MicroRNA-379-5p targets MAP3K2 to reduce autophagy and alleviate neuronal injury following cerebral ischemia via the JNK/c-Jun signaling pathway

Profiling immune cell-related gene features and immunoregulatory ceRNA in ischemic stroke

Molecules in immune cells plays a vital role in the pathogenesis of ischemic stroke (IS). The aim of this study is to profile the landscape of molecules on the basis of immune cells in IS peripheral blood and construct an immunoregulatory competing endogenous RNA (ceRNA) network. We collected and combined multiple public transcriptome datasets from the peripheral blood of IS patients and healthy controls. CIBERSORT deconvolution revealed that the proportions of CD8 and CD4 naive T cells, monocytes, and neutrophils changed significantly in the IS group. Intersecting the immune cell-related genes identified by weighted gene co-expression network analysis (WGCNA) and differential expression analysis, 38 overlapping candidate biomarkers were selected. Three machine learning algorithms, including least absolute shrinkage and selection operator (LASSO), support vector machine-recursive feature elimination (SVM-RFE), and random forest were applied, and 11 distinct immune cell-related genes were identified. We obtained the mRNA-miRNA and miRNA-lncRNA interactions from StarBase v3.0, and constructed a ceRNA network based on the differentially expressed mRNAs, miRNAs, and lncRNAs. The aberrant expression of HECW2-centered ceRNAs in the peripheral blood of in-house patients was validated using quantitative PCR. We also revealed that the expression of HECW2 was positively correlated with lncRNAs LINC02593 through miRNAs miR-130a-3p, miR-130b-3p and miR-148b-3p in cells. These results show that there are distinct immune features between IS patients and healthy controls. The ceRNA network may help elucidate the mechanism of immune cell-related genes in IS and may serve as a therapeutic target.

Brain microRNA profiles after exposure to heroin in rats

Heroin addiction is one of the neuropsychiatric burdens that affects many genetic and epigenetic systems. While it is known that heroin may change the expressions of some genes in the brain during dependence, there is no detailed study related to which gene are mostly affected. Therefore, in the current study, we aimed to determine alterations in the miRNA profiles of rats' brains for providing a detailed analysis of molecular mechanisms in heroin addiction-related toxicology. Next generation global miRNA sequencing was used to predict potential miRNAs in prefrontal cortex (PC), hippocampus, ventral tegmental area (VTA), striatum, and Nucleus accumbens (NA) of rats that exposed to heroin by intravenous injections. The total daily dose was started with 2 mg/kg and ended with 10 mg/kg on the 10th day. In the striatum, miR-18a, miR-17-5p, miR-20a-5p, miR-106a, miR-301a-3p, miR872-5p, miR-15a-5p, miR-500-3p, and miR-339-5p expressions were upregulated by nearly 2-to-4 times with heroin. The expressions of hippocampal miR-153-3p, miR-130a-3p, miR-204-5p, miR-15b-5p, and miR-137-3p and the expressions of miR-872, miR-183-5p, miR-20a-5p, miR-325-5p, miR-379-5p, and miR-340-5p in the VTA were 2-times higher in the heroin-addicted rats. While there was nearly 2-times increase in the miR-129-1-3p and miR-3068-3p expressions in the NA, no change was noted in the PC due to heroin. The only heroin-dependent downregulation was observed in the expressions of striatal miR-450b-3p and miR-103-1-5p of VTA. These results suggested that heroin addiction might give harm to brain by altering cytokine balance and increasing neuroinflammation and apoptosis. In addition, neurons also try to compensate these abnormalities by enhancing neurogenesis and angiogenesis through several miRNAs in the different brain regions. In conclusion, the present study may provide a more integrated view of the molecular mechanism and a potential biomarker that will aid in clinical diagnosis and treatment of heroin-dependence.

Involvement of extracellular vesicle microRNA clusters in developing healthy and Rett syndrome brain organoids

Rett syndrome (RTT) is a neurodevelopmental disorder caused by de novo mutations in the MECP2 gene. Although miRNAs in extracellular vesicles (EVs) have been suggested to play an essential role in several neurological conditions, no prior study has utilized brain organoids to profile EV-derived miRNAs during normal and RTT-affected neuronal development. Here we report the spatiotemporal expression pattern of EV-derived miRNAs in region-specific forebrain organoids generated from female hiPSCs with a MeCP2:R255X mutation and the corresponding isogenic control. EV miRNA and protein expression profiles were characterized at day 0, day 13, day 40, and day 75. Several members of the hsa-miR-302/367 cluster were identified as having a time-dependent expression profile with RTT-specific alterations at the latest developmental stage. Moreover, the miRNA species of the chromosome 14 miRNA cluster (C14MC) exhibited strong upregulation in RTT forebrain organoids irrespective of their spatiotemporal location. Together, our results suggest essential roles of the C14MC and hsa-miR-302/367 clusters in EVs during normal and RTT-associated neurodevelopment, displaying promising prospects as biomarkers for monitoring RTT progression.

