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Ramal M, Corral S, Kalisz M, Lapi E, Real FX. The urothelial gene regulatory network: understanding biology to improve bladder cancer management. Oncogene 2024; 43:1-21. [PMID: 37996699 DOI: 10.1038/s41388-023-02876-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 10/13/2023] [Accepted: 10/18/2023] [Indexed: 11/25/2023]
Abstract
The urothelium is a stratified epithelium composed of basal cells, one or more layers of intermediate cells, and an upper layer of differentiated umbrella cells. Most bladder cancers (BLCA) are urothelial carcinomas. Loss of urothelial lineage fidelity results in altered differentiation, highlighted by the taxonomic classification into basal and luminal tumors. There is a need to better understand the urothelial transcriptional networks. To systematically identify transcription factors (TFs) relevant for urothelial identity, we defined highly expressed TFs in normal human bladder using RNA-Seq data and inferred their genomic binding using ATAC-Seq data. To focus on epithelial TFs, we analyzed RNA-Seq data from patient-derived organoids recapitulating features of basal/luminal tumors. We classified TFs as "luminal-enriched", "basal-enriched" or "common" according to expression in organoids. We validated our classification by differential gene expression analysis in Luminal Papillary vs. Basal/Squamous tumors. Genomic analyses revealed well-known TFs associated with luminal (e.g., PPARG, GATA3, FOXA1) and basal (e.g., TP63, TFAP2) phenotypes and novel candidates to play a role in urothelial differentiation or BLCA (e.g., MECOM, TBX3). We also identified TF families (e.g., KLFs, AP1, circadian clock, sex hormone receptors) for which there is suggestive evidence of their involvement in urothelial differentiation and/or BLCA. Genomic alterations in these TFs are associated with BLCA. We uncover a TF network involved in urothelial cell identity and BLCA. We identify novel candidate TFs involved in differentiation and cancer that provide opportunities for a better understanding of the underlying biology and therapeutic intervention.
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Affiliation(s)
- Maria Ramal
- Epithelial Carcinogenesis Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Sonia Corral
- Epithelial Carcinogenesis Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Mark Kalisz
- Epithelial Carcinogenesis Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
- CIBERONC, Madrid, Spain
| | - Eleonora Lapi
- Epithelial Carcinogenesis Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
- CIBERONC, Madrid, Spain
| | - Francisco X Real
- Epithelial Carcinogenesis Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain.
- CIBERONC, Madrid, Spain.
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain.
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2
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Conci N, Tassinari E, Tateo V, Rosellini M, Marchetti A, Ricci C, Chessa F, Santoni M, Grande E, Mollica V, Massari F. How Do Molecular Classifications Affect the Neoadjuvant Treatment of Muscle-Invasive Urothelial Carcinoma? Mol Diagn Ther 2024; 28:37-51. [PMID: 37874465 DOI: 10.1007/s40291-023-00679-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/28/2023] [Indexed: 10/25/2023]
Abstract
Despite the significant improvements in the field of oncological treatments in recent decades, and the advent of targeted therapies and immunotherapy, urothelial carcinoma of the bladder remains a highly heterogeneous and difficult-to-treat neoplasm with a poor prognosis. In this context, owing to the new methods of genomic sequencing, numerous studies have analyzed the genetic features of muscle-invasive bladder cancer, providing a consensus set of molecular classes, to identify malignancies that may respond better to specific treatments (standard chemotherapy, immunotherapy, target therapy, local-regional treatment, or combinations) and improve the survival. The aim of the current review is to provide an overview of the current status of the molecular landscape of muscle-invasive bladder cancer, focusing our attention on therapeutic and prognostic implications in order to select the most effective and tailored therapeutic regimen for the individual patient.
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Affiliation(s)
- Nicole Conci
- Medical Oncology, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Via Albertoni 15, Bologna, Italy
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Bologna, Italy
| | - Elisa Tassinari
- Medical Oncology, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Via Albertoni 15, Bologna, Italy
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Bologna, Italy
| | - Valentina Tateo
- Medical Oncology, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Via Albertoni 15, Bologna, Italy
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Bologna, Italy
| | - Matteo Rosellini
- Medical Oncology, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Via Albertoni 15, Bologna, Italy
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Bologna, Italy
| | - Andrea Marchetti
- Medical Oncology, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Via Albertoni 15, Bologna, Italy
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Bologna, Italy
| | - Costantino Ricci
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Bologna, Italy
- Pathology Unit, Maggiore Hospital-AUSL Bologna, Bologna, Italy
| | - Francesco Chessa
- Division of Urology, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | | | - Enrique Grande
- Department of Medical Oncology, MD Anderson Cancer Center Madrid, Madrid, Spain
| | - Veronica Mollica
- Medical Oncology, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Via Albertoni 15, Bologna, Italy
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Bologna, Italy
| | - Francesco Massari
- Medical Oncology, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Via Albertoni 15, Bologna, Italy.
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Bologna, Italy.
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3
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Boll LM, Perera-Bel J, Rodriguez-Vida A, Arpí O, Rovira A, Juanpere N, Vázquez Montes de Oca S, Hernández-Llodrà S, Lloreta J, Albà MM, Bellmunt J. The impact of mutational clonality in predicting the response to immune checkpoint inhibitors in advanced urothelial cancer. Sci Rep 2023; 13:15287. [PMID: 37714872 PMCID: PMC10504302 DOI: 10.1038/s41598-023-42495-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 09/11/2023] [Indexed: 09/17/2023] Open
Abstract
Immune checkpoint inhibitors (ICI) have revolutionized cancer treatment and can result in complete remissions even at advanced stages of the disease. However, only a small fraction of patients respond to the treatment. To better understand which factors drive clinical benefit, we have generated whole exome and RNA sequencing data from 27 advanced urothelial carcinoma patients treated with anti-PD-(L)1 monoclonal antibodies. We assessed the influence on the response of non-synonymous mutations (tumor mutational burden or TMB), clonal and subclonal mutations, neoantigen load and various gene expression markers. We found that although TMB is significantly associated with response, this effect can be mostly explained by clonal mutations, present in all cancer cells. This trend was validated in an additional cohort. Additionally, we found that responders with few clonal mutations had abnormally high levels of T and B cell immune markers, suggesting that a high immune cell infiltration signature could be a better predictive biomarker for this subset of patients. Our results support the idea that highly clonal cancers are more likely to respond to ICI and suggest that non-additive effects of different signatures should be considered for predictive models.
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Affiliation(s)
| | | | - Alejo Rodriguez-Vida
- Hospital del Mar Research Institute, Barcelona, Spain
- Medical Oncology Department, Hospital del Mar, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Oncología (CIBERONC-ISCIII), Barcelona, Spain
| | - Oriol Arpí
- Hospital del Mar Research Institute, Barcelona, Spain
| | - Ana Rovira
- Hospital del Mar Research Institute, Barcelona, Spain
- Medical Oncology Department, Hospital del Mar, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Oncología (CIBERONC-ISCIII), Barcelona, Spain
| | | | | | | | - Josep Lloreta
- Hospital del Mar Research Institute, Barcelona, Spain
- Department of Medicine and Life Science, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - M Mar Albà
- Hospital del Mar Research Institute, Barcelona, Spain.
- Catalan Institute for Research and Advanced Studies (ICREA), Barcelona, Spain.
| | - Joaquim Bellmunt
- Hospital del Mar Research Institute, Barcelona, Spain.
- Dana Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.
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4
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Schwarzova L, Varchulova Novakova Z, Danisovic L, Ziaran S. Molecular classification of urothelial bladder carcinoma. Mol Biol Rep 2023; 50:7867-7877. [PMID: 37525073 PMCID: PMC10460735 DOI: 10.1007/s11033-023-08689-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 07/17/2023] [Indexed: 08/02/2023]
Abstract
Urothelial bladder carcinoma (UC) ranks among the top ten most commonly diagnosed cancers worldwide on an annual basis. The standardized classification system for urothelial bladder tumors is the Tumor, Node, Metastasis classification, which reflects differences between non-muscle-invasive bladder carcinoma (NMIBC) and muscle-invasive bladder carcinoma (MIBC) and it depends on the extent to which tumor has infiltrated the bladder wall and other tissues and organs. NMIBC and MIBC exhibit great intrinsic heterogeneity regarding different prognoses, survival, progression, and treatment outcomes. In recent years, studies based on mRNA expression profiling revealed the existence of biologically relevant molecular subtypes of UC, which show variant molecular features that can provide more precise stratification of UC patients. Here, we present a complex classification of UC based on mRNA expression studies and molecular subtypes of NMIBC and MIBC in detail with regard to different mRNA expression profiles, mutational signatures, and infiltration by non-tumor cells. The possible impact of molecular subtyping on treatment decisions and patients' outcomes is outlined, too.
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Affiliation(s)
- Lucia Schwarzova
- Institute of Medical Biology, Genetics and Clinical Genetics, Faculty of Medicine, Comenius University, Bratislava, Slovakia
| | - Zuzana Varchulova Novakova
- Institute of Medical Biology, Genetics and Clinical Genetics, Faculty of Medicine, Comenius University, Bratislava, Slovakia
| | - Lubos Danisovic
- Institute of Medical Biology, Genetics and Clinical Genetics, Faculty of Medicine, Comenius University, Bratislava, Slovakia.
| | - Stanislav Ziaran
- Department of Urology, Faculty of Medicine, Comenius University, Bratislava, Slovakia
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5
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Neyret-Kahn H, Fontugne J, Meng XY, Groeneveld CS, Cabel L, Ye T, Guyon E, Krucker C, Dufour F, Chapeaublanc E, Rapinat A, Jeffery D, Tanguy L, Dixon V, Neuzillet Y, Lebret T, Gentien D, Davidson I, Allory Y, Bernard-Pierrot I, Radvanyi F. Epigenomic mapping identifies an enhancer repertoire that regulates cell identity in bladder cancer through distinct transcription factor networks. Oncogene 2023; 42:1524-1542. [PMID: 36944729 PMCID: PMC10162941 DOI: 10.1038/s41388-023-02662-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 03/01/2023] [Accepted: 03/06/2023] [Indexed: 03/23/2023]
Abstract
Muscle-invasive bladder cancer (BLCA) is an aggressive disease. Consensus BLCA transcriptomic subtypes have been proposed, with two major Luminal and Basal subgroups, presenting distinct molecular and clinical characteristics. However, how these distinct subtypes are regulated remains unclear. We hypothesized that epigenetic activation of distinct super-enhancers could drive the transcriptional programs of BLCA subtypes. Through integrated RNA-sequencing and epigenomic profiling of histone marks in primary tumours, cancer cell lines, and normal human urothelia, we established the first integrated epigenetic map of BLCA and demonstrated the link between subtype and epigenetic control. We identified the repertoire of activated super-enhancers and highlighted Basal, Luminal and Normal-associated SEs. We revealed super-enhancer-regulated networks of candidate master transcription factors for Luminal and Basal subgroups including FOXA1 and ZBED2, respectively. FOXA1 CRISPR-Cas9 mutation triggered a shift from Luminal to Basal phenotype, confirming its role in Luminal identity regulation and induced ZBED2 overexpression. In parallel, we showed that both FOXA1 and ZBED2 play concordant roles in preventing inflammatory response in cancer cells through STAT2 inhibition. Our study furthers the understanding of epigenetic regulation of muscle-invasive BLCA and identifies a co-regulated network of super-enhancers and associated transcription factors providing potential targets for the treatment of this aggressive disease.
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Affiliation(s)
- Hélène Neyret-Kahn
- Molecular Oncology, PSL Research University, CNRS, UMR 144, Institut Curie, Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France.
- Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR144, 75005, Paris, France.
