Abstract Description Melanoma patients treated with anti-PD1 or anti-PD1/anti-CTLA4 present intrinsic or acquired resistance to these immune checkpoint blockade (ICB) treatments. However, the interactions between tumor-stromal-immune cells in the microenvironment (TME) underlying these resistances remain unclear. In this study, we used a cohort of melanoma patients (n = 61) treated with ICB, pre-treatment (n = 33) and post-progression (n = 28), for whole-exome sequencing, single-nucleus RNA sequencing and high-resolution spatial imaging. We developed a framework to analyze response and resistance (intrinsic and acquired) via tumor-intrinsic programs, immune features, and tumor-stromal-immune interactions. Patients with low immune infiltration exhibited enrichment of macrophages associated with hypoxia and angiogenesis phenotypes. Samples with high immune infiltrates displayed an enrichment in lymphocytes, particularly TCF7+ CD8+ T cells. Pre-treatment samples from patients experiencing durable clinical benefit are encriched in memory B cells and plasmablast-like B cells.The presence of Bcells and of follicular dendritic cells in non-lymph node biopsies support the presence of tertiary lymphoid structures within the TME. Lastly, the presence of a TIMD4-expressing macrophage subset correlates with lymphocyte infiltration, indicating its potential role in promoting anti-tumor immunity. Our work defines TME immune profile interaction with tumor-stromal cells associated with clinical outcomes in melanoma. Funding Sources NCI HTAN Topic Categories Tumor Immunology: Checkpoints, Prevention, and Treatment (TIPT)
Tarantino et al. (2025) studied this question.