Published online Feb 19, 2023. doi: 10.5498/wjp.v13.i2.36
Peer-review started: October 9, 2022
First decision: November 27, 2022
Revised: December 6, 2022
Accepted: January 23, 2023
Article in press: January 23, 2023
Published online: February 19, 2023
Processing time: 130 Days and 21.4 Hours
Major depressive disorder (MDD) is a common and serious mental illness. Many novel genes in MDD have been characterized by high-throughput methods such as microarrays or sequencing. Recently, noncoding RNAs (ncRNAs) were suggested to be involved in the complicated environmental-genetic regulatory network of MDD occurrence.
The interplay among RNA species, including protein-coding RNAs and ncRNAs, in MDD remains unclear.
To investigate the RNA expression datasets and construct a network based on differentially expressed long noncoding RNA (lncRNAs), miRNAs, and mRNAs between MDD and controls through data mining method.
Gene expression data were searched and downloaded from NCBI Gene Expression Omnibus database. Six array datasets from humans were related to the search term: GSE19738, GSE32280, GSE38206, GSE52790, GSE76826, and GSE81152. These datasets were processed for initial assessment and subjected to quality control and differential expression analysis. Differentially expressed lncRNAs, miRNAs, and mRNAs were determined, Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses were performed, and protein-protein interaction network was generated. The results were analyzed for their association with MDD.
After analysis, 3 miRNAs, 12 lncRNAs, and 33 mRNAs were identified in the ceRNA network. Two of these miRNAs were earlier shown to be involved in psychiatric disorders, and differentially expressed mRNAs were found to be highly enriched in pathways related to neurogenesis and neuroplasticity as per Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses. The expression of hub gene fatty acid 2-hydroxylase was enriched, and the encoded protein was found to be involved in myelin formation, indicating that neurological development and signal transduction are involved in MDD pathogenesis.
The present study presents candidate ncRNAs involved in the neurogenesis and neuroplasticity pathways related to MDD.
Bioinformatic data mining method can be an cost-effective way to explore potential biomarkers for complicated diseases. However, benchmark experiment is needed in the future to validate the results.