Dataset Information

Analysis of human stroke brain tissue resected during decompressive craniectomy or stroke-ectomy surgery

ABSTRACT: Purpose: Signaling pathways mediated by microRNAs (miRNAs) represent one of the mechanisms that regulate stroke progression and recovery. The goal of this study is to investigate miRNA expression signatures in freshly removed human stroke brain tissue. Methods: Human brain samples (5 stroke and 3 non-stroke samples) obtained at 48-72 hours after stroke onset during craniectomy and stroke-ectomy, were subjected to histopathological and immunofluorescence microscopy analyses. NGS sequencing was performed by Qiagen company and analyses were carried out using QIAseq miRNA Quantification workflow and RNA-seq Analysis tools within CLC Genomics Workbench (version 20.0.2). Reads were normalized for expression analysis using trimmed mean of M-values method (TMM). miRNA profiling was performed using the EdgeR in Bioconductor package. Whole transcriptome RNA-sequencing Analysis: The unmapped reads from the NGS miRNA analysis were extracted, deduplicated and mapped to the genome. Gene expressions were calculated by counting number of reads mapping to the annotated gene loci. Human miR-155 Targets RT2 Profiler PCR Array (Qiagen) was performed using 3 RNA samples per stroke and control groups. The PCR Array Data analysis was performed using an automated PCR Analysis Web Portal and GeneGlobe Data Analysis (Qiagen). Results: Human stroke brain tissue was characterized by classic ischemic changes, including significant neuronal and vascular damage, and prominent edema. The absence of monocytes and notable neutrophil infiltration indicated the early stage of leukocyte response to ischemia. miRNA NGS analysis detected 36 miRNAs with significantly aberrant expression in stroke tissue, as compared to non-stroke samples. Of these miRNAs, 19 were previously identified in stroke patient blood and CSF, while dysregulation of 16 miRNAs was newly detected in this study. Bioinformatics pathway enrichment analysis demonstrated a strong association of the identified miRNAs with stroke-related biological processes and signaling pathways Conclusions: Dysregulated miRNAs detected in our study could be regarded as potential candidates for biomarkers and/or targets for therapeutic intervention. The obtained data will serve for better understanding of the molecular basis of stroke and provide valuable information for the future functional studies in the experimental models of stroke.

ORGANISM(S): Homo sapiens

PROVIDER: GSE155257 | GEO | 2020/07/29

REPOSITORIES: GEO

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Project description:Purpose: Next-generation sequencing technologies allow miRNA detection at an unprecedented sensitivity.Early- to mid-gestational fetal mammalian skin wounds heal rapidly and without scarring. The goals of this study are to obtain the differently expressed miRNAs between late- and mid-gestational fetal Keratinocytes for further studies. Methods: Keratinocytes were obtained from six fetal skin samples dividied into two groups: a mid-gestation group and a late-gestation group. RNA extracted from Keratinocytes was used to prepare a small RNA library for next-generation sequencing (NGS) using an Illumina Genome Analyzer IIx. To uncover potentially novel microRNA (miRNAs), the mirTools 2.0 web server was used to identify candidate novel human miRNAs from the NGS data.UCSC Genome Browser and the Vienna RNAfold web server were used to further validate the novel miRNA candidates. The repeatability of the expression levels detected by NGS was confirmed by real-time quantitative RT-PCR. Results: Using an optimized data analysis workflow, we detected a total of 99,354,224 raw reads from the six samples, 85,252,341 (85.81%) were high-quality reads (≥ 18nt). After alignment to the human genome (GRCH38), the number of genome-aligned reads was 74,678,115 (87.60% of the high-quality reads). The number of sequence reads that correspond to known miRNAs was 61,587,749 (82.47% of the genome-matching reads), as was determined by perfect sequence matching to the database of known miRNAs (miRBase release 18). After removing the matched non-coding RNAs (Release 10), 8,755,258 reads remained for identification of novel miRNA candidates by mirTools 2.0. The results revealed the existence of 202 novel miRNA candidates and 29 known miRNAs that were not listed in miRBase release 18. Of the 202 potential novel miRNAs, 106 candidates were detected by at least 10 counts, by NGS, indicating that they have a higher probability of being novel human miRNAs. Using Student's t-test, 173 known miRNAs and 23 novel miRNA candidates were found to be statistically significant (P values < 0.05). The expression of 22 novel miRNA candidates and 88 known miRNAs was changed by more than 2.0-fold (known: 15 up-regulated and 73 down-regulated; novel: two up-regulated and 20 down-regulated). Conclusions: Our study represents the first detailed analysis of human miRNAs in fetal Keratinocytes. Using mirTools 2.0 web server, we have revealed the existence of 202 novel miRNA candidates. Of the 202 potential novel miRNAs, 106 candidates were detected by at least 10 counts, by NGS, indicating that they have a higher probability of being novel human miRNAs. Taken together, our results provide compelling evidence that dynamic expression of miRNAs in fetal Keratinocytes at different gestational ages. MiRNAs presenting altered expression at different gestational ages in fetal Keratinocytes may contribute to scarless wound healing in early- to mid-gestational fetal Keratinocytes, and thus may be new targets for potential scar prevention and reduction therapies.

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Analysis of human stroke brain tissue resected during decompressive craniectomy or stroke-ectomy surgery

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