Transcriptomic landscape of Kaposi sarcoma: Insights into therapeutic targeting of KSHV.

Abstract

e23526 Background: Kaposi sarcoma (KS) is a tumor caused by Kaposi sarcoma herpesvirus (KSHV), also known as human herpesvirus 8 (HHV-8). Unlike other virus-associated tumors, where disease progression often continues even after viral eradication, KS requires the persistent presence of KSHV for disease progression. This unique dependency underscores the potential of strategies targeting the virus to also target the tumor. This study aims to characterize the expression of KSHV viral proteins and identify factors associated with differences in viral gene expression, ultimately formulating treatment targets. Methods: A total of 43 unique samples were collected at a single academic institution between 2001 and 2024. RNA was extracted from formalin-fixed paraffin-embedded (FFPE) tissue blocks and subjected to bulk RNA sequencing. Reads were mapped to the human genome (GRCh38.p14) using STAR and to the KSHV genome (NC_009333) using Salmon. Transcript abundance in units of Transcripts Per Million (TPM) and estimated read counts to each transcript was quantified with Salmon. Clinical and demographic data from the time of sample collection were extracted from medical records. Differential gene expression analysis, PCA using DESeq2 and hierarchical clustering were done in R. Results: The 43 samples analyzed were derived from 25 patients, with 23 (92%) being male. Of the 18 patients with known HIV status, 4 (22%) were HIV-positive. None had a history of organ transplantation. Among the 14 patients with available disease status, 5 (38%) had disseminated disease at the time of sample collection. KSHV gene expression was detected in 42 out of 43 samples. The most consistently expressed genes across all samples were ORF75 (42 samples, proximal to the poly-A tail), ORF72/v-cyclin (42 samples), and ORF73/LANA (39 samples). A pronounced pattern of high expression was observed in the latency-associated region of the KSHV genome, which was conserved across all KS tumors. The three clusters of samples generated from hierarchical clustering exhibited different lytic and latent gene profile (lytic, latent, mixed), which are similar to previous studies. The differentially expressed genes between different tumor morphology or HIV status of the host showed a mix profile of lytic and latent genes. Conclusions: This study highlights the latency-associated region of KSHV as the most consistently and highly expressed region, regardless of baseline characteristics, presenting a potential conserved therapeutic target.