Expression profile analysis of long non-coding RNA in skeletal muscle of osteoporosis by microarray and bioinformatics

Shaojin Liu; Hongxing Huang; Shuang Chai; Hewei Wei; Jiachun Huang; Lei Wan

doi:10.1186/s13036-019-0180-5

Expression profile analysis of long non-coding RNA in skeletal muscle of osteoporosis by microarray and bioinformatics

J Biol Eng. 2019 May 31:13:50. doi: 10.1186/s13036-019-0180-5. eCollection 2019.

Authors

Shaojin Liu¹, Hongxing Huang², Shuang Chai¹, Hewei Wei², Jiachun Huang¹, Lei Wan^{2

3}

Affiliations

¹ 1Guangzhou University of Chinese Medicine, Guangzhou, 510405 China.
² 2Department of Orthopaedics, The Third Affiliated Hospital, Guangzhou University of Chinese Medicine, Guangzhou, 510378 China.
³ 3Lingnan Medical Research Center of Guangzhou University of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, 510405 China.

Abstract

Background: Osteoporosis (OP) is a condition featured by bone mass loss and bone tissue microarchitectural alterations due to impaired tissue homeostasis favoring excessive bone resorption versus deposition. The trigger of such an impairment and the downstream molecular pathways involved are yet to be clarified. Long non-coding RNA (lncRNA) plays a role in gene transcription, protein expression and epigenetic regulation; and altered expression results in immune or metabolism related desease development. To determine whether lncRNAs are involved in osteoporosis, we analyzed the expression profile of lncRNAs and mRNAs in osteoporosis.

Method: Three pairs of osteoporosis patients (OP group) and healthy people controls (NC group) were screened by microarray. Quantitative polymerase chain reaction (qRT-PCR) was performed to confirm dysregulated lncRNA expressions in 5 pairs of OP and NC group tissues samples. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed to construct the lncRNA-mRNA co-expression network.

Result: Through co-expression analysis, differently expressed transcripts were divided into modules, and lncRNAs were functionally annotated. We further analyzed the clinical significance of crucial lncRNAs from modules in public data. Finally, the expression of five lncRNAs, CUST_44695_PI430048170-GeneSymbol:CTA-384D8.35;CUST_39447_PI430048170,CUST_73298_PI430048170,CUST_108340_PI430048170,CUST_118927_PI430048170,this four lncRNAs have not been annotation genes and have not found GeneSymbols, and by quantitative RT-PCR, which may be associated with osteoporosis patients' overall survival.

Conclusion: Analysis of this study revealed that dysregulated lncRNAs and mRNAs in osteoporosis patients and health people controls could affect the immune or metabolism system and musculoskeletal cell differentiation. The biological functions of those lncRNAs need to be further validated.

Keywords: Microarray profile; Musculoskeletal; Osteoporosis; Quantitative real-time PCR; lncRNA.