Integrative Functional Genomics Analysis of Kaposis Sarcoma Cohorts

Kaposi's sarcoma (KS) is an AIDS-defining cancer and a significant global health challenge caused by Kaposi's sarcoma-associated herpesvirus (KSHV). KS lesions have been profiled by NGS-based approaches in a very limited number of studies compared with other neoplastic diseases. Here we present a compiled and harmonized dataset of 131 KS and non-tumor cutaneous samples in the context of their predicted pathway activities, immune infiltrate, KSHV and HIV gene expression profiles and their associated clinical data representing patient populations from Argentina, USA and Sub-Saharan Africa cohorts. First, RNA-seq data from 9 Argentinian KS lesions were generated and integrated with previously published datasets derived form USA and sub-Saharan African cohorts from Tanzania, Zambia and Uganda. Second, the compiled RNA-seq profile is shared with the research community through the UCSC Xena browser for further visualization, download and analysis (http://xena.ucsc.edu/). Third, unsupervised analysis of 131 KS related samples allowed us to identify four KS clusters based on their host and KSHV gene expression profiles, immune infiltrate and in the activity of specific signaling pathways. These resources will allow biologists without bioinformatics knowledge to explore and correlate the host and viral (KSHV and HIV) transcriptome in a curated dataset of different KS RNA-seq-based cohorts, which can lead to novel biological insights and biomarker discovery. Overall design: Nine KS skin lesions were collected from an Argentinian cohort of Men who have Sex with Men (MSM) and Transgender Women (TGW) with HIV.