Current Update on Synopsis of miRNA Dysregulation in Neurological Disorders

miR-874-3p Alleviates Macrophage-Mediated Inflammatory Injury in Intracerebral Hemorrhage by Targeting HIPK2

Macrophages mediate secondary inflammatory injury after intracerebral hemorrhage (ICH). This study aimed to investigate the role and molecular mechanisms of miR-874-3p in macrophage polarization. A mice model of ICH was constructed by autologous blood injection. Macrophages were treated with erythrocyte lysates to construct an ICH cell model. Real-time quantitative reverse transcription PCR (RT-qPCR) was used to detect miR-874-3p levels. Enzyme-Linked Immunosorbent Assay (ELISA) was used to detect macrophage polarization markers. Brain tissue water content and neurological deficit scores were used to assess the degree of inflammatory injury in ICH mice. RNA immunoprecipitation (RIP) and Dual-luciferase reporter (DLR) assays were used to analyze the targeting relationship between miR-874-3p and target mRNA. miR-874-3p levels were decreased in ICH mice and erythrocyte lysates-treated macrophages. miR-874-3p mimic alleviated inflammatory injury, decreased the levels of M1 macrophage markers, and increased the levels of M2 macrophage markers, suggesting that miR-874-3p is involved in ICH by regulating macrophage polarization. HIPK2 is the target mRNA of miR-874-3p and has the opposite expression pattern of miR-874-3p. Overexpression of HIPK2 attenuates the effect of elevated miR-874-3p levels on macrophage polarization and inflammatory brain injury in ICH mice. miR-874-3p regulates macrophage polarization in ICH by targeting HIPK2. Therefore, the miR-874-3p/HIPK2 axis may be a promising target for ICH treatment.

Therapeutic prospects of microRNAs derived from mesenchymal stem cell extracellular vesicles in rheumatoid arthritis: a comprehensive overview

Rheumatoid arthritis (RA) is a chronic autoimmune disorder characterized by inflammatory joint damage. Recent studies have focused on the significance of microRNAs (miRNAs) in the pathogenesis of RA. Mesenchymal stem cells (MSCs) have emerged as a potential therapeutic option for RA based on their regenerative and immunomodulatory properties. MSCs release extracellular vesicles (EVs) containing miRNAs that can modulate immune and inflammatory responses. This article provides a comprehensive overview of the current evidence on the existence of various MSCs-derived miRNAs involved in the pathophysiology, characterization, and treatment of RA. An overview of the miRNA profiles in MSC-EVs is provided, along with an examination of their impact on various cell types implicated in RA pathogenesis, including synovial fibroblasts, macrophages, and T cells. Furthermore, the therapeutic capability of MSC-EVs for miRNA-based therapies in RA is discussed. In total, this review can present an extensive view of the complex interaction between EVs and MSC-derived miRNAs in RA and thus suggest valuable strategies for developing new therapeutic approaches to target this debilitating disease.

MicroRNA Expression in Asymptomatic Welders: Implications for Biomarker Discovery for Environmentally-Linked Neurodegenerative Disorders

Chronic occupational exposure to metals in welding fumes has been implicated in the etiology of neurodegenerative diseases (NDDs), including Parkinson's disease (PD) and Alzheimer's disease (AD). Changes in microRNA (miRNA) expression have been associated with various neurodegenerative conditions. Circulating miRNAs, in particular, have emerged as promising, minimally invasive biomarkers for diagnosing and monitoring disease progression. This study was designed to characterize the expression of miRNAs in neuronally-enriched serum extracellular vesicles (EVs) among welders and non-welders to explore their potential link to metal concentrations and welding exposure measures and their potential as early diagnostic biomarkers for neurodegeneration. Serum samples from 39 welders and 27 healthy individuals were collected, and EV-enclosed miRNAs were extracted and analyzed. Also, whole blood metal concentrations and welding exposure measurements were obtained. Fifty miRNAs were found to be dysregulated in welders vs. non-welders, of which three (miR-16-5p, miR-93-5p, miR-486-5p) showing reduced expression and two (miR-4281 and miR-4417) exhibiting positive correlations with blood metal concentrations as well as with long- and short-term welding exposure measures. The dysregulation of these miRNAs suggests that exposure to metals could disrupt important biological processes, possibly contributing to an elevated risk of NDDs. These findings highlight the need for further research to validate the causal relationship between exposure to metals in welding fumes, the dysregulation of circulating miRNAs, and their role in neurodegenerative disease development, with implications for miRNA-based biomarkers in early disease detection and prevention.

MiRNA Dysregulation in Brain Injury: An In Silico Study to Clarify the Role of a MiRNA Set

BACKGROUND

The identification of specific circulating miRNAs has been proposed as a valuable tool for elucidating the pathophysiology of brain damage or injury and predicting patient outcomes.

OBJECTIVE

This study aims to apply several bioinformatic tools in order to clarify miRNA interactions with potential genes involved in brain injury, emphasizing the need of using a computational approach to determine the most likely correlations between miRNAs and target genes. Specifically, this study centers on elucidating the roles of miR-34b, miR-34c, miR-135a, miR-200c, and miR-451a.

METHODS

After a careful evaluation of different software available (analyzing the strengths and limitations), we applied three tools, one to perform an analysis of the validated targets (miRTarBase), and two to evaluate functional annotations (miRBase and TAM 2.0).

RESULTS

Research findings indicate elevated levels of miR-135a and miR-34b in patients with traumatic brain injury (TBI) within the first day post-injury, while miR-200c and miR-34c were found to be upregulated after 7 days. Moreover, miR-451a and miR-135a were found overexpressed in the serum, while miRNAs 34b, 34c, and 200c, had lower serum levels at baseline post brain injury.

