LncRNA and mRNA Expression Profiles in Methylprednisolone Stimulated Neural Stem Cells

Abstract

Spinal cord injury (SCI) is a devastating neurological disorder that affects thousands of individuals each year. Previously, our study in non-human primates with SCI demonstrated that methylprednisolone (MP) resulted in the dysfunction of neural stem cells (NSCs), which may help to explain the controversial roles of MP in SCI. However, the detailed mechanism is still unclear. In this manuscript, we investigated the LncRNA and mRNA expression profiles of NSCs treated with MP. A total of 63 differentially expressed LncRNAs and 174 differentially expressed mRNAs were identified. Gene ontology (GO) analysis showed that differentially expressed mRNAs were highly associated with terms related to regulation of external stimulation, secretion, and migration. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis results indicated that the PI3K–Akt signaling pathway contributed to the functions of MP treated NSCs. Besides, 3899 co-expression pairs were constructed among the differentially expressed LncRNA and mRNA, among which five predicted target mRNAs with the differentially expressed LncRNAs were identified. These results provide greater insight into the precise mechanisms of MP mediating NSC dysfunction in SCI.

Breast Cancer Cells Reprogram the Oncogenic lncRNAs/mRNAs Coexpression Networks in Three-Dimensional Microenvironment

“…LncRNAs are functionally involved in several biological processes; however, they are not represented in databases such as KEGG or gene ontology (GO), this makes it difficult to predict the biological processes and pathways in which they are involved. However, the identification of protein-coding genes that are co-expressed with lncRNAs can help to assign biological functions to lncRNAs [ 53 , 54 , 55 ]. To do this, we used the expression dataset from 4799 mRNAs modulated in BT-474 cell cultures in 3D conditions relative to 2D cultures (our unpublished data) to measure correlations between expressions of lncRNAs/mRNA pairs using Pearson’s correlation ( Supplementary Data S1 ), as previously reported [ 53 , 54 , 55 ].…”

“…However, the identification of protein-coding genes that are co-expressed with lncRNAs can help to assign biological functions to lncRNAs [ 53 , 54 , 55 ]. To do this, we used the expression dataset from 4799 mRNAs modulated in BT-474 cell cultures in 3D conditions relative to 2D cultures (our unpublished data) to measure correlations between expressions of lncRNAs/mRNA pairs using Pearson’s correlation ( Supplementary Data S1 ), as previously reported [ 53 , 54 , 55 ]. Correlation analyses were performed between the group of 290 lncRNAs and 1924 mRNAs over-expressed in 3D, and the group of 183 lncRNAs and 2875 mRNAs down-regulated in 3D cultures to identify lncRNAs/mRNAs pairs in co-expression.…”