Spatial and bulk transcriptomics reveal distinct molecular signatures in Kaposi sarcoma with and without other KSHV-associated diseases.

BACKGROUND: Kaposi sarcoma (KS) is an angioproliferative tumor caused by Kaposi sarcoma herpesvirus (KSHV) that occurs in people with HIV. Concurrent KSHV-associated diseases (KAD), including multicentric Castleman disease, primary effusion lymphoma, and KSHV-associated inflammatory cytokine syndrome may modify KS biology and impact clinical outcomes. Transcriptomic profiling of archival KS tissue enables investigation of molecular heterogeneity associated with these overlapping disease states. METHODS: Archival formalin-fixed paraffin-embedded (FFPE) KS skin biopsies from 42 patients with HIV-associated KS between 2017 and 2022 were analyzed based on confirmed histopathologic diagnosis, tissue adequacy for RNA profiling, and availability of linked clinical data. Bulk transcriptomic analyses were conducted using Nanostring nCounter PanCancer ImmunoOncology panel supplemented with KSHV-specific probes. Spatial RNA profiling was performed on four tissues from participants with KS and concurrent KAD (KS+KAD) using GeoMx digital spatial profiling (DSP) platform. Regions of interest were selected using LANA-1, CD45 and CD31 staining to characterize tumor (LANA-1+, CD31(+)), vessel (LANA-1-negative, CD31(+)) and immune cells (CD45(+)) areas. For bulk transcriptomic analyses and spatial transcriptomic analyses, p-values were adjusted for multiple comparisons using the Benjamin-Hochberg FDR approach, and adjusted p-values (padj) are reported. RESULTS: KS samples were obtained from 42 men with HIV (median age 40 years). Median HIV viral load of 27 copies/mL and median CD4(+) T-cell count was 211 cells/µL. Forty-eight percent had KS alone and 52% had KS+KAD. Patients with KS+KAD had worse survival compared to those with KS alone. Transcriptomic analyses identified increased expression of STC1 (log2FC = 2.02, padj = 0.001), a secreted glycoprotein, and MKI67 (log2FC = 1.11, padj = 0.02), a common proliferation marker, in KS+KAD lesions, along with lower expression of cytokine-associated pathways. Spatial RNA profiling from 4 KS samples from patients with KS+KAD identified increased abundance of lymphatic endothelial cells, elevated LYVE1 expression in LANA-1+ tumor areas as compared to LANA-negative areas. CONCLUSIONS: Bulk and spatial transcriptomic profiling of archival HIV-associated KS lesions revealed disease-specific molecular programs associated with concurrent KAD that altered tumor and microenvironment features. These findings demonstrate the heterogeneity of HIV-associated KS lesions that may guide future studies on KS pathogenesis and potential therapeutic targets. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12967-026-07976-8.