CONCLUSION

This study emphasizes the use of computational methods in determining the most likely relationships between miRNAs and target genes by investigating several bioinformatic techniques to elucidate miRNA interactions with potential genes. Specifically, this study focuses on the functions of miR-34b, miR-34c, miR-135a, miR-200c, and miR-451a, providing an up-to-date overview and suggesting future research directions for identifying theranomiRNAs related to brain injury, both at the tissue and serum levels.

MicroRNAs regulation in Parkinson's disease, and their potential role as diagnostic and therapeutic targets

MicroRNAs (miRNAs) are small non-coding RNA molecules that regulate gene expression by binding to target messenger RNA (mRNA) molecules and promoting their degradation or blocking their translation. Parkinson's disease (PD) is a neurodegenerative disorder caused by the loss of dopaminergic neurons in the substantia nigra. There is increasing evidence to suggest that miRNAs play a role in the pathogenesis of PD. Studies have identified several miRNAs that are dysregulated in the brains of PD patients, and animal models of the disease. MiRNA expression dysregulation contributes to the onset and progression of PD by modulating neuroinflammation, oxidative stress, and protein aggregation genes. Moreover, miRNAs have emerged as potential therapeutic targets for PD. This review elucidates the changes in miRNA expression profiles associated with PD, emphasising their potential as diagnostic biomarkers and therapeutic targets, and detailing specific miRNAs implicated in PD and their downstream targets. Integrated Insights into miRNA Function, Microglial Activation, Diagnostic, and Treatment Prospects in PD Note: This figure is an original figure created by the authors.

Sample-to-answer salivary miRNA testing: New frontiers in point-of-care diagnostic technologies

MicroRNA (miRNA), crucial non-coding RNAs, have emerged as key biomarkers in molecular diagnostics, prognosis, and personalized medicine due to their significant role in gene expression regulation. Salivary miRNA, in particular, stands out for its non-invasive collection method and ease of accessibility, offering promising avenues for the development of point-of-care diagnostics for a spectrum of diseases, including cancer, neurodegenerative disorders, and infectious diseases. Such development promises rapid and precise diagnosis, enabling timely treatment. Despite significant advancements in salivary miRNA-based testing, challenges persist in the quantification, multiplexing, sensitivity, and specificity, particularly for miRNA at low concentrations in complex biological mixtures. This work delves into these challenges, focusing on the development and application of salivary miRNA tests for point-of-care use. We explore the biogenesis of salivary miRNA and analyze their quantitative expression and their disease relevance in cancer, infection, and neurodegenerative disorders. We also examined recent progress in miRNA extraction, amplification, and multiplexed detection methods. This study offers a comprehensive view of the development of salivary miRNA-based point-of-care testing (POCT). Its successful advancement could revolutionize the early detection, monitoring, and management of various conditions, enhancing healthcare outcomes. This article is categorized under: Diagnostic Tools > Biosensing Diagnostic Tools > Diagnostic Nanodevices.

miR-154-5p Is a Novel Endogenous Ligand for TLR7 Inducing Microglial Activation and Neuronal Injury

Toll-like receptors (TLRs) are a collection of pattern recognition sensors that form a first line of defence by detecting pathogen- or damage-associated molecular patterns and initiating an inflammatory response. TLR activation in microglia, the major immune cells in the brain, can trigger the release of inflammatory molecules, which may contribute to various CNS diseases including Alzheimer's disease. Recently, some microRNAs were shown to serve as signalling molecules for TLRs. Here, we present miR-154-5p as a novel TLR7 ligand. Exposing microglia to miR-154-5p results in cytokine release and alters expression of the TLR signalling pathway dependent on TLR7. Additionally, miR-154-5p causes neuronal injury in enriched cortical neuron cultures and additive toxicity in the presence of microglia. Finally, intrathecal injection of miR-154-5p into mice leads to neuronal injury and accumulation of microglia in the cerebral cortex dependent on TLR7 expression. In conclusion, this study establishes miR-154-5p as a direct activator of TLR7 that can cause neuroinflammation and neuronal injury, which may contribute to CNS disease.

MicroRNA-148a-3p in pericyte-derived extracellular vesicles improves erectile function in diabetic mice by promoting cavernous neurovascular regeneration

BACKGROUND

To investigate the regulatory role of microRNA (miR)-148a-3p in mouse corpus cavernous pericyte (MCPs)-derived extracellular vesicles (EVs) in the treatment of diabetes-induced erectile dysfunction (ED).

METHODS

Mouse corpus cavernous tissue was used for MCP primary culture and EV isolation. Small-RNA sequencing analysis was performed to assess the type and content of miRs in MCPs-EVs. Four groups of mice were used: control nondiabetic mice and streptozotocin-induced diabetic mice receiving two intracavernous injections (days - 3 and 0) of phosphate buffered saline, MCPs-EVs transfected with reagent control, or MCPs-EVs transfected with a miR-148a-3p inhibitor. miR-148a-3p function in MCPs-EVs was evaluated by tube-formation assay, migration assay, TUNEL assay, intracavernous pressure, immunofluorescence staining, and Western blotting.

RESULTS

We extracted EVs from MCPs, and small-RNA sequencing analysis showed miR-148a-3p enrichment in MCPs-EVs. Exogenous MCPs-EV administration effectively promoted mouse cavernous endothelial cell (MCECs) tube formation, migration, and proliferation, and reduced MCECs apoptosis under high-glucose conditions. These effects were significantly attenuated in miR-148a-3p-depleted MCPs-EVs, which were extracted after inhibiting miR-148a-3p expression in MCPs. Repetitive intracavernous injections of MCPs-EVs improved erectile function by inducing cavernous neurovascular regeneration in diabetic mice. Using online bioinformatics databases and luciferase report assays, we predicted that pyruvate dehydrogenase kinase-4 (PDK4) is a potential target gene of miR-148a-3p.

