Single-cell profiling of acral melanoma infiltrating lymphocytes reveals a suppressive tumor microenvironment

Acral lentiginous melanoma (ALM) is the most common melanoma subtype in non-Caucasians. Despite advances in cancer immunotherapy, current immune checkpoint inhibitors remain unsatisfactory for ALM. Hence, we conducted comprehensive immune profiling using single-cell phenotyping with reactivity screening of the T cell receptors of tumor-infiltrating T lymphocytes (TILs) in ALM. Compared with cutaneous melanoma, ALM showed a lower frequency of tumor-reactive CD8 clusters and an enrichment of regulatory T cells with direct tumor recognition ability, suggesting a suppressive immune microenvironment in ALM. Tumor-reactive CD8 TILs showed heterogeneous expression of coinhibitory molecules, including KLRC1 (NKG2A), in subpopulations with therapeutic implications. Overall, our study provides a foundation for enhancing the efficacy of immunotherapy in ALM. Single-cell immune profiling of tumor-infiltrating lymphocytes from primary and metastatic human acral lentiginous melanoma was conducted. Individual cells were dissociated from fresh tumor resections, and tumor-infiltrating lymphocytes were isolated by FACS based on CD3CD45 staining. Single-cell 5' RNA-seq and paired full-length TCR-seq were performed using the 10X Genomics Chromium platform, and the samples were sequenced on the Illumina NextSeq HiSeq X Ten. RNA-seq data were obtained for the parental fresh tumor samples and the tumor cell line from two patients.