{
  "abstract": "Background Mucosal melanoma (MM) is a rare and aggressive subtype that responds poorly to immune checkpoint blockade (ICB), with low response rates and limited durable benefit—underscoring the need for novel therapeutic targets and biomarkers. The biological mechanisms driving ICB response and resistance in MM remain poorly understood. Notably, a small subset of patients achieves durable responses (DRs), suggesting fundamental differences from rapid progressors. We hypothesize that DRs harbor distinct genomic and microenvironmental features associated with ICB sensitivity.Methods We performed multimodal analysis—including whole-exome sequencing, bulk transcriptomics, H&E staining, and multiplexed imaging—on pre-treatment and post-progression tumor samples from 126 mucosal melanoma (MM) patients, focusing on 80 ICB-treated cases to identify features associated with response.Results Genomic analysis of 80 MM patients revealed that DRs (PFS≥1 year) had significantly fewer copy number alterations (CNAs) compared to patients with progressive disease (PFS≤6 months). Common MM driver mutations were identified, including SF3B1, KIT, NF1, and NRAS. Notably, SF3B1 mutations were predominantly found in anorectal primaries (10/17) and harbored fewer CNAs—a feature also enriched in DRs—suggesting SF3B1 mutations may promote genomic stability and enhance ICB responsiveness.RNAseq analysis (n=67) identified a tumor cluster enriched for epithelial-mesenchymal transition and hypoxia stress pathways—features associated with poor ICB outcomes—suggesting increased invasiveness and potential resistance, and present in 37% of MM tumors.Spatial analysis of primary and metastatic lesions revealed increased infiltration of CD8+ T cells and CD11C+ myeloid cells at metastatic sites. By delineating the tumor-stromal interface, we observed distinct localization of CD68+ macrophages, with enrichment at the tumor border in metastatic tumors, indicative of immune exclusion. In sinonasal tumors, non-metastatic patients had fewer tumor-associated macrophages (TAMs; CD163+/CD206+) in both the tumor center and border compared to those who later developed distant metastases, suggesting TAM infiltration may predict metastatic potential. We also identified colocalization of TAMs and regulatory T cells (Tregs; CD4+/FOXP3+) with a tumor subpopulation, indicating a structured immunosuppressive niche. Notably, vulvar/vaginal MM tumors—associated with the poorest outcomes—exhibited marked enrichment of this suppressive microenvironment, underscoring its role in disease progression.Multimodal analysis of a longitudinally sampled MM patient treated with ICB revealed distinct resistance clones associated with different microenvironments. Two lymph node metastases collected post-ICB showed clonal differences; one (harboring a SOX17 mutation) exhibited lower CD8+ T cell infiltration, suggesting divergent resistance mechanisms.Conclusions Our findings suggest that distinct genomic features, tumor states, and microenvironments differentiate ICB response and progression in MM, highlighting key tumor-intrinsic and microenvironmental factors associated with prognosis.",
  "authors": [
    {
      "affiliations": [
        "Harvard Medical School, Boston, MA, USA"
      ],
      "name": "Yingxiao Shi"
    },
    {
      "affiliations": [
        "Massachusetts General Hospital, Boston, MA, USA"
      ],
      "name": "Aikaterini Dedeilia"
    },
    {
      "affiliations": [
        "Harvard Medical School, Boston, MA, USA"
      ],
      "name": "Jia-Ren Lin"
    },
    {
      "affiliations": [
        "Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA, USA"
      ],
      "name": "Roxanne J Pelletier"
    },
    {
      "affiliations": [
        "Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA, USA"
      ],
      "name": "Tuulia Vallius"
    },
    {
      "affiliations": [
        "Harvard Medical School, Boston, MA, USA"
      ],
      "name": "Mariana Lopez"
    },
    {
      "affiliations": [
        "Harvard University, Boston, MA, USA"
      ],
      "name": "Shishir M Pant"
    },
    {
      "affiliations": [
        "Dana-Farber Cancer Institute, Boston, MA, USA"
      ],
      "name": "Giuseppe Tarantino"
    },
    {
      "affiliations": [
        "Massachusetts General Hospital, Boston, MA, USA"
      ],
      "name": "Annette Wang"
    },
    {
      "affiliations": [
        "Brigham and Women’s Hospital, Boston, MA, USA"
      ],
      "name": "Christine G Lian"
    },
    {
      "affiliations": [
        "Dana-Farber Cancer Institute, Boston, MA, USA"
      ],
      "name": "Elizabeth I Buchbinder"
    },
    {
      "affiliations": [
        "Harvard Medical School, Boston, MA, USA"
      ],
      "name": "Peter K Sorger"
    },
    {
      "affiliations": [
        "Massachusetts General Hospital, Boston, MA, USA"
      ],
      "name": "Genevieve M Boland"
    },
    {
      "affiliations": [
        "Dana-Farber Cancer Institute, Boston, MA, USA"
      ],
      "name": "David Liu"
    }
  ],
  "title": "488 Integrative molecular and spatial analysis to reveal tumor intrinsic and extrinsic drivers of immunotherapy response in mucosal melanoma",
  "uid": "090526fc-f02e-57da-80fa-382bbc9d5af5"
}