- INSERM U830, Equipe Labellisée LNCC, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, SIREDO Oncology Center, Institut Curie Research Center, Paris, France.
| | - Jacqueline Fontugne
- Molecular Oncology, PSL Research University, CNRS, UMR 144, Institut Curie, Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France
- Department of Pathology, Institut Curie, Saint-Cloud, France
- Université Versailles St-Quentin, Université Paris-Saclay, F-78180, Montigny-le-Bretonneux, France
| | - Xiang Yu Meng
- Molecular Oncology, PSL Research University, CNRS, UMR 144, Institut Curie, Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France
- Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR144, 75005, Paris, France
- College of Basic Medical Sciences, Medical School, Hubei Minzu University, Enshi, 445000, China
| | - Clarice S Groeneveld
- Molecular Oncology, PSL Research University, CNRS, UMR 144, Institut Curie, Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France
- Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR144, 75005, Paris, France
- Université de Paris, Centre de Recherche des Cordeliers, Paris, France
| | - Luc Cabel
- Molecular Oncology, PSL Research University, CNRS, UMR 144, Institut Curie, Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France
- Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR144, 75005, Paris, France
| | - Tao Ye
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Institut National de la Santé et de la Recherche Médicale (INSERM) U1258, Centre National de Recherche Scientifique (CNRS) UMR7104, Université de Strasbourg,1 rue Laurent Fries, 67404, Illkirch, France
| | - Elodie Guyon
- Molecular Oncology, PSL Research University, CNRS, UMR 144, Institut Curie, Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France
- Department of Pathology, Institut Curie, Paris, France
| | - Clémentine Krucker
- Molecular Oncology, PSL Research University, CNRS, UMR 144, Institut Curie, Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France
- Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR144, 75005, Paris, France
- Department of Pathology, Institut Curie, Saint-Cloud, France
| | - Florent Dufour
- Molecular Oncology, PSL Research University, CNRS, UMR 144, Institut Curie, Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France
- Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR144, 75005, Paris, France
| | - Elodie Chapeaublanc
- Molecular Oncology, PSL Research University, CNRS, UMR 144, Institut Curie, Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France
- Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR144, 75005, Paris, France
| | - Audrey Rapinat
- Department of Translational Research, Genomics Platform, Institut Curie, PSL Research University, Paris, France
| | - Daniel Jeffery
- Urology Medico-Scientific Program, Department of Translational Research, Institut Curie, PSL Research University, Paris, France
| | - Laura Tanguy
- Molecular Oncology, PSL Research University, CNRS, UMR 144, Institut Curie, Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France
- Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR144, 75005, Paris, France
| | - Victoria Dixon
- Molecular Oncology, PSL Research University, CNRS, UMR 144, Institut Curie, Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France
- Department of Pathology, Institut Curie, Saint-Cloud, France
| | - Yann Neuzillet
- Université Versailles St-Quentin, Université Paris-Saclay, F-78180, Montigny-le-Bretonneux, France
- Department of Urology, Hôpital Foch, Suresnes, France
| | - Thierry Lebret
- Université Versailles St-Quentin, Université Paris-Saclay, F-78180, Montigny-le-Bretonneux, France
- Department of Urology, Hôpital Foch, Suresnes, France
| | - David Gentien
- Department of Translational Research, Genomics Platform, Institut Curie, PSL Research University, Paris, France
| | - Irwin Davidson
- Department of Functional Genomics and Cancer, Institut de Genétique et de Biologie Moleculaire et Cellulaire, CNRS/INSERM/UDS, 67404, Illkirch Cedex, France
| | - Yves Allory
- Molecular Oncology, PSL Research University, CNRS, UMR 144, Institut Curie, Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France
- Department of Pathology, Institut Curie, Saint-Cloud, France
- Université Versailles St-Quentin, Université Paris-Saclay, F-78180, Montigny-le-Bretonneux, France
| | - Isabelle Bernard-Pierrot
- Molecular Oncology, PSL Research University, CNRS, UMR 144, Institut Curie, Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France
- Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR144, 75005, Paris, France
| | - François Radvanyi
- Molecular Oncology, PSL Research University, CNRS, UMR 144, Institut Curie, Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France
- Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR144, 75005, Paris, France
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6
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Xu HJ, Bai J, Tian Y, Feng X, Chen AP, Wang J, Wu J, Jin XR, Zhang F, Quan MY, Chen C, Lee KY, Zhang JS. ESE1/AGR2 axis antagonizes TGF-β-induced epithelial-mesenchymal transition in low-grade pancreatic cancer. Cancer Med 2023; 12:5979-5993. [PMID: 36329620 PMCID: PMC10028153 DOI: 10.1002/cam4.5397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 10/12/2022] [Accepted: 10/21/2022] [Indexed: 11/06/2022] Open
Abstract
Epithelium-specific ETS transcription factor 1 (ESE1) has been implicated in epithelial homeostasis, inflammation, as well as tumorigenesis, and cancer progression. However, numerous studies have reported contradictory roles-as an oncogene or a tumor suppressor of ESE1 in different cancers, and its function in the development and progression of pancreatic ductal adenocarcinoma (PDAC) has remained largely unexplored. Herein, we report that ESE1 was found upregulated in primary PDAC compared to normal pancreatic tissue, but high expression of ESE1 correlated to better relapse-free survival in patients with PDAC. Interestingly, ESE1 was found to exhibit dual roles in regulation of malignant properties of PDAC cells in that its overexpression promoted cell proliferation, whereas its downregulation enhanced epithelial-mesenchymal transition (EMT) phenotype. In the context of TGF-β-induced EMT, ESE1 is markedly downregulated at post-transcriptional level, and reconstituted ESE1 expression partially reversed TGF-β-induced EMT marker expression. Furthermore, we identify AGR2 as a novel transcriptional target of ESE1 that participates in TGF-β-induced EMT in PDAC. Collectively, our findings reveal an ESE1/AGR2 axis that interacts with TGF-β signaling to modulate EMT phenotype in PDAC.
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Affiliation(s)
- Hui-Jing Xu
- International Collaborative Center on Growth Factor Research, and School of Pharmaceutical Sciences, Wenzhou Medical University, Zhejiang, China
- College of Pharmacy and Research Institute of Drug Development, Chonnam National University, Gwangju, Republic of Korea
| | - Jing Bai
- International Collaborative Center on Growth Factor Research, and School of Pharmaceutical Sciences, Wenzhou Medical University, Zhejiang, China
| | - Ye Tian
- International Collaborative Center on Growth Factor Research, and School of Pharmaceutical Sciences, Wenzhou Medical University, Zhejiang, China
| | - Xiao Feng
- International Collaborative Center on Growth Factor Research, and School of Pharmaceutical Sciences, Wenzhou Medical University, Zhejiang, China
| | - Ai-Ping Chen
- International Collaborative Center on Growth Factor Research, and School of Pharmaceutical Sciences, Wenzhou Medical University, Zhejiang, China
| | - Jie Wang
- International Collaborative Center on Growth Factor Research, and School of Pharmaceutical Sciences, Wenzhou Medical University, Zhejiang, China
| | - Jin Wu
- International Collaborative Center on Growth Factor Research, and School of Pharmaceutical Sciences, Wenzhou Medical University, Zhejiang, China
| | - Xu-Ru Jin
- The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou People's Hospital, Zhejiang, China
| | - Feng Zhang
- The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou People's Hospital, Zhejiang, China
| | - Mei-Yu Quan
- Medical Research Center, and Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Wenzhou Medical University, Zhejiang, China
| | - Chengshui Chen
- The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou People's Hospital, Zhejiang, China
| | - Kwang-Youl Lee
- College of Pharmacy and Research Institute of Drug Development, Chonnam National University, Gwangju, Republic of Korea
| | - Jin-San Zhang
- The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou People's Hospital, Zhejiang, China
- Medical Research Center, and Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Wenzhou Medical University, Zhejiang, China
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7
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Identification of Prognostic Markers for Head and NeckSquamous Cell Carcinoma Based on Glycolysis-Related Genes. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2022; 2022:2762595. [PMID: 35845594 PMCID: PMC9283050 DOI: 10.1155/2022/2762595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Revised: 06/03/2022] [Accepted: 06/21/2022] [Indexed: 11/21/2022]
Abstract
Head and neck squamous cell carcinomas (HNSCCs) comprise a heterogeneous group of tumors. Many patients respond differently to treatment and prognosis due to molecular heterogeneity. There is an urgent need to identify novel biomarkers to predict the prognosis of patients with HNSCC. Glycolysis has an important influence on the progress of HNSCC. Therefore, we investigated the prognostic significance of glycolysis-related genes in HNSCC. Our results showed that ELF3, AURKA, and ADH7 of 20 glycolysis-related DEGs were significantly related to survival and were used to construct the risk signature. The risk score showed high accuracy in distinguishing the overall survival (OS) of HNSCC. The Kaplan–Meier curves demonstrated that the risk score was associated with an unfavorable prognosis in patients with female sex, male sex, grade 3, T1/2 stage, N+ stage, N2 stage, M0 stage, and clinical stage III/IV. Independent prognostic analysis showed that clinical stage and risk score were strongly associated with OS. Moreover, the risk score had higher accuracy in predicting 1-, 3-, and 5-year survival. AURKA and ADH7 were only significantly related to M1 macrophages and neutrophils, respectively, while ELF3 was significantly correlated with M2 macrophages and monocytes (all p < 0.05).The ceRNA network demonstrated that miR-335-5p and miR-9-5p may play core roles in the regulation of these three genes in HNSCC. The risk score constructed based on three glycolysis-related genes showed high accuracy in predicting the prognosis and clinicopathological characteristics of HNSCC.
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8
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Jafari NV, Rohn JL. The urothelium: a multi-faceted barrier against a harsh environment. Mucosal Immunol 2022; 15:1127-1142. [PMID: 36180582 PMCID: PMC9705259 DOI: 10.1038/s41385-022-00565-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 08/18/2022] [Accepted: 08/28/2022] [Indexed: 02/04/2023]
Abstract
All mucosal surfaces must deal with the challenge of exposure to the outside world. The urothelium is a highly specialized layer of stratified epithelial cells lining the inner surface of the urinary bladder, a gruelling environment involving significant stretch forces, osmotic and hydrostatic pressures, toxic substances, and microbial invasion. The urinary bladder plays an important barrier role and allows the accommodation and expulsion of large volumes of urine without permitting urine components to diffuse across. The urothelium is made up of three cell types, basal, intermediate, and umbrella cells, whose specialized functions aid in the bladder's mission. In this review, we summarize the recent insights into urothelial structure, function, development, regeneration, and in particular the role of umbrella cells in barrier formation and maintenance. We briefly review diseases which involve the bladder and discuss current human urothelial in vitro models as a complement to traditional animal studies.
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Affiliation(s)
- Nazila V Jafari
- Department of Renal Medicine, Division of Medicine, University College London, Royal Free Hospital Campus, London, UK
| | - Jennifer L Rohn
- Department of Renal Medicine, Division of Medicine, University College London, Royal Free Hospital Campus, London, UK.
