RNA sequencing-based identification of the regulatory mechanism of microRNAs, transcription factors, and corresponding target genes involved in vascular dementia

Abstract

Vascular dementia (VaD) is the second most common form of dementia with uncertain mechanisms and no effective treatments. microRNAs (miRNAs) and transcription factors (TFs) are considered regulatory factors of genes involved in many diseases. Therefore, this work investigated the aberrantly expressed miRNAs, TFs, corresponding target genes, and their co-regulatory networks in the cortex of rats with bilateral common carotid artery occlusion (2VO) to uncover the potential mechanism and biomarkers of VaD. Differentially expressed genes (DEGs), miRNAs (DEMs), and TFs (DETFs) were identified using RNA sequencing, and their interaction networks were constructed using Cytoscape. The results showed that rats with 2VO had declined cognitive abilities and neuronal loss in the cortex than sham rats. DEGs, DEMs, and DETFs were discriminated between rats with 2VO and sham rats in the cortex, as shown by the 13 aberrantly expressed miRNAs, 805 mRNAs, and 63 TFs. The miRNA-TF-target gene network was constructed, showing 523 nodes and 7237 edges. Five miRNAs (miR-5132-5p, miR-764-3p, miR-223-3p, miR-145-5p, and miR-122-5p), ten TFs (Mxi1, Nfatc4, Rxrg, Zfp523, Foxj2, Nkx6-1, Klf4, Klf5, Csrnp1, and Prdm6), and seven target genes (Serpine1, Nedd4l, Pxn, Col1a1, Plec, Trip12, and Tpm1) were chosen as the significant nodes to construct feed-forward loops (FFLs). Gene Ontology and pathway enrichment analysis revealed that these miRNA and TF-associated genes are mostly involved in the PI3K/Akt, neuroactive ligand–receptor interaction, calcium signaling, and Wnt signaling pathways, along with central locations around the cell membrane. They exert functions such as growth factor binding, integrin binding, and extracellular matrix structural constituent, with representative biological processes like vasculature development, cell–substrate adhesion, cellular response to growth factor stimulus, and synaptic transmission. Furthermore, the expression of three miRNAs (miR-145-5p, miR-122-5p, and miR-5132-5p), six TFs (Csrnp1, Klf4, Nfatc4, Rxrg, Foxj2, and Klf5), and five mRNAs (Serpine1, Plec, Nedd4l, Trip12, and Tpm1) were significantly changed in rats with VaD, in line with the outcome of RNA sequencing. In the potential FFL, miR-145-5p directly bound Csrnp1 and decreased its mRNA expression. These results might help the understanding of the underlying regulatory mechanisms of miRNA-TF-genes, providing potential therapeutic targets in VaD.

Trimethylamine N-oxide Aggravates Neuro-inflammation via lncRNA Fendrr/miR-145-5p/PXN axis in Vascular Dementia Rats

“…As an in ammatory gene [45], PXN expression was upregulated after middle cerebral artery occlusion in mice, especially following 1 hour of ischemia, and the upregulation of PXN may promote in ammation and the development of acute ischemic stroke [46,47]. Besides, a sequencing result observed that PXN was notably elevated in the cortex of 2VO rats [24]. Aligned with previous studies, we found elevated levels of PXN in the hippocampus of 2VO rats and con rmed its binding relationship with miR-145-5p.…”

“…Among these candidate genes, Trim2, PXN, and Nedd4l were reported to be signi cantly upregulated in the cortex of 2VO rats [24,27]. Then, the minimum free energies of binding between them and miR-145-5p were − 31.5, -35.1, and − 32.8 kcal/mol, respectively, predicted by the RNAhybrid (Fig.…”

Whole-Transcriptome Analysis of Repeated Low-Level Sarin-Exposed Rat Hippocampus and Identification of Cerna Networks to Investigate the Mechanism of Sarin-Induced Cognitive Impairment

“…Studies have shown that these miRNAs may be associated with neurological diseases. For example, miR-764-3p was down-regulated in the hippocampus of rats with dementia [ 70 ]. miR-741-3p was upregulated in attention-deficit/hyperactivity disorder rats [ 71 ].…”

Comprehensive analysis of dysregulated circular RNAs and construction of a ceRNA network involved in the pathology of Alzheimer’s disease in a 5 × FAD mouse model

“…After the MWM, the mice were euthanized via cervical dislocation, and the obtained samples were preserved in liquid nitrogen. The total RNA of the hippocampus was isolated with TRIzol reagent (Invitrogen, CA, United States) according to the previous protocol ( Zhao et al, 2022 ). The RNA sample used in this study was the same cohort as our reported investigation ( Cai et al, 2022 ).…”