Proteogenomic characterization unveils biomarkers associated with chemoresistance in muscle invasive bladder cancer
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ABSTRACT:
PROVIDER: PRJNA1262009 | ENA |
REPOSITORIES: ENA
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Project description:Proteogenomic characterization unveils biomarkers associated with chemoresistance in muscle invasive bladder cancer
| PRJNA1262010 | ENA
Project description:To explore potential chemoresistance mechanisms and identify therapeutic opportunities in muscle invasive bladder cancer (MIBC), we conducted comprehensive proteogenomic characterization of 46 pre- and 14 post-treatment MIBC tumors incorporating genomics, transcriptomics, proteomics, and phosphoproteomics. Multi-omics clustering not only recapitulated established molecular subtypes, but also revealed subtypes associated with chemotherapy sensitivity. Protein isoform level analysis identified protein abundance of a short isoform of ATAD1 and RAF family proteins as biomarkers of chemosensitivity. Integration of proteomic and phosphoproteomic data revealed Wnt signaling via GSK3B-S9 phosphorylation and the JAK/STAT pathway as potential targets to overcome chemoresistance. Correlations between PD-L1 and TROP-2/NECTIN-4 indicate an additive benefit of combination therapy targeting these proteins. Overall, this study serves as a valuable resource for researchers and clinicians aiming to better understand and treat chemoresistant MIBC.
2025-09-22 | PXD060290 | Pride
Project description:Fifty patient urine samples diagnosed as high-grade urothelial carcinoma (HGUC) or benign were evaluated for bladder cancer via urine cytology. RNA was isolated and analyzed by microarray to identify a panel of biomarkers differentially expressed in HGUC and benign.
2018-04-17 | GSE68020 | GEO
Project description:The biological behaviors, clinical treatment, prognosis of nonmuscle-invasive bladder cancers (NMIBCs) and muscle-invasive bladder cancers (MIBCs) are distinct. Therefore, we performed high-through microarray screening of mRNA expression in 30 bladder tumors, to filter out some of the differential expression genes in NMIBCs and MIBCs.A total of 11 Genes in MIBCs versus in NMIBCs were considered differentially transcribed if they were transcribed ≤2.0 fold change and p<0.001 by unpaired T-test, including 9 up-regulated genes and 2 down-regulated genes in MIBCs (NR4A2, PLK3, CYR61, APOLD1, C13ORF33, LIG4, RBMS3, PCK2, AK098422, HSD17B3, RTN4). These candidate genes were validated in further and provide further insight into the discovery of new putative markers to identify MIBCs preoperatively.
2018-12-01 | GSE77952 | GEO
Project description:Gene expression profiling of 82 human non-muscle invasive bladder carcinoma and 4 normal bladder samples, for a total of 86 tissues. A Cartes díIdentite des Tumeurs (CIT) study from the 'Institut Curie' and the french 'Ligue Nationale Contre le Cancer' (http://cit.ligue-cancer.net/).
2015-01-01 | E-MTAB-1940 | biostudies-arrayexpress
Project description:Transcriptional profiling of bladder cancer cell lines comparing control uninfected cells with KSHV-infected cells. Transcriptional profiling of bladder cancer cell lines comparing control uninfected cells with KSHV-infected cells.
2015-03-10 | E-GEOD-66682 | biostudies-arrayexpress
Project description:BackgroundThe majority of genetic biomarkers for human cancers are defined by statistical screening of high-throughput genomics data. While a large number of genetic biomarkers have been proposed for diagnostic and prognostic applications, only a small number have been applied in the clinic. Similarly, the use of proteomics methods for the discovery of cancer biomarkers is increasing. The emerging field of proteogenomics seeks to enrich the value of genomics and proteomics approaches by studying the intersection of genomics and proteomics data. This task is challenging due to the complex nature of transcriptional and translation regulatory mechanisms and the disparities between genomic and proteomic data from the same samples. In this study, we have examined tumor antigens as potential biomarkers for breast cancer using genomics and proteomics data from previously reported laser capture microdissected ER+ tumor samples.ResultsWe applied proteogenomic analyses to study the genetic aberrations of 32 tumor antigens determined in the proteomic data. We found that tumor antigens that are aberrantly expressed at the genetic level and expressed at the protein level, are likely involved in perturbing pathways directly linked to the hallmarks of cancer. The results found by proteogenomic analysis of the 32 tumor antigens studied here, capture largely the same pathway irregularities as those elucidated from large-scale screening of genomics analyses, where several thousands of genes are often found to be perturbed.ConclusionTumor antigens are a group of proteins recognized by the cells of the immune system. Specifically, they are recognized in tumor cells where they are present in larger than usual amounts, or are physiochemically altered to a degree at which they no longer resemble native human proteins. This proteogenomic analysis of 32 tumor antigens suggests that tumor antigens have the potential to be highly specific biomarkers for different cancers.
| S-EPMC4290786 | biostudies-literature
Project description:Tumor-associated blood vessels differ from normal vessels at the morphological and molecular level. Proteins that are only present on tumor vessels may serve as biomarkers and as therapeutic targets for inhibition of angiogenesis in cancer. Comparing the transcriptional profiles of blood vascular endothelium from human invasive bladder cancer and from normal bladder tissue, we found several markers that could serve as novel biomarkers or therapeutic targets. In this dataset, we include the expression data obtained from laser capture microdissected (LCM) vessels isolated from tumor and bladder normal tissue. 10 samples were analyzed. We compared expression of tumor associated blood vessels with expression of vessels in the normal bladder tissue using Genespring GX 12.
2013-03-08 | E-GEOD-41614 | biostudies-arrayexpress
Project description:We conducted a comprehensive proteogenomic analysis comprising proteomic and phosphoproteomic profiling on 98 pre-invasive and 99 invasive lung adenocarcinomas.
2023-12-05 | PXD047518 |
Project description:Although non muscle-invasive bladder cancer can be treated successfully by surgical resection, there is a high rate of recurrence, which frequently develops into an invasive form of cancer. Due to the lack of marker molecules to predict recurrence, it is currently recommended that after resection each patient is screened via cystoscopy at least twice a year. This results in a psychic burden to the patient and substantial economic costs to the health care system. Using antibody microarrays targeting 724 different cancer-related proteins, we studied protein profiles of patients with and without recurrence. The analysis revealed 255 proteins of differential abundance. Most are involved in the regulation and execution of apoptosis and cell proliferation. For prognosis, a signature of 20 proteins was determined that predicts bladder cancer recurrence with 100% sensitivity and 80% specificity. As a measure of overall accuracy, the area under the curve (AUC) value was found to be 90%. This is well within a clinically relevant window of quality and should support decision making about the stringency of surveillance or even different treatment options.
2014-04-07 | E-MEXP-3625 | biostudies-arrayexpress