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Screening and analysis of differentially expressed circRNAs and miRNAs in chronic diabetic extremity wounds

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Homo sapiens

PROVIDER: GSE212167 | GEO | 2022/08/30

REPOSITORIES: GEO

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Screening and analysis of differentially expressed circRNAs and miRNAs in chronic diabetic extremity wounds [array]

Project description:To investigate the expression of circRNAs, miRNAs, and related co-expression and competitive endogenous RNA (ceRNA) in diabetic chronic refractory wounds

2022-08-30 | GSE212163 | GEO

Screening and analysis of differentially expressed circRNAs and miRNAs in chronic diabetic extremity wounds [miRNA-Seq]

Project description:To investigate the expression of circRNAs, miRNAs, and related co-expression and competitive endogenous RNA (ceRNA) in diabetic chronic refractory wounds

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Screening and analysis of differentially expressed circRNAs and miRNAs in chronic diabetic extremity wounds

Project description:Screening and analysis of differentially expressed circRNAs and miRNAs in chronic diabetic extremity wounds

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Screening and analysis of differentially expressed circRNAs and miRNAs in chronic diabetic extremity wounds [array]

Project description:Screening and analysis of differentially expressed circRNAs and miRNAs in chronic diabetic extremity wounds [array]

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Screening and analysis of differentially expressed circRNAs and miRNAs in chronic diabetic extremity wounds [miRNA-Seq]

Project description:Screening and analysis of differentially expressed circRNAs and miRNAs in chronic diabetic extremity wounds [miRNA-Seq]

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Screening for differentially expressed circRNAs in ischemic stroke by RNA sequencing.

Project description:BackgroundIschemic stroke is a disease with high rate of death and disability worldwide. CircRNAs, as a novel type of non-coding RNAs, lacking 5' caps and 3' poly-A tails, has been associated with ischemic stroke. This study aimed to investigate key circRNAs related to ischemic stroke.MethodsRNA sequencing was performed obtain the circRNA expression profiles from peripheral whole blood of three ischemic stroke patients and three healthy individuals. Through bioinformatic analysis, differentially expressed circRNAs (DEcircRNAs) were identified, and GO and pathway analyses for the host genes of DEcircRNAs were conducted. The expression levels of selected circRNAs were analyzed with qRT-PCR. To further explore the functions of key circRNAs, a DEcircRNA-miRNA interaction network was constructed.ResultsA total of 736 DEcircRNAs were detected in ischemic stroke. Functional annotation of host genes of DEcircRNAs revealed several significantly enriched pathways, including Fc epsilon RI signaling pathway, B cell receptor signaling pathway, and T cell receptor signaling pathway. The qRT-PCR results were largely in keeping with our RNA-seq data. The ROC curve analyses indicated that hsa_circ_0000745, hsa_circ_0001459, hsa_circ_0003694 and hsa_circ_0007706 with relatively high diagnostic value. A circRNA-miRNA network, including 1544 circRNA-miRNA pairs, 456 circRNAs and 4 miRNAs, was obtained.ConclusionsThe results of our study may help to elucidate the specific mechanism underlying ischemic stroke.

| S-EPMC8464123 | biostudies-literature

Whole-Transcriptome Sequencing Identifies Key Differentially Expressed mRNAs, miRNAs, lncRNAs, and circRNAs Associated with CHOL.

Project description:To systematically evaluate the whole-transcriptome sequencing data of cholangiocarcinoma (CHOL) to gain more insights into the transcriptomic landscape and molecular mechanism of this cancer, we performed whole-transcriptome sequencing based on the tumorous (C) and their corresponding non-tumorous adjacent to the tumors (CP) from eight CHOL patients. Subsequently, differential expression analysis was performed on the C and CP groups, followed by functional interaction prediction analysis to investigate gene-regulatory circuits in CHOL. In addition, The Cancer Genome Atlas (TCGA) for CHOL data was used to validate the results. In total, 2,895 differentially expressed messenger RNAs (dif-mRNAs), 56 differentially expressed microRNAs (dif-miRNAs), 151 differentially expressed long non-coding RNAs (dif-lncRNAs), and 110 differentially expressed circular RNAs (dif-circRNAs) were found in CHOL samples compared with controls. Enrichment analysis on those differentially expressed genes (DEGs) related to miRNA, lncRNA, and circRNA also identified the function of spliceosome. The downregulated hsa-miR-144-3p were significantly enriched in the competing endogenous RNA (ceRNA) complex network, which also included 7 upregulated and 13 downregulated circRNAs, 7 upregulated lncRNAs, and 90 upregulated and 40 downregulated mRNAs. Moreover, most of the DEGs and a few of the miRNAs (such as hsa-miR-144-3p) were successfully validated by TCGA data. The genes involved in RNA splicing and protein degradation processes and miR-144-3p may play fundamental roles in the pathogenesis of CHOL.

