Gene expression profiling of host lipid metabolism in SARS-CoV-2 infected patients: a systematic review and integrated bioinformatics analysis.

Gene expression profiling of host lipid metabolism in SARS-CoV-2 infected patients: a systematic review and integrated bioinformatics analysis.

Publication date: Jan 23, 2024

The Coronavirus disease 2019 (COVID-19) pandemic occurred due to the dispersion of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Severe symptoms can be observed in COVID-19 patients with lipid-related comorbidities such as obesity and diabetes. Yet, the extensive molecular mechanisms of how SARS-CoV-2 causes dysregulation of lipid metabolism remain unknown. Here, an advanced search of articles was conducted using PubMed, Scopus, EBSCOhost, and Web of Science databases using terms from Medical Subject Heading (MeSH) like SARS-CoV-2, lipid metabolism and transcriptomic as the keywords. From 428 retrieved studies, only clinical studies using next-generation sequencing as a gene expression method in COVID-19 patients were accepted. Study design, study population, sample type, the method for gene expression and differentially expressed genes (DEGs) were extracted from the five included studies. The DEGs obtained from the studies were pooled and analyzed using the bioinformatics software package, DAVID, to determine the enriched pathways. The DEGs involved in lipid metabolic pathways were selected and further analyzed using STRING and Cytoscape through visualization by protein-protein interaction (PPI) network complex. The analysis identified nine remarkable clusters from the PPI complex, where cluster 1 showed the highest molecular interaction score. Three potential candidate genes (PPARG, IFITM3 and APOBEC3G) were pointed out from the integrated bioinformatics analysis in this systematic review and were chosen due to their significant role in regulating lipid metabolism. These candidate genes were significantly involved in enriched lipid metabolic pathways, mainly in regulating lipid homeostasis affecting the pathogenicity of SARS-CoV-2, specifically in mechanisms of viral entry and viral replication in COVID-19 patients. Taken together, our findings in this systematic review highlight the affected lipid-metabolic pathways along with the affected genes upon SARS-CoV-2 invasion, which could be a potential target for new therapeutic strategies study in the future.

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Concepts Keywords
Diabetes Bioinformatics
Homeostasis Gene expression
Molecular Lipid metabolism
Pandemic Next-generation sequencing
Viral SARS-CoV-2

Semantics

Type Source Name
disease IDO host
disease MESH Coronavirus disease 2019
disease VO Severe acute respiratory syndrome coronavirus 2
disease MESH obesity
disease MESH causes
disease VO study design
disease VO population
pathway KEGG Metabolic pathways
pathway KEGG Viral replication
disease MESH Long Covid
pathway REACTOME Reproduction
disease MESH Infectious Diseases
disease MESH severe acute respiratory syndrome
disease IDO pathogen
disease VO Betacoronavirus
disease VO Orthocoronavirinae
disease MESH infection
disease MESH inflammation
disease MESH chest pain
disease MESH cancer
disease MESH morbidities
disease MESH pulmonary inflammation
disease VO effectiveness
disease VO vaccination
disease IDO blood
pathway KEGG Fatty acid metabolism
pathway KEGG Cholesterol metabolism
pathway KEGG Sphingolipid metabolism
drug DRUGBANK Cholesterol
disease IDO cell
drug DRUGBANK Corticorelin
disease IDO process
disease IDO quality
disease MESH critically ill
disease VO time
disease MESH atherosclerosis
disease MESH alcoholic fatty liver
drug DRUGBANK Palmitic Acid
disease IDO biological process
disease MESH non alcoholic fatty liver disease
disease MESH virus infection
pathway KEGG Apoptosis
pathway KEGG Peroxisome
disease IDO algorithm
drug DRUGBANK Coenzyme M
disease IDO immune response
disease VO storage
pathway KEGG PPAR signaling pathway
disease MESH insulin resistance
pathway KEGG Insulin resistance
disease IDO replication
drug DRUGBANK NADH
pathway KEGG Chemokine signaling pathway
drug DRUGBANK Serine
drug DRUGBANK L-Threonine
pathway KEGG Estrogen signaling pathway
pathway KEGG Ribosome
drug DRUGBANK Methylergometrine
drug DRUGBANK Cytidine
disease IDO site
drug DRUGBANK Uracil
drug DRUGBANK Propylthiouracil
disease VO Viruses
disease MESH mutation rate
drug DRUGBANK Probucol
pathway KEGG Lysosome
drug DRUGBANK Angiotensin II
disease VO vaccine
disease VO NAP
disease VO gene
disease MESH Influenza
disease MESH hypercholesterolemia
disease MESH dyslipidemia
disease IDO intervention
disease MESH Syndrome
disease MESH complications
disease MESH pulmonary fibrosis
disease VO Gap
drug DRUGBANK Esomeprazole
disease MESH Mayaro virus infection
disease VO organ

Original Article

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