Homo sapiens Raw sequence reads

Inadequate T-cell control of Kaposi sarcoma-associated herpesvirus infection is thought to contribute to the development of Kaposi sarcoma, but little is known about the T-cell response to KSHV. Postulating that KS tumors are likely to contain abundant T-cells specific for KSHV, we defined the T-cell receptor repertoire of 299 KS tumor biopsies and 64 samples of uninvolved axillary skin from 106 adults with epidemic KS and 38 with endemic KS from Uganda. We also performed transcriptional profiling of 51 KS tumors using bulk RNA sequencing and 27 tumors using targeted gene expression analysis, respectively. Deconvolution of immune cell types from the bulk RNA-Seq data suggests that the tumor micro-environment in KS contains CD8 T-cells and abundant macrophages with M2 polarization, and targeted gene expression analysis confirms increased expression of M2 macrophage and CD8 T-cell markers. Repertoire analysis reveals that the populations of T-cells infiltrating KS tumors are diverse and largely private to the individual from which they were obtained but shared across non-contiguous tumors obtained from the same individual and across metachronous lesions biopsied at different time points over one year. T-cells with predicted specificity for pathogens such as CMV, EBV, HIV-1, and Mtb, or defined human tissue antigens, comprise less than 1 percent of the tumor-infiltrating lymphocytes in KS tumors. Clusters of T-cells with computationally predicted shared major histocompatibility complex associated specificity for unknown antigens - a subset of which we hypothesize are encoded by KSHV comprise approximately 25 percent of KS TIL. These specificity groups are shared not only across synchronous and metachronous lesions from individual subjects but also across individuals sharing one or more MHC alleles. We performed TCR alpha/beta chain sequencing and transcriptional profiling of single T-cells in 20 peripheral blood samples from 9 individuals in our cohort, 5 with epidemic and 4 with endemic KS, and captured the TCRs expressed in 14,698 cells from these putative KSHV-specific T-cell clusters, 4,283 of which were unique. Collectively, our results support the existence of a systemic, persistent, MHC-restricted KSHV-specific T-cell response in individuals with KS that is potentially inhibited by M2 macrophages within the TME, and lay a foundation for future studies to define the specificity of that T-cell response at large scale.