Microarray Data Analysis of Molecular Mechanism Associated with Stroke Progression

Identification of aberrantly expressed lncRNAs and ceRNA networks in multiple myeloma: a combined high-throughput sequencing and microarray analysis

Background

This study aimed to explore the potential effects of long non-coding RNAs (lncRNAs) in multiple myeloma (MM) patients using two detection methods: high-throughput sequencing and microarray.

Methods

In this study, lncRNAs were detected in 20 newly diagnosed MM patients, with 10 patients analyzed by whole transcriptome-specific RNA sequencing and 10 patients analyzed by microarray (Affymetrix Human Clariom D). The expression levels of lncRNAs, microRNAs, and messenger RNAs (mRNAs) were analyzed, and the differentially expressed lncRNAs identified by both methods were selected. The significant differentially expressed lncRNAs were further validated using PCR.

Results

This study established the aberrant expression of certain lncRNAs involved in the occurrence of MM, with AC007278.2 and FAM157C showing the most significant differences. The top 5 common pathways identified by the Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis were the chemokine signaling pathway, inflammatory mediator regulation, Th17 cell differentiation, apoptosis, and NF-kappa B signaling pathway. Furthermore, three microRNAs (miRNAs) (miR-4772-3p, miR-617, and miR-618) were found to constitute competing endogenous RNA (ceRNA) networks in both sequencing and microarray analyses.

Conclusions

By the combination analysis, our understanding of lncRNAs in MM will be increased significantly. More overlapping differentially expressed lncRNAs were found to predict therapeutic targets precisely.

A Systematic Review of Body Fluids Biomarkers Associated With Early Neurological Deterioration Following Acute Ischemic Stroke

Biomarkers are objectively measured biological properties of normal and pathological processes. Early neurological deterioration (END) refers to the deterioration of neurological function in a short time after the onset of acute ischemic stroke (AIS) and is associated with adverse outcomes. Although multiple biomarkers have been found to predict END, there are currently no suitable biomarkers to be applied in routine stroke care. According to the Preferred Reporting Items for Systematic Review standards, we present a systematic review, concentrating on body fluids biomarkers that have shown potential to be transferred into clinical practice. We also describe newly reported body fluids biomarkers that can supply different insights into the mechanism of END. In our review, 40 scientific papers were included. Depending on the various mechanisms, sources or physicochemical characteristics of body fluids biomarkers, we classified related biomarkers as inflammation, protease, coagulation, metabolism, oxidative stress, and excitatory neurotoxicity. The body fluids biomarkers whose related articles are limited or mechanisms are unknown are categorized as other biomarkers. The inflammation-related biomarkers, such as neutrophil-to-lymphocyte ratio and hypersensitive C-reactive protein, play a crucial role among the mentioned biomarkers. Considering the vast heterogeneity of stroke progression, using a single body fluids biomarker may not accurately predict the risk of stroke progression, and it is necessary to combine multiple biomarkers (panels, scores, or indices) to improve their capacity to estimate END.

Detecting Key Functional Components Group and Speculating the Potential Mechanism of Xiao-Xu-Ming Decoction in Treating Stroke

Stroke is a cerebrovascular event with cerebral blood flow interruption which is caused by occlusion or bursting of cerebral vessels. At present, the main methods in treating stroke are surgical treatment, statins, and recombinant tissue-type plasminogen activator (rt-PA). Relatively, traditional Chinese medicine (TCM) has widely been used at clinical level in China and some countries in Asia. Xiao-Xu-Ming decoction (XXMD) is a classical and widely used prescription in treating stroke in China. However, the material basis of effect and the action principle of XXMD are still not clear. To solve this issue, we designed a new system pharmacology strategy that combined targets of XXMD and the pathogenetic genes of stroke to construct a functional response space (FRS). The effective proteins from this space were determined by using a novel node importance calculation method, and then the key functional components group (KFCG) that could mediate the effective proteins was selected based on the dynamic programming strategy. The results showed that enriched pathways of effective proteins selected from FRS could cover 99.10% of enriched pathways of reference targets, which were defined by overlapping of component targets and pathogenetic genes. Targets of optimized KFCG with 56 components can be enriched into 166 pathways that covered 80.43% of 138 pathways of 1,012 pathogenetic genes. A component potential effect score (PES) calculation model was constructed to calculate the comprehensive effective score of components in the components-targets-pathways (C-T-P) network of KFCGs, and showed that ferulic acid, zingerone, and vanillic acid had the highest PESs. Prediction and docking simulations show that these components can affect stroke synergistically through genes such as MEK, NFκB, and PI3K in PI3K-Akt, cAMP, and MAPK cascade signals. Finally, ferulic acid, zingerone, and vanillic acid were tested to be protective for PC12 cells and HT22 cells in increasing cell viabilities after oxygen and glucose deprivation (OGD). Our proposed strategy could improve the accuracy on decoding KFCGs of XXMD and provide a methodologic reference for the optimization, mechanism analysis, and secondary development of the formula in TCM.

