Single-cell RNA-sequencing of herpes simplex virus 1-infected cells connects NRF2 activation to an antiviral program

Abstract

Herpesvirus infection initiates a range of perturbations in the host cell, which remain poorly understood at the level of individual cells. Here, we quantify the transcriptome of single human primary fibroblasts during the first hours of lytic infection with HSV-1. By applying a generalizable analysis scheme, we define a precise temporal order of early viral gene expression and propose a set-wise emergence of viral genes. We identify host cell genes and pathways relevant for 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 correlates with increased resistance to infection, implicates the transcription factor NRF2. Consequently, Bardoxolone methyl and Sulforaphane, two known NRF2 agonists, impair virus production, suggesting that NRF2 activation restricts viral infection. Our study provides insights into early stages of HSV-1 infection and serves as a general blueprint for the investigation of heterogeneous cell states in virus infection.

Bulk and single-cell gene expression profiling of SARS-CoV-2 infected human cell lines identifies molecular targets for therapeutic intervention

“…RNA was isolated from Trizol using the RNA clean and concentrator kit (Zymo). The RNA was reverse transcribed using maxima RT and subjected to qPCR as described [26]. Primers used for qPCR are listed in supplementary table 5.…”

“…All analysis shown in figure 4-6 was done similar as described previously [26] using Seurat and ggplot2 packages [101,102].…”

“…A recent in-depth analysis of the transcriptional response to SARS-CoV-2 in comparison to other respiratory viruses in cells and animal models revealed a virus-specific inflammatory response [21]. Of particular interest are methods such as single-cell RNAsequencing (scRNA-seq), which allow the characterization of heterogeneity over the course of infection, which may be masked at the population level [22][23][24][25][26][27], but also small RNA sequencing, which reveals miRNAs and other small RNAs [28,29].…”

VIRTUS: a pipeline for comprehensive virus analysis from conventional RNA-seq data

“…We next applied VIRTUS to droplet-based single-cell RNA-seq data of human primary fibroblasts infected with Herpes simplex virus 1 (HSV-1) (Wyler et al, 2019) ( Fig.1d,e). First, we conducted pooled screening of viruses, in which all reads from all cells were assigned at once, and detected HSV-1 in the samples.…”

Nrf2 Activator PB125®as a Potential Therapeutic Agent Against COVID-19

“…Among the types of virus studied are influenza virus, respiratory syncytial virus (RSV), and human metapneumovirus (hMPV) [9][10][11][12][13]. The phenomenon is also seen in non-respiratory viruses including Dengue virus (DENV) [14], rotavirus [15], herpes simplex virus [16], Zika virus [17], and HIV [18], suggesting that regulation of oxidative stress may be a need common to most, if not all viruses, and that Nrf2 activators may offer multiple ways to regain control of important pathways to increase resistance and slow viral replication. We recently described a phytochemical composition, PB125, that potently activates Nrf2 by controlling multiple steps involved in the process, especially via the Akt1/PI3K/GSK3/Fyn pathway [19].…”