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9
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Barrier-Forming Potential of Epithelial Cells from the Exstrophic Bladder. THE AMERICAN JOURNAL OF PATHOLOGY 2022; 192:943-955. [PMID: 35358476 PMCID: PMC9194657 DOI: 10.1016/j.ajpath.2022.03.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 02/04/2022] [Accepted: 03/03/2022] [Indexed: 11/20/2022]
Abstract
Bladder exstrophy (BEX) is a rare developmental abnormality resulting in an open, exposed bladder plate. Although normal bladder urothelium is a mitotically quiescent barrier epithelium, histologic studies of BEX epithelia report squamous and proliferative changes that can persist beyond surgical closure. The current study examined whether patient-derived BEX epithelial cells in vitro were capable of generating a barrier-forming epithelium under permissive conditions. Epithelial cells isolated from 11 BEX samples, classified histologically as transitional (n = 6) or squamous (n = 5), were propagated in vitro. In conditions conducive to differentiated tight barrier formation by normal human urothelial cell cultures, 8 of 11 BEX lines developed transepithelial electrical resistances of more than 1000 Ω.cm2, with 3 squamous lines failing to generate tight barriers. An inverse relationship was found between expression of squamous KRT14 transcript and barrier development. Transcriptional drivers of urothelial differentiation PPARG, GATA3, and FOXA1 showed reduced expression in squamous BEX cultures. These findings implicate developmental interruption of urothelial transcriptional programming in the spectrum of transitional to squamous epithelial phenotypes found in BEX. Assessment of BEX epithelial phenotype may inform management and treatment strategies, for which distinction between reversible versus intractably squamous epithelium could identify patients at risk of medical complications or those who are most appropriate for reconstructive tissue engineering strategies.
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10
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Identification of the gene expression changes and gene regulatory aspects in ELF3 mutant bladder cancer. Mol Biol Rep 2022; 49:3135-3147. [PMID: 35199247 DOI: 10.1007/s11033-022-07145-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 01/12/2022] [Indexed: 10/19/2022]
Abstract
BACKGROUND Recent genome-wide studies revealed the molecular subtypes and mutational landscape of bladder cancer, which is the 10th most common cancer causing many deaths. ELF3 is one of the frequently mutated genes in bladder cancer with 14% alteration rate. It mainly functions as an epithelial transcription factor and its proper function is critical for the urothelium development. However, the impact of ELF3 mutations in bladder cancer is currently unknown. METHODS AND RESULTS In this study, we analysed the gene expression data available for primary bladder cancer and bladder cancer cell lines according to the mutation status of ELF3. Our results show that de-regulated genes common in cell lines and primary tissue are primarily involved in ameboidal type cell migration and cell-cell junction organization. Additionally, we identify that ELF3-mutant cases in primary samples significantly overexpress PIK3C2B and ELF3 and PIK3C2B and ELF3 are significantly co-mutated in many cancer types. Our integrative analysis with existing Hi-C data further revealed the genes proximally located to ELF3, including PIK3C2B to be upregulated in ELF3 mutant cases, potentially as a result of truncated ELF3 protein product and subsequent changes in regulatory interactions. CONCLUSIONS Our results provide important insights about how ELF3 mutation contributes to bladder tumorigenesis and uncover previously unknown dependencies.
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11
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Alterations of Chromatin Regulators in the Pathogenesis of Urinary Bladder Urothelial Carcinoma. Cancers (Basel) 2021; 13:cancers13236040. [PMID: 34885146 PMCID: PMC8656749 DOI: 10.3390/cancers13236040] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 11/29/2021] [Accepted: 11/29/2021] [Indexed: 12/14/2022] Open
Abstract
Simple Summary Urinary bladder cancer is one of the ten major cancers worldwide, with higher incidences in males, in smokers, and in highly industrialized countries. New therapies beyond cytotoxic chemotherapy are urgently needed to improve treatment of these tumors. A better understanding of the mechanisms underlying their development may help in this regard. Recently, it was discovered that a group of proteins regulating the state of chromatin and thus gene expression is exceptionally and frequently affected by gene mutations in bladder cancers. Altered function of these mutated chromatin regulators must therefore be fundamental in their development, but how and why is poorly understood. Here we review the current knowledge on changes in chromatin regulators and discuss their possible consequences for bladder cancer development and options for new therapies. Abstract Urothelial carcinoma (UC) is the most frequent histological type of cancer in the urinary bladder. Genomic changes in UC activate MAPK and PI3K/AKT signal transduction pathways, which increase cell proliferation and survival, interfere with cell cycle and checkpoint control, and prevent senescence. A more recently discovered additional category of genetic changes in UC affects chromatin regulators, including histone-modifying enzymes (KMT2C, KMT2D, KDM6A, EZH2), transcription cofactors (CREBBP, EP300), and components of the chromatin remodeling complex SWI/SNF (ARID1A, SMARCA4). It is not yet well understood how these changes contribute to the development and progression of UC. Therefore, we review here the emerging knowledge on genomic and gene expression alterations of chromatin regulators and their consequences for cell differentiation, cellular plasticity, and clonal expansion during UC pathogenesis. Our analysis identifies additional relevant chromatin regulators and suggests a model for urothelial carcinogenesis as a basis for further mechanistic studies and targeted therapy development.
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12
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Liu Y, Wang S, Zhou R, Li W, Zhang G. Overexpression of E74-like transformation-specific transcription factor 3 promotes cellular proliferation and predicts poor prognosis in ovarian cancer. Oncol Lett 2021; 22:710. [PMID: 34457065 PMCID: PMC8358619 DOI: 10.3892/ol.2021.12971] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Accepted: 07/12/2021] [Indexed: 01/24/2023] Open
Abstract
E74-like E26 transformation-specific (ETS) transcription factor 3 (ELF3), is a member of the ETS transcription factor family, and has been characterized as an epithelial cell-specific transcription factor. The role of ELF3 in tumor progression remains to be elucidated. Previous studies have indicated that loss of ELF3 mRNA and protein expression was associated with poor outcomes in ovarian cancer (OC). By contrast, the present study demonstrated that ELF3 was upregulated in OC, using data from The Cancer Genome Atlas, and elevated expression levels of ELF3 were associated with a poor prognosis. ELF3 promoted OC cell proliferation in vitro and in vivo. The present study revealed that ELF3 inhibited apoptosis and reduced the cisplatin sensitivity of OC cells. Furthermore, the mTOR pathway was found to be activated by ELF3. Collectively, the results of the present study indicated the role of ELF3 in the development and pathogenesis of OC.
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Affiliation(s)
- Yao Liu
- Department of Gynecology and Obstetrics, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, P.R. China
| | - Shourong Wang
- Department of Gynecology and Obstetrics, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, P.R. China
| | - Ruiqi Zhou
- Department of Gynecology and Obstetrics, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, P.R. China
| | - Wenxue Li
- Department of Gynecology and Obstetrics, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, P.R. China
| | - Guiyu Zhang
- Department of Gynecology and Obstetrics, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, P.R. China
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13
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Peng L, Li BY, Wang W, Gao XS, Zeng X, Luo DY. Identification of key genes in human urothelial cells corresponding to interstitial cystitis/bladder pain syndrome in a lipopolysaccharide-induced cystitis model. Neurourol Urodyn 2021; 40:1720-1729. [PMID: 34245600 DOI: 10.1002/nau.24743] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Revised: 06/18/2021] [Accepted: 06/22/2021] [Indexed: 02/05/2023]
Abstract
AIMS The cellular functions of bladder urothelial cells in interstitial cystitis/bladder pain syndrome (IC/BPS) have not been well revealed and understood. Thus, the study aims to identify key genes and significant pathways in urothelium corresponding to IC/BPS in a lipopolysaccharide (LPS)-induced cystitis model and provide novel clues related to diagnosis and treatment of IC/BPS. METHODS Human urothelial cells (HUCs) were incubated with LPS (50 μg/ml for 24 h). Microarray was applied to analyze the differentially expressed genes (DEGs) between HUCs under LPS treatment and the control group. DEGs in the two groups were identified and then used for enrichment analysis. Subsequently, protein-protein interaction (PPI) network based on DEGs was constructed. Lastly, the top five key genes were identified through the Cytoscape (version 3.7.2) using the "Clustering Coefficient" algorithm. RESULTS One hundred and seventy-one DEGs (96 upregulated genes and 75 downregulated genes) were identified between the LPS treatment and control group. The established PPI network was composed of 169 nodes and 678 edges. Moreover, C19orf33, TRIM31, MUC21, ELF3, and IFI27 were identified as hub genes in the PPI network. Subsequently, a statistically increased expression level of TRIM31 and ELF3 was validated by real-time quantitative-polymerase chain reaction and immunohistochemistry in bladder tissues from 20 patients with IC/BPS. CONCLUSIONS TRIM31 and ELF3 may be the two hub genes in urothelium corresponding to IC/BPS. More studies are warranted to further validate the findings. The identified marker genes may be useful targets for further studies to develop diagnostic tools and more effective therapies for a broader group of women with IC/PBS.
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Affiliation(s)
- Liao Peng
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Bo-Ya Li
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Wei Wang
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Xiao-Shuai Gao
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Xiao Zeng
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - De-Yi Luo
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, Sichuan, China
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14
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Goutas D, Tzortzis A, Gakiopoulou H, Vlachodimitropoulos D, Giannopoulou I, Lazaris AC. Contemporary Molecular Classification of Urinary Bladder Cancer. In Vivo 2021; 35:75-80. [PMID: 33402452 DOI: 10.21873/invivo.12234] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 10/28/2020] [Accepted: 10/30/2020] [Indexed: 12/14/2022]
Abstract
The significant heterogeneity in the clinical outcome among patients with bladder cancer has highlighted the existence of different biological subtypes of muscle-invasive and non-muscle-invasive bladder cancer. Transcriptional profiling studies revealed that primary bladder cancers can be grouped into 'intrinsic' basal and luminal molecular subtypes. Luminal tumors have a papillary configuration and express markers of urothelial differentiation (uroplakins, cytokeratin 20) fibroblast growth factor 3 (FGFR3), E-cadherin and early cell-cycle genes. On the contrary, basal tumors express markers of the basal layer of the urothelium (cluster of differentiation 44, cytokeratin 5/6 and cytokeratin 14); some show squamous differentiation. Patients with basal tumors respond better to immune checkpoint inhibitors and have a worse prognosis than those with luminal tumors, who respond better to FGFR3 and human epidermal growth factor receptor 2. Patients with squamous differentiation tumors show better response to agents targeting epidermal growth factor receptor. The aim of this review was to highlight the chronological order of research performed in the field of the molecular classification of bladder cancer, with particular emphasis on prototypical research projects and recent advances. If prospective studies confirm the association of bladder cancer molecular subtypes with different responses and prognoses to targeted therapies, molecular subtyping will be incorporated into bladder cancer management.
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Affiliation(s)
- Dimitrios Goutas
- First Department of Pathology, School of Medicine, The National and Kapodistrian University of Athens - Laikon General Hospital of Athens, Athens, Greece;
| | - Andrianos Tzortzis
- First Department of Pathology, School of Medicine, The National and Kapodistrian University of Athens - Laikon General Hospital of Athens, Athens, Greece
| | - Harikleia Gakiopoulou
- First Department of Pathology, School of Medicine, The National and Kapodistrian University of Athens - Laikon General Hospital of Athens, Athens, Greece
| | | | - Ioanna Giannopoulou
- First Department of Pathology, School of Medicine, The National and Kapodistrian University of Athens - Laikon General Hospital of Athens, Athens, Greece
| | - Andreas C Lazaris
- First Department of Pathology, School of Medicine, The National and Kapodistrian University of Athens - Laikon General Hospital of Athens, Athens, Greece
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15
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Wezel F, Lustig J, Azoitei A, Liu J, Meessen S, Najjar G, Zehe V, Faustmann P, Zengerling F, John A, Martini T, Bolenz C, Günes C. Grainyhead-Like 3 Influences Migration and Invasion of Urothelial Carcinoma Cells. Int J Mol Sci 2021; 22:ijms22062959. [PMID: 33803949 PMCID: PMC8000182 DOI: 10.3390/ijms22062959] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 03/06/2021] [Accepted: 03/08/2021] [Indexed: 12/25/2022] Open
Abstract
Invasive urothelial carcinomas of the bladder (UCB) characteristically show a loss of differentiation markers. The transcription factor Grainyhead-like 3 (GRHL3) plays an important role in the development and differentiation of normal urothelium. The contribution to UCB progression is still elusive. Differential expression of GRHL3 was assessed in normal human urothelium and in non-invasive and invasive bladder cancer cell lines. The contribution of GRHL3 to cell proliferation, viability and invasion in UCB cell lines was determined by gain- and loss-of-function assays in vitro and in an organ culture model using de-epithelialized porcine bladders. GRHL3 expression was detectable in normal human urothelial cells and showed significantly higher mRNA and protein levels in well-differentiated, non-invasive RT4 urothelial carcinoma cells compared to moderately differentiated RT112 cells. GRHL3 expression was absent in anaplastic and invasive T24 cells. Ectopic de novo expression of GRHL3 in T24 cells significantly impaired their migration and invasion properties in vitro and in organ culture. Its downregulation improved the invasive capacity of RT4 cells. The results indicate that GRHL3 may play a role in progression and metastasis in UCB. In addition, this work demonstrates that de-epithelialized porcine bladder organ culture can be a useful, standardized tool to assess the invasive capacity of cancer cells.