In silico analysis suggests the RNAi-enhancing antibiotic enoxacin as a potential inhibitor of SARS-CoV-2 infection

COVID-19 has currently become the biggest challenge in the world. There is still no specific medicine for COVID-19, which leaves a critical gap for the identification of new drug candidates for the disease. Recent studies have reported that the small-molecule enoxacin exerts an antiviral activity by enhancing the RNAi pathway. The aim of this study is to analyze if enoxacin can exert anti-SARS-CoV-2 effects. We exploit multiple computational tools and databases to examine (i) whether the RNAi mechanism, as the target pathway of enoxacin, could act on the SARS-CoV-2 genome, and (ii) microRNAs induced by enoxacin might directly silence viral components as well as the host cell proteins mediating the viral entry and replication. We find that the RNA genome of SARS-CoV-2 might be a suitable substrate for DICER activity. We also highlight several enoxacin-enhanced microRNAs which could target SARS-CoV-2 components, pro-inflammatory cytokines, host cell components facilitating viral replication, and transcription factors enriched in lung stem cells, thereby promoting their differentiation and lung regeneration. Finally, our analyses identify several enoxacin-targeted regulatory modules that were critically associated with exacerbation of the SARS-CoV-2 infection. Overall, our analysis suggests that enoxacin could be a promising candidate for COVID-19 treatment through enhancing the RNAi pathway.

Circulating miRNA-3552 as a Potential Biomarker for Ischemic Stroke in Rats

Objective

With the growing incidence of ischemic stroke worldwide, there is an urgent need to identify blood biomarkers for ischemic stroke patients. Thus, our aim was to identify potential circulating microRNA (miRNA) as a potential biomarker and to explore its potential mechanism for ischemic stroke in rats.

Methods

The mRNA dataset GSE97537 and miRNA dataset GSE97532 were downloaded from the Gene Expression Omnibus (GEO) GSE97537 including 7 middle cerebral artery occlusion (MCAO) rat brain tissues and 5 sham-operated rat brain tissues GSE97532 including 6 MCAO rat blood samples and 3 sham-operated rat blood samples. Differentially expressed mRNAs and miRNAs with corrected p value ≤ 0.01 and fold change ≥2 or ≤0.05 were identified. To explore potential biological processes and pathways of differentially expressed mRNAs, functional enrichment analysis was performed. The target mRNAs of differentially expressed miRNAs were predicted using DNA Intelligent Analysis (DIANA)-microT tools. The target mRNAs and differentially expressed mRNAs were intersected.

Results

1228 differentially expressed mRNAs in MCAO rat brain tissues were identified. Highly expressed mRNAs were mainly enriched in the inflammatory responses. Nine differentially expressed miRNAs were identified in MCAO rat blood samples. A total of 673 target mRNAs were predicted to significantly bind these differentially expressed miRNAs. Among them, 54 target mRNAs were differentially expressed in MCAO rat blood samples. Enrichment analysis results showed that these 54 target mRNAs were closely related to neurological diseases and immune responses. Among all miRNA-mRNA relationship, miR-3552-CASP3 interaction was identified, indicating that CASP3 might be mediated by miR-3552. Functional enrichment analysis revealed that CASP3 was involved in the apoptosis pathway, indicating that miR-3552 might participate in apoptosis by CASP3.

Conclusion

Our findings reveal that circulating miR-3552 shows promise as a potential biomarker for ischemic stroke in rats.

Upregulated C-C Motif Chemokine Ligand 2 Promotes Ischemic Stroke via Chemokine Signaling Pathway

BACKGROUND

This study aims to evaluate the potential effect and the underlying mechanism of C-C motif chemokine ligand 2 (CCL2) in ischemic stroke.

METHODS

An integrated bioinformatics analysis was performed to identify the differentially expressed (DE) genes and their related pathways in ischemic stroke. In vivo study of a rat model of middle cerebral artery occlusion (MCAO) was further established to assess the effect of CCL2 on severity of neurologic impairments. The expression levels of proinflammatory cytokines were also evaluated using the ELISA assay, and Western blot was also used to determine the expression of CCL2 and other DE proteins in the related pathways.

RESULTS

A total of 88 DE genes were identified from the microarray dataset of ischemic stroke. The bioinformatics analysis revealed that CCL2 was highly expressed in ischemic stroke tissue and promoted the ischemic stroke progression via activation of the chemokine signaling pathway and cytokine-cytokine receptor interaction pathway. The in vivo study of the ischemic stroke rat model also showed that the CCL2 expression was elevated in the MCAO/R rats, with significant neurological impairments and ischemic infarct area in the brain tissue being observed. The administration of CCL2 inhibitors significantly inhibited the inflammatory response, attenuated the neurological impairments, and decreased the ischemic infarct area in the MCAO/R rats. Furthermore, the downregulation of CCL2 also inhibited the expression of the pathway-related proteins including CCL7, CCR2, CXCL16, and TNF-α.

CONCLUSIONS

These results indicate that the CCL2/chemokine signaling pathway is responsible for ischemic stroke progression and might represent a potential therapeutic target for ischemic stroke treatment.