UROMOL 2020 - RNA-seq data
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ABSTRACT:
PROVIDER: EGAS00001004693 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:The molecular landscape in non-muscle-invasive bladder cancer (NMIBC) is characterized by large biological heterogeneity with variable clinical outcomes. Here, we performed a large integrative multi-omics analysis of patients diagnosed with NMIBC (n=834). Transcriptomic analysis identifies four classes (1, 2a, 2b and 3) reflecting tumor biology and disease aggressiveness. Both transcriptome-based subtyping and the level of chromosomal instability provide independent prognostic value beyond established prognostic clinicopathological parameters.
| EGAS00001004862 | EGA
Project description:Non-muscle-invasive bladder cancer (NMIBC) is clinically heterogeneous, and many NMIBC patients fail to respond to treatment and frequently experience disease relapse. We aim to identify a prognostic and predictive signature of the NMIBC heterogeneity. We constructed a transcriptomic data set by RNA-seq experiments from an independent NMIBC patient cohort (n=32). This cohort contains the patients stratified into three prognostic subgroups: Group 1 (patients with non-relapse; n=15), Group 2 (patients experiencing recurrence, n=9), and Group 3 (patients experiencing progression; n=8).
2021-02-16 | GSE163899 | GEO
Project description:Improved risk stratification and predictive biomarkers of treatment response are needed for non–muscle-invasive bladder cancer (NMIBC). Here we assessed the clinical utility of targeted RNA and DNA molecular profiling in NMIBC. We performed RNA-based profiling by NanoString nCounter on non–muscle-invasive bladder cancer (NMIBC) clinical specimens and found that a novel expression signature of an inflamed tumor microenvironment (TME), but not molecular subtyping, was associated with improved recurrence-free survival after bacillus Calmette-Guérin (BCG) immunotherapy. We further demonstrated that immune checkpoint gene expression was not associated with higher recurrence rates after BCG.
2021-10-05 | GSE185264 | GEO
Project description:Although recent advances in high-throughput technology and data-driven approach have provided many insights into non-muscle invasive bladder cancer (NMIBC), previous studies are still limited in their ability to predict the clinical behavior of NMIBC including response to intravesical therapy. We aim to develop a prognostic index (PI) consisting of a small gene group that predicts the NMIBC progression and response to intravesical bacillus calmette-guérin (BCG) therapy. We analyzed progression-associated genes using Cox regression analysis and validated their predictive values using a fully connected neural network (FNN) algorithm. By applying a pathway enrichment analysis to these genes, a PI system consisting of small core genes for NMIBC progression was developed. Gene expression profiling in NMIBC patients identified a prognostic gene set for predicting NMIBC progression in multiple patient cohorts. Pathway enrichment analysis revealed a 23-gene signature. We incorporated these genes into the PI system, which was a significant prognostic indicator of NMIBC progression. The PI system was shown to be an independent risk factor by a multivariate analysis and subset stratification according to stage and grade. The subset analysis also revealed that the PI system could identify patients who would benefit from BCG immunotherapy. The 23-gene-based PI represents a promising diagnostic tool for identifying high-risk NMIBC patients who would display different clinical behaviors and response to BCG immunotherapy.
2024-02-01 | GSE224248 | GEO
Project description:Spinal muscular atrophy (SMA) genes SMN1/SMN2 produce multiplecircular RNAs (circRNAs), including C2A-2B-3-4that encompassesearly exons 2A, 2B, 3 and 4. Here we report the transcriptome-and proteome-wide effects of overexpression of C2A-2B-3-4 in inducible HEK293 cells. Our RNA-Seq analysisrevealedaltered expression of ~15% genes (4,172 genes) by C2A-2B-3-4. About half of the affected genes by C2A-2B-3-4 remained unaffected by L2A-2B-3-4, a linear transcript encompassing exons 2A, 2B, 3 and 4 of SMN1/SMN2.These findings underscore theuniquerole of the structural context of C2A-2B-3-4 in gene regulation. A surprisingly high numberof upregulated genes by C2A-2B-3-4 were located on chromosomes 4 and 7, whereas many of the downregulated genes were located on chromosomes 10 and X. Supporting a cross-regulation of SMN1/SMN2transcripts, C2A-2B-3-4 and L2A-2B-3-4upregulated and downregulatedSMN1/SMN2mRNAs, respectively. Proteome analysis revealed 61 upregulated and 57 downregulated proteins by C2A-2B-3-4 with very limited overlap with those affected by L2A-2B-3-4. Independent validations confirmed the effect ofC2A-2B-3-4on expression ofgenesassociated with chromatin remodeling, transcription, spliceosome function, ribosome biogenesis, lipid metabolism, cytoskeletal formation, cell proliferationand neuromuscular junction formation. Our findings reveal a broad role of C2A-2B-3-4, a universally expressed circRNA produced by SMN1/SMN2.
