Item request has been placed! ×
Item request cannot be made. ×
loading  Processing Request

Integrative bioinformatics analysis reveals novel insights into osteoarthritis pathogenesis and diagnostic biomarkers.

Item request has been placed! ×
Item request cannot be made. ×
loading   Processing Request
Read Online Read More Add to Saved list
  • Additional Information
    • Source:
      Publisher: BioMed Central Country of Publication: England NLM ID: 100968565 Publication Model: Electronic Cited Medium: Internet ISSN: 1471-2474 (Electronic) Linking ISSN: 14712474 NLM ISO Abbreviation: BMC Musculoskelet Disord Subsets: MEDLINE
    • Publication Information:
      Original Publication: London : BioMed Central, [2000-
    • Subject Terms:
      Computational Biology* ; Osteoarthritis*/genetics ; Osteoarthritis*/diagnosis ; Protein Interaction Maps* ; Gene Expression Profiling* ; Biomarkers*/metabolism ; Biomarkers*/analysis; Humans ; Gene Regulatory Networks ; Nomograms ; Transcriptome ; Female ; Cysteine-Rich Protein 61/genetics ; Male
    • Abstract:
      Competing Interests: Declarations. Ethics approval and consent to participate: This study was approved by the Ethical Committee of Heilongjiang University of Traditional Chinese Medicine. All procedures were conducted in accordance with the Declaration of Helsinki. Prior to participation, patients provided their written informed consent. Consent for publication: Not applicable. Competing interests: The authors declare no competing interests.
      Background: Osteoarthritis (OA) is a prevalent joint disorder characterized by degeneration and inflammation. Understanding its molecular mechanisms is crucial for diagnosis and treatment.
      Methods: We employed bioinformatics analyses to study OA using gene expression data. Differential expression analysis, weighted gene co-expression network analysis (WGCNA), and protein-protein interaction (PPI) network analysis were conducted. Enrichment analyses were performed to elucidate the biological significance of identified genes. Additionally, signature genes were identified using LASSO regression analysis, and a diagnostic nomogram was developed. qRT-PCR was conducted to confirm the expression levels of signature genes.
      Results: We identified 200 differentially expressed genes (DEGs) and a lightgreen module strongly correlated with OA. Within this module, 97 core genes were identified. Fifteen core lipopolysaccharide-related genes (LRGs) were found, enriched in immune and inflammatory pathways. Three hub genes (CCL3, ZFP36, and CCN1) emerged as potential biomarkers for OA diagnosis, with a nomogram showing high predictive accuracy, and validated by using clinical samples. Gene set enrichment analysis (GSEA) revealed distinct signaling pathways associated with the signature genes. Immunological analysis indicated altered immune profiles in OA, with the signature genes influencing immune cell infiltration and immune response pathways.
      Conclusion: Our study provides insights into OA pathogenesis and identifies potential diagnostic biomarkers. The developed nomogram shows promise for accurate OA diagnosis. Furthermore, the signature genes play crucial roles in modulating the immune microenvironment in OA, suggesting their therapeutic potential.
      Clinical Trial Number: Not applicable.
      (© 2024. The Author(s).)
    • References:
      Osteoarthritis Cartilage. 2020 May;28(5):555-561. (PMID: 31982565)
      Front Immunol. 2017 Mar 30;8:356. (PMID: 28424692)
      Ann Phys Rehabil Med. 2016 Jun;59(3):134-138. (PMID: 26904959)
      Arthritis Res Ther. 2013;15(5):R111. (PMID: 24020912)
      Oral Surg Oral Med Oral Pathol Oral Radiol. 2017 Sep;124(3):315-322. (PMID: 28732700)
      J Immunol Res. 2022 Jun 13;2022:5600190. (PMID: 35733917)
      J Immunol. 2012 Jun 1;188(11):5776-84. (PMID: 22547695)