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16
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Dalghi MG, Montalbetti N, Carattino MD, Apodaca G. The Urothelium: Life in a Liquid Environment. Physiol Rev 2020; 100:1621-1705. [PMID: 32191559 PMCID: PMC7717127 DOI: 10.1152/physrev.00041.2019] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 03/02/2020] [Accepted: 03/14/2020] [Indexed: 02/08/2023] Open
Abstract
The urothelium, which lines the renal pelvis, ureters, urinary bladder, and proximal urethra, forms a high-resistance but adaptable barrier that surveils its mechanochemical environment and communicates changes to underlying tissues including afferent nerve fibers and the smooth muscle. The goal of this review is to summarize new insights into urothelial biology and function that have occurred in the past decade. After familiarizing the reader with key aspects of urothelial histology, we describe new insights into urothelial development and regeneration. This is followed by an extended discussion of urothelial barrier function, including information about the roles of the glycocalyx, ion and water transport, tight junctions, and the cellular and tissue shape changes and other adaptations that accompany expansion and contraction of the lower urinary tract. We also explore evidence that the urothelium can alter the water and solute composition of urine during normal physiology and in response to overdistension. We complete the review by providing an overview of our current knowledge about the urothelial environment, discussing the sensor and transducer functions of the urothelium, exploring the role of circadian rhythms in urothelial gene expression, and describing novel research tools that are likely to further advance our understanding of urothelial biology.
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Affiliation(s)
- Marianela G Dalghi
- Department of Medicine, Renal-Electrolyte Division, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Nicolas Montalbetti
- Department of Medicine, Renal-Electrolyte Division, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Marcelo D Carattino
- Department of Medicine, Renal-Electrolyte Division, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Gerard Apodaca
- Department of Medicine, Renal-Electrolyte Division, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
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17
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Kamoun A, de Reyniès A, Allory Y, Sjödahl G, Robertson AG, Seiler R, Hoadley KA, Groeneveld CS, Al-Ahmadie H, Choi W, Castro MAA, Fontugne J, Eriksson P, Mo Q, Kardos J, Zlotta A, Hartmann A, Dinney CP, Bellmunt J, Powles T, Malats N, Chan KS, Kim WY, McConkey DJ, Black PC, Dyrskjøt L, Höglund M, Lerner SP, Real FX, Radvanyi F. A Consensus Molecular Classification of Muscle-invasive Bladder Cancer. Eur Urol 2019; 77:420-433. [PMID: 31563503 PMCID: PMC7690647 DOI: 10.1016/j.eururo.2019.09.006] [Citation(s) in RCA: 663] [Impact Index Per Article: 132.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 09/02/2019] [Indexed: 01/10/2023]
Abstract
Background: Muscle-invasive bladder cancer (MIBC) is a molecularly diverse disease with heterogeneous clinical outcomes. Several molecular classifications have been proposed, but the diversity of their subtype sets impedes their clinical application. Objective: To achieve an international consensus on MIBC molecular subtypes that reconciles the published classification schemes. Design, setting, and participants: We used 1750 MIBC transcriptomic profiles from 16 published datasets and two additional cohorts. Outcome measurements and statistical analysis: We performed a network-based analysis of six independent MIBC classification systems to identify a consensus set of molecular classes. Association with survival was assessed using multivariable Cox models. Results and limitations: We report the results of an international effort to reach a consensus on MIBC molecular subtypes. We identified a consensus set of six molecular classes: luminal papillary (24%), luminal nonspecified (8%), luminal unstable (15%), stroma-rich (15%), basal/squamous (35%), and neuroendocrine-like (3%). These consensus classes differ regarding underlying oncogenic mechanisms, infiltration by immune and stromal cells, and histological and clinical characteristics, including outcomes. We provide a single-sample classifier that assigns a consensus class label to a tumor sample’s transcriptome. Limitations of the work are retrospective clinical data collection and a lack of complete information regarding patient treatment. Conclusions: This consensus system offers a robust framework that will enable testing and validation of predictive biomarkers in future prospective clinical trials. Patient summary: Bladder cancers are heterogeneous at the molecular level, and scientists have proposed several classifications into sets of molecular classes. While these classifications may be useful to stratify patients for prognosis or response to treatment, a consensus classification would facilitate the clinical use of molecular classes. Conducted by multidisciplinary expert teams in the field, this study proposes such a consensus and provides a tool for applying the consensus classification in the clinical setting.
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Affiliation(s)
- Aurélie Kamoun
- Cartes d'Identité des Tumeurs (CIT) Program, Ligue Nationale Contre le Cancer, Paris, France.
| | - Aurélien de Reyniès
- Cartes d'Identité des Tumeurs (CIT) Program, Ligue Nationale Contre le Cancer, Paris, France
| | - Yves Allory
- Department of Pathology, Institut Curie, Saint-Cloud, France; Institut Curie, PSL Research University, CNRS, UMR144, Equipe Labellisée Ligue Contre le Cancer, Paris, France
| | - Gottfrid Sjödahl
- Division of Urological Research, Department of Translational Medicine, Lund University, Skåne University Hospital, Malmö, Sweden
| | - A Gordon Robertson
- Canada's Michael Smith Genome Sciences Center, BC Cancer Agency, Vancouver, BC, Canada
| | - Roland Seiler
- Department of Urology, Bern University Hospital, Bern, Switzerland
| | - Katherine A Hoadley
- Department of Genetics, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Clarice S Groeneveld
- Cartes d'Identité des Tumeurs (CIT) Program, Ligue Nationale Contre le Cancer, Paris, France; Institut Curie, PSL Research University, CNRS, UMR144, Equipe Labellisée Ligue Contre le Cancer, Paris, France; Bioinformatics and Systems Biology Laboratory, Federal University of Paraná, Polytechnic Center, Curitiba, Brazil
| | - Hikmat Al-Ahmadie
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Woonyoung Choi
- Johns Hopkins Greenberg Bladder Cancer Institute and Brady Urological Institute, Johns Hopkins University, Baltimore, MD, USA
| | - Mauro A A Castro
- Bioinformatics and Systems Biology Laboratory, Federal University of Paraná, Polytechnic Center, Curitiba, Brazil
| | - Jacqueline Fontugne
- Department of Pathology, Institut Curie, Saint-Cloud, France; Institut Curie, PSL Research University, CNRS, UMR144, Equipe Labellisée Ligue Contre le Cancer, Paris, France
| | - Pontus Eriksson
- Division of Oncology and Pathology, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Qianxing Mo
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Jordan Kardos
- Department of Genetics, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Alexandre Zlotta
- Division of Urology, Department of Surgery, University of Toronto, Mount Sinai Hospital and University Health Network, Toronto, ON, Canada
| | - Arndt Hartmann
- Institute of Pathology, University Erlangen-Nürnberg, Erlangen, Germany
| | - Colin P Dinney
- Department of Urology, University of Texas MD Anderson Cancer Center, Houston, TX, USA; Department of Cancer Biology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Joaquim Bellmunt
- Bladder Cancer Center, Dana-Farber/Brigham and Women's Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Thomas Powles
- Barts Cancer Institute ECMC, Barts Health and the Royal Free NHS Trust, Queen Mary University of London, London, UK
| | - Núria Malats
- Genetic and Molecular Epidemiology Group, Spanish National Cancer Research Centre (CNIO), CIBERONC, Madrid, Spain
| | - Keith S Chan
- Cedars-Sinai Samuel Oschin Cancer Institute, Los Angeles, CA, USA
| | - William Y Kim
- Department of Genetics, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Medicine, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - David J McConkey
- Johns Hopkins Greenberg Bladder Cancer Institute and Brady Urological Institute, Johns Hopkins University, Baltimore, MD, USA
| | - Peter C Black
- Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Lars Dyrskjøt
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Mattias Höglund
- Division of Oncology and Pathology, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Seth P Lerner
- Scott Department of Urology, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Francisco X Real
- Epithelial Carcinogenesis Group, Spanish National Cancer Research Centre (CNIO), CIBERONC, Madrid, Spain
| | - François Radvanyi
- Institut Curie, PSL Research University, CNRS, UMR144, Equipe Labellisée Ligue Contre le Cancer, Paris, France
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18
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The Transcription Factor Elf3 Is Essential for a Successful Mesenchymal to Epithelial Transition. Cells 2019; 8:cells8080858. [PMID: 31404945 PMCID: PMC6721682 DOI: 10.3390/cells8080858] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 07/22/2019] [Accepted: 07/27/2019] [Indexed: 12/13/2022] Open
Abstract
The epithelial to mesenchymal transition (EMT) and the mesenchymal to epithelial transition (MET) are two critical biological processes that are involved in both physiological events such as embryogenesis and development and also pathological events such as tumorigenesis. They present with dramatic changes in cellular morphology and gene expression exhibiting acute changes in E-cadherin expression. Despite the comprehensive understanding of EMT, the regulation of MET is far from being understood. To find novel regulators of MET, we hypothesized that such factors would correlate with Cdh1 expression. Bioinformatics examination of several expression profiles suggested Elf3 as a strong candidate. Depletion of Elf3 at the onset of MET severely impaired the progression to the epithelial state. This MET defect was explained, in part, by the absence of E-cadherin at the plasma membrane. Moreover, during MET, ELF3 interacts with the Grhl3 promoter and activates its expression. Our findings present novel insights into the regulation of MET and reveal ELF3 as an indispensable guardian of the epithelial state. A better understanding of MET will, eventually, lead to better management of metastatic cancers.
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19
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Gondkar K, Patel K, Krishnappa S, Patil A, Nair B, Sundaram G, Zea T, Kumar P. E74 like ETS transcription factor 3 (ELF3) is a negative regulator of epithelial- mesenchymal transition in bladder carcinoma. Cancer Biomark 2019; 25:223-232. [DOI: 10.3233/cbm-190013] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Kirti Gondkar
- Institute of Bioinformatics, International Technology Park, Bangalore, India
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam, India
| | - Krishna Patel
- Institute of Bioinformatics, International Technology Park, Bangalore, India
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam, India
| | - Shobha Krishnappa
- Department of Surgical Oncology, Kidwai Memorial Institute of Oncology, Bangalore, India
| | - Akkamahadevi Patil
- Department of Pathology, Kidwai Memorial Institute of Oncology, Bangalore, India
| | - Bipin Nair
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam, India
| | | | - Tan Tuan Zea
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Prashant Kumar
- Institute of Bioinformatics, International Technology Park, Bangalore, India
- Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, India
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20
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Luk IY, Reehorst CM, Mariadason JM. ELF3, ELF5, EHF and SPDEF Transcription Factors in Tissue Homeostasis and Cancer. Molecules 2018; 23:molecules23092191. [PMID: 30200227 PMCID: PMC6225137 DOI: 10.3390/molecules23092191] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 08/23/2018] [Accepted: 08/23/2018] [Indexed: 02/07/2023] Open
Abstract
The epithelium-specific ETS (ESE) transcription factors (ELF3, ELF5, EHF and SPDEF) are defined by their highly conserved ETS DNA binding domain and predominant epithelial-specific expression profile. ESE transcription factors maintain normal cell homeostasis and differentiation of a number of epithelial tissues, and their genetic alteration and deregulated expression has been linked to the progression of several epithelial cancers. Herein we review the normal function of the ESE transcription factors, the mechanisms by which they are dysregulated in cancers, and the current evidence for their role in cancer progression. Finally, we discuss potential therapeutic strategies for targeting or reactivating these factors as a novel means of cancer treatment.
