Abstract 6550: Biopsy analysis of trial S1616: Ipilimumab plus nivolumab versus ipilimumab alone in patients with anti-PD-1 refractory melanoma

Abstract Background: The phase II randomized trial S1616 (NCT03033576) showed that patients with melanoma refractory to anti-PD-1-based therapy had improved progression free survival (HR=0.63, p=0.037) and objective response (28% vs 9%) to the combination of ipilimumab with nivolumab compared to ipilimumab. Here, we report molecular and spatial proteomic features of biopsies collected from patients on S1616, both prior to and during therapy. Methods: Biopsies collected from patients from both arms at baseline (N=68 patients total) and early on-therapy (N=51; 43 with paired timepoints) were analyzed by whole exome sequencing (n=185 samples), RNA sequencing (n=105), histopathologic staining (n=149), and multiplexed ion beam imaging (n=45). Multiple biopsies were available for some patients. Mutations, gene expression, and tumor microenvironment were compared across timepoints and response to combination (N=18 responders [CR/PR], N=44 nonresponders [SD/PD]). Results: Baseline biopsies from patients responsive to combination had increased expression of genes (n=482, FDR<0.05) associated with coagulation and complement, fatty acid metabolism, oxidative phosphorylation, hypoxia, and interferon gamma response gene sets (FDR<0.05), compared to nonresponsive biopsies. Baseline biopsies from responders also had low levels of effector CD8 T cells (PD1+, TIM-3+, GZMB+, Ki67+) colocalized with tumor cells and myeloid populations expressing higher levels of MHC Class II. On-therapy biopsies from responders showed decreased detection of driver mutations by genomics, reduced gene expression of pathways enriched at baseline (oxidative phosphorylation, complement) by transcriptomics, and increased CD8 T cell to tumor cell ratios by histopathology, supporting observations of tumor regression. On-therapy biopsies from responders also had increased gene expression of genes related to inflammatory cytokine signaling. This correlated with increased proportions of effector CD8 T cells, compared to paired baseline or nonresponding biopsies, and increased organization of nonactivated CD8 T cells near mature endothelial structures (SMA+, CD31+ regions) adjacent to tumor. Biopsies from nonresponders did not demonstrate these dynamics and instead contained exhausted CD8 T cells (PD1+, TIM-3+, granzyme B-, Ki67-) colocalized with FOXP3+, CD4+ Tregs and CD163+, PD-L1+ M2 macrophages, both at baseline and on-therapy. Conclusion: In patients with melanoma refractory to anti-PD-1, addition of anti-CTLA-4 facilitates tumor-reactive CD8 T-cell infiltration and decreased suppressor cell dynamics, resulting in regression of some tumors with distinct transcriptome features. Conversely, biopsies from patients whose tumors progress on combination therapy lack expression of metabolic pathways and show CD8 T-cells restricted in proximity to M2 macrophages and Tregs. Citation Format: Katie M. Campbell, Zaid Bustami, Daniel G. Chen, Egmidio Medina, Cynthia R. Gonzalez, Nataly Naser Aldeen, Ignacio Baselga-Carretero, Agustin Vega-Crespo, Jessica Maxey, Jia M. Chen, Lawrence F. Kuklinski, Kari L. Kendra, Bartosz Chmielowski, Thach-Giao Truong, Nikhil I. Khushalani, Frances Collichio, Alexandra Ikeguchi, Adrienne I. Victor, Kim Margolin, Jeffrey A. Sosman, Sapna P. Patel, Siwen Hu-Lieskovan, James Moon, Shay Bellasea, Daniel K. Wells, Christine N. Spencer, Marshall A. Thompson, Michael Wu, Philip O. Scumpia, Ari VanderWalde, Antoni Ribas. Biopsy analysis of trial S1616: Ipilimumab plus nivolumab versus ipilimumab alone in patients with anti-PD-1 refractory melanoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 6550.