The autophagy in ischemic stroke: A regulatory role of non-coding-RNAs

Ischemic stroke (IS) is a central nervous system neurological disorder ascribed to an acute focal trauma, with high mortality and disability, leading to a heavy burden on family and society. Autophagy is a self-digesting process by which damaged organelles and useless proteins are recycled to maintain cellular homeostasis, and plays a pivotal role in the process of IS. Non-coding RNAs (ncRNAs), mainly contains microRNA, long non-coding RNA and circular RNA, have been extensively investigated on regulation of autophagy in human diseases. Recent studies have implied that ncRNAs-regulating autophagy participates in pathophysiological process of IS, including cell apoptosis, inflammation, oxidative stress, blood-brain barrier damage and glial activation, which indicates that regulating autophagy by ncRNAs may be beneficial for IS treatment. This review summarizes the role of autophagy in IS, as well as focuses on the role of ncRNAs-mediated autophagy in IS, for the development of potential therapeutic strategies in this disease.

Pro-fibrotic and apoptotic activities of circARAP1 in myocardial ischemia-reperfusion injury

Reperfusion modality can cause damage to cardiomyocytes, known as myocardial ischemia-reperfusion injury (MI/RI). Circular RNAs (circRNAs) are fundamental regulators associated with many cardiac diseases, including MI/RI. However, their functional impact on cardiomyocyte fibrosis and apoptosis remains elusive. Therefore, this study aimed to explore possible molecular mechanisms of circARPA1 in animal models and in hypoxia/reoxygenation (H/R)-treated cardiomyocytes. GEO dataset analysis showed that has_circ_0023461 (circARPA1) was differentially expressed in myocardial infarction samples. Real-time quantitative PCR further supported that circARPA1 was expressed at high levels in animal models and in H/R-triggered cardiomyocytes. Then, loss-of-function assays were performed to show that circARAP1 suppression effectively ameliorated cardiomyocyte fibrosis and apoptosis in MI/RI mice. Mechanistic experiments showed that miR-379-5p, KLF9 and Wnt signaling pathways were associated with circARPA1. circARPA1 can sponge miR-379-5p to regulate KLF9 expression, thereby activating the wnt/β-catenin pathway. Finally, gain-of-function assays revealed that circARAP1 aggravated MI/RI in mice and H/R-induced cardiomyocyte injury by regulating the miR-379-5p/KLF9 axis to activate Wnt/β-catenin signaling.

Isoflurane Postconditioning Alleviates Ischemic Neuronal Injury Via MiR-384-5p Regulated Autophagy

The purpose of the study was to investigate the effect of isoflurane postconditioning on neuron injury in MCAO (middle cerebral artery occlusion) rats and its molecular mechanism of affecting autophagy through miR-384-5p/ATG5 (autophagy-related protein 5). HT22 cells (mouse hippocampal neuronal cell line) were exposed to 1.5% isoflurane for 30 min after OGD/R (oxygen-glucose deprivation/reoxygenation). Flow cytometry and CCK-8 kit were used to analyze changes in apoptosis and cell viability. The level of miR-384-5p was detected by qRT-PCR. Targetscan database prediction combined with dual luciferase reporter gene assay confirmed ATG5 as a target molecule downstream of miR-384-5p. In addition, western blot results confirmed that isoflurane postconditioning regulated miR-384-5p/ATG5 and significantly inhibited the expression of apoptosis-related proteins. Meanwhile, immunofluorescence staining for LC3II positivity combined with western blot results revealed that isoflurane postconditioning significantly inhibited autophagy. In vivo, MCAO induced neuronal injury for 90 min, followed by 24-h reperfusion. Isoflurane postconditioning (Iso) group underwent 1.5% isoflurane postconditioning for 60 min after reperfusion. Neurological scoring and TTC staining were used to evaluate the protective effect of isoflurane post-treatment on neurological injury, respectively. TUNEL staining and western blot results confirmed that isoflurane post-conditioning could regulate miR-384-5p and inhibit apoptosis. Immunofluorescence staining and western blot results confirmed that isoflurane post-conditioning inhibited autophagy in MCAO rats. Based on the above results, we speculated that the molecular mechanism of isoflurane post-conditioning to alleviate ischemic neuronal injury may be related to the regulation of miR-384-5p/ATG5-mediated autophagy.

