Aberrant expression of miRNAs in epilepsy

Ghafouri‐Fard, Soudeh; Hussen, Bashdar Mahmud; Abak, Atefe; Taheri, Mohammad; Khoshnoud, Reza Jalili

doi:10.1007/s11033-022-07188-5

Cited by 21 publications

(12 citation statements)

References 71 publications

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“…Third, there are some miRNAs which have been reported to be related to SE, but for which we did not find statistically significant fold-changes, such as miR-134, 181a, 181a-5p, 181b, 155, 34c-5p, 935, 10a-5p, 142a-5p, 431-5p, 141, 184, 421, 25-3p, and 15a [ 38 , 46 , 48 , 55 ].…”

Section: Discussionmentioning

confidence: 79%

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Stage- and Subfield-Associated Hippocampal miRNA Expression Patterns after Pilocarpine-Induced Status Epilepticus

Dheen

Tang

et al. 2022

Biomedicines

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Objective: To investigate microRNA (miRNA) expression profiles before and after pilocarpine-induced status epilepticus (SE) in the cornu ammonis (CA) and dentated gyrus (DG) areas of the mouse hippocampus, and to predict the downstream proteins and related pathways based on bioinformatic analysis. Methods: An epileptic mouse model was established using a pilocarpine injection. Brain tissues from the CA and DG were collected separately for miRNA analysis. The miRNAs were extracted using a kit, and the expression profiles were generated using the SurePrint G3 Mouse miRNA microarray and validated. The intersecting genes of TargetScan and miRanda were selected to predict the target genes of each miRNA. For gene ontology (GO) studies, the parent-child-intersection (pci) method was used for enrichment analysis, and Benjamini-Hochberg was used for multiple test correction. The Kyoto Encyclopedia of Genes and Genomes (KEGG) was used to detect disease-related pathways among the large list of miRNA-targeted genes. All analyses mentioned above were performed at the time points of control, days 3, 14, and 60 post-SE. Results: Control versus days 3, 14, and 60 post-SE: in the CA area, a total of 131 miRNAs were differentially expressed; 53, 49, and 26 miRNAs were upregulated and 54, 10, and 22 were downregulated, respectively. In the DG area, a total of 171 miRNAs were differentially expressed; furthermore, 36, 32, and 28 miRNAs were upregulated and 78, 58, and 44 were downregulated, respectively. Of these, 92 changed in both the CA and DG, 39 only in the CA, and 79 only in the DG area. The differentially expressed miRNAs target 11–1630 genes. Most of these proteins have multiple functions in epileptogenesis. There were 15 common pathways related to altered miRNAs: nine different pathways in the CA and seven in the DG area. Conclusions: Stage- and subfield-associated hippocampal miRNA expression patterns are closely related to epileptogenesis, although the detailed mechanisms need to be explored in the future.

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Section: Discussionmentioning

confidence: 79%

“…Transcription factor-related miRNAs include downregulated miR-124 [ 42 ]. Apoptosis-related miRNAs include upregulated miR-21 [ 43 ], miR-34a (CA) [ 44 ], miR-129-5p [ 45 ], and downregulated miR-139-5p [ 46 ]. Ion channel-related miRNAs include downregulated miR-324-5p (DG) [ 47 ].…”

Section: Discussionmentioning

confidence: 99%

Stage- and Subfield-Associated Hippocampal miRNA Expression Patterns after Pilocarpine-Induced Status Epilepticus

Dheen

Tang

et al. 2022

Biomedicines

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“…Both miR-155 and miR-146a have been shown to be involved in complementary regulatory pathways activated during the inflammatory response, being the first pro-inflammatory and the second anti-inflammatory [ 53 ]. We showed that both miRNAs are overexpressed, in an age-dependent manner in brains from Epm2a-/- and Epm2b-/- mice models [ 30 ].…”

