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

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

ORGANISM(S): Homo sapiens

PROVIDER: GSE236932 | 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

Comprehensive circular RNA expression profiling and competitive endogenous RNAs regulatory networks in distal cholangiocarcinoma

Project description:To explore the differentially expressed (DE) circular (circ)RNAs, competing endogenous RNAs networks, and potential biomarkers in distal cholangiocarcinoma (dCCA), using microarray analysis, a comprehensive circRNA expression profiling was constructed with six paired dCCA tumor and adjacent normal samples. A total of 171 DE circRNAs were identified. Three upregulated (hsa_circ_0060144, hsa_circ_0008274, and hsa_circ_0000673) and two downregulated circRNAs (hsa_circ_0139402 and hsa_circ_0001714) were validated with RT-qPCR in 40 dCCA patients. Among them, hsa_circ_0000673 had an idea prognostic efficiency (AUC=0.85, p<0.01) and high level of hsa_circ_0000673 was associated with late tumor stage (p<0.01), poor histodifferentiation (p=0.041), and residual tumor (p=0.044). Gene ontology analysis of the host genes of 171 DE circRNAs showed that “response to nutrient”, “adherens junction”, and “cell adhesion molecule binding” were mainly enriched in terms of biological process, cellular component, and molecular functions respectively. Nine target micro(mi)RNAs of the five DE circRNAs were screened out and enriched in cancer associated pathways. Thereafter, 188 DE mRNAs were predicted as target genes of the nine miRNAs. Finally, protein-protein interaction networks were constructed and 20 hubgenes were identified. This research provided a landscape of DE circRNAs in dCCA, constructed circRNA-miRNA-mRNA regulating networks, and identified hsa_circ_0000673 as a potential biomarker and target for treating dCCA.

2020-12-31 | GSE148561 | GEO

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

Project description:This SuperSeries is composed of the SubSeries listed below.

2023-07-15 | GSE236935 | 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

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 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

Hsa_circ_0001944 promotes the growth and metastasis in bladder cancer cells by acting as a competitive endogenous RNA for miR-548.

Project description:BackgroundBladder cancer (BC) is a common genitourinary malignancy worldwide. Circular RNAs (circRNAs) participate in cancer development, including BC; thus, the roles of circRNAs in this process have attracted significant attention.MethodsIn this study, high-throughput sequencing was used to analyze circRNA expression profiles in BC tissues. We performed RT-qPCR to determine hsa_circ_0001944 expression in BC tissues. We used fluorescence in situ hybridization (FISH) to detect hsa_circ_0001944 expression and hsa_circ_0001944 subcellular localization in BC tissues. hsa_circ_0001944 expression in BC cells was selectively regulated. We employed CCK8, transwell, and wound healing assays to monitor cell proliferation, invasion, and migration, respectively. We employed the dual-luciferase reporter and RNA pulldown assays to verify the relationships among hsa_circ_0001944, miR-548, and PROK2. We examined the effects of hsa_circ_0001944 on BC cell metastasis and proliferation in vivo using a subcutaneous xenograft model and an intravenous tail injection model in nude mice.ResultsThe results showed that hsa_circ_0001944 expression was significantly increased in BC samples. Furthermore, high hsa_circ_0001944 expression predicted unfavorable prognoses in BC. Functional assays validated that downregulating hsa_circ_0001944 decreased BC invasion and proliferation in vivo and in vitro. Further studies showed that hsa_circ_0001944 expression promoted BC progression via sponging miR-548 and enhancing PROK2 expression. Luciferase reporter experiments validated the interactions between hsa_circ_0001944, miR-548, and PROK2. This study also found that downregulating miR-548 or overexpressing PROK2 restored BC cell invasion and proliferation after silencing hsa_circ_0001944.ConclusionsTaken together, we found that hsa_circ_0001944 is a tumor-promoting circRNA in BC that functions as a competing endogenous RNA to regulate PROK2 expression via sponging miR-548.

| S-EPMC7490907 | biostudies-literature

Single cell RNA seq of mouse bladder and bladder assembloids

Project description:To investigate whether the bladder assembloids recapitulate cell compositions, in addition to the gene expression patterns of each cell type in the adult bladder, we performed single-cell RNA-seq of bladder assembloids and mouse adult bladders, and compared the transcriptional profiles between them at the single-cell level.

2020-09-27 | GSE141348 | GEO

High-throughput RNA sequencing on circular RNA profiles of human bladder cancer tissues and normal bladder tissues

Project description:In order to find out circular RNAs profiles in human bladder cancer tissues and normal bladder tissues, we characterized circuclar RNA transcripts by performing RNA-Seq on ribosomal RNA-depleted total RNA from three pairs of human bladder cancer tissues and paired normal bladder tissues.A computational pipeline based on the anchor alignment of unmapped reads was used to identify circular RNAs. Collectively, we identified16,535 distict circular RNAs, most of them origined from exons (88.96%), others from introns, linc RNA, intergenic region, 3’UTR and 5’UTR. Among all these circRNAs, 571 circRNAs were differentially expressed between bladder cancer tissues and normal bladder tissues, and 524 circRNAs were downregulated in bladder cancer tissues (91.2%), others were upreguluated. These significantly differential expressed circular RNA might have regulatory function in bladder cancer, and worth to be further explored.

2017-08-04 | GSE97239 | GEO

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