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Integration of miRNA in exosomes and single-cell RNA-seq profiles in endemic osteoarthritis, Kashin-Beck disease

ABSTRACT: Integration of miRNA in exosomes and single-cell RNA-seq profiles in endemic osteoarthritis, Kashin-Beck disease

PROVIDER: PRJNA1031539 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR26495072.fastq.gz	Fastqsanger.gz
	SRR26495073.fastq.gz	Fastqsanger.gz
	SRR26495074.fastq.gz	Fastqsanger.gz
	SRR26495075.fastq.gz	Fastqsanger.gz
	SRR26495076.fastq.gz	Fastqsanger.gz

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Integration of miRNA in exosomes and single-cell RNA-seq profiles in endemic osteoarthritis, Kashin-Beck disease

Project description:Kashin-Beck disease (KBD) is an endemic, chronic degenerative joint disease in China. Exosomes miRNAs, as signaling molecules in intercellular communication, can transfer specific biological martials into target cell to regulate the their function and might participate in the pathogenesis of KBD. We isolated serum and chondrocytes-derived exosomes, miRNA sequencing revealed exosomes miRNA profiles and differentially expressed miRNAs (DE-miRNAs) were identified. The target genes were predicted of known and novel DE-miRNAs with TargetScan 5.0 and miRanda 3.3a database. Single-cell RNA sequencing (scRNA-seq) was performed to identify chondrocyte clusters and their gene signatures in KBD. And we performed comparative analysis between the serum and chondrocytes-derived exosomes DE-miRNA target genes and differentially expressed genes of each cell clusters.A total of 20 DE-miRNAs were identified in serum-derived exosomes. In the miRNA expression of chondrocytes-derived exosomes, 53 DE-miRNAs were identified. 16063 predicted targets were identified as the target genes in the serum-derived exosomes, 57316 predicted targets were identified as the target genes in the chondrocytes-derived exosomes. Seven clusters were labelled by cell type according to the expression of previously described markers. 315 common genes were found among serum/chondrocytes-derived exosomes DE-miRNA target genes and DEGs identified by scRNA-seq analysis. We firstly integratly analyzed the serum and chondrocytes exosomes miRNA with single-cell RNA sequencing (scRNA-seq) data of KBD chondrocyte, the results showed that DE-miRNAs in exosomes might play a potential role in regulating genes expression in different KBD chondrocytes clusters by exosomes mediating cell-cell communications functions, which could improve the new diagnosis and treatment methods for KBD.

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Transcription profiling by array of Kashin-beck disease and osteoarthritis

Project description:We compared genome-wide gene expression profiles of articular cartilage derived from 4 Kashin-beck disease patients and 4 Primary osteoarthritis. Total RNA was isolated from cartilage samples following by being amplified, labeled and hybridized to Agilent Human 4M-W44k Whole Genome microarray (G4112F).

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Genome-Wide Differentially Methylated Region Analysis to Reveal Epigenetic Differences of Articular Cartilage in Kashin-Beck Disease and Osteoarthritis

Project description:Kashin-Beck disease (KBD) is a degenerative osteoarticular disorder, and displays the significant differences with osteoarthritis (OA) regarding the etiology and molecular changes in articular cartilage. However, the underlying dysfunctions of molecular mechanisms in KBD and OA remain unclear. Here, we performed the various genome-wide differentially methylated region analyses to reveal the distinct differentially methylated regions (DMRs) and corresponding differentially methylated genes (DMGs), and enriched functional pathways/GO terms for KBD and OA.

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Human Peripheral blood mononuclear cells (PBMCs): Control vs. Kashin-Beck Disease

Project description:Objective:To identify an accurate blood-based gene signature for early detection of Kashin-Beck disease (KBD). Methods: Gene expression analysis was conducted of peripheral blood samples from 100 patients with KBD and 100 controls randomly chosen from two KBD-endemic areas

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Human Peripheral blood mononuclear cells (PBMCs): Control vs. Kashin-Beck Disease

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Project description:Kashin-Beck disease (KBD) is an endemic and chronic osteochondropathy with unknown etiology. The disease mostly occurs in children between the ages of 3 and 13 in a diagonal belt-like area ranging from Northeast to Southwest China. We carried out this microarray analysis to investigate the differences in gene expression levels between KBD patients and healthy controls. Total RNA was isolated from peripheral blood mononuclear cells (PBMCs).

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Project description:Objective: To investigate the differences between the gene expression profiles in peripheral blood mononuclear cells (PBMC) from normal controls and patients with Kashin-Beck disease (KBD). Methods: Twenty KBD patients and 12 normal subjects were selected from a KBD-endemic area and divided into four pairs of KBD vs. control (KBD, n=5 per pair; control, n=3 per pair). RNAs were respectively isolated from KBD PBMCs and normal PBMCs. Gene expression profiles were analyzed by oligonucleotide microarray.

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