Dataset Information

Expression profiling dataset of competing endogenous RNA in pre-eclampsia.

ABSTRACT: This data descriptor is an extended version of the methodologies which have been described in a related paper [1]; its purpose is to disseminate the raw data and analyzed data produced in this experiment. For more insight please see the research article, "competing endogenous RNA expression profiling in pre-eclampsia identifies hsa_circ_0036877 as a potential novel blood biomarker for early pre-eclampsia" (Xiaopeng Hu and Junping Ao, 2018) [1]. Using microarray analysis, we investigated competing endogenous RNA (ceRNA) expression profiles in placentas of women with severe pre-eclampsia (SPE) and normal pregnancies. Competing endogenous RNA (ceRNA) refer to RNA transcripts, such as messenger RNA (mRNA), long noncoding RNA (lncRNA), and circular RNA (circRNA) that can regulate each other by competing for the same pool of miRNAs. CircRNAs, lncRNAs, and mRNAs differentially expressed between human normal and SPE placentas were obtained in the study. Metadata files were submitted to the Gene Expression Omnibus repository (GEO), with GEO accession number GSE102897. These data are potential useful for further study on the pathogenesis of PE and early prediction of PE onset.

SUBMITTER: Hu X

PROVIDER: S-EPMC6881654 | biostudies-literature | 2019 Dec

REPOSITORIES: biostudies-literature

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Expression profiling dataset of competing endogenous RNA in pre-eclampsia.

Hu Xiaopeng X Hu Xiaopeng X Li Xinyue X Tian Geng G GG Zhang Huijuan H Cheng Weiwei W Wu Ji J

Data in brief 20191112

This data descriptor is an extended version of the methodologies which have been described in a related paper [1]; its purpose is to disseminate the raw data and analyzed data produced in this experiment. For more insight please see the research article, "competing endogenous RNA expression profiling in pre-eclampsia identifies hsa_circ_0036877 as a potential novel blood biomarker for early pre-eclampsia" (Xiaopeng Hu and Junping Ao, 2018) [1]. Using microarray analysis, we investigated competin ...[more]

PMID: 31799347

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Project description:BackgroundOsteoarthritis (OA) is one of the most common diseases in elderly people; however, the correlation between molecular alterations and the occurrence and progression of OA are still not well understood. We conducted this study to investigate the molecular changes in OA via the competing endogenous ribonucleic acid (ceRNA) network.MethodsWe downloaded the messenger RNA (mRNA) data set, GSE48556, the microRNA (miRNA) data set, GSE105027, and the long non-coding (lncRNA) data set, GSE126963 from the Gene Expression Omnibus (GEO) database, and examined the differentially expressed genes (DEGs) in these data sets. Further, we constructed a ceRNA network of the differentially expressed miRNAs, mRNAs, and lncRNAs. To determine the biological functions of the ceRNA network, we performed Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional enrichment analyses. Finally, we conducted an immune cell infiltration analysisusing single-sample gene set enrichment analysis to examine the abundance of immune cells in healthy and OA patients, and compared the infiltration of 28 immune cells between the healthy and OA samples. We also analyzed the relationship between the abundance of immune cells and mRNA expression levels in the ceRNA network.ResultsUltimately hsa-mir-425-3p, dual specificity phosphatase 1, and 24 lncRNAs were identified in the ceRNA network. The functional enrichment analyses showed that these lncRNAs, miRNAs, and mRNAs are involved in various significant biological process, such as the regulation of leukocyte migration, Mitogen-Activated Protein (MAP) kinase tyrosine/serine/threonine phosphatase activity, the interleukin-17 signaling pathway, the tumor necrosis factor signaling pathway, and osteoclast differentiation, and can also have a strong effect on immune cell infiltration.ConclusionsThe dual-specificity phosphatase 1-specific ceRNA network can be used as a diagnostic tool to assess the progression of OA patients.

Project description:ObjectiveMany primary tumors have insufficient supply of molecular oxygen, called hypoxia. Hypoxia is one of the leading characteristics of solid tumors resulting in a higher risk of local failure and distant metastasis. It is quite necessary to investigate the hypoxia associated molecular hallmarks in breast cancer.Materials and methodsAccording to the published studies, we selected 13 hypoxia related gene expression signature to define the hypoxia status of breast cancer using ConsensusClusterPlus package based on the data from The Cancer Genome Atlas (TCGA). Subsequently, we characterized the infiltration of 24 immune cell types under different hypoxic conditions. Furthermore, the differentially expressed hypoxia associated microRNAs, mRNAs and related signaling pathways were analyzed and depicted. On this basis, a series of prognostic markers related to hypoxia were identified and ceRNA co-expression networks were constructed.ResultsTwo subgroups (cluster1 and cluster2) were identified and the 13 hypoxia related gene signature were all up-regulated in cluster1. Thus, we defined the cluster1 as "hypoxic subgroup" compared with cluster2. The infiltration of CD8+ T cell and CD4+ T cell were lower in cluster1 while the nTreg cell and iTreg cell were higher, indicating that there was immunosuppressive status in cluster1. We observed widespread hypoxia-associated dysregulation of microRNAs and mRNAs. Next, a risk signature for predicting prognosis of breast cancer patients was established based on 12 dysregulated hypoxia associated prognostic genes. Two microRNAs, hsa-miR-210-3p and hsa-miR-190b, with the most significant absolute logFC value were related to unfavorable and better prognosis, respectively. Several long non-coding RNAs were predicted to be microRNA targets and positively correlated with two selected mRNAs, CPEB2 and BCL11A. Predictions based on the SNHG16-hsa-miR-210-3p-CPEB2 and LINC00899/PSMG3-AS1/PAXIP-AS1-hsa-miR-190b-BCL11A ceRNA regulation networks indicated that the two genes might act as tumor suppressor and oncogene, respectively.ConclusionHypoxia plays an important role in the initiation and progression of breast cancer. Our research provides potential mechanisms into molecular-level understanding of tumor hypoxia.

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Expression profiling dataset of competing endogenous RNA in pre-eclampsia.

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Expression profiling dataset of competing endogenous RNA in pre-eclampsia.

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