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Diving into the proteomic atlas of SARS-CoV-2 infected cells: insights of viral infection in different cell types

ABSTRACT: The COVID-19 pandemic was initiated by the rapid spread of a SARS-CoV-2 strain. Though mainly classified as a respiratory disease, SARS-CoV-2 infects multiple tissues throughout the human body, leading to a wide range of symptoms in patients. To better understand how SARS-CoV-2 affects the proteome from cells with different ontologies, this work generated an infectome atlas of 9 cell models, including cells from brain, blood, digestive system, and adipocyte tissue. Our data shows that SARS-CoV-2 infection mainly trigger dysregulations on proteins related to cellular structure and energy metabolism. Despite these pivotal processes, heterogeneity of infection was also observed, highlighting many proteins and pathways uniquely dysregulated in one cell type or ontological group. These data have been made searchable online via a tool that will permit future submissions of proteomic data (https://reisdeoliveira.shinyapps.io/Infectome_App/) to enrich and expand this knowledgebase.

INSTRUMENT(S): Synapt MS

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Cell Culture

SUBMITTER: Licia C. Silva-Costa

LAB HEAD: Daniel Martins-de-Souza

PROVIDER: PXD050226 | Pride | 2024-02-29

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	CACO2.rar	Other
	CACO_2021_Pride_Complete_submission.DerivedFromSearchc6cf4331-1874-42ef-ae07-2ccc3982bc30.mgf	Mgf
	CACO_2021_Pride_Complete_submission.mzid.gz	Mzid
	CACO_Peptides.csv	Csv
	CACO_Proteins.csv	Csv

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Project description:Coronaviruses belong to a well-known family of enveloped RNA viruses and the causative agent of the common cold. Although the seasonal coronaviruses do not pose a threat to human life, three members of this family, i.e., SARS-CoV, MERS-CoV and recently, SARS-CoV2, may cause severe acute respiratory syndrome that may lead to death. Unfortunately, COVID-19 has already caused more than 4,4 million deaths worldwide. Although much is better understood about the immunopathogenesis of the lung disease, important information about systemic disease is still missing, mainly concerning neurological parameters. In this context, we sought to evaluate immunometabolic changes using in vitro and in vivo models of hamsters infected with SARS-CoV2. Here show that, besides infecting and replicating in glial cells, SARS-CoV2 induces important changes in protein expression and metabolic pathways, specially involved in carbon metabolism, glycolysis, and mitochondrial respiration. Interestingly, many of the differentially expressed proteins during SARS-CoV2 infection overlapped with proteins correlated with neurological diseases, such as Parkinsons's Disease, multiple sclerosis, amyotrophic lateral sclerosis and Huntington's disease. Metabolic analysis by high resolution real-time respirometry evidenced hyperactivation of glycolysis and mitochondrial respiration, which was confirmed by metabolomics. Brain infection with SARS-CoV2 was confirmed in vivo as hippocampus, cortex and olfactory bulb of infected hamsters were positive for viral genome both at 4 and 7 days post-infection. Unexpectedly, we observed that glutamine was significantly reduced in mixed glial cells infected with SARS-CoV2 and that the blockade of glutaminolysis significantly reduced viral replication and pro-inflammatory response. Altogether, our data confirms the infection of brain cells by SARS-CoV2 but, most importantly, there is an important change in overall protein expression profile, mostly of proteins related to metabolic pathways. This may suggest that some of the neurological impairments observed during COVID-19, as the brain fog and cognitive impairment, may rely on altered protein expression and unbalanced glutamine/glutamate levels, whose importance for adequate brain function is unquestionable.

Project description:Background: Type I interferons (IFNs) are essential to the clearance of viral diseases, in part by initiating upregulation of IFN regulated genes (IRGs). A clear distinction between genes upregulated directly by virus and genes upregulated by secondary IFN production has not been made. Here we investigated the genes regulated by IFN-a2b compared to the genes regulated by SARS-CoV infection in ferrets. Methods: We characterized early host immune responses in peripheral blood and lung necropsies of ferrets injected with IFN-a2b or infected with SARS-CoV/Tor 2 strain, using microarray analysis on the Affymetrix platform. Results: We identified a common IRG signature that was upregulated in both SARS-CoV infected ferrets as well as in ferrets injected with IFN-a2b. We also identified unique patterns of gene expression for leukocyte activation, cell adhesion and complement pathways between IFN-a2b injection and SARS-CoV infection. Conclusions: Our results define the effects of IFN-a2b on the immune system of ferrets highlighting genes regulated by IFN during SARS-CoV infection. We have shown the similarities and differences of top funcional gene groups as well as pathways that play key roles in early immune responses in ferrets in response to IFN-a2b or SARS-CoV. Key words: ferret, gene expression, SARS, interferon. Keywords: time course In experiments with IFN-a2b, for peripheral blood, 15 ferrets were randomly allocated to 3 groups: Day 0, 5 ferrets (no IFN injection), day 1, 6 ferrets (injected), and day 2, 4 ferrets (injected). For lung necropsies of injected ferrets with IFN-a2b, we used 12 ferrets in 3 groups: 4 ferrets, day 0 (no IFN injection), 4 ferrets, day 1 (injected) and 4 ferrets, day 2 (injected). Experimental groups for SARS-CoV infection was as follows: For peripheral blood, 3 and 4 ferrets for day 0 (no infection) and day 2 (infection) respectively. For lung neceropsies, a total of 9 ferrets in 3 groups, each with 3 replicates for day 0 (no infection), day 1 (infection) and day 2 (infection).

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Diving into the proteomic atlas of SARS-CoV-2 infected cells: insights of viral infection in different cell types

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