Comparative Transcriptomic Analyses of Peripheral Blood Mononuclear Cells of COVID-19 Patients without Pneumonia and with Severe Pneumonia in the First Year of Follow-Up

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dc.authoridARGUN BARIS, SERAP/0000-0002-4429-9441
dc.authoridbaydar, oya/0000-0001-7320-976X
dc.authoridELDEM, VAHAP/0000-0003-3767-5661
dc.authoridTomruk Erdem, Aysegul/0000-0002-5346-9107
dc.authoridBayram, Hasan/0000-0002-5236-766X
dc.authoridDeniz, Pelin Pinar/0000-0002-9047-7608
dc.authoridRajabi, Hadi/0000-0001-6086-591X
dc.contributor.authorKayalar, Ozgecan
dc.contributor.authorCetinkaya, Pelin Duru
dc.contributor.authorEldem, Vahap
dc.contributor.authorBaris, Serap Argun
dc.contributor.authorKokturk, Nurdan
dc.contributor.authorKuralay, Selim Can
dc.contributor.authorRajabi, Hadi
dc.date.accessioned2025-10-11T20:47:41Z
dc.date.available2025-10-11T20:47:41Z
dc.date.issued2024
dc.departmentDüzce Üniversitesien_US
dc.description.abstractThe multisystemic effects of COVID-19 may continue for a longer time period following the acute phase, depending on the severity of the disease. However, long-term systemic transcriptomic changes associated with COVID-19 disease and the impact of disease severity are not fully understood. We aimed to investigate the impact of COVID-19 and its severity on transcriptomic alterations in peripheral blood mononuclear cells (PBMCs) following 1 year of the disease. PBMCs were isolated from the peripheral blood of healthy control donors who did not have COVID-19 (C; n = 13), from COVID-19 patients without pneumonia (NP; n = 11), and from COVID-19 patients with severe pneumonia (SP; n = 10) after 1-year of follow-up. Following RNA isolation from PBMCs, high-quality RNAs were sequenced after creating a library. Differentially expressed genes (DEGs) and differentially expressed long non-coding RNAs (DElncRNAs) were identified using Benjamini-Hochberg correction and they were analysed for hierarchical clustering and principal component analysis (PCA). Intergroup comparisons (C vs. NP, C vs. SP, and NP vs. SP) of DEGs and DElncRNAs were performed and hub genes were determined. Functional enrichment analyses of DEGs and DElncRNAs were made using Metascape (v3.5.20240101) and the first version of NCPATH. The RNA sequencing analysis revealed 4843 DEGs and 1056 DElncRNAs in C vs. NP, 1651 DEGs and 577 DElncRNAs in C vs. SP, and 954 DEGs and 148 DElncRNAs in NP vs. SP, with 291 DEGs and 70 DElncRNAs shared across all groups, respectively. We identified 14 hub genes from 291 DEGs, with functional enrichment analysis showing upregulated DEGs mainly linked to inflammation and osteoclast differentiation and downregulated DEGs to viral infections and immune responses. The analysis showed that 291 common and 14 hub genes were associated with pneumonia and that these genes could be regulated by the transcription factors JUN and NF kappa B1 carrying the NF kappa B binding site. We also revealed unique immune cell signatures across DEG categories indicating that the upregulated DEGs were associated with neutrophils and monocytes, while downregulated DEGs were associated with CD4 memory effector T cells. The comparative transcriptomic analysis of NP and SP groups with 52 gene signatures suggestive of IPF risk showed a lower risk of IPF in the SP group than the NP patients. Our findings suggest that COVID-19 may cause long term pathologies by modulating the expression of various DEGs, DeLncRNAs, and hub genes at the cellular level.en_US
dc.description.sponsorshipResearch Support Fund of the Turkish Thoracic Society (TTD)en_US
dc.description.sponsorshipResearch Support Fund of the Turkish Thoracic Societyen_US
dc.description.sponsorshipThis study was funded by the Research Support Fund of the Turkish Thoracic Society (TTD).en_US
dc.identifier.doi10.3390/v16081211
dc.identifier.issn1999-4915
dc.identifier.issue8en_US
dc.identifier.pmid39205185en_US
dc.identifier.scopus2-s2.0-85202518321en_US
dc.identifier.scopusqualityN/Aen_US
dc.identifier.urihttps://doi.org/10.3390/v16081211
dc.identifier.urihttps://hdl.handle.net/20.500.12684/21525
dc.identifier.volume16en_US
dc.identifier.wosWOS:001307492100001en_US
dc.identifier.wosqualityQ2en_US
dc.indekslendigikaynakWeb of Scienceen_US
dc.indekslendigikaynakScopusen_US
dc.indekslendigikaynakPubMeden_US
dc.language.isoenen_US
dc.publisherMdpien_US
dc.relation.ispartofViruses-Baselen_US
dc.relation.publicationcategoryMakale - Uluslararası Hakemli Dergi - Kurum Öğretim Elemanıen_US
dc.rightsinfo:eu-repo/semantics/openAccessen_US
dc.snmzKA_WOS_20250911
dc.subjectCOVID-19en_US
dc.subjecttranscriptomic analysisen_US
dc.subjectperipheral blood mononuclear cells (PBMC)en_US
dc.subjectlong-term effectsen_US
dc.subjectinflammatory responsesen_US
dc.subjectpneumoniaen_US
dc.titleComparative Transcriptomic Analyses of Peripheral Blood Mononuclear Cells of COVID-19 Patients without Pneumonia and with Severe Pneumonia in the First Year of Follow-Upen_US
dc.typeArticleen_US

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