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Affiliation(s)
- Ian Y Luk
- Olivia Newton-John Cancer Research Institute, Heidelberg, Victoria 3084, Australia.
- School of Cancer Medicine, La Trobe University, Bundoora, Victoria 3086, Australia.
| | - Camilla M Reehorst
- Olivia Newton-John Cancer Research Institute, Heidelberg, Victoria 3084, Australia.
- School of Cancer Medicine, La Trobe University, Bundoora, Victoria 3086, Australia.
| | - John M Mariadason
- Olivia Newton-John Cancer Research Institute, Heidelberg, Victoria 3084, Australia.
- School of Cancer Medicine, La Trobe University, Bundoora, Victoria 3086, Australia.
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21
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Hustler A, Eardley I, Hinley J, Pearson J, Wezel F, Radvanyi F, Baker SC, Southgate J. Differential transcription factor expression by human epithelial cells of buccal and urothelial derivation. Exp Cell Res 2018; 369:284-294. [PMID: 29842880 PMCID: PMC6092173 DOI: 10.1016/j.yexcr.2018.05.031] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 05/24/2018] [Accepted: 05/25/2018] [Indexed: 12/29/2022]
Abstract
Identification of transcription factors expressed by differentiated cells is informative not only of tissue-specific pathways, but to help identify master regulators for cellular reprogramming. If applied, such an approach could generate healthy autologous tissue-specific cells for clinical use where cells from the homologous tissue are unavailable due to disease. Normal human epithelial cells of buccal and urothelial derivation maintained in identical culture conditions that lacked significant instructive or permissive signaling cues were found to display inherent similarities and differences of phenotype. Investigation of transcription factors implicated in driving urothelial-type differentiation revealed buccal epithelial cells to have minimal or absent expression of PPARG, GATA3 and FOXA1 genes. Retroviral overexpression of protein coding sequences for GATA3 or PPARy1 in buccal epithelial cells resulted in nuclear immunolocalisation of the respective proteins, with both transductions also inducing expression of the urothelial differentiation-associated claudin 3 tight junction protein. PPARG1 overexpression alone entrained expression of nuclear FOXA1 and GATA3 proteins, providing objective evidence of its upstream positioning in a transcription factor network and identifying it as a candidate factor for urothelial-type transdifferentiation or reprogramming.
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Affiliation(s)
- Arianna Hustler
- Jack Birch Unit for Molecular Carcinogenesis, Department of Biology, University of York, York YO10 5DD, United Kingdom
| | - Ian Eardley
- Pyrah Department of Urology, St. James's University Hospital, Leeds LS9 7TF, United Kingdom
| | - Jennifer Hinley
- Jack Birch Unit for Molecular Carcinogenesis, Department of Biology, University of York, York YO10 5DD, United Kingdom
| | - Joanna Pearson
- Jack Birch Unit for Molecular Carcinogenesis, Department of Biology, University of York, York YO10 5DD, United Kingdom
| | - Felix Wezel
- Jack Birch Unit for Molecular Carcinogenesis, Department of Biology, University of York, York YO10 5DD, United Kingdom
| | - Francois Radvanyi
- Oncologie Moléculaire, Institut Curie, Centre de Recherche, 75248 Paris cedex 05, France
| | - Simon C Baker
- Jack Birch Unit for Molecular Carcinogenesis, Department of Biology, University of York, York YO10 5DD, United Kingdom
| | - Jennifer Southgate
- Jack Birch Unit for Molecular Carcinogenesis, Department of Biology, University of York, York YO10 5DD, United Kingdom.
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22
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Liu S, Chen H, Ronquist S, Seaman L, Ceglia N, Meixner W, Chen PY, Higgins G, Baldi P, Smale S, Hero A, Muir LA, Rajapakse I. Genome Architecture Mediates Transcriptional Control of Human Myogenic Reprogramming. iScience 2018; 6:232-246. [PMID: 30240614 PMCID: PMC6137960 DOI: 10.1016/j.isci.2018.08.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 06/23/2018] [Accepted: 07/31/2018] [Indexed: 12/21/2022] Open
Abstract
Genome architecture has emerged as a critical element of transcriptional regulation, although its role in the control of cell identity is not well understood. Here we use transcription factor (TF)-mediated reprogramming to examine the interplay between genome architecture and transcriptional programs that transition cells into the myogenic identity. We recently developed new methods for evaluating the topological features of genome architecture based on network centrality. Through integrated analysis of these features of genome architecture and transcriptome dynamics during myogenic reprogramming of human fibroblasts we find that significant architectural reorganization precedes activation of a myogenic transcriptional program. This interplay sets the stage for a critical transition observed at several genomic scales reflecting definitive adoption of the myogenic phenotype. Subsequently, TFs within the myogenic transcriptional program participate in entrainment of biological rhythms. These findings reveal a role for topological features of genome architecture in the initiation of transcriptional programs during TF-mediated human cellular reprogramming. 4D Nucleome analysis of direct human fibroblast to muscle reprogramming A space-time bifurcation marks transit to a new cell identity Chromatin reorganization precedes significant transcriptional changes Myogenic master regulators have a role in entraining biological rhythms
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Affiliation(s)
- Sijia Liu
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA; Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, MI 48109, USA
| | - Haiming Chen
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Scott Ronquist
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Laura Seaman
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Nicholas Ceglia
- Department of Computer Science, University of California-Irvine, Irvine, CA 92697, USA
| | - Walter Meixner
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Pin-Yu Chen
- AI Foundations, IBM T. J. Watson Research Center, Yorktown Heights, NY 10598, USA
| | - Gerald Higgins
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Pierre Baldi
- Department of Computer Science, University of California-Irvine, Irvine, CA 92697, USA
| | - Steve Smale
- Department of Mathematics, City University of Hong Kong, Hong Kong 999077, China; Department of Mathematics, University of California, Berkeley, CA 94720, USA
| | - Alfred Hero
- Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, MI 48109, USA
| | - Lindsey A Muir
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Indika Rajapakse
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA; Department of Mathematics, University of Michigan, Ann Arbor, MI 48109, USA.
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23
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Retinoic acid signaling maintains epithelial and mesenchymal progenitors in the developing mouse ureter. Sci Rep 2017; 7:14803. [PMID: 29093497 PMCID: PMC5665985 DOI: 10.1038/s41598-017-14790-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 10/16/2017] [Indexed: 12/27/2022] Open
Abstract
The differentiated cell types of the mature ureter arise from the distal ureteric bud epithelium and its surrounding mesenchyme. Uncommitted epithelial cells first become intermediate cells from which both basal and superficial cells develop. Mesenchymal progenitors give rise to separated layers of adventitial fibrocytes, smooth muscle cells and lamina propria fibrocytes. How progenitor expansion and differentiation are balanced is poorly understood. Here, we addressed the role of retinoic acid (RA) signaling in these programs. Using expression analysis of components and target genes, we show that pathway activity is restricted to the mesenchymal and epithelial progenitor pools. Inhibition of RA signaling in ureter explant cultures resulted in tissue hypoplasia with a relative expansion of smooth muscle cells at the expense of lamina propria fibroblasts in the mesenchyme, and of superficial cells at the expense of intermediate cells in the ureteric epithelium. Administration of RA led to a slight reduction of smooth muscle cells, and almost completely prevented differentiation of intermediate cells into basal and superficial cells. We identified cellular programs and transcriptional targets of RA signaling that may account for this activity. We conclude that RA signaling is required and sufficient to maintain mesenchymal and epithelial progenitors in early ureter development.
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24
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Choi W, Ochoa A, McConkey DJ, Aine M, Höglund M, Kim WY, Real FX, Kiltie AE, Milsom I, Dyrskjøt L, Lerner SP. Genetic Alterations in the Molecular Subtypes of Bladder Cancer: Illustration in the Cancer Genome Atlas Dataset. Eur Urol 2017; 72:354-365. [PMID: 28365159 PMCID: PMC5764190 DOI: 10.1016/j.eururo.2017.03.010] [Citation(s) in RCA: 168] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 03/06/2017] [Indexed: 12/14/2022]
Abstract
CONTEXT Recent whole genome mRNA expression profiling studies revealed that bladder cancers can be grouped into molecular subtypes, some of which share clinical properties and gene expression patterns with the intrinsic subtypes of breast cancer and the molecular subtypes found in other solid tumors. The molecular subtypes in other solid tumors are enriched with specific mutations and copy number aberrations that are thought to underlie their distinct progression patterns, and biological and clinical properties. OBJECTIVE The availability of comprehensive genomic data from The Cancer Genome Atlas (TCGA) and other large projects made it possible to correlate the presence of DNA alterations with tumor molecular subtype membership. Our overall goal was to determine whether specific DNA mutations and/or copy number variations are enriched in specific molecular subtypes. EVIDENCE We used the complete TCGA RNA-seq dataset and three different published classifiers developed by our groups to assign TCGA's bladder cancers to molecular subtypes, and examined the prevalence of the most common DNA alterations within them. We interpreted the results against the background of what was known from the published literature about the prevalence of these alterations in nonmuscle-invasive and muscle-invasive bladder cancers. EVIDENCE SYNTHESIS The results confirmed that alterations involving RB1 and NFE2L2 were enriched in basal cancers, whereas alterations involving FGFR3 and KDM6A were enriched in luminal tumors. CONCLUSIONS The results further reinforce the conclusion that the molecular subtypes of bladder cancer are distinct disease entities with specific genetic alterations. PATIENT SUMMARY Our observation showed that some of subtype-enriched mutations and copy number aberrations are clinically actionable, which has direct implications for the clinical management of patients with bladder cancer.
