Identification of key biomolecules in rheumatoid arthritis through the reconstruction of comprehensive disease-specific biological networks

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dc.authoridGOV, ESRA/0000-0002-5256-4778
dc.authoridComertpay, Betul/0000-0002-3515-1461
dc.contributor.authorComertpay, Betul
dc.contributor.authorGov, Esra
dc.date.accessioned2025-01-06T17:44:38Z
dc.date.available2025-01-06T17:44:38Z
dc.date.issued2020
dc.description.abstractRheumatoid arthritis (RA) frequently seen chronic synovial inflammation causing joint destruction, chronic disability and reduced life expectancy. The pathogenesis of RA is not completely known. In this study, several gene expression data including synovial tissue and macrophages from synovial tissues were integrated with a holistic perspective and the molecular targets and signatures in RA were determined. Differentially expressed genes (DEGs) were identified from each dataset by comparing diseased and healthy samples. Afterward, the RA-specific protein-protein interaction (PPI) and the transcriptional regulatory network were reconstructed by using several biomolecule interaction data. Key biomolecules were determined through a statistical test employing the hypergeometric probability density function by using the physical interactions of transcriptional regulators and PPI. The integrative analyses of DEGs indicated that there were 110 and 494 common genes between synovial tissues and macrophages related datasets, respectively. Common DEGs of all datasets were identified as 25 genes and these core genes which might be feasible to uncover the mutual biological mechanism insights behind the RA pathogenesis were used for disease specific biological networks reconstruction. It was determined the hub proteins, novel key biomolecules (i.e. receptor, transcription factors and miRNAs) and biomolecules interactions by using the core DEGs. It was identified STAT1, RAC2 and KYNU as hub proteins, PEPD as a receptor, NR4A1, MEOX2, KLF4, IRF1 and MYB as TFs, miR-299, miR-8078, miR-146a, miR-3659 and miR-6882 as key miRNAs. It was determined that biomolecule interaction scenarios using identified key biomolecules and novel biomolecules including RAC2, PEPD, NR4A1, MEOX2, miR-299, miR-8078, miR-3659 and miR-6882 in RA. Our novel findings could be a crucial resource for the understanding of RA molecular mechanism and may be considered as drug targets and development of novel diagnostic strategies. Corresponding genes and miRNAs should be validated via experimental studies.
dc.identifier.doi10.1080/08916934.2020.1722107
dc.identifier.endpage166
dc.identifier.issn0891-6934
dc.identifier.issn1607-842X
dc.identifier.issue3
dc.identifier.pmid32013628
dc.identifier.scopus2-s2.0-85084618532
dc.identifier.scopusqualityQ2
dc.identifier.startpage156
dc.identifier.urihttps://doi.org/10.1080/08916934.2020.1722107
dc.identifier.urihttps://hdl.handle.net/20.500.14669/3131
dc.identifier.volume53
dc.identifier.wosWOS:000512505100001
dc.identifier.wosqualityQ4
dc.indekslendigikaynakWeb of Science
dc.indekslendigikaynakScopus
dc.indekslendigikaynakPubMed
dc.language.isoen
dc.publisherTaylor & Francis Ltd
dc.relation.ispartofAutoimmunity
dc.relation.publicationcategoryMakale - Uluslararası Hakemli Dergi - Kurum Öğretim Elemanı
dc.rightsinfo:eu-repo/semantics/closedAccess
dc.snmzKA_20241211
dc.subjectTranscriptome
dc.subjectautoimmunity
dc.subjectmolecular signatures
dc.subjectnetwork medicine
dc.subjectrheumatoid arthritis
dc.titleIdentification of key biomolecules in rheumatoid arthritis through the reconstruction of comprehensive disease-specific biological networks
dc.typeArticle

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