Quantitative Proteomics Analysis of Lytic KSHV Infection in Human Endothelial Cells Reveals Targets of Viral Immune Modulation

Kaposi’s sarcoma herpesvirus (KSHV) is an oncogenic human virus and the leading cause of mortality in HIV infection. KSHV reactivation from latent- to lytic-stage infection initiates a cascade of viral gene expression. Here we show how these changes remodel the host cell proteome to enable viral replication. By undertaking a systematic and unbiased analysis of changes to the endothelial cell proteome following KSHV reactivation, we quantify >7,000 cellular proteins and 71 viral proteins and provide a temporal profile of protein changes during the course of lytic KSHV infection. Lytic KSHV induces >2-fold downregulation of 291 cellular proteins, including PKR, the key cellular sensor of double-stranded RNA. Despite the multiple episomes per cell, CRISPR-Cas9 efficiently targets KSHV genomes. A complementary KSHV genome-wide CRISPR genetic screen identifies K5 as the viral gene responsible for the downregulation of two KSHV targets, Nectin-2 and CD155, ligands of the NK cell DNAM-1 receptor. [Display omitted] •Quantitative proteomics identifies changes in host proteins induced by lytic KSHV•Targeting KSHV with CRISPR identifies CD155 and Nectin-2 as KSHV K5 substrates•Lytic KSHV downregulates protein kinase R in human endothelial cells•Kinetic profiling of lytic KSHV unravels PAA-sensitive and ORF57-dependent proteins Gabaev et al. describe how a human oncogenic herpesvirus, KSHV, changes the proteome of endothelial cells and modulates the host immune system. By targeting KSHV with CRISPR, they show that viral K5 protein downregulates ligands for the NK cell DNAM-1 receptor and antiviral protein PKR is depleted in an K5-independent manner.