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Whole transcriptome sequencing of kidney tissues in lupus nephritis

ABSTRACT: Lupus nephritis (LN) is a well-known complication of SLE, which is the leading cause of morbidity and mortality. mRNA and non-coding RNAs, including long non-coding RNA (lncRNA), circular RNA (circRNA) and microRNA(miRNA), could play important roles in LN onset and development. In this study, we identified differential lncRNA/miRNA/circRNA and mRNA expression profiles of renal tissues from LN patients compared with the healthy renal tissues by whole transcriptome sequencing. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed to investigate the potential functions of these DE mRNAs and ncRNAs. Besides, the competing endogenous RNA (ceRNA) networks (circRNA-miRNA-mRNA network) were also constructed to understand the internal regulating relationships of these mRNAs and circRNAs. And key ceRNA relationships were verified by dual-luciferase reporter experiments. Moreover, gene function enrichment analysis showed that dysregulated RNAs were mostly related to innate and adaptive immune response, especially against virus infection. The analysis for these DE mRNAs and ncRNAs in LN patients provided a new perspective for the pathophysiology, diagnosis, and treatment of LN.

ORGANISM(S): Homo sapiens

PROVIDER: GSE157293 | GEO | 2021/01/04

REPOSITORIES: GEO

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Comprehensive analyses of function and molecular interaction of differential expressed non-coding RNAs and mRNA in Hantaan virus infection

Project description:Hantaan virus (HTNV), the prevalent prototype of the hantavirus in Asia, causes hemorrhagic fever with renal syndrome (HFRS) with high mortality in human being. However, the pathogenesis of HTNV infection remains elusive. Accumulating evidences indicate that non-coding RNAs (ncRNAs), including long non-coding RNA (lncRNA), circular RNA (circRNA) and microRNA (miRNA) play crucial roles in the progression of virus infection. Here, we identified differential lncRNA/miRNA/circRNA and mRNA expression profiles of HTNV-infected human umbilical vein endothelial cells (HUVECs) compared with mock-infected HUVECs by whole transcriptome sequencing. Subsequently, comprehensive bioinformatics analyses established miRNA-mRNA co-expression, protein-protein interaction and competing endogenous RNA (ceRNA) networks in miRNA-lncRNA-circRNA-mRNA regulatory axis. The trans or cis regulatory roles of identified RNAs on HTNV infection were ascertained by RNA interference and key ceRNA relationships were verified by dual-luciferase reporter experiments. Moreover, gene ontology (GO) enrichment analysis showed that dysregulated RNAs were mostly related to antiviral innate immune response. In conclusion, our findings firstly revealed that circRNAs and ceRNA network were involved in regulating HTNV infection, and also confirmed several key lncRNAs and miRNAs which had vital effects on HTNV infection. The identification and characterization of RNAs provide the new insights on ceRNA networks in HTNV-host interactions, which lays the foundation for future research of the potential roles of ncRNAs in the pathogenesis of HFRS.

2020-04-06 | GSE133319 | GEO

Comprehensive analyses of function and molecular interaction of differentially expressed non-coding RNAs and mRNA in Hantaan virus infection

2020-04-06 | GSE133751 | GEO

Comprehensive analyses of function and molecular interaction of differential expressed non-coding RNAs and mRNA in Hantaan virus infection

2020-04-06 | GSE133634 | GEO

Systematic identification of aberrant non-coding RNAs and their mediated modules in rotator cuff tears [miRNA-seq]

Project description:The purpose of this study is to identify dysregulated ncRNAs and understand how they influence Rotator cuff tears (RCT). We performed RNA sequencing and miRNA sequencing on 5 pairs of torn supraspinatus muscles and matched unharmed subscapularis muscles to identify RNAs dysregulated in RCT patients. Based on the results of differential expression analysis and miRNA targeting information, we constructed lncRNA/circRNA-associated dysregulated ceRNA networks in RCT. We found the largest module in the ceRNA network and identified several important ncRNAs in this module, which may have critical roles in RCT.

2022-04-21 | GSE199485 | GEO

Systematic identification of aberrant non-coding RNAs and their mediated modules in rotator cuff tears [mRNA-lncRNA/circRNA]

2022-04-21 | GSE199484 | GEO

Changing expression profiles of mRNA, miRNA, lncRNA, and circRNA reveal the key regulators and interaction networks of ceRNA in pulmonary fibrosis [miRNA-seq]