CONCLUSIONS

Our findings provide new and reliable evidence that miR-148a-3p in MCPs-EVs significantly enhances cavernous neurovascular regeneration by inhibiting PDK4 expression in diabetic mice.

The Role of MicroRNA in Migraine: A Systemic Literature Review

Migraine is a common primary headache disorder, affecting about 14% of the population. Importantly, it was indicated as the second cause of disability globally and the leading cause among young women. Despite the widespread prevalence, migraine remains underdiagnosed and undertreated. The possible solution may be microRNAs-small, non-coding molecules. Until now, multiple studies have shown the great value of microRNA in both the diagnosis and treatment of different human diseases. Furthermore, a significant role in neurological disorders has been suggested. Little research regarding the utility of microRNA in migraine has been conducted, however, the results so far appear to be promising. We performed an electronic article search through PubMed and Embase Database to further explore the topic. After the analysis, according to PRISMA 2020 guidelines, we included 21 studies. The dysregulation was observed in migraine in general, as well as in different types and phases; thus, miRNAs emerge as promising diagnostic biomarkers. Additionally, some studies showed the influence of the intervention with miRNA levels on neuroinflammation and the expression of peptides, which are crucial in migraine pathogenesis. This review aims to summarize the current knowledge about the role of miRNAs in migraine and encourage to further research in this field.Kindly check and confirm the edit made in the title.I checked and confirm.

microRNA Detection via Nanostructured Biochips for Early Cancer Diagnostics

MicroRNA (miRNA) are constituted of approximately 22 nucleotides and play an important role in the regulation of many physiological functions and diseases. In the last 10 years, an increasing interest has been recorded in studying the expression profile of miRNAs in cancer. Real time-quantitative polymerase chain reaction (RT-qPCR), microarrays, and small RNA sequencing represent the gold standard techniques used in the last 30 years as detection methods. The advent of nanotechnology has allowed the fabrication of nanostructured biosensors which are widely exploited in the diagnostic field. Nanostructured biosensors offer many advantages: (i) their small size allows the construction of portable, wearable, and low-cost products; (ii) the large surface-volume ratio enables the loading of a great number of biorecognition elements (e.g., probes, receptors); and (iii) direct contact of the recognition element with the analyte increases the sensitivity and specificity inducing low limits of detection (LOD). In this review, the role of nanostructured biosensors in miRNA detection is explored, focusing on electrochemical and optical sensing. In particular, four types of nanomaterials (metallic nanoparticles, graphene oxide, quantum dots, and nanostructured polymers) are reported for both detection strategies with the aim to show their distinct properties and applications.

Antagonistic Interactions in Mitochondria ROS Signaling Responses to Manganese

Antagonistic interaction refers to opposing beneficial and adverse signaling by a single agent. Understanding opposing signaling is important because pathologic outcomes can result from adverse causative agents or the failure of beneficial mechanisms. To test for opposing responses at a systems level, we used a transcriptome-metabolome-wide association study (TMWAS) with the rationale that metabolite changes provide a phenotypic readout of gene expression, and gene expression provides a phenotypic readout of signaling metabolites. We incorporated measures of mitochondrial oxidative stress (mtOx) and oxygen consumption rate (mtOCR) with TMWAS of cells with varied manganese (Mn) concentration and found that adverse neuroinflammatory signaling and fatty acid metabolism were connected to mtOx, while beneficial ion transport and neurotransmitter metabolism were connected to mtOCR. Each community contained opposing transcriptome-metabolome interactions, which were linked to biologic functions. The results show that antagonistic interaction is a generalized cell systems response to mitochondrial ROS signaling.

3D genome-selected microRNAs to improve Alzheimer's disease prediction

Introduction

Alzheimer's disease (AD) is a type of neurodegenerative disease that has no effective treatment in its late stage, making the early prediction of AD critical. There have been an increase in the number of studies indicating that miRNAs play an important role in neurodegenerative diseases including Alzheimer's disease via epigenetic modifications including DNA methylation. Therefore, miRNAs may serve as excellent biomarkers in early AD prediction.

Methods

Considering that the non-coding RNAs' activity may be linked to their corresponding DNA loci in the 3D genome, we collected the existing AD-related miRNAs combined with 3D genomic data in this study. We investigated three machine learning models in this work under leave-one-out cross-validation (LOOCV): support vector classification (SVC), support vector regression (SVR), and knearest neighbors (KNNs).

Results

The prediction results of different models demonstrated the effectiveness of incorporating 3D genome information into the AD prediction models.

Discussion

With the assistance of the 3D genome, we were able to train more accurate models by selecting fewer but more discriminatory miRNAs, as witnessed by several ML models. These interesting findings indicate that the 3D genome has great potential to play an important role in future AD research.

Evaluation of miR-526b-3p, miR-1179, miR-3529-3p, miR-5011-5p as potential diagnostic biomarkers in isolated cervical dystonia

BACKGROUND

Cervical dystonia (CD) also named spasmodic torticollis is the most common type of focal dystonias and characterized by abnormal head, neck, and shoulder movements due to involuntary muscular spasm. Although CD is mostly idiopathic, to date, several genes have been associated with CD. However, to the best of our knowledge, microRNAs (miRNAs) which are interacted with CD-associated genes have been not evaluated yet. miRNAs are regulatory small non-coding RNAs and are suggested as potential biomarkers for many diseases through their stability in clinical samples. Therefore, we aimed to assess the expression levels of miRNAs (miR-526b-3p, miR-1179, miR-3529-3p, miR-5011-5p) which are targeted the CD-associated genes, and evaluate their performance as diagnostic biomarkers.