2024-05-23 | PXD048160 | Pride
Project description:To investigate the effects of inactivation of the transcription factors AP-2a and/or AP-2b in the adult mouse skin.
2023-12-20 | GSE248372 | GEO
Project description:Spinal muscular atrophy (SMA) genes, SMN1 and SMN2, produce multiple circular RNAs (circRNAs), including C2A-2B-3-4 that encompasses early exons 2A, 2B, 3 and 4. Here we report the transcriptome- and proteome-wide effects of overexpression of C2A-2B-3-4 in inducible HEK293 cells. Our RNA-Seq analysis revealed altered expression of ~15% genes (4,172 genes) by C2A-2B-3-4. About half of the affected genes by C2A-2B-3-4 remained unaffected by L2A-2B-3-4, a linear transcript encompassing exons 2A, 2B, 3 and 4 of SMN1/SMN2. These findings underscore the unique role of the structural context of C2A-2B-3-4 in gene regulation. A surprisingly high number of upregulated genes by C2A-2B-3-4 were located on chromosomes 4 and 7, whereas many of the downregulated genes were located on chromosomes 10 and X. Supporting a cross-regulation of SMN1/SMN2 transcripts, C2A-2B-3-4 and L2A-2B-3-4 upregulated and downregulated SMN1/SMN2 mRNAs, respectively. Proteome analysis revealed 61 upregulated and 57 downregulated proteins by C2A-2B-3-4 with very limited overlap with those affected by L2A-2B-3-4. Independent validations confirmed the effect of C2A-2B-3-4 on expression of genes associated with chromatin remodeling, transcription, spliceosome function, ribosome biogenesis, lipid metabolism, cytoskeletal formation, cell proliferation and neuromuscular junction formation. Our findings reveal a broad role of C2A-2B-3-4, a universally expressed circRNA produced by SMN1/SMN2.
2024-02-14 | GSE255511 | GEO
Project description:Breast cancer was one of the first cancer types where molecular subtyping led to explanation of interpersonal heterogeneity and resulted in improvement of treatment regimen. Several multigene classifiers have been developed and in particular those defining molecular signatures of early breast cancers possess significant prognostic information. Hence since 2014, molecular subtyping of primary breast cancers was implemented as a part of routine diagnostics with direct impact of therapy assignment. In this study, we evaluate direct and potential benefits of molecular subtyping in low-risk breast cancers as well as present the advantages of a robust molecular signature in regard to patient work-up among high-risk breast cancers.
2017-12-01 | E-MTAB-5724 | biostudies-arrayexpress
Project description:The DNA methylation patterns associated with the development and progression of cancer. The aim of the present study was to identify novel methylation markers that can discriminate between normal and Non-muscle-invasive bladder cancer (NMIBC), and between good and poor prognosis using microarray analysis of DNA methylation and RNA expression patterns in NMIBC patients. From the 24 matched microarray-based DNA methylation and gene expression profiling data set, tumor specific hypermethylated genes were selected and clinical relevance of these genes were verified by quantitative PQS analyses. Methylation statues of several genes were significantly associated with decreased gene expression levels and aggressive clinicopathological characteristics. In multivariate regression analyses, hypermethylation of these genes were the independent predictors of recurrence and progression.
2013-05-03 | GSE37815 | GEO
Project description:The DNA methylation patterns associated with the development and progression of cancer. The aim of the present study was to identify novel methylation markers that can discriminate between normal and Non-muscle-invasive bladder cancer (NMIBC), and between good and poor prognosis using microarray analysis of DNA methylation and RNA expression patterns in NMIBC patients. From the 24 matched microarray-based DNA methylation and gene expression profiling data set, tumor specific hypermethylated genes were selected and clinical relevance of these genes were verified by quantitative PQS analyses. Methylation statues of several genes were significantly associated with decreased gene expression levels and aggressive clinicopathological characteristics. In multivariate regression analyses, hypermethylation of these genes were the independent predictors of recurrence and progression.
2013-05-03 | GSE37816 | GEO