Endoplasmic reticulum stress-mediated upregulation of miR-29a enhances sensitivity to neuronal apoptosis.

Disturbance of homeostasis within the endoplasmic reticulum (ER) lumen leads to the accumulation of unfolded and misfolded proteins. This results in the activation of an evolutionary conserved stress response termed ER stress that, if unresolved, induces apoptosis. Previously the Bcl-2 homology domain 3-Only Protein Puma was identified as a mediator of ER stress-induced apoptosis in neurons. In the search of alternative contributors to ER stress-induced apoptosis, a downregulation of the anti-apoptotic Bcl-2 family protein Mcl-1 was noted during ER stress in both mouse cortical neurons and human SH-SY5Y neuroblastoma cells. Downregulation of Mcl-1 was associated with an upregulation of microRNA-29a (miR-29a) expression, and subsequent experiments showed that miR-29a targeted the 3\u27-untranslated region of the anti-apoptotic Bcl-2 family protein, Mcl-1. Inhibition of miR-29a expression using sequence-specific antagomirs or the overexpression of Mcl-1 decreased cell death following tunicamycin treatment, while gene silencing of Mcl-1 increased cell death. miR-29a did not alter the signalling branches of the ER stress response, rather its expression was controlled by the ER stress-induced transcription factor activating-transcription-factor-4 (ATF4). The current data demonstrate that the ATF4-mediated upregulation of miR-29a enhances the sensitivity of neurons to ER stress-induced apoptosis

A systems approach delivers a functional microRNA catalog and expanded targets for seizure suppression in temporal lobe epilepsy

Temporal lobe epilepsy is the most common drug-resistant form of epilepsy in adults. The reorganization of neural networks and the gene expression landscape underlying pathophysiologic network behavior in brain structures such as the hippocampus has been suggested to be controlled, in part, by microRNAs. To systematically assess their significance, we sequenced Argonaute-loaded microRNAs to define functionally engaged microRNAs in the hippocampus of three different animal models in two species and at six time points between the initial precipitating insult through to the establishment of chronic epilepsy. We then selected commonly up-regulated microRNAs for a functional in vivo therapeutic screen using oligonucleotide inhibitors. Argonaute sequencing generated 1.44 billion small RNA reads of which up to 82% were microRNAs, with over 400 unique microRNAs detected per model. Approximately half of the detected microRNAs were dysregulated in each epilepsy model. We prioritized commonly up-regulated microRNAs that were fully conserved in humans and designed custom antisense oligonucleotides for these candidate targets. Antiseizure phenotypes were observed upon knockdown of miR-10a-5p, miR-21a-5p, and miR-142a-5p and electrophysiological analyses indicated broad safety of this approach. Combined inhibition of these three microRNAs reduced spontaneous seizures in epileptic mice. Proteomic data, RNA sequencing, and pathway analysis on predicted and validated targets of these microRNAs implicated derepressed TGF-\u3b2 signaling as a shared seizure-modifying mechanism. Correspondingly, inhibition of TGF-\u3b2 signaling occluded the antiseizure effects of the antagomirs. Together, these results identify shared, dysregulated, and functionally active microRNAs during the pathogenesis of epilepsy which represent therapeutic antiseizure targets

Development of Bioinformatics Software Tools for Network- and Pathway-Based Exploration of miRNA Target Interactions

