Fig. 4: Immune microenvironment of uveal melanomas with V(D)J recombination repertoire sequencing of B- and T- lymphocytes.

a t-SNE plot of 9441 single immune cells present in the TME. b Heatmap of averaged RNA expression of immune cell clusters. c Three-dimensional bar chart of immune cell subtypes as a percentage of immune cell population for each tumor. d Single-cell V(D)J recombination repertoire sequencing of T cells from 10 primary and metastatic UMs and B cells from an indolent class 1B metastasis. Red, clonotypes ≥4% T cell frequency; purple, clonotypes <4% and ≥2.5% T cell frequency; blue, clonotypes <2.5% and ≥1.5% T cell frequency; gray, all remaining clonotypes <1.5% T cell frequency. Source data are provided as a Source Data file. e Ridge plot of CD8⁺ T cell subset demonstrating strong expression of LAG3, moderate expression of TIGIT, and minimal expression of PD1, CTLA4, TIM3, and TNFRSF9. f Quantification of multi-color IHC for CD8, LAG3, PD1, CTLA4, and DAPI. 18 total samples were analyzed by IHC including 7 that were analyzed by scRNA-seq and an additional 11 samples. Metastatic samples include BSSR0022 and UMM067L. Other samples represent primary tumors. Quantitation of each sample was performed by whole-slide scanning of a single slide. Source data are provided as a Source Data file. g Representative multi-color IHC images of a primary and a metastatic class 2 UM stained for CD8, LAG3, PD1, CTLA4, and DAPI (scale bar, 50 μm).