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Affiliation(s)
- Woonyoung Choi
- Department of Urology, U.T. M.D. Anderson Cancer Center, Houston, Texas, USA; Department of Cancer Biology, U.T. M.D. Anderson Cancer Center, Houston, Texas, USA
| | - Andrea Ochoa
- Department of Urology, U.T. M.D. Anderson Cancer Center, Houston, Texas, USA; Department of Cancer Biology, U.T. M.D. Anderson Cancer Center, Houston, Texas, USA
| | - David J McConkey
- Department of Urology, U.T. M.D. Anderson Cancer Center, Houston, Texas, USA; Department of Cancer Biology, U.T. M.D. Anderson Cancer Center, Houston, Texas, USA.
| | - Mattias Aine
- Division of Oncology and Pathology, Department of Clinical Sciences, Faculty of Medicine, Lund University, Lund, Sweden
| | - Mattias Höglund
- Division of Oncology and Pathology, Department of Clinical Sciences, Faculty of Medicine, Lund University, Lund, Sweden
| | - William Y Kim
- University of North Carolina, Chapel Hill, North Carolina, USA
| | - Francisco X Real
- Epithelial Carcinogenesis Group, Spanish National Cancer Research Centre-CNIO, Madrid, Spain; Departament de Ciències Experimentalsi de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
| | - Anne E Kiltie
- Department of Oncology, University of Oxford, Oxford, UK
| | - Ian Milsom
- Institute of Clinical Sciences, Sahlgrenska Academy at Gothenburg University, Gothenburg, Sweden
| | - Lars Dyrskjøt
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Seth P Lerner
- TCGA Analysis Working Group, Baylor College of Medicine, Houston, Texas, USA
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25
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Sjödahl G, Eriksson P, Liedberg F, Höglund M. Molecular classification of urothelial carcinoma: global mRNA classification versus tumour-cell phenotype classification. J Pathol 2017; 242:113-125. [PMID: 28195647 PMCID: PMC5413843 DOI: 10.1002/path.4886] [Citation(s) in RCA: 233] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Revised: 01/12/2017] [Accepted: 02/07/2017] [Indexed: 12/17/2022]
Abstract
Global mRNA expression analysis is efficient for phenotypic profiling of tumours, and has been used to define molecular subtypes for almost every major tumour type. A key limitation is that most tumours are communities of both tumour and non‐tumour cells. This problem is particularly pertinent for analysis of advanced invasive tumours, which are known to induce major changes and responses in both the tumour and the surrounding tissue. To identify bladder cancer tumour‐cell phenotypes and compare classification by tumour‐cell phenotype with classification by global gene expression analysis, we analysed 307 advanced bladder cancers (cystectomized) both by genome gene expression analysis and by immunohistochemistry with antibodies for 28 proteins. According to systematic analysis of gene and protein expression data, focusing on key molecular processes, we describe five tumour‐cell phenotypes of advanced urothelial carcinoma: urothelial‐like, genomically unstable, basal/SCC‐like, mesenchymal‐like, and small‐cell/neuroendocrine‐like. We provide molecular pathological definitions for each subtype. Tumours expressing urothelial differentiation factors show inconsistent and abnormal protein expression of terminal differentiation markers, suggesting pseudo‐differentiation. Cancers with different tumour‐cell phenotypes may co‐cluster (converge), and cases with identical tumour‐cell phenotypes may cluster apart (diverge), in global mRNA analyses. This divergence/convergence suggests that broad global commonalities related to the invasive process may exist between muscle‐invasive tumours regardless of specific tumour‐cell phenotype. Hence, there is a systematic disagreement in subtype classification determined by global mRNA profiling and by immunohistochemical profiling at the tumour‐cell level. We suggest that a combination of molecular pathology (tumour‐cell phenotype) and global mRNA profiling (context) is required for adequate subtype classification of muscle‐invasive bladder cancer. © 2017 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Gottfrid Sjödahl
- Division of Urological Research, Department of Translational Medicine, Lund University, Skåne University Hospital, Malmö, Sweden
| | - Pontus Eriksson
- Division of Oncology and Pathology, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Fredrik Liedberg
- Division of Urological Research, Department of Translational Medicine, Lund University, Skåne University Hospital, Malmö, Sweden
| | - Mattias Höglund
- Division of Oncology and Pathology, Department of Clinical Sciences, Lund University, Lund, Sweden
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26
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Kullmann FA, Clayton DR, Ruiz WG, Wolf-Johnston A, Gauthier C, Kanai A, Birder LA, Apodaca G. Urothelial proliferation and regeneration after spinal cord injury. Am J Physiol Renal Physiol 2017; 313:F85-F102. [PMID: 28331065 DOI: 10.1152/ajprenal.00592.2016] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Revised: 02/21/2017] [Accepted: 03/16/2017] [Indexed: 11/22/2022] Open
Abstract
The basal, intermediate, and superficial cell layers of the urothelium undergo rapid and complete recovery following acute injury; however, the effects of chronic injury on urothelial regeneration have not been well defined. To address this discrepancy, we employed a mouse model to explore urothelial changes in response to spinal cord injury (SCI), a condition characterized by life-long bladder dysfunction. One day post SCI there was a focal loss of umbrella cells, which are large cells that populate the superficial cell layer and normally express uroplakins (UPKs) and KRT20, but not KRT5, KRT14, or TP63. In response to SCI, regions of urothelium devoid of umbrella cells were replaced with small superficial cells that lacked KRT20 expression and appeared to be derived in part from the underlying intermediate cell layer, including cells positive for KRT5 and TP63. We also observed KRT14-positive basal cells that extended thin cytoplasmic extensions, which terminated in the bladder lumen. Both KRT14-positive and KRT14-negative urothelial cells proliferated 1 day post SCI, and by 7 days, cells in the underlying lamina propria, detrusor, and adventitia were also dividing. At 28 days post SCI, the urothelium appeared morphologically patent, and the number of proliferative cells decreased to baseline levels; however, patches of small superficial cells were detected that coexpressed UPKs, KRT5, KRT14, and TP63, but failed to express KRT20. Thus, unlike the rapid and complete restoration of the urothelium that occurs in response to acute injuries, regions of incompletely differentiated urothelium were observed even 28 days post SCI.
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Affiliation(s)
- F Aura Kullmann
- University of Pittsburgh School of Medicine, Department of Medicine, Pittsburgh, Pennsylvania
| | - Dennis R Clayton
- University of Pittsburgh School of Medicine, Department of Medicine, Pittsburgh, Pennsylvania
| | - Wily G Ruiz
- University of Pittsburgh School of Medicine, Department of Medicine, Pittsburgh, Pennsylvania
| | - Amanda Wolf-Johnston
- University of Pittsburgh School of Medicine, Department of Medicine, Pittsburgh, Pennsylvania
| | - Christian Gauthier
- University of Pittsburgh School of Medicine, Department of Medicine, Pittsburgh, Pennsylvania
| | - Anthony Kanai
- University of Pittsburgh School of Medicine, Department of Medicine, Pittsburgh, Pennsylvania.,University of Pittsburgh School of Medicine, Department of Pharmacology and Chemical Biology, Pittsburgh, Pennsylvania; and
| | - Lori A Birder
- University of Pittsburgh School of Medicine, Department of Medicine, Pittsburgh, Pennsylvania.,University of Pittsburgh School of Medicine, Department of Pharmacology and Chemical Biology, Pittsburgh, Pennsylvania; and
| | - Gerard Apodaca
- University of Pittsburgh School of Medicine, Department of Medicine, Pittsburgh, Pennsylvania; .,University of Pittsburgh School of Medicine, Department of Cell Biology, Pittsburgh, Pennsylvania
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27
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Fishwick C, Higgins J, Percival-Alwyn L, Hustler A, Pearson J, Bastkowski S, Moxon S, Swarbreck D, Greenman CD, Southgate J. Heterarchy of transcription factors driving basal and luminal cell phenotypes in human urothelium. Cell Death Differ 2017; 24:809-818. [PMID: 28282036 PMCID: PMC5423105 DOI: 10.1038/cdd.2017.10] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2016] [Revised: 01/10/2017] [Accepted: 01/11/2017] [Indexed: 02/06/2023] Open
Abstract
Cell differentiation is affected by complex networks of transcription factors that co-ordinate re-organisation of the chromatin landscape. The hierarchies of these relationships can be difficult to dissect. During in vitro differentiation of normal human uro-epithelial cells, formaldehyde-assisted isolation of regulatory elements (FAIRE-seq) and RNA-seq was used to identify alterations in chromatin accessibility and gene expression changes following activation of the nuclear receptor peroxisome proliferator-activated receptor gamma (PPARγ) as a differentiation-initiating event. Regions of chromatin identified by FAIRE-seq, as having altered accessibility during differentiation, were found to be enriched with sequence-specific binding motifs for transcription factors predicted to be involved in driving basal and differentiated urothelial cell phenotypes, including forkhead box A1 (FOXA1), P63, GRHL2, CTCF and GATA-binding protein 3 (GATA3). In addition, co-occurrence of GATA3 motifs was observed within subsets of differentiation-specific peaks containing P63 or FOXA1. Changes in abundance of GRHL2, GATA3 and P63 were observed in immunoblots of chromatin-enriched extracts. Transient siRNA knockdown of P63 revealed that P63 favoured a basal-like phenotype by inhibiting differentiation and promoting expression of basal marker genes. GATA3 siRNA prevented differentiation-associated downregulation of P63 protein and transcript, and demonstrated positive feedback of GATA3 on PPARG transcript, but showed no effect on FOXA1 transcript or protein expression. This approach indicates that as a transcriptionally regulated programme, urothelial differentiation operates as a heterarchy, wherein GATA3 is able to co-operate with FOXA1 to drive expression of luminal marker genes, but that P63 has potential to transrepress expression of the same genes.
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Affiliation(s)
- Carl Fishwick
- Jack Birch Unit for Molecular Carcinogenesis, Department of Biology, University of York, York YO10 5DD, UK
| | - Janet Higgins
- Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
| | | | - Arianna Hustler
- Jack Birch Unit for Molecular Carcinogenesis, Department of Biology, University of York, York YO10 5DD, UK
| | - Joanna Pearson
- Jack Birch Unit for Molecular Carcinogenesis, Department of Biology, University of York, York YO10 5DD, UK
| | | | - Simon Moxon
- Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
| | - David Swarbreck
- Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
| | - Chris D Greenman
- School of Computing Sciences, University of East Anglia, Norwich NR4 7TJ, UK
| | - Jennifer Southgate
- Jack Birch Unit for Molecular Carcinogenesis, Department of Biology, University of York, York YO10 5DD, UK
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28
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Archer LK, Frame FM, Maitland NJ. Stem cells and the role of ETS transcription factors in the differentiation hierarchy of normal and malignant prostate epithelium. J Steroid Biochem Mol Biol 2017; 166:68-83. [PMID: 27185499 DOI: 10.1016/j.jsbmb.2016.05.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Revised: 04/25/2016] [Accepted: 05/07/2016] [Indexed: 12/18/2022]
Abstract
Prostate cancer is the most common cancer of men in the UK and accounts for a quarter of all new cases. Although treatment of localised cancer can be successful, there is no cure for patients presenting with invasive prostate cancer and there are less treatment options. They are generally treated with androgen-ablation therapies but eventually the tumours become hormone resistant and patients develop castration-resistant prostate cancer (CRPC) for which there are no further successful or curative treatments. This highlights the need for new treatment strategies. In order to prevent prostate cancer recurrence and treatment resistance, all the cell populations in a heterogeneous prostate tumour must be targeted, including the rare cancer stem cell (CSC) population. The ETS transcription factor family members are now recognised as a common feature in multiple cancers including prostate cancer; with aberrant expression, loss of tumour suppressor function, inactivating mutations and the formation of fusion genes observed. Most notably, the TMPRSS2-ERG gene fusion is present in approximately 50% of prostate cancers and in prostate CSCs. However, the role of other ETS transcription factors in prostate cancer is less well understood. This review will describe the prostate epithelial cell hierarchy and discuss the evidence behind prostate CSCs and their inherent resistance to conventional cancer therapies. The known and proposed roles of the ETS family of transcription factors in prostate epithelial cell differentiation and regulation of the CSC phenotype will be discussed, as well as how they might be targeted for therapy.
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Affiliation(s)
- Leanne K Archer
- Cancer Research Unit, Department of Biology, University of York, York, YO10 5DD, United Kingdom
| | - Fiona M Frame
- Cancer Research Unit, Department of Biology, University of York, York, YO10 5DD, United Kingdom
| | - Norman J Maitland
- Cancer Research Unit, Department of Biology, University of York, York, YO10 5DD, United Kingdom.
