Single-cell RNA-sequencing of Herpes simplex virus 1-infected cells identifies NRF2 activation as an antiviral program

Abstract

<jats:title>Abstract</jats:title><jats:p>Herpesvirus infection initiates a range of perturbations in the host cell, which remain poorly understood at the level of individual cells. Here, we quantified the transcrips of single human primary fibroblasts during the first hours of lytic infection with HSV-1. By applying a generalizable analysis scheme, we defined a precise temporal order of early viral gene expression and found unexpected bifurcations and bottlenecks. We identified individual host cell genes and pathways relevant in early infection by combining three different computational approaches: gene and pathway overdispersion analysis, prediction of cell-state transition probabilities as well as future cell states. One transcriptional program, which was turned on in infected cells and correlated with increased resistance to infection, implicated the transcription factor NRF2. Consequently, Bardoxolone methyl, a known NRF2 agonist, impaired virus production, suggesting that NRF2 activation restricts the progression of viral infection. Our study provides novel insights into early stages of HSV-1 infection and serves as a general blueprint for the investigation of heterogenous cell states in virus infection.</jats:p>

Functional single-cell genomics of human cytomegalovirus infection

“…Measuring tens of thousands of singlecell transcriptomes provides a massively parallel way of testing large numbers of genetic perturbations under controlled conditions with a high-dimensional readout. The single-cell nature of this approach makes it particularly well suited for studying virus infection, a process with great inherent vari-ability from cell to cell (42)(43)(44)(45)(46). To lay the groundwork for the Perturb-seq analysis, we explored the spectrum of cellular states in response to infection by recording single-cell transcriptomes from cells sampled from eight time points with two multiplicities of infection each ( Fig.…”

Single-virus genomics and beyond

“…Studying virus-hosts pairs goes beyond DNA; for example, single-cell RNA sequencing has reveals valuable biological insights into the interactions of single cells infected with one virus in different human infections, such as dengue, herpes simplex or influenza [140][141][142] . Single-cell RNA-seq of herpex simplex virus 1-infected cells has shed some light into early stages of infection and connected metabolic activation of viral pathways with antiviral programs 142 .…”

Immunology Driven by Large-Scale Single-Cell Sequencing

“…Recent studies identified marker genes that defined populations of human CD4 + T cells that were more prone to HIV-1 infection than others [62]; moreover, transcriptional programs defining HIV-1 latency and reactivation in host cells were analyzed simultaneously, revealing that not all cells were infected in the same way, and that the rate of CD4 + T cell invasion could be affected by the virus genotype [63]. Viral molecules can also be sequenced together with the host transcriptome to quantify viral loads of infected cells, which can have a significant impact in the interpretation of immune responses to intracellular pathogens [64][65][66][67].…”