Trend analysis of differentially expressed genes in retinoic acid-induced neural tube defects in mouse model

Abstract

Objective·To explore the molecular regulatory mechanism of neural tube defect (NTD) induced by retinoic acid (RA) in mouse embryos, and reveal the gene expression regularity of neural tube closure in mice.Methods·Based on the high-quality brain vesicle transcriptome data of mouse embryo during the critical period of neural tube closure [embryonic day 8.5 (E8.5), E9.5 and E10.5], the gene expression trend data of the NTD group and the control group were obtained by using Short Time-series Expression Miner (STEM) software. Gene Ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis were performed for genes with different expression trends between the NTD group and the control group. Some candidate genes were screened for validation. Pregnant mice were divided into the NTD group and control group, with 9 mice in each group. Pregnant mice in the NTD group were treated with RA and those in the control group were treated with sesame oil by gavage at E7.5. Foetal rat brain vesicle tissues were collected at E8.5, E9.5 and E10.5 for experiments. Based on the above animal tissues, the screened candidate genes were validated by quantitative real-time PCR (RT-PCR).Results·A total of 18 255 genes were detected in the transcriptome data of the control group, and the expression patterns of these genes could be summarized into 7 significant profiles. A total of 19 037 gene expression data were detected in the transcriptome data of the NTD group, and gene expression patterns could be summarized into 6 profiles with significant significance. A total of 46 genes in the control group showed an upward trend but a downward trend in the NTD group. They were enriched in the positive and negative regulation of organ development, neuronal apoptosis, oligodendrocyte proliferation, and fibroblast growth factor signaling pathway at the biological process level. At the cellular component level, they were mainly involved in the basic structure of cells and neurons; At the molecular functional level, they were mainly related to the binding of fibroblast growth factor receptor. A total of 61 genes showed a downward trend in the control group but an upward trend in the NTD group. These genes were enriched in functions such as cell lysis and amino acid/ion transport at the biological process level. At the cellular component level, they were enriched in intracellular molecules, particles, extracellular region, intercellular space, etc. At the molecular function level, they were related to the activity of a series of enzymes and transporters. The results of RT-qPCR showed that the transcriptome sequencing data were authentic and reliable.Conclusion·RA intervention causes abnormal cellular activities and stress responses during mouse embryo development, leading to abnormal embryo development, activation of signalling pathways related to organismal self-protection, and suppression of genes that maintain normal embryo development.

Keywords

• retinoic acid
• neural tube defect
• gene expression
• trend analysis