Identification of biomarkers and regulatory networks for cartilage damage patients

Baohong Liu; Xingxing Xiao

doi:10.31083/j.fbl2702050

Identification of biomarkers and regulatory networks for cartilage damage patients

Front Biosci (Landmark Ed). 2022 Feb 11;27(2):50. doi: 10.31083/j.fbl2702050.

Authors

Baohong Liu¹, Xingxing Xiao²

Affiliations

¹ State Key Laboratory of Veterinary Etiological Biology; Key Laboratory of Veterinary Parasitology of Gansu Province; Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, 730046 Lanzhou, Gansu, China.
² Wenzhou Key Laboratory of Sanitary Microbiology; Key Laboratory of Laboratory Medicine, Ministry of Education; School of Laboratory Medicine and Life Science, Wenzhou Medical University, 325035 Wenzhou, Zhejiang, China.

PMID: 35226993
DOI: 10.31083/j.fbl2702050

Abstract

Background: The aim of this study was to mine cartilage damage and regeneration-related biomarkers and identify the gene regulatory networks of cartilage damage.

Methods: A gene expression data set (GSE129147) containing damaged and control samples collected from the knee of the same patients was employed. R package limma was used to identify differentially expressed genes (DEGs), and clusterProfiler was performed for the GO and KEGG functional enrichment analysis. Cytoscape plug-ins of CytoHubba and MCODE were applied to investigate protein-protein interaction (PPI) network, modules, and hub genes.

Results: We identified 422 DEGs that were involved in skeletal system development, bone development, ossification, mesenchyme development, mesenchymal cell differentiation, connective tissue development, osteoblast differentiation, and extracellular matrix. We dug out 30 hub genes, identified three PPI modules, and constructed a miRNA regulatory network for DEGs. The miRNAs of the DEGs were predicted by miRNet, and the miRNA-mRNA network displayed some important miRNAs such as miR-335-5p, miR-92a-3p, and miR-98-5p.

Conclusions: Collectively, these results have the potential to clarify the mechanism of cartilage damage and to assist us in discovering the damage and repair-related biomarkers.

Keywords: Biomarkers; Cartilage damage; Protein-protein interaction (PPI) network; miRNA.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Biomarkers
Cartilage / metabolism
Computational Biology* / methods
Gene Expression Profiling
Gene Regulatory Networks
Humans
MicroRNAs* / genetics
MicroRNAs* / metabolism

Substances

Biomarkers
MIRN98 microRNA, human
MicroRNAs