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29
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Al-Kurdi B. Hierarchical transcriptional profile of urothelial cells development and differentiation. Differentiation 2017; 95:10-20. [PMID: 28135607 DOI: 10.1016/j.diff.2016.10.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2016] [Revised: 10/09/2016] [Accepted: 10/14/2016] [Indexed: 11/27/2022]
Abstract
The urothelial lining of the lower urinary tract is the most efficient permeability barrier in animals, exhibiting a highly differentiated phenotype and a remarkable regenerative capacity upon wounding. During development and possibly during repair, cells undergo a sequence of hierarchical transcriptional events that mark the transition of these cells from the least differentiated urothelial phenotype characteristic of the basal cell layer, to the most differentiated cellular phenotype characteristic of the superficial cell layer. Unraveling normal urothelial differentiation program is essential to uncover the underlying causes of many congenital abnormalities and for the development of an appropriate differentiation niche for stem cells, for future use in urinary tract tissue engineering and organ reconstruction. Kruppel like factor-5 appears to be at the top of the hierarchy activating several downstream transcription factors, the most prominent of which is peroxisome proliferator activator receptor-γ. Eventually those lead to the activation of transcription factors that directly regulate the expression of uroplakin proteins along with other proteins that mediate the permeability function of the urothelium. In this review, we discuss the most recent findings in the area of urothelial cellular differentiation and transcriptional regulation, aiming for a comprehensive overview that aids in a refined understanding of this process.
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Affiliation(s)
- Ban Al-Kurdi
- Cell Therapy Center, The University of Jordan, Amman, Jordan.
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30
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Warrick JI, Walter V, Yamashita H, Chung E, Shuman L, Amponsa VO, Zheng Z, Chan W, Whitcomb TL, Yue F, Iyyanki T, Kawasawa YI, Kaag M, Guo W, Raman JD, Park JS, DeGraff DJ. FOXA1, GATA3 and PPARɣ Cooperate to Drive Luminal Subtype in Bladder Cancer: A Molecular Analysis of Established Human Cell Lines. Sci Rep 2016; 6:38531. [PMID: 27924948 PMCID: PMC5141480 DOI: 10.1038/srep38531] [Citation(s) in RCA: 93] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 11/10/2016] [Indexed: 12/22/2022] Open
Abstract
Discrete bladder cancer molecular subtypes exhibit differential clinical aggressiveness and therapeutic response, which may have significant implications for identifying novel treatments for this common malignancy. However, research is hindered by the lack of suitable models to study each subtype. To address this limitation, we classified bladder cancer cell lines into molecular subtypes using publically available data in the Cancer Cell Line Encyclopedia (CCLE), guided by genomic characterization of bladder cancer by The Cancer Genome Atlas (TCGA). This identified a panel of bladder cancer cell lines which exhibit genetic alterations and gene expression patterns consistent with luminal and basal molecular subtypes of human disease. A subset of bladder cancer cell lines exhibit in vivo histomorphologic patterns consistent with luminal and basal subtypes, including papillary architecture and squamous differentiation. Using the molecular subtype assignments, and our own RNA-seq analysis, we found overexpression of GATA3 and FOXA1 cooperate with PPARɣ activation to drive transdifferentiation of a basal bladder cancer cells to a luminial phenotype. In summary, our analysis identified a set of human cell lines suitable for the study of molecular subtypes in bladder cancer, and furthermore indicates a cooperative regulatory network consisting of GATA3, FOXA1, and PPARɣ drive luminal cell fate.
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Affiliation(s)
- Joshua I Warrick
- Department of Pathology, Pennsylvania State University Milton S. Hershey Medical Center, Hershey, PA, USA.,Department of Surgery, Division of Urology, Pennsylvania State University College of Medicine, PA, USA
| | - Vonn Walter
- Department of Biochemistry and Molecular Biology, Pennsylvania State University College of Medicine, PA, USA.,Department of Public Health Sciences, Pennsylvania State University College of Medicine, PA, USA
| | - Hironobu Yamashita
- Department of Pathology, Pennsylvania State University Milton S. Hershey Medical Center, Hershey, PA, USA
| | - Eunah Chung
- Division of Pediatric Urology and Developmental Biology, Cincinnati Children's Hospital Medical Center, OH, USA
| | - Lauren Shuman
- Department of Pathology, Pennsylvania State University Milton S. Hershey Medical Center, Hershey, PA, USA.,Department of Surgery, Division of Urology, Pennsylvania State University College of Medicine, PA, USA
| | - Vasty Osei Amponsa
- Department of Pathology, Pennsylvania State University Milton S. Hershey Medical Center, Hershey, PA, USA
| | - Zongyu Zheng
- Department of Pathology, Pennsylvania State University Milton S. Hershey Medical Center, Hershey, PA, USA
| | - Wilson Chan
- Department of Pathology, Pennsylvania State University Milton S. Hershey Medical Center, Hershey, PA, USA.,Department of Surgery, Division of Urology, Pennsylvania State University College of Medicine, PA, USA
| | - Tiffany L Whitcomb
- Department of Comparative Medicine, Pennsylvania State University College of Medicine, PA, USA
| | - Feng Yue
- Department of Biochemistry and Molecular Biology, Pennsylvania State University College of Medicine, PA, USA.,Institute for Personalized Medicine, Pennsylvania State University College of Medicine, PA, USA
| | - Tejaswi Iyyanki
- Department of Biochemistry and Molecular Biology, Pennsylvania State University College of Medicine, PA, USA
| | - Yuka I Kawasawa
- Department of Biochemistry and Molecular Biology, Pennsylvania State University College of Medicine, PA, USA.,Institute for Personalized Medicine, Pennsylvania State University College of Medicine, PA, USA
| | - Matthew Kaag
- Department of Surgery, Division of Urology, Pennsylvania State University College of Medicine, PA, USA
| | - Wansong Guo
- Department of Surgery, Division of Urology, Changchun Central Hospital, Changchun, China
| | - Jay D Raman
- Department of Biochemistry and Molecular Biology, Pennsylvania State University College of Medicine, PA, USA
| | - Joo-Seop Park
- Division of Pediatric Urology and Developmental Biology, Cincinnati Children's Hospital Medical Center, OH, USA
| | - David J DeGraff
- Department of Pathology, Pennsylvania State University Milton S. Hershey Medical Center, Hershey, PA, USA.,Department of Surgery, Division of Urology, Pennsylvania State University College of Medicine, PA, USA.,Department of Biochemistry and Molecular Biology, Pennsylvania State University College of Medicine, PA, USA
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31
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Abstract
Genomic and transcriptional studies have identified discrete molecular subtypes of bladder cancer. These observations could be the starting point to identify new treatments. Several members of the forkhead box (FOX) superfamily of transcription factors have been found to be differentially expressed in the different bladder cancer subtypes. In addition, the FOXA protein family are key regulators of embryonic bladder development and patterning. Both experimental and clinical data support a role for FOXA1 and FOXA2 in urothelial carcinoma. FOXA1 is expressed in embryonic and adult urothelium and its expression is altered in urothelial carcinomas and across disparate molecular bladder cancer subtypes. FOXA2 is normally absent from the adult urothelium, but developmental studies identified FOXA2 as a marker of a transient urothelial progenitor cell population during bladder development. Studies also implicate FOXA2 in bladder cancer and several other FOX proteins might be involved in development and/or progression of this disease; for example, FOXA1 and FOXO3A have been associated with clinical patient outcomes. Future studies should investigate to what extent and by which mechanisms FOX proteins might be directly involved in bladder cancer pathogenesis and treatment responses.
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32
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Scholz GM, Sulaiman NS, Al Baiiaty S, Kwa MQ, Reynolds EC. A novel regulatory relationship between RIPK4 and ELF3 in keratinocytes. Cell Signal 2016; 28:1916-1922. [PMID: 27667567 DOI: 10.1016/j.cellsig.2016.09.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Revised: 09/19/2016] [Accepted: 09/21/2016] [Indexed: 12/16/2022]
Abstract
Keratinocytes are central to the barrier functions of surface epithelia, such as the gingiva and epidermis. RIPK4 is a key regulator of keratinocyte differentiation; however, the signalling pathways in which it functions remain poorly defined. In this study, we identified a regulatory relationship between RIPK4 and ELF3, an ETS family transcription factor. RIPK4 was shown to be important for the upregulation of ELF3 gene expression by the PKC agonist PMA in both oral and epidermal keratinocytes. RIPK4 promotes keratinocyte differentiation in part by phosphorylating and thereby activating the IRF6 transcription factor. Significantly, silencing of IRF6 inhibited the PMA-inducible expression of ELF3. A role for the GRHL3 transcription factor, a downstream target gene of IRF6, in the regulation of ELF3 expression was similarly demonstrated. ELF3 has previously been shown to regulate the expression of SPPR1A and SPRR1B, small proline-rich proteins that contribute to the cornification of keratinocytes. Consistently, RIPK4 and IRF6 were important for the PMA-inducible expression of SPRR1A and SPRR1B. They were also important for the upregulation of TGM1, a transglutaminase that catalyses the cross-linking of proteins, including small proline-rich proteins, during keratinocyte cornification. RIPK4 was also shown to upregulate the expression of TGM2 independently of IRF6. Collectively, our findings position RIPK4 upstream of a hierarchal IRF6-GRHL3-ELF3 transcription factor pathway in keratinocytes, as well as provide insight into a potential role for RIPK4 in the regulation of keratinocyte cornification.
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Affiliation(s)
- Glen M Scholz
- Oral Health Cooperative Research Centre, Melbourne Dental School, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Victoria 3010, Australia
| | - Nur S Sulaiman
- Oral Health Cooperative Research Centre, Melbourne Dental School, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Victoria 3010, Australia
| | - Sahar Al Baiiaty
- Oral Health Cooperative Research Centre, Melbourne Dental School, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Victoria 3010, Australia
| | - Mei Qi Kwa
- Oral Health Cooperative Research Centre, Melbourne Dental School, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Victoria 3010, Australia
| | - Eric C Reynolds
- Oral Health Cooperative Research Centre, Melbourne Dental School, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Victoria 3010, Australia.
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Zhang M, Li H, Zou D, Gao J. Ruguo key genes and tumor driving factors identification of bladder cancer based on the RNA-seq profile. Onco Targets Ther 2016; 9:2717-23. [PMID: 27217782 PMCID: PMC4863592 DOI: 10.2147/ott.s92529] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Aim This study aimed to select several signature genes associated with bladder cancer, thus to investigate the possible mechanism in bladder cancer. Methods The mRNA expression profile data of GSE31614, including ten bladder tissues and ten control samples, was downloaded from the Gene Expression Omnibus. The differentially expressed genes (DEGs) in bladder cancer samples compared with the control samples were screened using the Student’s t-test method. Functional analysis for the DEGs was analyzed using the Database for Annotation, Visualization, and Integrated Discovery from the Gene Ontology database, followed by the transcription function annotation of DEGs from Tumor-Associated Gene database. Motifs of genes that had transcription functions in promoter region were analyzed using the Seqpos. Results A total of 1,571 upregulated and 1,507 downregulated DEGs in the bladder cancer samples were screened. ELF3 and MYBL2 involved in cell cycle and DNA replication were tumor suppressors. MEG3, APEX1, and EZH2 were related with the cell epigenetic regulation in bladder cancer. Moreover, HOXB9 and EN1 that have their own motif were the transcription factors. Conclusion Our study has identified several key genes involved in bladder cancer. ELF3 and MYBL2 are tumor suppressers, HOXB9 and EN1 are the main regulators, while MEG3, APEX1, and EZH2 are driving factors for bladder cancer progression.
