Abstract 5014: Integrative molecular and spatial analysis to reveal tumor intrinsic and extrinsic drivers of immunotherapy response in mucosal melanoma
Authors: Yingxiao Shi, Tuulia Vallius, Aikaterini Dedeilia, Roxanne Pelletier, Jia-Ren Lin, Mariana Lopez Leon, Christine Lian, Shishir Pant, Giuseppe Tarantino, Annette Wang, Jiajia Chen, Elizabeth I. Buchbinder, Peter K. Sorger, David Liu, Genevieve M. Boland
Journal: Cancer Research (2025)

Abstract Background: Mucosal melanoma (MM) is a rare subtype of melanoma that responds poorly to immune checkpoint blockade (ICB), exhibiting low response rates and few durable responses. The biological mechanisms underlying ICB response and resistance in MM remain poorly understood, highlighting the need for novel therapeutic targets and biomarkers to improve patient outcomes. Hypothesis: While most MM patients respond poorly to ICB, a subset of durable responders (DRs) exists. We hypothesize that DRs have distinct biological and genomic features compared to rapid progressors. Methods: We performed multimodal analysis - including whole exome sequencing, bulk transcriptomics, H&amp;E, and multiplexed Cyclic Immunofluorescence (CyCIF) imaging - on pre-treatment and post-progression tumor samples from 126 MM patients, with a focus on a subset of 80 patients treated with ICB to identify features associated with response. Results: Our genomic analysis of 80 MM patients revealed that DRs (PFS ≥ 1 year) had significantly fewer copy number alterations (CNAs) compared to those with progressive diseases (PFS ≤ 6 months). The most common MM driver mutations were identified including SF3B1, KIT, NF1, and NRAS. Notably, SF3B1 mutations were primarily found in anorectal primary tumors (10/17) and had fewer CNAs, a feature also observed in DRs, suggesting it may be associated with better ICB responses in MM. Bulk RNAseq analysis (n = 67) identified a tumor cluster enriched for epithelial-mesenchymal transition and hypoxia stress pathways, suggesting increased invasiveness and potential ICB resistance. These signatures were observed in 37% of our MM primary tumors, underscoring the aggressive nature of MM. CyCIF analysis of primary and metastatic MM lesions revealed increased CD8+ T cells and CD11C+ myeloid cells in metastatic sites. By defining the tumor/stromal border, we found fewer antitumorigenic CD68+ macrophages in the tumor center but more at the tumor border at the metastatic site compared to the primary sites, suggesting immune exclusion. In sinonasal primary tumors, non-metastatic patients had fewer protumorigenic CD163+ macrophages in both tumor center and border compared to those with distant metastases. Multimodal analysis of a longitudinally sampled MM patient treated with ICB showed distinct resistance clones associated with different microenvironments. Two lymph node metastases collected simultaneously after ICB showed clonal differences, with one (harboring a SOX17 mutation) exhibiting lower CD8+ T cell infiltration, suggesting the evolution of diverse resistance mechanisms. Conclusion: Our preliminary findings suggest that distinct genomic features, tumor states, and microenvironments differentiated ICB response and disease progression in MM, highlighting key tumor-intrinsic and microenvironmental factors associated with patient prognosis. Citation Format: Yingxiao Shi, Tuulia Vallius, Aikaterini Dedeilia, Roxanne Pelletier, Jia-Ren Lin, Mariana Lopez Leon, Christine Lian, Shishir Pant, Giuseppe Tarantino, Annette Wang, Jiajia Chen, Elizabeth I. Buchbinder, Peter K. Sorger, David Liu, Genevieve M. Boland. Integrative molecular and spatial analysis to reveal tumor intrinsic and extrinsic drivers of immunotherapy response in mucosal melanoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 5014.