Sarcoma, Kaposi study with OTHER data on dbGaP (16 participants)

phs003800 — Single-Cell Transcriptomic Analysis of Kaposi Sarcoma

Summary: Single-cell transcriptome analysis of skin and blood samples from individuals with Kaposi's sarcoma Aims: Elucidate the cellular composition and gene expression profiles of Kaposi sarcoma herpesvirus (KSHV) infected cells and non-infected tumor infiltrating cells, and peripheral blood samples from the same individuals, with or without specific therapies, such as antiretroviral therapy for HIV, immunotherapies (such as immune checkpoint inhibitors and immune modulator drugs like pomalidomide), or angiogenesis inhibitory agents. Population: Age 18 and older, both genders, including individuals from North America and other areas of the world (including Africa). Individuals with or without HIV are included. Molecular Technologies: Single-cell RNAseq using 10x Genomics Principal Findings: <ol><li>Two distinct populations of endothelial cells were found infected with KSHV, one <a href="https://www.ncbi.nlm.nih.gov/gene/947">CD34</a>+ and one <a href="https://www.ncbi.nlm.nih.gov/gene/947">CD34</a>-</li><li>Both clusters include lytic and latent KSHV gene expression</li><li>The KSHV infected cell clusters differ in expression of housekeeping genes, proliferative markers, ribosomal and secretory vesicle genes</li><li>Biomarkers of KSHV infected cells were identified, including sodium channel <a href="https://www.ncbi.nlm.nih.gov/gene/6335">SCN9A</a> </li><li>Changes in cell composition with therapy are noted </li><li>Clonal amplification of TCR+ T-cells were noted in the skin and blood </li></ol>Data Available through dbGaP: scRNA-seq dataversion 2 of this study adds data for a single case (KS14) that was submitted for publication as a case report.