Section: Discussionmentioning

confidence: 99%

Exploring miRNA–target gene pair detection in disease with coRmiT

Cordoba-Caballero,

Perkins,

García-Criado

et al. 2024

Briefings in Bioinformatics

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A wide range of approaches can be used to detect micro RNA (miRNA)–target gene pairs (mTPs) from expression data, differing in the ways the gene and miRNA expression profiles are calculated, combined and correlated. However, there is no clear consensus on which is the best approach across all datasets. Here, we have implemented multiple strategies and applied them to three distinct rare disease datasets that comprise smallRNA-Seq and RNA-Seq data obtained from the same samples, obtaining mTPs related to the disease pathology. All datasets were preprocessed using a standardized, freely available computational workflow, DEG_workflow. This workflow includes coRmiT, a method to compare multiple strategies for mTP detection. We used it to investigate the overlap of the detected mTPs with predicted and validated mTPs from 11 different databases. Results show that there is no clear best strategy for mTP detection applicable to all situations. We therefore propose the integration of the results of the different strategies by selecting the one with the highest odds ratio for each miRNA, as the optimal way to integrate the results. We applied this selection-integration method to the datasets and showed it to be robust to changes in the predicted and validated mTP databases. Our findings have important implications for miRNA analysis. coRmiT is implemented as part of the ExpHunterSuite Bioconductor package available from https://bioconductor.org/packages/ExpHunterSuite.

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“…Alteration in the gene expression pattern result in changes in neuronal firing threshold in epilepsy. Processes related to apoptosis, neurodegeneration and inflammation and oxidative stress, which are affected by changes in gene expression, are crucial for development of diseases in the brain ( Dichter, 2009 ; Ghafouri-Fard et al, 2022 ). This abnormal brain function is mediated by changes in transcription factors, epigenetic pathways such as DNA methylation and histone modifications and post-transcriptional regulation.…”

Section: Hippocampal Mirnas In Epilepsymentioning

confidence: 99%

The role of microRNAs in neurobiology and pathophysiology of the hippocampus

Rashidi,

Kalirad,

Rafie

et al. 2023

Front. Mol. Neurosci.

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MicroRNAs (miRNAs) are short non-coding and well-conserved RNAs that are linked to many aspects of development and disorders. MicroRNAs control the expression of genes related to different biological processes and play a prominent role in the harmonious expression of many genes. During neural development of the central nervous system, miRNAs are regulated in time and space. In the mature brain, the dynamic expression of miRNAs continues, highlighting their functional importance in neurons. The hippocampus, as one of the crucial brain structures, is a key component of major functional connections in brain. Gene expression abnormalities in the hippocampus lead to disturbance in neurogenesis, neural maturation and synaptic formation. These disturbances are at the root of several neurological disorders and behavioral deficits, including Alzheimer’s disease, epilepsy and schizophrenia. There is strong evidence that abnormalities in miRNAs are contributed in neurodegenerative mechanisms in the hippocampus through imbalanced activity of ion channels, neuronal excitability, synaptic plasticity and neuronal apoptosis. Some miRNAs affect oxidative stress, inflammation, neural differentiation, migration and neurogenesis in the hippocampus. Furthermore, major signaling cascades in neurodegeneration, such as NF-Kβ signaling, PI3/Akt signaling and Notch pathway, are closely modulated by miRNAs. These observations, suggest that microRNAs are significant regulators in the complicated network of gene regulation in the hippocampus. In the current review, we focus on the miRNA functional role in the progression of normal development and neurogenesis of the hippocampus. We also consider how miRNAs in the hippocampus are crucial for gene expression mechanisms in pathophysiological pathways.

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Aberrant expression of miRNAs in epilepsy

Cited by 21 publications

References 71 publications

Stage- and Subfield-Associated Hippocampal miRNA Expression Patterns after Pilocarpine-Induced Status Epilepticus

Stage- and Subfield-Associated Hippocampal miRNA Expression Patterns after Pilocarpine-Induced Status Epilepticus

Exploring miRNA–target gene pair detection in disease with coRmiT

The role of microRNAs in neurobiology and pathophysiology of the hippocampus

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