Spatial and bulk transcriptomic analysis of skin Kaposi sarcoma lesions: Differences by disease characteristics.

Abstract

11530 Background: Kaposi sarcoma (KS) is an angioproliferative tumor caused by Kasposi sarcoma herpesvirus (KSHV) that typically manifests as skin lesions. Other KSHV-associated disease (KAD) that can occur with KS include multicentric Castleman disease (MCD), primary effusion lymphoma (PEL) and KSHV-associated inflammatory cytokine syndrome (KICS). KS with concurrent KAD, which occurs frequently in people with HIV (PWH), contributes to morbidity and mortality. Novel sequencing technologies that evaluate archival KS may further our understanding of HIV-associated KS pathogenesis. Methods: Gene expression profiling of archival KS skin samples of 42 PWH was performed with the custom nCounter PanCancer ImmunoOncology panel with the addition of KSHV probes. Spatial RNA profiling was performed using GeoMx digital spatial profiling (DSP) platform on 4 formalin fixed paraffin-embedded tissue sections randomly selected from patients (pts) with concurrent KS and KAD. LANA, CD45, and CD31 expression in samples identified KS (LANA + , CD31 +) ) and other areas of interest (AOIs) including vessels (LANA - , CD31 + ) and immune cells (CD45 + ) on tissue sections. Gene Set Enrichment analysis was performed using R package ClusterProfiler. Results: Samples were taken from 42 men with HIV with a median age of 40 years. The median CD4 T cell count was 211 cells/ µl and a median HIV viral load of 27 copies/ml. Fifty-two percent of pts with KS had a concurrent KAD, most commonly KICS with KS (30%) followed by MCD with KS (19%). In nCounter analyses, samples from pts with KS alone demonstrated upregulation of STC1, a secreted glycoprotein, (log2FC=2.02, padj=0.001) and MKI67, a proliferation marker, (log2FC=1.11, padj=0.02) as compared to pts with KS and concurrent KAD. Pathway analyses highlighted reduced enrichment in specific cytokine activity profiles (padj = 0.01), natural killer cell activation markers (padj=0.02), and B cell proliferation (padj=0.004), in KS with concurrent KAD specimens. Cell deconvolution analyses showed increased abundance of CD8 T cells and regulatory T cells in KS alone specimens as compared to those with KS and other KAD. DSP of 4 samples of pts with KS and concurrent KAD (2 pts with MCD+ KS, 2 pts with KICS+ KS) identified higher expression of TSPAN (log2FC=1.32, padj=0.04) and LYVE1 (log2FC=1.82, padj=9.17e-5) in LANA+ tumor regions than vessel and immune AOIs, and lower ICAM1 (log2FC=-1.08, padj=3.95e-6), highlighting the role of virus-infected areas in oncogenesis and modulating immune activity. Conclusions: Sequencing data of archival HIV-associated KS samples highlighted distinct gene expression profiles by concurrent KAD, particularly in MCD or KICS, demonstrating disruptions in immune activity and increased cell proliferation thus shedding light on the molecular pathways driving KS pathogenesis and avenues for future targeted study.