Analysis of long non-coding RNA expression profiles in disuse osteoporosis using microarray and bioinformatics

WZ Wei; B Li; JX Lin; J Zhao; XF Zhang; XQ Wang; Z Lv; J Liu

doi:10.23812/21-246-A

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Analysis of long non-coding RNA expression profiles in disuse osteoporosis using microarray and bioinformatics

WZ Wei, B Li, JX Lin, J Zhao, XF Zhang, XQ Wang, Z Lv, J Liu

Article ID: 4035
Vol 35, Issue 4, 2021

DOI: https://doi.org/10.23812/21-246-A

Received: 8 September 2021; Accepted: 8 September 2021; Available online: 8 September 2021; Issue release: 8 September 2021

Abstract

Disuse osteoporosis (DOP) is one of the major consequences of long space flights. DOP also occurs in patients with spinal cord injuries and prolonged bedridden states that can have a severe impact on human health. Bone marrow mesenchymal stem cells (BMSCs) are multipotent stromal cells that play an important role in bone homeostasis. Long non-coding RNAs (lncRNAs) are involved in regulating osteogenic differentiation of BMSCs, and their abnormal expression might lead to the formation of orthopedic diseases. However, the specific mechanism of DOP has not yet been elucidated. All sequencing data were obtained from Gene Expression Omnibus (GEO) datasets. The limma package of R was applied to identify DEmRNAs and DElncRNAs. Pearson correlation coefficients (PCC) between DElncRNADEmRNA expression levels were calculated. Functional annotation was performed for DEmRNAs coexpressed with DElncRNAs. In addition, the Cytohubba plug-in in Cytoscape was applied to determine the top 10 hub genes. Finally, connectivity map (CMap) analysis was used to identify potential therapeutic drugs for DOP. The gene expression data, GSE100930 and GSE17696, were retrieved from the GEO database. A total of 2,212 differentially expressed mRNAs (DEmRNAs) and 22 differentially expressed lncRNAs (DElncRNAs) were obtained. Gene ontology (GO) functional terms, Kyoto Encyclopedia of Genes, and Genomes (KEGG) pathway enrichment analysis reveal 30 significant GO terms and 13 significant pathways. A coding-non-coding gene co-expression (CNC) network was constructed to study the potential role of hub-DElncRNAs and their co-expressed DEmRNAs in DOP. The lncRNAs, GSNAS1, SNHG12, and EPB41LA4A-AS1, were significant in the CNC network and potential regulators of DOP development. Three bioactive compounds (scoulerine, kinetin riboside, dexanabinol) with potential therapeutic significance for DOP were obtained through the Connectivity Map (CMAP) analysis. Our study revealed a new mechanism for a lineage shift of bone marrow mesenchymal stem cells under microgravity, and linked the function of protein-coding mRNAs with ncRNAs, which may contribute to the development of new therapies for DOP.

Keywords

Bone Mesenchymal Stem Cells (BMSCs);Connectivity Map (CMAP);bioinformatics;disuse osteoporosis;long non-coding RNAs;miR-361-3p

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Medical Genetics, University of Torino Medical School, Italy

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Department of Biomedical, Surgical and Dental Sciences, University of Milan, Italy

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