METHODS

Peripheral blood samples were obtained from 30 patients with isolated CD (ICD) and 25 healthy controls. The expression levels of miR-526b-3p, miR-1179, miR-3529-3p, and miR-5011-5p were analyzed via quantitative real-time PCR (qRT-PCR), and receiver operating characteristic (ROC) curves were generated to evaluate the diagnostic values.

RESULTS

miR-526b-3p, miR-1179, and miR-3529-3p were significantly up-regulated while miR-5011-5p was significantly down-regulated in ICD patients compared to healthy controls. ROC analysis revealed that all miRNAs, especially miR-1179 and miR-3529-3p were statistically significant with the area under the curve (AUC) of 0.905 and 0.933, respectively.

CONCLUSION

Altered expression levels of aforementioned miRNAs may be associated with CD pathogenesis. Our findings suggest using these four miRNAs as remarkable biomarkers in the diagnosis of ICD.

miRNA in Parkinson's disease: From pathogenesis to theranostic approaches

Parkinson's disease (PD) is an age associated neurological disorder which is specified by cardinal motor symptoms such as tremor, stiffness, bradykinesia, postural instability, and non-motor symptoms. Dopaminergic neurons degradation in substantia nigra region and aggregation of αSyn are the classic signs of molecular defects noticed in PD pathogenesis. The discovery of microRNAs (miRNA) predicted to have a pivotal part in various processes regarding regularizing the cellular functions. Studies on dysregulation of miRNA in PD pathogenesis has recently gained the concern where our review unravels the role of miRNA expression in PD and its necessity in clinical validation for therapeutic development in PD. Here, we discussed how miRNA associated with ageing process in PD through molecular mechanistic approach of miRNAs on sirtuins, tumor necrosis factor-alpha and interleukin-6, dopamine loss, oxidative stress and autophagic dysregulation. Further we have also conferred the expression of miRNAs affected by SNCA gene expression, neuronal differentiation and its therapeutic potential with PD. In conclusion, we suggest more rigorous studies should be conducted on understanding the mechanisms and functions of miRNA in PD which will eventually lead to discovery of novel and promising therapeutics for PD.

SFGAE: a self-feature-based graph autoencoder model for miRNA-disease associations prediction

Increasing evidence has suggested that microRNAs (miRNAs) are important biomarkers of various diseases. Numerous graph neural network (GNN) models have been proposed for predicting miRNA-disease associations. However, the existing GNN-based methods have over-smoothing issue-the learned feature embeddings of miRNA nodes and disease nodes are indistinguishable when stacking multiple GNN layers. This issue makes the performance of the methods sensitive to the number of layers, and significantly hurts the performance when more layers are employed. In this study, we resolve this issue by a novel self-feature-based graph autoencoder model, shortened as SFGAE. The key novelty of SFGAE is to construct miRNA-self embeddings and disease-self embeddings, and let them be independent of graph interactions between two types of nodes. The novel self-feature embeddings enrich the information of typical aggregated feature embeddings, which aggregate the information from direct neighbors and hence heavily rely on graph interactions. SFGAE adopts a graph encoder with attention mechanism to concatenate aggregated feature embeddings and self-feature embeddings, and adopts a bilinear decoder to predict links. Our experiments show that SFGAE achieves state-of-the-art performance. In particular, SFGAE improves the average AUC upon recent GAEMDA [1] on the benchmark datasets HMDD v2.0 and HMDD v3.2, and consistently performs better when less (e.g. 10%) training samples are used. Furthermore, SFGAE effectively overcomes the over-smoothing issue and performs stably well on deeper models (e.g. eight layers). Finally, we carry out case studies on three human diseases, colon neoplasms, esophageal neoplasms and kidney neoplasms, and perform a survival analysis using kidney neoplasm as an example. The results suggest that SFGAE is a reliable tool for predicting potential miRNA-disease associations.

HT-SELEX-based identification of binding pre-miRNA hairpin-motif for small molecules

Selective targeting of biologically relevant RNAs with small molecules is a long-standing challenge due to the lack of clear understanding of the binding RNA motifs for small molecules. The standard SELEX procedure allows the identification of specific RNA binders (aptamers) for the target of interest. However, more effort is needed to identify and characterize the sequence-structure motifs in the aptamers important for binding to the target. Herein, we described a strategy integrating high-throughput (HT) sequencing with conventional SELEX followed by bioinformatic analysis to identify aptamers with high binding affinity and target specificity to unravel the sequence-structure motifs of pre-miRNA, which is essential for binding to the recently developed new water-soluble small-molecule CMBL3aL. To confirm the fidelity of this approach, we investigated the binding of CMBL3aL to the identified motifs by surface plasmon resonance (SPR) spectroscopy and its potential regulatory activity on dicer-mediated cleavage of the obtained aptamers and endogenous pre-miRNAs comprising the identified motif in its hairpin loop. This new approach would significantly accelerate the identification process of binding sequence-structure motifs of pre-miRNA for the compound of interest and would contribute to increase the spectrum of biomedical application.

Extracellular Vesicles, Stem Cells and the Role of miRNAs in Neurodegeneration

There are different modalities of intercellular communication governed by cellular homeostasis. In this review, we will explore one of these forms of communication called extracellular vesicles (EVs). These vesicles are released by all cells in the body and are heterogeneous in nature. The primary function of EVs is to share information through their cargo consisting of proteins, lipids and nucleic acids (mRNA, miRNA, dsDNA etc.) with other cells, which have a direct consequence on their microenvironment. We will focus on the role of EVs of mesenchymal stem cells (MSCs) in the nervous system and how these participate in intercellular communication to maintain physiological function and provide neuroprotection. However, deregulation of this same communication system could play a role in several neurodegenerative diseases, such as Alzheimer's disease, Parkinson's disease, Amyotrophic lateral sclerosis, multiple sclerosis, prion disease and Huntington's disease. The release of EVs from a cell provides crucial information to what is happening inside the cell and thus could be used in diagnostics and therapy. We will discuss and explore new avenues for the clinical applications of using engineered MSC-EVs and their potential therapeutic benefit in treating neurodegenerative diseases.