      World J Clin Cases. 2019 Aug 26;7(16):2134-2142. (PMID: 31531309)
      Curr Opin Rheumatol. 2020 Jan;32(1):80-91. (PMID: 31724972)
      Med Clin North Am. 2020 Mar;104(2):293-311. (PMID: 32035570)
      Front Immunol. 2022 Jul 04;13:937886. (PMID: 35865542)
      Int J Environ Res Public Health. 2019 Nov 26;16(23):. (PMID: 31779104)
      Biostatistics. 2007 Jan;8(1):118-27. (PMID: 16632515)
      Clin Geriatr Med. 2022 May;38(2):181-192. (PMID: 35410675)
      Clin Transl Oncol. 2016 Aug;18(8):782-91. (PMID: 26563146)
      Cell Mol Life Sci. 2011 Oct;68(19):3149-63. (PMID: 21805345)
      Br J Radiol. 2018 May;91(1085):20170349. (PMID: 29271229)
      Ann Med. 2021 Dec;53(1):2380-2390. (PMID: 34933614)
      Int J Mol Sci. 2022 Oct 05;23(19):. (PMID: 36233118)
      Clin Chim Acta. 2020 Nov;510:323-329. (PMID: 32653484)
      Front Immunol. 2022 Jun 06;13:871008. (PMID: 35734177)
      BMC Bioinformatics. 2012 Dec 24;13:335. (PMID: 23259851)
      Front Immunol. 2022 Jul 04;13:907750. (PMID: 35860250)
      Immunity. 1996 May;4(5):445-54. (PMID: 8630730)
      Mediators Inflamm. 2014;2014:561459. (PMID: 24876674)
      Rheumatol Ther. 2023 Aug;10(4):793-808. (PMID: 37227653)
      Bone. 2012 Aug;51(2):249-57. (PMID: 22387238)
      Ann Rheum Dis. 2015 Apr;74(4):703-10. (PMID: 24363360)
      Reumatologia. 2023;61(3):191-201. (PMID: 37522140)
      Free Radic Biol Med. 2019 Feb 20;132:90-100. (PMID: 30236789)
      Prog Mol Biol Transl Sci. 2017;148:305-325. (PMID: 28662824)
      J Biol Regul Homeost Agents. 2020 Sep-Oct;34(5 Suppl. 1):51-55. IORS Special Issue on Orthopedics. (PMID: 33739005)
      Curr Opin Rheumatol. 2023 Mar 1;35(2):128-134. (PMID: 36695054)
      Front Immunol. 2021 Jul 21;12:632798. (PMID: 34367124)
      Acta Biomater. 2022 Mar 1;140:23-42. (PMID: 34896634)
      Int J Mol Sci. 2022 Jan 04;23(1):. (PMID: 35008966)
      Arthritis Rheum. 2009 Dec;60(12):3602-12. (PMID: 19950293)
      Front Cell Dev Biol. 2022 Jan 18;9:789948. (PMID: 35118075)
      Nat Rev Rheumatol. 2016 Feb;12(2):123-9. (PMID: 26656661)
      Immunol Res. 2014 May;58(2-3):234-9. (PMID: 24791905)
      PLoS One. 2014 Sep 04;9(9):e106632. (PMID: 25187949)
      Brief Bioinform. 2019 Nov 27;20(6):1981-1996. (PMID: 30084940)
      Clin Exp Rheumatol. 2019 Sep-Oct;37 Suppl 120(5):57-63. (PMID: 31621560)
      Sci Rep. 2020 Jul 2;10(1):10868. (PMID: 32616761)
      J Clin Med. 2022 Oct 12;11(20):. (PMID: 36294334)
      BMC Bioinformatics. 2008 Dec 29;9:559. (PMID: 19114008)
      Cells. 2019 Jul 17;8(7):. (PMID: 31319599)
      Signal Transduct Target Ther. 2023 Feb 3;8(1):56. (PMID: 36737426)
      Arthritis Rheumatol. 2022 Feb;74(2):227-236. (PMID: 34423918)
      Osteoarthritis Cartilage. 2022 Feb;30(2):207-215. (PMID: 34801671)
      Ann Transl Med. 2021 Oct;9(20):1552. (PMID: 34790758)
      Hum Gene (Amst). 2023 Feb;35:201135. (PMID: 37521006)
      Pharmgenomics Pers Med. 2023 Dec 23;16:1127-1143. (PMID: 38152411)
      Osteoarthritis Cartilage. 2016 Oct;24(10):1769-1775. (PMID: 27216281)
      Immunology. 2000 Apr;99(4):607-14. (PMID: 10792509)
      Biochem Soc Trans. 2016 Oct 15;44(5):1321-1337. (PMID: 27911715)
      Open Life Sci. 2023 Oct 14;18(1):20220747. (PMID: 37854319)
      Nat Rev Dis Primers. 2016 Oct 13;2:16072. (PMID: 27734845)
      JAMA. 2021 Feb 9;325(6):568-578. (PMID: 33560326)
    • Contributed Indexing:
      Keywords: Bacterial lipopolysaccharide; Immune cell infiltration; Nomogram; Osteoarthritis
    • Accession Number:
      0 (Biomarkers)
      0 (CCN1 protein, human)
      0 (Cysteine-Rich Protein 61)
    • Publication Date:
      Date Created: 20241205 Date Completed: 20241206 Latest Revision: 20241208
    • Publication Date:
      20250114
    • Accession Number:
      PMC11619307
    • Accession Number:
      10.1186/s12891-024-08124-3
    • Accession Number:
      39639239