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Identification of Differentially Expressed circRNAs, miRNAs, and Genes in Patients Associated with Cartilaginous Endplate Degeneration.

Project description:BackgroundIntervertebral disc degeneration (IDD) disease is a global challenge because of its predominant pathogenic factor in triggering low back pain, whereas cartilaginous endplate degeneration (CEPD) is the main cause of IDD. Accumulating evidence have indicated that the differentially expressed microRNAs (DEMs) and differentially expressed genes (DEGs) have been determined to be involved in multiple biological processes to mediate CEPD progression. However, the differentially expressed circular RNAs (DECs) and their potential biofunctions in CEPD have not been identified.MethodsGSE153761 dataset was analyzed using R software to predict DECs, DEMs, and DEGs. Pathway enrichment analysis of DEGs and host genes of DECs and protein-protein interaction network of DEGs were conducted to explore their potential biofunctions. Furthermore, we explore the potential relationship between DEGs and DECs.ResultsThere were 74 DECs, 17 DEMs, and 68 DEGs upregulated whereas 50 DECs, 16 DEMs, and 67 DEGs downregulated in CEPD group. Pathway analysis unveiled that these RNAs might regulate CEPD via mediating inflammatory response, ECM metabolism, chondrocytes apoptosis, and chondrocytes growth. A total of 17 overlapping genes were predicted between the host genes of DEGs and DECs, such as SDC1 and MAOA. Moreover, 6 upregulated DECs, of which hsa_circ_0052830 was the most upregulated circRNA in CEPD, were derived from the host genes SDC1, whereas 8 downregulated DECs were derived from the host genes MAOA.ConclusionThis will provide novel clues for future experimental studies to elucidate the pathomechanism of CEPD and therapeutic targets for CEPD-related diseases.

| S-EPMC8158415 | biostudies-literature

Screening of differentially expressed circRNAs in renal cortex of mice with diabetic kidney injury

Project description:To determine the circRNA expression profile in DKI and normal mice, we uesed circRNA microArray analysis form Arraystar to examine the expression of circRNAs in DKI and normal mice Kidney cortex tissues.

2022-09-23 | GSE213955 | GEO

Patterns of Differentially Expressed circRNAs in Human Thymocytes.

Project description:Circular RNAs (circRNAs) are suggested to play a discriminative role between some stages of thymocyte differentiation. However, differential aspects of the stage of mature single-positive thymocytes remain to be explored. The purpose of this study is to investigate the differential expression pattern of circRNAs in three different development stages of human thymocytes, including mature single-positive cells, and perform predictions in silico regarding the ability of specific circRNAs when controlling the expression of genes involved in thymocyte differentiation. We isolate human thymocytes at three different stages of intrathymic differentiation and determine the expression of circRNAs and mRNA by RNASeq. We show that the differential expression pattern of 50 specific circRNAs serves to discriminate between the three human thymocyte populations. Interestingly, the downregulation of RAG2, a gene involved in T-cell differentiation in the thymus, could be simultaneously controlled by the downregulation of two circRNASs (hsa_circ_0031584 and hsa_circ_0019079) through the hypothetical liberation of hsa-miR-609. Our study provides, for the first time, significant insights into the usefulness of circRNAs in discriminating between different stages of thymocyte differentiation and provides new potential circRNA-miRNA-mRNA networks capable of controlling the expression of genes involved in T-cell differentiation in the thymus.

| S-EPMC9030292 | biostudies-literature

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