MiR-218 steps down to a threshold of motor impairment

In this issue of Neuron, Amin et al. (2021) generate genetic tools to titrate down levels of miR-218, a motor neuron-enriched microRNA, in vivo. Varying miR-218 dose alters target selection, results in distinct dose-response curves reflecting 3' UTR features, and reveals a miR-218 threshold below which motor neuron deficits emerge.

A hidden threshold in motor neuron gene networks revealed by modulation of miR-218 dose

Disruption of homeostatic microRNA (miRNA) expression levels is known to cause human neuropathology. However, the gene regulatory and phenotypic effects of altering a miRNA's in vivo abundance (rather than its binary gain or loss) are not well understood. By genetic combination, we generated an allelic series of mice expressing varying levels of miR-218, a motor neuron-selective gene regulator associated with motor neuron disease. Titration of miR-218 cellular dose unexpectedly revealed complex, non-ratiometric target mRNA dose responses and distinct gene network outputs. A non-linearly responsive regulon exhibited a steep miR-218 dose-dependent threshold in repression that, when crossed, resulted in severe motor neuron synaptic failure and death. This work demonstrates that a miRNA can govern distinct gene network outputs at different expression levels and that miRNA-dependent phenotypes emerge at particular dose ranges because of hidden regulatory inflection points of their underlying gene networks.

Melatonin as a promising modulator of aging related neurodegenerative disorders: Role of microRNAs

One of the host risk factors involved in aging-related diseases is coupled with the reduction of endogenous melatonin (MLT) synthesis in the pineal gland. MLT is considered a well-known pleiotropic regulatory hormone to modulate a multitude of biological processes such as the regulation of circadian rhythm attended by potent anti-oxidant, anti-inflammatory, and anti-cancer properties. It has also been established that the microRNAs family, as non-coding mRNAs regulating post-transcriptional processes, also serve a crucial role to promote MLT-related advantageous effects in both experimental and clinical settings. Moreover, the anti-aging impact of MLT and miRNAs participation jointly are of particular interest, recently. In this review, we aimed to scrutinize recent advances concerning the therapeutic implications of MLT, particularly in the brain tissue in the face of aging. We also assessed the possible interplay between microRNAs and MLT, which could be considered a therapeutic strategy to slow down the aging process in the nervous system.

Description of a CSF-Enriched miRNA Panel for the Study of Neurological Diseases

Background: The study of circulating miRNAs in CSF has gained tremendous attention during the last years, as these molecules might be promising candidates to be used as biomarkers and provide new insights into the disease pathology of neurological disorders. Objective: The main aim of this study was to describe an OpenArray panel of CSF-enriched miRNAs to offer a suitable tool to identify and characterize new molecular signatures in different neurological diseases. Methods: Two hundred and fifteen human miRNAs were selected to be included in the panel, and their expression and abundance in CSF samples were analyzed. In addition, their stability was studied in order to propose suitable endogenous controls for CSF miRNA studies. Results: miR-143-3p and miR-23a-3p were detected in all CSF samples, while another 80 miRNAs were detected in at least 70% of samples. miR-770-5p was the most abundant miRNA in CSF, presenting the lowest mean Cq value. In addition, miR-26b-5p, miR-335-5p and miR-92b-3p were the most stable miRNAs and could be suitable endogenous normalizers for CSF miRNA studies. Conclusions: These OpenArray plates might be a suitable and efficient tool to identify and characterize new molecular signatures in different neurological diseases and would improve the yield of miRNA detection in CSF.

Emerging role of microRNAs in the pathogenesis of amyotrophic lateral sclerosis

Amyotrophic lateral sclerosis (ALS) is a deadly motor neuron disease (MND) and the most frequent MND in adults. ALS is recognized by degenerative alterations in both upper and lower motor neurons. This disorder is classified to familial and sporadic classes. Disease-causing mutations in SOD1, C9ORF72, FUS, and TARDBP have been recognized in familial ALS cases. However, in spite of conduction of several genetic association studies, heritable genetic risk elements in sporadic have not been identified completely. Several miRNAs have been dysregulated in the serum samples or brain tissues of ALS patients. Moreover, a number of miRNAs have been suggested as putative biomarkers for sporadic ALS. In the current manuscript, we review of miRNAs in the development of ALS.

Clustering of Alzheimer's and Parkinson's disease based on genetic burden of shared molecular mechanisms

One of the visions of precision medicine has been to re-define disease taxonomies based on molecular characteristics rather than on phenotypic evidence. However, achieving this goal is highly challenging, specifically in neurology. Our contribution is a machine-learning based joint molecular subtyping of Alzheimer's (AD) and Parkinson's Disease (PD), based on the genetic burden of 15 molecular mechanisms comprising 27 proteins (e.g. APOE) that have been described in both diseases. We demonstrate that our joint AD/PD clustering using a combination of sparse autoencoders and sparse non-negative matrix factorization is reproducible and can be associated with significant differences of AD and PD patient subgroups on a clinical, pathophysiological and molecular level. Hence, clusters are disease-associated. To our knowledge this work is the first demonstration of a mechanism based stratification in the field of neurodegenerative diseases. Overall, we thus see this work as an important step towards a molecular mechanism-based taxonomy of neurological disorders, which could help in developing better targeted therapies in the future by going beyond classical phenotype based disease definitions.

miRNA degradation in the mammalian brain

MicroRNAs (miRNAs) are short, noncoding RNAs that are evolutionarily conserved across many different species. miRNA regulation of gene expression, specifically in the context of the mammalian brain, has been well characterized; however, the regulation of miRNA degradation is still a focus of ongoing research. This review focuses on recent findings concerning the cellular mechanisms that govern miRNA degradation, with an emphasis on target-mediated miRNA degradation and how this phenomenon is uniquely poised to maintain homeostasis in neuronal systems.