miRNAs are short, non-coding RNA involved in the post-transcriptional regulation of mRNA in both health and disease. A single miRNA can target hundreds or even thousands of mRNAs. Similarly, a single mRNA can be targeted by multiple miRNAs simultaneously. Moreover, the functional impact of miRNA targeting can be difficult to elucidate due to overlapping and redundant targeting, heterogenous tissue expression, direct and indirect effects, and convergent signalling mechanisms.The large interest in miRNA research and miRNA-target interactions (MTIs) has led to the development of many publicly available MTI databases (DBs) and other tools. The use of individual DBs and tools, however, is error-prone, due to rapidly evolving miRNA nomenclature guidelines and resultant naming inconsistencies within publications and other resources, similar naming inconsistencies across molecular identifiers and gene symbols, and the use of deprecated resources. MTI prediction algorithms also suffer from a high level of false positives.A standard workflow for MTI investigation can include miRNA target identification, functional annotation of miRNA targets, computation of overlapping targets, and pathway enrichment analysis, all of which require application of individual tools and software packages. Further errors, however, caused by ID mismatches and data inconsistencies within and across combined resources, can be introduced at many points in these workflows, leading to irreproducible research and potentially incorrect conclusions. At worst, these issues have directly contributed to the retraction of publications.To address these challenges, we here developed and applied three software tools to perform optimised miRNA and MTI research: 1) miRNAmeConverter, an R-package and web application that performs high-throughput miRNA name translation. 2) GeneNameGenie, a molecular ID graph database and translation framework that maps relationships between 47 molecular ID types and facilitates rapid translation of common IDs, including miRNAs. GeneNameGenie also performs integrated Reactome pathway enrichment analysis. 3) miRGIK builds on the GeneNameGenie graph database and enriches it with more than 48 million MTIs and their metadata, gene-tissue expression data, and transcription factor (TF) target information. miRGIK is a complete, standalone MTI graph database resource and research tool which enables sophisticated MTI identification and filtering including tissue expression, top-down (pathway - gene - miRNA) and bottom-up (miRNA - gene - pathway) functional analysis of miRNA direct and indirect targeting, computation of overlapping and redundant targets, detailed TF targeting investigation, and pathway enrichment analysis. The developed software tools can complement wet-lab research to facilitate holistic investigation of miRNA functions in a biological context, and were herein applied to analyse the functional role of miRNAs dysregulated in ischaemic neuronal injury (Pfeiffer et al., 2021) and epilepsy (Venø et al., 2020).</p

miRNAmeConverter: an R/bioconductor package for translating mature miRNA names to different miRBase versions.

Summary: The miRBase database is the central and official repository for miRNAs and the current release is miRBase version 21.0. Name changes in different miRBase releases cause inconsistencies in miRNA names from version to version. When working with only a small number of miRNAs the translation can be done manually. However, with large sets of miRNAs, the necessary correction of such inconsistencies becomes burdensome and error-prone. We developed miRNAmeConverter , available as a Bioconductor R package and web interface that addresses the challenges associated with mature miRNA name inconsistencies. The main algorithm implemented enables high-throughput automatic translation of species-independent mature miRNA names to user selected miRBase versions. The web interface enables users less familiar with R to translate miRNA names given in form of a list or embedded in text and download of the results. Availability and Implementation: The miRNAmeConverter R package is open source under the Artistic-2.0 license. It is freely available from Bioconductor ( http://bioconductor.org/packages/miRNAmeConverter ). The web interface is based on R Shiny and can be accessed under the URL http://www.systemsmedicineireland.ie/tools/mirna-name-converter/ . The database that miRNAmeConverter depends on is provided by the annotation package miRBaseVersions.db and can be downloaded from Bioconductor ( http://bioconductor.org/packages/miRBaseVersions.db ). Minimum R version 3.3.0 is required. Contact: [email protected]. Supplementary information: Supplementary data are available at Bioinformatics online

AMPK‐regulated miRNA‐210‐3p is activated during ischaemic neuronal injury and modulates PI3K‐p70S6K signalling

