Proteomic landscape of Japanese encephalitis virus-infected fibroblasts

Abstract

Advances in proteomics have enabled a comprehensive understanding of host–pathogen interactions. Here we have characterized Japanese encephalitis virus (JEV) infection-driven changes in the mouse embryonic fibroblast (MEF) proteome. Through tandem mass tagging (TMT)-based mass spectrometry, we describe changes in 7.85 % of the identified proteome due to JEV infection. Pathway enrichment analysis showed that proteins involved in innate immune sensing, interferon responses and inflammation were the major upregulated group, along with the immunoproteasome and poly ADP-ribosylation proteins. Functional validation of several upregulated anti-viral innate immune proteins, including an active cGAS–STING axis, was performed. Through siRNA depletion, we describe a crucial role of the DNA sensor cGAS in restricting JEV replication. Further, many interferon-stimulated genes (ISGs) were observed to be induced in infected cells. We also observed activation of TLR2 and inhibition of TLR2 signalling using TLR1/2 inhibitor CU-CPT22-blocked production of inflammatory cytokines IL6 and TNF-α from virus-infected N9 microglial cells. The major proteins that were downregulated by infection were involved in cell adhesion (collagens), transport (solute carrier and ATP-binding cassette transporters), sterol and lipid biosynthesis. Several collagens were found to be transcriptionally downregulated in infected MEFs and mouse brain. Collectively, our data provide a bird’s-eye view into how fibroblast protein composition is rewired following JEV infection.

Human Guanylate-Binding Protein 1 Positively Regulates Japanese Encephalitis Virus Replication in an Interferon Gamma Primed Environment

“…Robust activation of GBPs in response to JEV infection at both the transcript and protein levels has been shown in our previous studies on human monocyte derived dendritic cells and mouse embryonic fibroblasts ( Chauhan et al., 2021 ; Sharma et al., 2021a ). Here, we found that GBP1 expression was markedly induced in human epithelial HeLa cells upon JEV infection, and interestingly GBP1 strongly colocalized with JEV-NS1 protein that marks the virus replication complex.…”

“…A detailed understanding of the host-virus interaction is critical for the development of effective antivirals ( Turtle and Solomon, 2018 ; Sharma et al., 2021b ). While there are a few reports that have suggested the induction of various interferon-stimulated genes (ISGs) at both transcription and protein levels during JEV infection ( Yang et al., 2011 ; Zhang et al., 2013 ; Chauhan et al., 2021 ; Sharma et al., 2021a ), the finer details of the innate immune landscape during JEV infection remain largely unexplored.…”

Deep proteomics network and machine learning analysis of human cerebrospinal fluid in Japanese encephalitis virus infection

“…There have been a handful of studies utilizing ELISA methods to target specific proteins, however these rarely used power calculations in their experimental design, nor did they include adequate controls (48)(49)(50)(51)(52)(53). Analysis of the transcriptome and proteome in animal models (54)(55)(56)(57)(58) and cell culture (48,54,(59)(60)(61)(62)(63)(64) have been performed, however the comparability to human CSF and comparison with other neurological infections is limited. Furthermore, mRNA expression does not directly correlate with that of the corresponding protein (65).…”

Let’s Get Physical: Flavivirus-Host Protein–Protein Interactions in Replication and Pathogenesis

“…Even though disrupting this interaction did not affect virus replication, it led to lower protein aggregates in mouse brain and reduced neurological symptoms. For JEV, Sharma et al (2021) have shown that autophagy acts as an antiviral response during JEV infection in neuronal cells. They also observed NS1 colocalization with LC3-I, an important autophagy protein whose depletion caused decreased viral titers.…”