Noncoding RNAs and Intracerebral Hemorrhage

BACKGROUND & OBJECTIVE

Intracerebral hemorrhage (ICH) is the most devastating subtype of stroke, for which there are few effective interventions. Computed tomography is accepted as the gold standard for diagnosis, whereas surgical evacuation is the main treatment for ICH. However, in emergency rooms, time is limited and information regarding a patient's clinical status or tolerance is typically not available. Many studies over the last decade have investigated the fundamental mechanisms of ICH and especially hematoma, which not only cause physical damage but also release toxins that have detrimental effects. However, there remain many gaps in our understanding of ICH. Compared to ischemic stroke, there is little known about the ICH pathogenesis and treatment options, and few specific biomarkers are available for monitoring disease progression, which include hematoma enlargement and perihematoma edema. Noncoding RNAs (ncRNAs) are involved in various biological processes and are potential biomarkers and therapeutic tools in central nervous system diseases. Recent studies have examined the role of ncRNAs including microRNAs, long noncoding RNAs, and circular RNAs-the three main subgroups associated with stroke-in ICH models. A deeper understanding of the functions of ncRNAs in different biological processes can provide a basis for developing more effective therapeutic strategies to prevent neuronal damage following ICH. In clinical settings, ncRNAs can serve as biomarkers for predicting the degree of injury resulting from ICH.

CONCLUSION

In this review, we discuss the current state of knowledge of the role of ncRNAs in ICH.

Droplet digital polymerase chain reaction-based quantification of circulating microRNAs using small RNA concentration normalization

Quantification of plasma microRNAs (miRNAs) as non-invasive disease biomarkers is subject to multiple technical variabilities. This study aimed to develop an optimized protocol for miRNA quantification from rodent plasma. We hypothesized that a fixed small RNA concentration input for reverse transcription (RT) reaction will provide better miRNA quantification than a fixed RNA volume input. For this, tail-vein plasma was collected from 30 naïve, adult male Sprague-Dawley rats. Plasma hemolysis was measured with NanoDrop-1000 and Denovix DS-11 spectrophotometers. Plasma was then pooled, and RNA was extracted from 50-μl, 100-μl or 200-μl pool aliquots. Small RNA concentration was measured with Qubit miRNA assay. A fixed RNA volume (un-normalized) or a fixed small RNA concentration was used for RT (concentration-normalized). The method was setup with miR-23a-3p and validated with miR-103a-3p and miR-451a. Hemolysis measurements from Denovix and NanoDrop strongly correlated. Qubit revealed increased small RNA concentrations with increasing starting plasma volumes. With concentration-normalization, miRNA levels from 100-µl and 200-µl plasma volume groups mostly normalized to the level of the 50-µl in ddPCR. Our results indicate that miRNA quantification with ddPCR should be performed with small RNA concentration-normalization to minimize variations in eluted RNA concentrations occuring during RNA extraction.

Modeling Parkinson's Disease Using Induced Pluripotent Stem Cells

Parkinson's disease (PD) is the second most common neurodegenerative disease. The molecular mechanisms of PD at the cellular level involve oxidative stress, mitochondrial dysfunction, autophagy, axonal transport, and neuroinflammation. Induced pluripotent stem cells (iPSCs) with patient-specific genetic background are capable of directed differentiation into dopaminergic neurons. Cell models based on iPSCs are powerful tools for studying the molecular mechanisms of PD. The iPSCs used for PD studies were mainly from patients carrying mutations in synuclein alpha (SNCA), leucine-rich repeat kinase 2 (LRRK2), PTEN-induced putative kinase 1 (PINK1), parkin RBR E3 ubiquitin protein ligase (PARK2), cytoplasmic protein sorting 35 (VPS35), and variants in glucosidase beta acid (GBA). In this review, we summarized the advances in molecular mechanisms of Parkinson's disease using iPSC models.

Role of MicroRNAs in Parkinson's Disease

Parkinson's disease (PD) is a disabling neurodegenerative disease that manifests with resting tremor, bradykinesia, rigidity and postural instability. Since the discovery of microRNAs (miRNAs) in 1993, miRNAs have been shown to be important biological molecules involved in diverse processes to maintain normal cellular functions. Over the past decade, many studies have reported dysregulation of miRNA expressions in PD. Here, we identified 15 miRNAs from 34 reported screening studies that demonstrated dysregulation in the brain and/or neuronal models, cerebrospinal fluid (CSF) and blood. Specific miRNAs-of-interest that have been implicated in PD pathogenesis include miR-30, miR-29, let-7, miR-485 and miR-26. However, there are several challenges and limitations in drawing definitive conclusions due to the small sample size in clinical studies, varied laboratory techniques and methodologies and their incomplete penetrance of the blood-brain barrier. Developing an optimal delivery system and unravelling druggable targets of miRNAs in both experimental and human models and clinical validation of the results may pave way for novel therapeutics in PD.

miR‑223‑3p/TIAL1 interaction is involved in the mechanisms associated with the neuroprotective effects of dexmedetomidine on hippocampal neuronal cells in vitro

