS; p = 0.010). ScRNA-seq was performed on tumors from 17 pts (8 with baseline only, 7 with progression only, and 2 with paired baseline and progression samples) across 7 trial sites. Trajectory inference analysis of tumor-infiltrating T cells revealed a bifurcating structure, starting with naïve T cells and ending either in terminally exhausted CD8+ T cells or SLAMF7+ CD8+ T cells. Surprisingly, the SLAMF7+ T cell population expressed high levels of cytotoxic genes (including GZMA, GZMB, GNLY) and markers of tissue residency ( ZNF683/HOBIT and ITGAE/CD103). Of the 14 pts with at least 100 sequenced tumor-infiltrating T cells, the presence of a higher percentage of SLAMF7+ CD8+ T cells (relative to total T cells) was associated with primary resistance to nivo (mean percentage in PD [n = 4] pts 32.7%; stable disease [n = 4] pts, 9.1%; CR/PR [n = 6] pts, 2.2%; p = 0.019 for CR/PR vs PD). Of 172 pre-treatment tumors from the nivo arms of the CheckMate-009/010/025 trials that we analyzed by bulk RNA-seq, a signature score derived using genes expressed in the SLAMF7+ CD8+ T cell trajectory branch was enriched in pts with PD compared to CR/PR as best response (p = 0.032). Conclusions: Bulk genomic and single-cell transcriptomic analyses uncovered somatic alterations (amp11q13) and infiltrating T cell populations ( SLAMF7+ CD8+) associated with resistance to frontline nivo monotherapy in a phase II study in RCC. Additional independent and functional validation studies are in progress.