Molecular characterizaion of neuroendocrine-like bladder cancer
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ABSTRACT:
PROVIDER: PRJNA528581 | ENA |
REPOSITORIES: ENA
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Project description:Neuroendocrine bladder cancer is an aggressive variant of bladder cancer with significant metastatic potential and high risk of mortality. Diagnosis of these tumors is currently dependent on morphological criteria and staining for neuroendocrine markers. Using machine learning and multiple validation cohorts in different clinical settings, we developed a model that identifies tumors with transcriptomic profiles consistent with NE bladder cancers with an absence of NE features by morphological criteria. Early and accurate identification of these patients by genomic analysis may improve outcomes through treatment intensification and adaptation of standard treatment regimens.
2019-03-23 | GSE128702 | GEO
Project description:Muscle invasive bladder cancer (MIBC) is highly heterogeneous, both at the molecular level and in terms of clinical progression. Several molecular classifications have been proposed to understand this heterogeneity and contribute to diagnosis and treatment. Although the neuroendocrine-like subtype is the most aggressive and exhibits the worst survival rate when compared to other subtypes, molecular mechanisms underlying neuroendocrine differentiation have not yet been understood. The nuclear localization of β-catenin is known to be associated with the activation of the Wnt/β-catenin pathway, and it is linked to disease progression and aggressiveness in various cancer types. To decipher the mechanisms underlying the neuroendocrine differentiation of bladder cancer, we determined β-catenin expression profiles of 169 T2-stage primary MIBC samples. Immunohistochemistry analysis revealed increased expression of the most widely used NE markers SYP, CGA, and CD56 in β-catenin positive MIBC tumors. As a result of our transcriptomic analysis, we observed higher expression of neuroendocrine differentiation-related genes, and lower expression of basal differentiation and urothelial differentiation-related genes in β-catenin positive MIBC tumors. Furthermore, we applied a molecular consensus classifier to β-catenin positive and negative samples, and the NE score was significantly higher in β-catenin positive MIBC compared to others. By comparing transcriptome profiles, we reveal that β-catenin positive MIBC harbor unique gene modules and gene expression profiles that are divergent from the β-catenin negative MIBC. GO term and KEGG pathway analyses showed that various neurogenesis-related pathways as well as regulation of gene expression and chromatin remodeling were significantly enriched at β-catenin positive MIBC. Our results collectively revealed that β-catenin expression contributes to neuroendocrine differentiation of bladder cancer.
2024-07-16 | GSE253064 | GEO
Project description:Molecular Basis of Neuroendocrine Prostate Cancer
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Project description:Three subtypes of small cell/neuroendocrine bladder cancers (SCBCs) were identified: ASCL1, NEUROD1, and POU2F3. These subtypes are with neuroendocrine (NE) level, immune signature, and antibody-drug conjugate (ADC) target implications.
2024-06-13 | GSE269750 | GEO
Project description:MicroRNAs play an important role in the pathogenesis of different types of cancer including bladder cancer. MiR-21 has been identified to have an oncogenic function, while its inhibition suppresses tumor growth. Here, we followed an integrated bioinformatics and molecular analyses to identify the molecular mediators of miR-21 oncogenic function in bladder cancer and evaluate the therapeutic potential of a chemically-modified miR-21 inhibitor in bladder xenografts. MiR-21 expression was found to up-regulated in human bladder cancers relative to normal tissues and miR-21 inhibition suppressed bladder cancer cell properties, including growth, invasiveness and anchorage-independence. Intravenous administration of an antisense oligonucleotide against miR-21 harboring locked-nucleic-acid (LNA-miR-21) modifications blocked bladder tumor growth in vivo. Transcriptomic analysis of 28 bladder cancer cell lines revealed a gene signature that negatively correlated with miR-21 expression levels. Bioinformatics and 3’UTR luciferase assay analyses revealed a direct interaction between miR-21 the 3’UTR of PPP2R2A gene. Inhibition of PPP2R2A expression induced bladder cancer growth, suggesting its tumor suppressor function. Gene profiling followed by IPA network analysis revealed that PPP2R2A regulates the ERK1/2 molecular network. Taken together, PPP2R2A is the functional mediator of miR-21 oncogenic activity on bladder cancer and LNA-miR-21 could have a therapeutic potential in bladder cancer patients.
2018-04-19 | GSE97782 | GEO
Project description:Nucleocytoplasmic β‐Catenin expression contributes to neuroendocrine differentiation in muscle invasive bladder cancer
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Project description:Neuroendocrine prostate cancer models
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Project description:Previous studies successfully revealed molecular characteristics of bladder cancers, dealing with non-muscle invasive bladder cancer and muscle invasive bladder cancer, separately. At the molecular level, however, there is a great need to aggregate these subtypes, which may share biological characteristics. This study aimed to identify distinct molecular subtypes of BC and the clinical and/or biological characteristics of each subtype. We used seven gene expression data sets for bladder cancer, which included data from 118 primary bladder cancer samples and 27 recurrent bladder tumor tissues from the Yonsei University Severance Hospital. Hierarchical clustering revealed four molecular subtypes of BC with different clinical outcomes: class 1 with low-grade NMIBC and the best prognosis; class 2 characterized by active FGFR3 and inhibited immune response pathways; class 3 with high-grade NMIBC and the worst progression-free survival; and class 4 mainly comprised of MIBC along with EMT activation. By applying the classifier based on these characteristics, we stratified all BC samples into newly identified molecular subtypes. When comparing previously reported subtypes, our subtypes well agreed with their molecular characteristics regardless of breast cancer-based biology, and showed a strong prognostic relevance in class 3. Integrative analysis of mutation and gene expression suggested that class 3 may have the potential benefit from anti-PD-L1 immunotherapy. Our classifier, constructed by NMIBC and MIBC integration, successfully stratified BC patients into distinct subtypes with different clinical outcomes and a possible treatment option.
2018-10-03 | GSE120736 | GEO
Project description:Bladder cancer (BCa) is one of the most common malignancy of the urinary tract. In order to improve the diagnosis, prevention and treatment of BCa, the details of molecular mechanisms underlying the tumorigenesis and development needs to be clarified. Results provide insight into molecular mechanisms underlying the mRNA and miRNA interactions in BCa. 3 human bladder cancer tissues and 3 normal bladder tissues were analyzed using microarray. The alteration of mRNA and miRNA expression between the 2 groups were detected.
2017-02-22 | GSE76211 | GEO
Project description:Patients with bladder cancer need frequent controls over long follow-up time due to high recurrence rate and risk of conversion to muscle invasive cancer with poor prognosis. We identified cancer-related molecular signatures in apparently healthy bladder in patients with subsequent muscular invasiveness during follow-up. Global proteomics of the normal tissue biopsies revealed specific proteome fingerprints in these patients prior to subsequent muscular invasiveness. In these presumed normal samples, we detected modulations of proteins previously associated with different cancer types. This study indicates that analyzing apparently healthy tissue of a cancer-invaded organ may predict disease progression.
2018-10-26 | PXD010260 | Pride