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Comprehensive analysis of circRNA expression profiles and circRNA associated competing endogenous RNA networks in IgA nephropathy

ABSTRACT: Comprehensive analysis of circRNA expression profiles and circRNA associated competing endogenous RNA networks in IgA nephropathy

PROVIDER: PRJNA644922 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR12174886_1.fastq.gz	Fastqsanger.gz
	SRR12174886_2.fastq.gz	Fastqsanger.gz
	SRR12174887_1.fastq.gz	Fastqsanger.gz
	SRR12174887_2.fastq.gz	Fastqsanger.gz
	SRR12174888_1.fastq.gz	Fastqsanger.gz

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Project description:BackgroundImmunoglobulin A nephropathy (IgAN) is immune-mediated primary glomerulonephritis, which is the most common reason leading to renal failure worldwide. The exact pathogenesis of IgAN is not well defined. Accumulating evidence indicates that circular RNAs (circRNAs) play crucial roles in the immune disease by involving in the competing endogenous RNA (ceRNA) network mechanism. At present, the studies of the circRNA profiles and circRNA-associated ceRNA networks in the IgAN are still scarce. This study aimed to elucidate the potential roles of circRNA-associated ceRNA networks of peripheral blood mononuclear cells (PBMCs) in IgAN patients.MethodCircRNA sequencing was used to identify the differential expressed circRNAs (DEcircRNAs) of PBMCs in IgAN and healthy controls; limma packages from data sets GSE25590 and GSE73953 in the Gene Expression Omnibus (GEO) database, were used to identify differentially expressed micro RNAs (miRNAs) and message RNAs (mRNAs). A circRNA-miRNA-mRNA ceRNA network was constructed to further investigate the mechanisms of IgAN. Then, GO analysis and KEGG enrichment analyses were used to annotate the genes involved in the circRNA-associated ceRNA network. Further, Protein-protein interaction (PPI) networks were established to screen potential hub genes, by using Search Tool for the Retrieval of Interacting Genes/Proteins (STRING). Last, a quantitative real-time polymerase chain reaction (qRT-PCR) was applied to verify the hub genes in the ceRNA network.ResultA total of 145 circRNAs, 22 miRNAs, and 1,117 mRNAs were differentially expressed in IgAN compared with controls (P < 0.05). A ceRNA network was constructed which contained 16 DEcircRNAs, 72 differential expressed mRNAs (DEmRNAs) and 11 differential expressed miRNAs (DEmiRNAs). KEGG pathway enrichment analysis illustrated the underlying biological functions of the ceRNA-associated genes, such as Nitrogen compound metabolic process, COPII-coated ER to Golgi transport vesicle, CAMP response element protein binding process (P < 0.01); meanwhile, Hepatitis B, GnRH signaling, and Prion disease were the most significant enrichment GO terms (P < 0.01). PPI network based on STRING analysis identified 4 potentially hub genes. Finally, Ankyrin repeat and SOCS box containing 16 (ASB16), SEC24 homolog C, COPII coat complex component (SEC24C) were confirmed by qRT-PCR (P < 0.05) and were identified as the hub genes of the ceRNA network in our study.ConclusionOur study identified a novel circRNA-mediated ceRNA regulatory network mechanisms in the pathogenesis of IgAN.

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Comprehensive analysis of circRNA expression profiles and circRNA associated competing endogenous RNA networks in IgA nephropathy

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