Dexmedetomidine (DEX), an α2 adrenoceptor agonist, is a commonly used anesthetic drug in surgical procedures. Previous studies have indicated that DEX exerts neuroprotective effects. However, the molecular mechanism underlying this process remains to be elucidated. The present study investigated a potential implication of microRNA (miR)-223-3p in the DEX-induced anti-oxidative effect on neuronal cells. The results indicated that following hydrogen peroxide (H₂O₂)-mediated induction of oxidative stress, the viability of human hippocampal neuronal cells was markedly decreased, as determined by an MTT assay. In addition, treatment with H₂O₂ induced cell apoptosis, the release of lactate dehydrogenase, accumulation of intracellular calcium, phosphorylation of calmodulin-2, and production of malondialdehyde and reactive oxygen species. Furthermore, treatment with H₂O₂ inhibited the expression of mir-223-3p and enhanced the expression of its target cytotoxic granule associated RNA binding protein like 1 (TIAL1), and these effects were reversed by treatment with DEX. Mechanistic studies demonstrated that the 3′-untranslated region of TIAL1 is a direct target of mir-223-3p. The results of the present study demonstrated that DEX may induce its neuroprotective effects by regulating the interaction between miR-223-3p and TIAL1. Therefore, the manipulation of miR-223-3p/TIAL1 interaction may be involved in the neuroprotective effects of DEX.

Elevated microRNA-520d-5p in the serum of patients with Parkinson's disease, possibly through regulation of cereloplasmin expression

Iron metabolism dysfunction and redox-active iron-induced oxidative stress in the brain may contribute to the pathogenesis of Parkinson's disease. We have previously demonstrated that reduced serum ceruloplasmin level exacerbates nigral iron deposition in Parkinson's disease, although the underlying cause of the low serum ceruloplasmin level in Parkinson's disease remains unknown. Fluorescent quantitative real-time polymerase chain reaction analysis revealed that patients with Parkinson's disease had higher serum levels of microRNA (miR)-520d-5p than controls (p = 0.0011). Patients with Alzheimer's disease or multiple system atrophy did not have significantly elevated miR-520d-5p levels. Expression of miR-520d-5p did not correlate with disease severity or the motor phenotype of Parkinson's disease. Luciferase assays confirmed that miR-520d-5p was associated with ceruloplasmin gene expression, as predicted by the TargetScan tool and miRBase. In vitro experiments showed that miR-520d-5p reduced ceruloplasmin gene expression in the U251 astrocyte cell line. Our data suggest that miR-520d-5p may be a potential regulator of ceruloplasmin gene expression in vitro.

Identifying and Exploiting Potential miRNA-Disease Associations With Neighborhood Regularized Logistic Matrix Factorization

With the rapid development of biological research, microRNAs (miRNA) have become an attractive topic because lots of experimental studies have revealed the significant associations between miRNAs and diseases. However, considering that experiments are expensive and time-consuming, computational methods for predicting associations between miRNAs and diseases have become increasingly crucial. In this study, we proposed a neighborhood regularized logistic matrix factorization method for miRNA-disease association prediction (NRLMFMDA) by integrating miRNA functional similarity, disease semantic similarity, Gaussian interaction profile kernel similarity, and experimentally validation of disease-miRNA association. We used Gaussian interaction profile kernel similarity to cover the shortage of the traditional similarity to make it more reasonable and complete. Furthermore, NRLMFMDA also considered the important influences of the neighborhood information and took full advantage of them to improve the accuracy of the miRNA-disease association prediction. We also improved the accuracy by giving higher weights to the known association data in the process of calculating the potential association probabilities. In the global and the local leave-one-out cross validation, NRLMFMDA got the AUCs of 0.9068 and 0.8239, respectively. Moreover, the average AUC of NRLMFMDA in 5-fold cross validation was 0.8976 ± 0.0034. All the three kinds of cross validations have shown significant advantages to a number of previous models. In the case studies of breast neoplasms, esophageal neoplasms and lymphoma according to known miRNA-disease associations in the recent version of HMDD database, there were 78, 80, and 74% of top 50 predicted related miRNAs verified to have associations with these three diseases, respectively. In the further case studies for new disease without any known related miRNAs and the previous version of HMDD database, there were also high proportions of the predicted miRNAs verified by experimental reports. All the validation experiment results have demonstrated the effectiveness and practicability of NRLFMDA to predict the potential miRNA-disease associations.

TLHNMDA: Triple Layer Heterogeneous Network Based Inference for MiRNA-Disease Association Prediction

In recent years, microRNAs (miRNAs) have been confirmed to be involved in many important biological processes and associated with various kinds of human complex diseases. Therefore, predicting potential associations between miRNAs and diseases with the huge number of verified heterogeneous biological datasets will provide a new perspective for disease therapy. In this article, we developed a novel computational model of Triple Layer Heterogeneous Network based inference for MiRNA-Disease Association prediction (TLHNMDA) by using the experimentally verified miRNA-disease associations, miRNA-long noncoding RNA (lncRNA) interactions, miRNA function similarity information, disease semantic similarity information and Gaussian interaction profile kernel similarity for lncRNAs into an triple layer heterogeneous network to predict new miRNA-disease associations. As a result, the AUCs of TLHNMDA are 0.8795 and 0.8795 ± 0.0010 based on leave-one-out cross validation (LOOCV) and 5-fold cross validation, respectively. Furthermore, TLHNMDA was implemented on three complex human diseases to evaluate predictive ability. As a result, 84% (kidney neoplasms), 78% (lymphoma) and 76% (prostate neoplasms) of top 50 predicted miRNAs for the three complex diseases can be verified by biological experiments. In addition, based on the HMDD v1.0 database, 98% of top 50 potential esophageal neoplasms-associated miRNAs were confirmed by experimental reports. It is expected that TLHNMDA could be a useful model to predict potential miRNA-disease associations with high prediction accuracy and stability.