Research progress on astrocyte autophagy in ischemic stroke

Ischemic stroke is a highly disabling and potentially fatal disease. After ischemic stroke, autophagy plays a key regulatory role as an intracellular catabolic pathway for misfolded proteins and damaged organelles. Mounting evidence indicates that astrocytes are strongly linked to the occurrence and development of cerebral ischemia. In recent years, great progress has been made in the investigation of astrocyte autophagy during ischemic stroke. This article summarizes the roles and potential mechanisms of astrocyte autophagy in ischemic stroke, briefly expounds on the crosstalk of astrocyte autophagy with pathological mechanisms and its potential protective effect on neurons, and reviews astrocytic autophagy-targeted therapeutic methods for cerebral ischemia. The broader aim of the report is to provide new perspectives and strategies for the treatment of cerebral ischemia and a reference for future research on cerebral ischemia.

A comprehensive comparison of multilocus association methods with summary statistics in genome-wide association studies

BACKGROUND

Multilocus analysis on a set of single nucleotide polymorphisms (SNPs) pre-assigned within a gene constitutes a valuable complement to single-marker analysis by aggregating data on complex traits in a biologically meaningful way. However, despite the existence of a wide variety of SNP-set methods, few comprehensive comparison studies have been previously performed to evaluate the effectiveness of these methods.

RESULTS

We herein sought to fill this knowledge gap by conducting a comprehensive empirical comparison for 22 commonly-used summary-statistics based SNP-set methods. We showed that only seven methods could effectively control the type I error, and that these well-calibrated approaches had varying power performance under the simulation scenarios. Overall, we confirmed that the burden test was generally underpowered and score-based variance component tests (e.g., sequence kernel association test) were much powerful under the polygenic genetic architecture in both common and rare variant association analyses. We further revealed that two linkage-disequilibrium-free P value combination methods (e.g., harmonic mean P value method and aggregated Cauchy association test) behaved very well under the sparse genetic architecture in simulations and real-data applications to common and rare variant association analyses as well as in expression quantitative trait loci weighted integrative analysis. We also assessed the scalability of these approaches by recording computational time and found that all these methods can be scalable to biobank-scale data although some might be relatively slow.

CONCLUSION

In conclusion, we hope that our findings can offer an important guidance on how to choose appropriate multilocus association analysis methods in post-GWAS era. All the SNP-set methods are implemented in the R package called MCA, which is freely available at https://github.com/biostatpzeng/ .

Identification of Novel Circulating miRNAs in Patients with Acute Ischemic Stroke

Ischemic strokes are associated with significant morbidity and mortality, but currently there are no reliable prognostic or diagnostic blood biomarkers. MicroRNAs (miRNAs) regulate various molecular pathways and may be used as biomarkers. Using RNA-Seq, we conducted comprehensive circulating miRNA profiling in patients with ischemic stroke compared with healthy controls. Samples were collected within 24 h of clinical diagnosis. Stringent analysis criteria of discovery (46 cases and 95 controls) and validation (47 cases and 96 controls) cohorts led to the identification of 10 differentially regulated miRNAs, including 5 novel miRNAs, with potential diagnostic significance. Hsa-miR-451a was the most significantly upregulated miRNA (FC; 4.8, FDR; 3.78 × 10-85), while downregulated miRNAs included hsa-miR-574-5p and hsa-miR-142-3p, among others. Importantly, we computed a multivariate classifier based on the identified miRNA panel to differentiate between ischemic stroke patients and healthy controls, which showed remarkably high sensitivity (0.94) and specificity (0.99). The area under the ROC curve was 0.97 and it is superior to other current available biomarkers. Moreover, in samples collected one month following stroke, we found sustained upregulation of hsa-miR-451a and downregulation of another 5 miRNAs. Lastly, we report 3 miRNAs that were significantly associated with poor clinical outcomes of stroke, as defined by the modified Rankin scores. The clinical translation of the identified miRNA panel may be explored further.