Project description:Pulmonary fibrosis is a kind of interstitial lung disease with architectural remodeling of tissues and excessive matrix deposition. Apart from mRNA, microRNA, long non-coding RNA (lncRNA) and circular RNA (circRNA) could also play important roles in the regulatory processes of occurrence and progression of pulmonary fibrosis. In the present study, whole transcriptome sequencing analysis was applied to investigate the expression profiles of mRNAs, lncRNAs, circRNAs and miRNAs. After comparing bleomycin-induced pulmonary fibrosis model lung samples and controls, 286 lncRNAs, 192 mRNAs, 605 circRNAs, and 32 miRNAs were found to be differentially expressed. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed to investigate the potential functions of these DE mRNAs and ncRNAs. Various related GO-BP terms such as “inflammatory response”, “positive regulation of interleukin-2 biosynthetic process”, “Regulation of actin cytoskeleton”, “Notch signaling pathway”, “negative regulation of cellular response to vascular endothelial growth factor stimulus”, and KEGG signal pathways such as “Wnt signaling pathway”, “TNF signaling pathway”, “MAPK signaling pathway”, “Regulation of actin cytoskeleton” were enriched implying potential roles in regulatory process. In addition, two co-expression networks (lncRNA-miRNA-mRNA, circRNA-miRNA-mRNA) were also constructed to understand the internal regulating relationships of these mRNAs and ncRNAs. Our study provides a systematic perspective on the potential functions of these DE mRNAs and ncRNAs during PF process, and could help pave the way for effective therapeutics for this devastating and complex disease.

2020-08-21 | GSE153294 | GEO

Changing expression profiles of mRNA, miRNA, lncRNA, and circRNA reveal the key regulators and interaction networks of ceRNA in pulmonary fibrosis [ncRNA-seq]

2020-08-21 | GSE153278 | GEO

circRNA expression in human myometrium during labor

Project description:The maintenance of coordinated powerful episodic contractions of the uterus is the crucial factor for normal labor. The uterine contractility is gradually enhanced with the progression of labor, which is related to the gene expression of myometrium, competing endogenous RNA (ceRNA) can also regulate the gene expression. To better understand the role of ceRNA network in labor, transcriptome sequencing was performed on the myometrium of 17 parturients at different labor duration. Furthermore, an correlated analysis was performed to identify mRNA, long non-coding RNA (lncRNA), circular RNA (circRNA), and microRNA (miRNA) which correlated with their expression levels and labor duration. Then, targeting relationships between mRNAs, lncRNAs, circRNAs and miRNAs were predicted, and the ceRNA regulatory network was established.This analysis identified 934 RNAs positively correlated with labor duration (859 mRNAs, 28 lncRNAs, 45 circRNAs, and 2 miRNAs) and 153 RNAs negatively correlated with labor duration (122 mRNAs, 28 lncRNAs, and 3 miRNAs).

2022-01-01 | GSE188873 | GEO

miRNA of human myometrium in labor

2022-01-01 | GSE188407 | GEO

Whole-transcriptome analysis and construction of vernalization-related ceRNA-miRNA-target gene regulatory network in Chinese cabbage (Brassica campestris L. ssp. pekinensis) [seed miRNA]

Project description:The transition from vegetative growth to reproductive growth involves many pathways. Vernalization is crucial to the formation of floral organs, the regulation of flowering time and plant breeding. The purpose of this study was to identify the mRNA, microRNA (miRNA), long non-coding RNA (lncRNA), and circular RNA (circRNA) related to vernalization of Chinese cabbage, and to construct a competitive endogenous RNA (ceRNA) network, so as to provide valuable information for exploring the molecular mechanism of vernalization of Chinese cabbage. Results: The results of whole-transcriptome sequencing showed that 2702 mRNAs, 151 lncRNAs, 16 circRNA, and 233 miRNAs were differentially expressed in vernalized (‘Ver’) and non-vernalized (‘Nor’) seeds of Chinese cabbage. Some transcription factors and regulatory proteins that play important roles in vernalization pathway have been identified, such as the transcription factors of WRKY, MYB, NAC, bHLH, and MADS-box, zinc finger protein CONSTANS like gene and B3 domain protein. We constructed vernalization-related ceRNA-miRNA-target gene network and obtained 199 pairs of ceRNA relationships, including 108 DEmiRNA-DEmRNA, 67 DEmiRNA-DElncRNA, and 12 DEmiRNA-DEcircRNA interactions in Chinese cabbage. Meanwhile, several important vernalization-related genes and their interacting lncRNAs, circRNAs, and miRNAs were identified, which were involved in the regulation of flowering time, floral organ formation, bolting and flowering. Conclusions: The candidate differentially expressed mRNA, miRNA, lncRNA and circRNA for vernalization of Chinese cabbage were identified by the whole-transcriptome sequencing, and the ceRNA network was constructed. This study laid a foundation for further study on the molecular mechanism of vernalization in Chinese cabbage.

2021-11-17 | GSE171708 | GEO

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