Comparative analysis of lncRNA and mRNA expression profiles between periodontal ligament stem cells and gingival mesenchymal stem cells

Oral tissue-derived mesenchymal stem cells, such as periodontal ligament stem cells (PDLSCs) and gingival mesenchymal stem cells (GMSCs), possess different biological characteristics, but the molecular mechanism remains unclear, which restricts their application in tissue engineering. Long noncoding RNAs (lncRNAs) are known to be significant regulators of gene expression, but our knowledge about their roles in the regulation of stem cell biological properties is still limited. This study compared the lncRNA and mRNA expression profiles between PDLSCs and GMSCs through microarray analysis, and applied bioinformatics methods to analyze and predict the function and connection of differentially expressed genes, aiming to screen potential key regulators of diverse biological characteristics in PDLSCs and GMSCs. Microarray analysis showed that 2162 lncRNAs and 1347 mRNAs were significantly differentially expressed between PDLSCs and GMSCs. Gene ontology (GO) analysis and pathway analysis indicated that these differentially expressed genes were involved in diverse biological processes and signaling pathways. The gene signal network and pathway relation network predicted some potentially important regulators. The coding-noncoding gene coexpression network (CNC network) revealed many potential lncRNA-mRNA connection pairs that participated in the regulation of biological behaviors. These results stressed the roles of lncRNAs in controlling stem cell biological behaviors and provided guides for molecular mechanistic study of different biological characteristics in PDLSCs and GMSCs.