ArticlePloS one2012
Integrated genomic and gene expression profiling identifies two major genomic circuits in urothelial carcinoma.
Article in PloS one, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 121 papers, 3 of them syntheses that pooled it.
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Who cites it
121 citing papers in PubMed, 3 syntheses or guidelines pooled it, 227 citations in OpenAlex.
- Pooled it
- Genetic alterations of histone lysine methyltransferases and their significance in breast cancer.Oncotarget · 2015Pooled it
- A meta-analysis of multiple matched copy number and transcriptomics data sets for inferring gene regulatory relationships.PloS one · 2014Pooled it
- An integrated molecular classification system identifies distinct prognostic clusters of non-muscle-invasive bladder cancer.Functional & integrative genomics · 2026Article
- Multi-omic profiling defines three distinct molecular subtypes of urothelial carcinoma with implications for precision therapy.Clinical and translational medicine · 2026Article
- Integration of bulk and single-cell transcriptomic sequencing reveals the neutrophil heterogeneity in bladder cancer and establishes a prognostic model.Discover oncology · 2026Article
- PRECOG update: an augmented resource of clinical outcome associations with gene expression for adult, pediatric, and immunotherapy cohorts.Nucleic acids research · 2026Article
- PSMD8 cooperates with USP14 to promote bladder cancer progression by inhibiting ferroptosis.iScience · 2025Article
- Glutamine metabolism reprogramming promotes bladder cancer progression via PYCR1: a multi-omics and functional validation study.Journal of translational medicine · 2025Article
- Identification of E3 ubiquitin ligase-based molecular subtypes and prognostic signature regarding prognosis and immune landscape in bladder cancer.Cancer cell international · 2025Article
- Tertiary Lymphoid Structures are Linked to Enhanced Antitumor Immunity and Better Prognosis in Muscle-Invasive Bladder Cancer.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Machine Learning and Experimental Validation Reveal MYH11 as a Novel Prognostic Biomarker and Therapeutic Target in Bladder Cancer.Journal of inflammation research · 2025Article
- Epigenetic dysregulation-induced metabolic reprogramming fuels tumor progression in bladder cancer.Frontiers in molecular biosciences · 2025Article
- IGF2BP2 Shapes the Tumor Microenvironment by Regulating Monocyte and Macrophage Recruitment in Bladder Cancer.Cancer medicine · 2024Article
- Integrating single cell and bulk RNA sequencing data identifies RBM17 as a novel response biomarker for immunotherapy in bladder cancer.Virchows Archiv : an international journal of pathology · 2024Article
- Mevalonate pathway inhibition reduces bladder cancer metastasis by modulating RhoB protein stability and integrin β1 localization.Communications biology · 2024Article
- Article
- Article
- Biomarker Profiling of Upper Tract Urothelial Carcinoma Only and with Synchronous or Metachronous Bladder Cancer.Biomedicines · 2024Article
- Poor Prognosis among Radiation-Associated Bladder Cancer Is Defined by Clinicogenomic Features.Cancer research communications · 2024Article
61 more citing papers are in PubMed but not listed here.
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Authors and funding
12 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Similar to other malignancies, urothelial carcinoma (UC) is characterized by specific recurrent chromosomal aberrations and gene mutations. However, the interconnection between specific genomic alterations, and how patterns of chromosomal alterations adhere to different molecular subgroups of UC, is less clear. We applied tiling resolution array CGH to 146 cases of UC and identified a number of regions harboring recurrent focal genomic amplifications and deletions. Several potential oncogenes were included in the amplified regions, including known oncogenes like E2F3, CCND1, and CCNE1, as well as new candidate genes, such as SETDB1 (1q21), and BCL2L1 (20q11). We next combined genome profiling with global gene expression, gene mutation, and protein expression data and identified two major genomic circuits operating in urothelial carcinoma. The first circuit was characterized by FGFR3 alterations, overexpression of CCND1, and 9q and CDKN2A deletions. The second circuit was defined by E3F3 amplifications and RB1 deletions, as well as gains of 5p, deletions at PTEN and 2q36, 16q, 20q, and elevated CDKN2A levels. TP53/MDM2 alterations were common for advanced tumors within the two circuits. Our data also suggest a possible RAS/RAF circuit. The tumors with worst prognosis showed a gene expression profile that indicated a keratinized phenotype. Taken together, our integrative approach revealed at least two separate networks of genomic alterations linked to the molecular diversity seen in UC, and that these circuits may reflect distinct pathways of tumor development.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.