Transcriptional Profiling of SARS-CoV-2-Infected Calu-3 Cells Reveals Immune-Related Signaling Pathways

Eric Petterson Viana Pereira; Stela Mirla da Silva Felipe; Raquel Martins de Freitas; José Ednésio da Cruz Freire; Antonio Rocha Oliveira; Natália Canabrava; Paula Matias Soares; Mauricio Fraga van Tilburg; Maria Izabel Florindo Guedes; Chad Grueter; Vânia Ceccatto

doi:10.3390/pathogens12111373

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Transcriptional Profiling of SARS-CoV-2-Infected Calu-3 Cells Reveals Immune-Related Signaling Pathways

Journal article

Open access

Peer reviewed

Transcriptional Profiling of SARS-CoV-2-Infected Calu-3 Cells Reveals Immune-Related Signaling Pathways

Eric Petterson Viana Pereira, Stela Mirla da Silva Felipe, Raquel Martins de Freitas, José Ednésio da Cruz Freire, Antonio Rocha Oliveira, Natália Canabrava, Paula Matias Soares, Mauricio Fraga van Tilburg, Maria Izabel Florindo Guedes, Chad Grueter, …

Pathogens (Basel), Vol.12(11), 1373

11/01/2023

DOI: 10.3390/pathogens12111373

PMCID: PMC10674242

PMID: 38003837

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Abstract

The COVID-19 disease, caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), emerged in late 2019 and rapidly spread worldwide, becoming a pandemic that infected millions of people and caused significant deaths. COVID-19 continues to be a major threat, and there is a need to deepen our understanding of the virus and its mechanisms of infection. To study the cellular responses to SARS-CoV-2 infection, we performed an RNA sequencing of infected vs. uninfected Calu-3 cells. Total RNA was extracted from infected (0.5 MOI) and control Calu-3 cells and converted to cDNA. Sequencing was performed, and the obtained reads were quality-analyzed and pre-processed. Differential expression was assessed with the EdgeR package, and functional enrichment was performed in EnrichR for Gene Ontology, KEGG pathways, and WikiPathways. A total of 1040 differentially expressed genes were found in infected vs. uninfected Calu-3 cells, of which 695 were up-regulated and 345 were down-regulated. Functional enrichment analyses revealed the predominant up-regulation of genes related to innate immune response, response to virus, inflammation, cell proliferation, and apoptosis. These transcriptional changes following SARS-CoV-2 infection may reflect a cellular response to the infection and help to elucidate COVID-19 pathogenesis, in addition to revealing potential biomarkers and drug targets.

Apoptosis

Biomarkers

Gene Expression

Gene Regulation

Genes

Immune System

Pathogenesis

Public Health

Respiratory Diseases

RNA

Viral Infections

Cell proliferation

Coronaviruses

COVID-19

Disease transmission

Enrichment

Gene sequencing

Genomes

Immune response

Infections

Innate immunity

Medical research

Pandemics

Reproducibility

Ribonucleic acid

Severe acute respiratory syndrome coronavirus 2

Therapeutic targets

Viral diseases

Viruses

Details

Title: Subtitle: Transcriptional Profiling of SARS-CoV-2-Infected Calu-3 Cells Reveals Immune-Related Signaling Pathways
Creators: Eric Petterson Viana Pereira - Universidade Estadual do Ceará
Stela Mirla da Silva Felipe - Universidade Estadual do Ceará
Raquel Martins de Freitas
José Ednésio da Cruz Freire - Universidade Estadual do Ceará
Antonio Rocha Oliveira
Natália Canabrava
Paula Matias Soares - Universidade Estadual do Ceará
Mauricio Fraga van Tilburg - Universidade Estadual do Ceará
Maria Izabel Florindo Guedes - Universidade Estadual do Ceará
Chad Grueter - University of Iowa
Vânia Ceccatto - Universidade Estadual do Ceará
Resource Type: Journal article
Publication Details: Pathogens (Basel), Vol.12(11), 1373
DOI: 10.3390/pathogens12111373
PMID: 38003837
PMCID: PMC10674242
NLM abbreviation: Pathogens
ISSN: 2076-0817
eISSN: 2076-0817
Publisher: MDPI AG
Grant note: DOI: 10.13039/501100006507, name: Inova FIOCRUZ, award: FIO-0167-00015.01.00/20; name: Oswaldo Cruz Foundation; name: Foundation to Support Scientific and Technological Development of Ceará—FUNCAP/Brazil; name: the Brazilian National Council for Scientific and Technological Development.—CNPq/Brazil
Language: English
Date published: 11/01/2023
Academic Unit: Cardiovascular Medicine; Craniofacial Anomalies Research Center; Internal Medicine
Record Identifier: 9984528121502771

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