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Whole Transcriptome Sequencing Identifies a Competitive Endogenous RNA Network that Regulates the Immunity of Bladder Cancer

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

ORGANISM(S): Homo sapiens

PROVIDER: GSE236935 | GEO | 2023/07/15

REPOSITORIES: GEO

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Whole Transcriptome Sequencing Identifies a Competitive Endogenous RNA Network that Regulates the Immunity of Bladder Cancer [miRNA-seq]

Project description:In this study, we performed whole-transcriptome sequencing of bladder tumors and their peritumoral tissues to identify differentially expressed circ-, lnc-, mi-, and mRNAs.

2023-07-15 | GSE236933 | GEO

Whole Transcriptome Sequencing Identifies a Competitive Endogenous RNA Network that Regulates the Immunity of Bladder Cancer [RNA-seq]

Project description:In this study, we performed whole-transcriptome sequencing of bladder tumors and their peritumoral tissues to identify differentially expressed circ-, lnc-, mi-, and mRNAs.

2023-07-15 | GSE236932 | GEO

Whole Transcriptome Sequencing Identifies a Competitive Endogenous RNA Network that Regulates the Immunity of Bladder Cancer

Project description:Whole Transcriptome Sequencing Identifies a Competitive Endogenous RNA Network that Regulates the Immunity of Bladder Cancer

| PRJNA993143 | ENA

Whole Transcriptome Sequencing Identifies a Competitive Endogenous RNA Network that Regulates the Immunity of Bladder Cancer [RNA-seq]

Project description:Whole Transcriptome Sequencing Identifies a Competitive Endogenous RNA Network that Regulates the Immunity of Bladder Cancer [RNA-seq]

| PRJNA993150 | ENA

Whole Transcriptome Sequencing Identifies a Competitive Endogenous RNA Network that Regulates the Immunity of Bladder Cancer [miRNA-seq]

Project description:Whole Transcriptome Sequencing Identifies a Competitive Endogenous RNA Network that Regulates the Immunity of Bladder Cancer [miRNA-seq]

| PRJNA993154 | ENA

Whole-transcriptome analysis of periodontal tissue and construction of immune-related competitive endogenous RNA network

Project description:Background In periodontitis, noncoding RNAs may play a regulatory role in the immune microenvironment through competitive endogenous RNA. We aimed to profile noncoding RNA expression and construct immune-related ceRNA network in periodontitis. Methods Five inflamed periodontal tissue and five healthy gingivae were collected for whole-transcriptome sequencing. Differential gene, functional enrichment, and protein–protein interaction network analysis were performed to explore the function of differentially expressed genes. CIBERSORTx was used to analyze level of immune cell infiltration in the periodontal tissue. An immune-related competitive endogenous RNA network was constructed and expression of key regulators in the network was validated. Results Compared with healthy gingiva, 200 mRNAs, 90 long noncoding RNAs, 65 microRNAs, and 518 circular RNAs were differentially expressed, and cell chemotaxis was significantly enhanced in inflamed periodontal tissue. Immune cell infiltration analysis showed that neutrophils, macrophages M1, T follicular helper cells, and naive B cells were significantly increased in periodontitis. Key regulators including JUN, FOS, THBS1, KLF2, WIF1, were identified and their expression was then validated. Conclusion We constructed an immune-related competitive endogenous RNA network in periodontal tissue, which provided new insights into immune homeostasis in periodontitis and laid a foundation for further study of noncoding RNAs. Key regulators in this network may be promising targets for future periodontitis treatment. Supplementary Information The online version contains supplementary material available at 10.1186/s12903-022-02401-0.

| S-EPMC9429583 | biostudies-literature

Identification of bladder cancer prognostic biomarkers using an ageing gene-related competitive endogenous RNA network.

