Background Acral melanoma (AM) is a rare cancer with distinct genotypic and phenotypic characteristics as compared to cutaneous melanoma (CM). While UV radiation-induced CM exhibits a relatively high response rate to immune checkpoint inhibitors (ICI), the response in AM is poor.¹ Tumor-intrinsic mechanisms of immune exclusion have been identified in many cancers but less studied in AM.^{2 3}

Methods We characterized clinically annotated tumors from patients diagnosed with AM at our institution in correlation with ICI response using whole transcriptome RNAseq, whole exome sequencing, CD8 immunohistochemistry, and multispectral immunofluorescence imaging. A defined interferon-γ-associated T cell-inflamed gene signature was used to categorize tumors into non-T cell-inflamed and T cell-inflamed phenotypes. In combination with AM tumors from two published studies, we systematically assessed the immune landscape of AM and detected differential gene expression and pathway activation in a non-T cell-inflamed tumor microenvironment (TME). Two single-cell(sc) RNAseq AM cohorts and 11 bulk RNAseq cohorts of various tumor types from 891 patients were used for independent validation on pathways associated with lack of ICI response.

Results A majority of AM tumors showed low expression of the T cell-inflamed gene signature (72.5%), including 23.9% grouped as non-T cell-inflamed. Patients of low CD3⁺CD8⁺PD1⁺ intratumoral T cell density showed poor prognosis. We identified 11 oncogenic pathways significantly upregulated in non-T cell-inflamed relative to T cell-inflamed TME shared across all three acral cohorts (MYC, HGF, MITF, VEGF, EGFR, SP1, ERBB2, TFEB, SREBF1, SOX2, and CCND1). scRNAseq analysis revealed that tumor cell-expressing pathway scores were significantly higher in low vs high T cell-infiltrated AM tumors. We further demonstrated that the 11 pathways were enriched in ICI non-responders compared to responders across cancers, including acral melanoma (figure 1A), cutaneous melanoma (figure 1B), triple-negative breast cancer, and non-small cell lung cancer. Pathway activation was associated with low expression of interferon stimulated genes, suggesting suppression of antigen presentation. Across the 11 pathways, fatty acid synthase and CXCL8 were unifying downstream target molecules suggesting potential nodes for therapeutic intervention.

Conclusions A unique set of pathways is associated with immune exclusion and ICI resistance in AM. These data may inform immunotherapy combinations for immediate clinical translation.

References

1. Nakamura Y, Namikawa K, Yoshino K, et al. Anti-PD1 checkpoint inhibitor therapy in acral melanoma: a multicenter study of 193 Japanese patients. Ann Oncol. 2020;31(9):1198–1206. doi:10.1016/j.annonc.2020.05.031

2. Riaz N, Havel JJ, Makarov V, et al. Tumor and Microenvironment Evolution during Immunotherapy with Nivolumab. Cell. 2017;171(4):934–949.e16. doi:10.1016/j.cell.2017.09.028

3. Liu D, Schilling B, Liu D, et al. Integrative molecular and clinical modeling of clinical outcomes to PD1 blockade in patients with metastatic melanoma. Nat Med. 2019;25(12):1916–1927. doi:10.1038/s41591-019-0654-5

Ethics Approval This study was approved by the University of Pittsburgh Institutional Review Board (Protocol No. 20090109).

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Abstract 888 Figure 1

(A) Comparison of 11 pathways in acral melanoma (AM) samples from patients who showed clinical benefit (CB) or not (NCB) to ICI (Hillman Cancer Center (HCC) AM cohort, n = 14 shown). (B) Comparison of 11 pathways in cutaneous melanoma (CM) samples from patients who received ICI [2,3]. * P <0.05 after FDR adjustment for multiple comparisons.