Commonalities in Biological Pathways, Genetics, and Cellular Mechanism between Alzheimer Disease and Other Neurodegenerative Diseases: An In Silico-Updated Overview

BACKGROUND

Alzheimer's disease (AD) is the most common and well-studied neurodegenerative disease (ND). Biological pathways, pathophysiology and genetics of AD show commonalities with other NDs viz. Parkinson's disease (PD), Amyotrophic lateral sclerosis (ALS), Huntington's disease (HD), Prion disease and Dentatorubral-pallidoluysian atrophy (DRPLA). Many of the NDs, sharing the common features and molecular mechanisms suggest that pathology may be directly comparable and be implicated in disease prevention and development of highly effective therapies.

METHOD

In this review, a brief description of pathophysiology, clinical symptoms and available treatment of various NDs have been explored with special emphasis on AD. Commonalities in these fatal NDs provide support for therapeutic advancements and enhance the understanding of disease manifestation.

CONCLUSION

The studies concentrating on the commonalities in biological pathways, cellular mechanisms and genetics may provide the scope to researchers to identify few novel common target(s) for disease prevention and development of effective common drugs for multi-neurodegenerative diseases.

Emerging preclinical pharmacological targets for Parkinson's disease

Parkinson's disease (PD) is a progressive neurological condition caused by the degeneration of dopaminergic neurons in the basal ganglia. It is the most prevalent form of Parkinsonism, categorized by cardinal features such as bradykinesia, rigidity, tremors, and postural instability. Due to the multicentric pathology of PD involving inflammation, oxidative stress, excitotoxicity, apoptosis, and protein aggregation, it has become difficult to pin-point a single therapeutic target and evaluate its potential application. Currently available drugs for treating PD provide only symptomatic relief and do not decrease or avert disease progression resulting in poor patient satisfaction and compliance. Significant amount of understanding concerning the pathophysiology of PD has offered a range of potential targets for PD. Several emerging targets including AAV-hAADC gene therapy, phosphodiesterase-4, potassium channels, myeloperoxidase, acetylcholinesterase, MAO-B, dopamine, A2A, mGlu5, and 5-HT-1A/1B receptors are in different stages of clinical development. Additionally, alternative interventions such as deep brain stimulation, thalamotomy, transcranial magnetic stimulation, and gamma knife surgery, are also being developed for patients with advanced PD. As much as these therapeutic targets hold potential to delay the onset and reverse the disease, more targets and alternative interventions need to be examined in different stages of PD. In this review, we discuss various emerging preclinical pharmacological targets that may serve as a new promising neuroprotective strategy that could actually help alleviate PD and its symptoms.

Excessive expression of miR-27 impairs Treg-mediated immunological tolerance

MicroRNAs (miRs) are tightly regulated in the immune system, and aberrant expression of miRs often results in hematopoietic malignancies and autoimmune diseases. Previously, it was suggested that elevated levels of miR-27 in T cells isolated from patients with multiple sclerosis facilitate disease progression by inhibiting Th2 immunity and promoting pathogenic Th1 responses. Here we have demonstrated that, although mice with T cell-specific overexpression of miR-27 harbor dysregulated Th1 responses and develop autoimmune pathology, these disease phenotypes are not driven by miR-27 in effector T cells in a cell-autonomous manner. Rather, dysregulation of Th1 responses and autoimmunity resulted from a perturbed Treg compartment. Excessive miR-27 expression in murine T cells severely impaired Treg differentiation. Moreover, Tregs with exaggerated miR-27-mediated gene regulation exhibited diminished homeostasis and suppressor function in vivo. Mechanistically, we determined that miR-27 represses several known as well as previously uncharacterized targets that play critical roles in controlling multiple aspects of Treg biology. Collectively, our data show that miR-27 functions as a key regulator in Treg development and function and suggest that proper regulation of miR-27 is pivotal to safeguarding Treg-mediated immunological tolerance.

miRNAs as Circulating Biomarkers for Alzheimer's Disease and Parkinson's Disease

Detection of biomarkers for neurodegenerative disorders (NDDs) within brain tissues of Alzheimer's disease (AD) and Parkinson's disease (PD) patients has always been hampered by our inability to access and biopsy tissue of key brain regions implicated in disease occurrence and progression. Currently, diagnosis of NDDs is principally based on clinical observations of symptoms that present at later stages of disease progression, followed by neuroimaging and, possibly, CSF evaluation. One way to potentially detect and diagnose NDDs at a far earlier stage is to screen for abnormal levels of specific disease markers within the peripheral circulation of patients with NDDs. Increasing evidence suggests that there is dysregulation of microRNAs (miRNAs) in NDDs. Peripheral blood mononuclear cells, as well as biofluids, such as plasma, serum, urine and cerebrospinal fluid, contain miRNAs that can be identified and quantified. Circulating miRNAs within blood and other biofluids may thus be characterized and used as non-invasive, diagnostic biomarkers that facilitate the early detection of disease and potentially the continual monitoring of disease progression for NDDs such as AD and PD. Plainly, such a screen is only possible with a clear understanding of which miRNAs change with disease, and when these changes occur during the progression of AD and PD. Such information is becoming increasingly available and, in the near future, may not only support disease diagnosis, but provide the opportunity to evaluate therapeutic interventions earlier in the disease process.

Molecular regulation of miRNAs and potential biomarkers in the progression of hepatic steatosis to NASH

Increasing evidence suggests that microRNAs regulate diverse biological functions in the liver and play a very important function in metabolic-related disorders such as nonalcoholic fatty liver disease via regulating their target genes expression. In this review, we summarized the most recent progress in identification of miRNAs involving in the progression of liver steatosis and discussed the possible mechanisms by which miRNAs contribute to the diverse pathogenic liver injuries. We provide insights into the functional network of miRNAs by connecting miRNAs, their targets and biological pathways associated to hepatic steatosis and fibrosis, with important implications for our understanding of phenotypic-based disease pathogenesis. We also discuss the possible roles and challenges of miRNAs as biomarkers for drug-induced liver injury.