Project description:Competitive endogenous RNAs (ceRNAs) are a newly proposed RNA interaction mechanism that has been associated with the initiation and progression of various cancers. In this study, we constructed an ageing gene related ceRNA network (AgeingCeNet) in bladder cancer. Network analysis revealed that ageing gene ceRNAs have a larger degree and closeness centrality than ageing genes themselves. Notably, the difference of betweenness centrality of ageing genes and their ceRNAs is not significant, suggesting that the ceRNAs of ageing genes and ageing genes themselves both play important communication roles in AgeingCeNet. KEGG pathway enrichment analysis for genes in AgeingCeNet revealed that AgeingCeNet genes are enriched in cancer pathways and several cancer related singaling pathways. We also identified 37 core modules from AgeingCeNet using CFinder software. Next, we identified 2 potential prognostic modules, named K11M14 and K13M4, whose prognostic ability is better than that of age and gender. Finally, we identified microRNAs (miRNAs) regulating the two modules, which include miR-15b-5p, miR-195-5p, miR-30 family members, and several other cancer-related miRNAs. Our study demonstrated that constructing an ageing gene related ceRNA network is a feasible strategy to explore the mechanism of initiation and progression of bladder cancer, which might benefit the treatment of this disease.

| S-EPMC5762356 | biostudies-literature

Whole transcriptome sequencing identifies increased CXCR2 expression in PNH granulocytes.

Project description:The aetiology of paroxysmal nocturnal haemoglobinuria (PNH) is a somatic mutation in the X-linked phosphatidylinositol glycan class A gene (PIGA), resulting in global deficiency of glycosyl phosphatidylinositol-anchored proteins (GPI-APs). This study applied RNA-sequencing to examine functional effects of the PIGA mutation in human granulocytes. CXCR2 expression was increased in GPI-AP- compared to GPI-AP+ granulocytes. Macrophage migration inhibitory factor, a CXCR2 agonist, was significantly higher in plasma of PNH patients. Nuclear factor-κB phosphorylation was upregulated in GPI-AP- compared with GPI-AP+ granulocytes. Our data suggest novel mechanisms in PNH, not obviously predicted by decreased production of the GPI moiety.

| S-EPMC5378616 | biostudies-literature

Ouroboros resembling competitive endogenous loop (ORCEL) in circular RNAs revealed through transcriptome sequencing dataset analysis.

Project description:BACKGROUND:Emerging evidence indicates that Circular RNAs (circRNAs) exert post-transcriptional regulation of gene expression. A subclass of circRNA was found enriched with miRNA target sites. This evidence suggests that this kind of circRNA functions as natural miRNA sponge. Noticing the potential impacts of circular RNA research, we were motivated to identify novel circRNAs as well as putative circRNA-miRNA interactions through retroactive sourced transcriptome sequencing samples. RESULTS:Through the analysis in 465 RNA-seq runs and 22 reports published in recent years, putatively circRNA sponged miRNA that had been experimentally verified targeting circRNA host gene were found. From this observation, supporting evidence of the competitive endogenous relationship of circRNAs and miRNAs targeting circRNA host genes can be observed. Given the self-regulation and self-induction nature of these circRNAs, this kind of hypothetical phenomenon was hereby called Ouroboros Resembling Competitive Endogenous Loop (ORCEL) in circular RNAs. CONCLUSIONS:The fact that miRNA sponge circRNA originated from region miRNA target sites enriched regions, while genes encoded from these regions are conserved to be miRNA targets rationalize the existence of ORCEL.

| S-EPMC5954272 | biostudies-literature

Transcriptome sequencing identifies ANLN as a promising prognostic biomarker in bladder urothelial carcinoma.

Project description:The prognosis of bladder urothelial carcinoma (BLCA) varies greatly even for patients with similar pathological characteristics. We conducted transcriptome sequencing on ten pairs of BLCA samples and adjacent normal tissues to identify differentially expressed genes. Anillin (ANLN) was identified as a transcript that was significantly up-regulated in BLCA samples compared with normal tissues. Prognostic power of candidate gene was studied using qRT-PCR and immunohistochemistry on 40 and 209 patients, respectively. Patients with elevated ANLN expression level was correlated with poorer cancer-specific (median, 22.4 vs. 37.3 months, p = 0.001), progression-free (median, 19.7 vs. 27.9 months, p = 0.001) and recurrence-free survival (median, 17.1 vs. 25.2 months, p = 0.011) compared with low ANLN expression. Public datasets TCGA and NCBI-GEO were analyzed for external validation. Knockdown of ANLN in J82 and 5637 cells using small interfering RNA significantly inhibited cell proliferation, migration, and invasion ability. Moreover, knockdown of ANLN resulted in G2/M phase arrest and decreased expression of cyclin B1 and D1. Microarray analysis suggested that ANLN played a major role in cell migration and was closely associated with several cancer-related signaling pathways. In conclusion, ANLN was identified as a promising prognostic biomarker which could be used to stratify different risks of BLCA.

| S-EPMC5466664 | biostudies-literature

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