AbstractProgressive neuronal injury following ischaemic stroke is associated with glutamate‐induced depolarization, energetic stress and activation of AMP‐activated protein kinase (AMPK). We here identify a molecular signature associated with neuronal AMPK activation, as a critical regulator of cellular response to energetic stress following ischaemia. We report a robust induction of microRNA miR‐210‐3p both in vitro in primary cortical neurons in response to acute AMPK activation and following ischaemic stroke in vivo. Bioinformatics and reverse phase protein array analysis of neuronal protein expression changes in vivo following administration of a miR‐210‐3p mimic revealed altered expression of phosphatase and tensin homolog (PTEN), 3‐phosphoinositide‐dependent protein kinase 1 (PDK1), ribosomal protein S6 kinase (p70S6K) and ribosomal protein S6 (RPS6) signalling in response to increasing miR‐210‐3p. In vivo, we observed a corresponding reduction in p70S6K activity following ischaemic stroke. Utilizing models of glutamate receptor over‐activation in primary neurons, we demonstrated that induction of miR‐210‐3p was accompanied by sustained suppression of p70S6K activity and that this effect was reversed by miR‐210‐3p inhibition. Collectively, these results provide new molecular insight into the regulation of cell signalling during ischaemic injury, and suggest a novel mechanism whereby AMPK regulates miR‐210‐3p to control p70S6K activity in ischaemic stroke and excitotoxic injury. imag

AMPK-regulated miRNA-210-3p is activated during ischaemic neuronal injury and modulates P13K-p70S6K signalling

Progressive neuronal injury following ischaemic stroke is associated with glutamate-induced depolarization, energetic stress and activation of AMP-activated protein kinase (AMPK). We here identify a molecular signature associated with neuronal AMPK activation, as a critical regulator of cellular response to energetic stress following ischaemia. We report a robust induction of microRNA miR-210-3p both in vitro in primary cortical neurons in response to acute AMPK activation and following ischaemic stroke in vivo. Bioinformatics and reverse phase protein array analysis of neuronal protein expression changes in vivo following administration of a miR-210-3p mimic revealed altered expression of phosphatase and tensin homolog (PTEN), 3-phosphoinositide-dependent protein kinase 1 (PDK1), ribosomal protein S6 kinase (p70S6K) and ribosomal protein S6 (RPS6) signalling in response to increasing miR-210-3p. In vivo, we observed a corresponding reduction in p70S6K activity following ischaemic stroke. Utilizing models of glutamate receptor over-activation in primary neurons, we demonstrated that induction of miR-210-3p was accompanied by sustained suppression of p70S6K activity and that this effect was reversed by miR-210-3p inhibition. Collectively, these results provide new molecular insight into the regulation of cell signalling during ischaemic injury, and suggest a novel mechanism whereby AMPK regulates miR-210-3p to control p70S6K activity in ischaemic stroke and excitotoxic injury.<br

A systems approach delivers a functional microRNA catalog and expanded targets for seizure suppression in temporal lobe epilepsy.

Temporal lobe epilepsy is the most common drug-resistant form of epilepsy in adults. The reorganization of neural networks and the gene expression landscape underlying pathophysiologic network behavior in brain structures such as the hippocampus has been suggested to be controlled, in part, by microRNAs. To systematically assess their significance, we sequenced Argonaute-loaded microRNAs to define functionally engaged microRNAs in the hippocampus of three different animal models in two species and at six time points between the initial precipitating insult through to the establishment of chronic epilepsy. We then selected commonly up-regulated microRNAs for a functional in vivo therapeutic screen using oligonucleotide inhibitors. Argonaute sequencing generated 1.44 billion small RNA reads of which up to 82% were microRNAs, with over 400 unique microRNAs detected per model. Approximately half of the detected microRNAs were dysregulated in each epilepsy model. We prioritized commonly up-regulated microRNAs that were fully conserved in humans and designed custom antisense oligonucleotides for these candidate targets. Antiseizure phenotypes were observed upon knockdown of miR-10a-5p, miR-21a-5p, and miR-142a-5p and electrophysiological analyses indicated broad safety of this approach. Combined inhibition of these three microRNAs reduced spontaneous seizures in epileptic mice. Proteomic data, RNA sequencing, and pathway analysis on predicted and validated targets of these microRNAs implicated derepressed TGF-β signaling as a shared seizure-modifying mechanism. Correspondingly, inhibition of TGF-β signaling occluded the antiseizure effects of the antagomirs. Together, these results identify shared, dysregulated, and functionally active microRNAs during the pathogenesis of epilepsy which represent therapeutic antiseizure targets.</p