Virus host interactions in clinical samples

Division Of Basic Sciences - Nci

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Abstract

In collaboration with Drs. Yarchoan, Ramaswami, Lurain, and Krug in HAMB, we have been investigating human and viral gene expression patterns in normal tissue, in Kaposi sarcoma (KS), and other KSHV-infected pathological tissues. Little is known about cellular and viral RNA transcripts in KS lesions and how these factors are influenced by prior therapy, concurrent KSHV-associated diseases, or the tissue location of KS lesions. We sought to understand how human gene expression and viral transcripts are altered in KS as compared to normal tissue using matched patient samples. In this study of participants with well-annotated clinical characteristics, we also investigated both skin and GI KS to determine differences in the viral and host transcripts between these lesions. We determined whether there were differences in immune environment by the location of the KS lesion or clinical characteristics. Specific cellular genes of interest that were linked to pathogenesis of KS or KSHV infection were investigated with in vitro studies using lymphatic endothelial cells (LECs) infected with KSHV to study and determine the significance of these findings from patient samples. We compared the cellular and KSHV gene expression signatures of skin and GI KS lesions. Skin and GI KS were compared to normal matched samples using bulk RNA sequencing. Twenty-two paired samples of KS and normal tissue were obtained (skin (10 pairs) and GI (12 pairs)) from 19 patients with KS of whom 17 had concurrent HIV infection. Seven paired samples were from patients who had received prior KS therapy. Three patients provided both skin and GI samples at the same timepoint. These analyses identified 370 differentially expressed genes unique to cutaneous KS and 58 DEGs unique to GI KS compared to normal skin or GI tissues. Twenty-six differentially expressed genes overlapped between skin and GI KS, which included FLT4, which encodes for a VEGF-C and VEGF-D receptor, and STC1. KSHV infection of primary lymphatic endothelial cells (LECs) resulted in increased angiogenesis, and repression of STC1 or FLT4 inhibited angiogenesis. The analyses of KSHV expression from KS lesions identified certain lytic genes, specifically ORF75, that were consistently expressed, and these expression patterns differed from laboratory infection of LECs with KSHV and KSHV gene expression in PEL cell lines. This study demonstrates that complex patterns of gene expression are found in KS tissue that differ from the canonical latent/lytic programs seen in KSHV cell lines and also demonstrates differences in viral gene and clinically relevant host gene expression in skin and GI KS that may offer insights into the pathogenesis of these forms of KS.