Comprehensive RNA expression profile of therapeutic adipose-derived mesenchymal stem cells co-cultured with degenerative nucleus pulposus cells

Stem cell-based therapy is a promising alternative to conventional approaches to treating intervertebral disc degeneration (IDD). However, comprehensive understanding of stem cell-based therapy at the gene level is still lacking. In the present study, we identified the expression profiles of messenger RNAs (mRNAs) and long non-coding RNAs (lncRNAs) expressed within a co-culture system of adipose-derived mesenchymal stem cells (ASCs) and degenerative nucleus pulposus cells (NPCs) and explored the signaling pathways involved and their regulatory networks. Microarray analysis was used to compare ASCs co-cultured with degenerative NPCs to ASCs cultured alone, and the underlying regulatory pattern, including the signaling pathways and competing endogenous RNA (ceRNA) network, was analyzed with robust bioinformatics methods. The results showed that 360 lncRNAs and 1757 mRNAs were differentially expressed by ASCs, and the microarray results were confirmed by quantitative PCR. Moreover, 589 Gene Ontology terms were upregulated, whereas 661 terms were downregulated. A total of 299 signaling pathways were significantly altered. A Path-net and a Signal-net were built to show interactions among differentially expressed genes. An mRNA-lncRNA co-expression network was constructed to reveal the interplay among differentially expressed mRNAs and lncRNAs, whereas a ceRNA network was built to investigate their connections with microRNAs involved in IDD. To the best of our knowledge, this original and comprehensive exploration reveals differentially expressed lncRNAs and mRNAs of ASCs stimulated by degenerative NPCs, underscoring the regulation pattern within the co-culture system at the gene level. These data may further understanding of NPC-directed differentiation of ASCs and facilitate the application of ASCs in future treatments for IDD.