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Affiliation(s)
- Minglei Zhang
- Department of Orthopedics, Division of Tumor and Trauma Surgery, China-Japan Union Hospital of Jilin University, Changchun, People's Republic of China
| | - Hongyan Li
- Department of Urology, China-Japan Union Hospital of Jilin University, Changchun, People's Republic of China
| | - Di Zou
- Department of Nephrology, The First Affiliated Hospital of Changchun University of Chinese Medicine, Changchun, People's Republic of China
| | - Ji Gao
- Department of Urology, China-Japan Union Hospital of Jilin University, Changchun, People's Republic of China
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Lerner SP, McConkey DJ, Hoadley KA, Chan KS, Kim WY, Radvanyi F, Höglund M, Real FX. Bladder Cancer Molecular Taxonomy: Summary from a Consensus Meeting. Bladder Cancer 2016; 2:37-47. [PMID: 27376123 PMCID: PMC4927916 DOI: 10.3233/blc-150037] [Citation(s) in RCA: 157] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The advent of Omics technologies has been key to the molecular subclassification of urothelial bladder cancer. Several groups have used different strategies to this aim, with partially overlapping findings. The meeting at the Spanish National Cancer Research Center-CNIO was held to discuss such classifications and reach consensus where appropriate. After updated presentations on the work performed by the teams attending the meeting, a consensus was reached regarding the existence of a group of Basal-Squamous-like tumors – designated BASQ – charaterized the high expression of KRT5/6 and KRT14 and low/undetectable expression of FOXA1 and GATA3. An additional tumor subgroup with urothelial differentiation features was recognized whose optimal molecular definition is required. For other subtypes described, more work is needed to determine how robust they are and how to best define them at the molecular level.
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Affiliation(s)
- Seth P Lerner
- Scott Department of Urology, Dan L. Duncan Cancer Center, Baylor College of Medicine , Houston, TX, USA
| | - David J McConkey
- Department of Urology and Department of Cancer Biology, U.T. M.D. Anderson Cancer Center , Houston, TX, USA
| | - Katherine A Hoadley
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapell Hill , Chapell Hill, NC, USA
| | - Keith S Chan
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Program in Translational Biology and Molecular Medicine, Dan L. Duncan Cancer Center for Cell Gene & Therapy, Scott Departmentof Urology, Baylor College of Medicine , Houston, TX, USA
| | - William Y Kim
- Department of Genetics, Department of Medicine, Lineberger ComprehensiveCancer Center, University of North Carolina at Chapell Hill , Chapell Hill, NC, USA
| | - François Radvanyi
- CNRS, UMR 144, Oncologie Moléculaire, Institut Curie , Paris, France
| | - Mattias Höglund
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University , Lund, Sweden
| | - Francisco X Real
- Epithelial Carcinogenesis Group, Spanish National Cancer Research Centre-CNIO, Madrid, Spain and Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra , Barcelona, Spain
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Eriksson P, Aine M, Veerla S, Liedberg F, Sjödahl G, Höglund M. Molecular subtypes of urothelial carcinoma are defined by specific gene regulatory systems. BMC Med Genomics 2015; 8:25. [PMID: 26008846 PMCID: PMC4446831 DOI: 10.1186/s12920-015-0101-5] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Accepted: 05/20/2015] [Indexed: 12/13/2022] Open
Abstract
Background Molecular stratification of bladder cancer has revealed gene signatures differentially expressed across tumor subtypes. While these signatures provide important insights into subtype biology, the transcriptional regulation that governs these signatures is not well characterized. Methods In this study, we use publically available ChIP-Seq data on regulatory factor binding in order to link transcription factors to gene signatures defining molecular subtypes of urothelial carcinoma. Results We identify PPARG and STAT3, as well as ADIRF, a novel regulator of fatty acid metabolism, as putative mediators of the SCC-like phenotype. We link the PLK1-FOXM1 axis to the rapidly proliferating Genomically Unstable and SCC-like subtypes and show that differentiation programs involving PPARG/RXRA, FOXA1/GATA3 and HOXA/HOXB are differentially expressed in UC molecular subtypes. We show that gene signatures and regulatory systems defined in urothelial carcinoma operate in breast cancer in a subtype specific manner, suggesting similarities at the gene regulatory level of these two tumor types. Conclusions At the gene regulatory level Urobasal, Genomically Unstable and SCC-like tumors represents three fundamentally different tumor types. Urobasal tumors maintain an apparent urothelial differentiation axis composed of PPARG/RXRA, FOXA1/GATA3 and anterior HOXA and HOXB genes. Genomically Unstable and SCC-like tumors differ from Urobasal tumors by a strong increase of proliferative activity through the PLK1-FOXM1 axis operating in both subtypes. However, whereas SCC-like tumors evade urothelial differentiation by a block in differentiation through strong downregulation of PPARG/RXRA, FOXA1/GATA3, our data indicates that Genomically Unstable tumors evade differentiation in a more dynamic manner. Electronic supplementary material The online version of this article (doi:10.1186/s12920-015-0101-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Pontus Eriksson
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Skåne, SE-223 81, Sweden.
| | - Mattias Aine
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Skåne, SE-223 81, Sweden.
| | - Srinivas Veerla
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Skåne, SE-223 81, Sweden.
| | - Fredrik Liedberg
- Division of Urological Research, Department of Clinical Sciences Malmö, Lund University, Malmö, Skåne, SE-205 02, Sweden.
| | - Gottfrid Sjödahl
- Division of Urological Research, Department of Clinical Sciences Malmö, Lund University, Malmö, Skåne, SE-205 02, Sweden.
| | - Mattias Höglund
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Skåne, SE-223 81, Sweden.
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Smith NJ, Hinley J, Varley CL, Eardley I, Trejdosiewicz LK, Southgate J. The human urothelial tight junction: claudin 3 and the ZO-1α + switch. Bladder (San Franc) 2015; 2:e9. [PMID: 26269793 PMCID: PMC4530542 DOI: 10.14440/bladder.2015.33] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Objective Tight junctions are multicomponent structures, with claudin proteins defining paracellular permeability. Claudin 3 is a candidate for the exceptional “tightness” of human urothelium, being localised to the terminal tight junction (TJ) of superficial cells. Our aim was to determine whether claudin 3 plays an instigating and/or a functional role in the urothelial TJ. Materials and Methods Normal human urothelial (NHU) cells maintained as non-immortalised cell lines were retrovirally-transduced to over-express or silence claudin 3 expression. Stable sublines induced to stratify or differentiate were assessed for TJ formation by immunocytochemistry and transepithelial electrical resistance (TER). Expression of claudin 3, ZO-1 and ZO-1α+ was examined in native urothelium by immunohistochemistry. Results Claudin 3 expression was associated with differentiation and development of a tight barrier and along with ZO-1 and ZO-1α+ was localised to the apical tight junction in native urothelium. Knockdown of claudin 3 inhibited formation of a tight barrier in three independent cell lines, however, overexpression of claudin 3 was not sufficient to induce tight barrier development in the absence of differentiation. A differentiation-dependent induction of the ZO-1α+ isoform was found to coincide with barrier formation. Whereas claudin 3 overexpression did not induce the switch to co-expression of ZO-1α−/ZO-1α+, claudin 3 knockdown decreased localisation of ZO-1 to the TJ and resulted in compromised barrier function. Conclusions Urothelial cytodifferentiation is accompanied by induction of claudin 3 which is essential for the development of a terminal TJ. A coordinated switch to the ZO-1α+ isotype was also observed and for the first time may indicate that ZO-1α+ is involved in the structural assembly and function of the urothelial terminal TJ.
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Affiliation(s)
- Nicholas J Smith
- Jack Birch Unit of Molecular Carcinogenesis, Department of Biology, University of York, York YO10 5DD, United Kingdom ; Pyrah Department of Urology, St James's University Hospital, Leeds LS9 7TF, United Kingdom
| | - Jennifer Hinley
- Jack Birch Unit of Molecular Carcinogenesis, Department of Biology, University of York, York YO10 5DD, United Kingdom
| | - Claire L Varley
- Jack Birch Unit of Molecular Carcinogenesis, Department of Biology, University of York, York YO10 5DD, United Kingdom
| | - Ian Eardley
- Pyrah Department of Urology, St James's University Hospital, Leeds LS9 7TF, United Kingdom
| | - Ludwik K Trejdosiewicz
- Jack Birch Unit of Molecular Carcinogenesis, Department of Biology, University of York, York YO10 5DD, United Kingdom
| | - Jennifer Southgate
- Jack Birch Unit of Molecular Carcinogenesis, Department of Biology, University of York, York YO10 5DD, United Kingdom
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Ureter growth and differentiation. Semin Cell Dev Biol 2014; 36:21-30. [DOI: 10.1016/j.semcdb.2014.07.014] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Revised: 07/22/2014] [Accepted: 07/22/2014] [Indexed: 12/25/2022]
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Greife A, Knievel J, Ribarska T, Niegisch G, Schulz WA. Concomitant downregulation of the imprinted genes DLK1 and MEG3 at 14q32.2 by epigenetic mechanisms in urothelial carcinoma. Clin Epigenetics 2014; 6:29. [PMID: 25741387 PMCID: PMC4348104 DOI: 10.1186/1868-7083-6-29] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Accepted: 11/07/2014] [Indexed: 01/01/2023] Open
Abstract
Background The two oppositely imprinted and expressed genes, DLK1 and MEG3, are located in the same gene cluster at 14q32. Previous studies in bladder cancer have suggested that tumor suppressor genes are located in this region, but these have not been identified. Results We observed that both DLK1 and MEG3 are frequently silenced in urothelial cancer tissues and cell lines. The concomitant downregulation of the two genes is difficult to explain by known mechanisms for inactivating imprinted genes, namely deletion of active alleles or epitype switching. Indeed, quantitative PCR revealed more frequent copy number gains than losses in the gene cluster that were, moreover, consistent within each sample, excluding gene losses as the cause of downregulation. Instead, we observed distinctive epigenetic alterations at the three regions controlling DLK1 and MEG3 expression, namely the DLK1 promoter; the intergenic (IG) and MEG3 differentially methylated regions (DMRs). Bisulfite sequencing and pyrosequencing revealed novel patterns of DNA methylation in tumor cells, which were distinct from that of either paternal allele. Furthermore, chromatin immunoprecipitation demonstrated loss of active and gain of repressive histone modifications at all regulatory sequences. Conclusions Our data support the idea that the main cause of the prevalent downregulation of DLK1 and MEG3 in urothelial carcinoma is epigenetic silencing across the 14q32 imprinted gene cluster, resulting in the unusual concomitant inactivation of oppositely expressed and imprinted genes. Electronic supplementary material The online version of this article (doi:10.1186/1868-7083-6-29) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Annemarie Greife
- Department of Urology, Medical Faculty, Heinrich-Heine University, Moorenstr. 5, Düsseldorf, 40225 Germany
| | - Judith Knievel
- Department of Urology, Medical Faculty, Heinrich-Heine University, Moorenstr. 5, Düsseldorf, 40225 Germany
| | - Teodora Ribarska
- Department of Urology, Medical Faculty, Heinrich-Heine University, Moorenstr. 5, Düsseldorf, 40225 Germany
| | - Günter Niegisch
- Department of Urology, Medical Faculty, Heinrich-Heine University, Moorenstr. 5, Düsseldorf, 40225 Germany
| | - Wolfgang A Schulz
- Department of Urology, Medical Faculty, Heinrich-Heine University, Moorenstr. 5, Düsseldorf, 40225 Germany
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Abstract
PURPOSE OF REVIEW This review addresses significant changes in our understanding of urothelial development and regeneration. Understanding urothelial differentiation will be important in the push to find new methods of bladder reconstruction and augmentation, as well as identification of bladder cancer stem cells. RECENT FINDINGS This review will cover recent findings including the identification of novel progenitor cells in the embryo and adult urothelium, function of the urothelium, and regeneration of the urothelium. Using Cre-lox recombination with cell-type-specific Cre lines, lineage studies from our laboratory have revealed novel urothelial cell types and progenitors that are critical for formation and regeneration of the urothelium. Interestingly, our studies indicate that Keratin-5-expressing basal cells, which have previously been proposed to be urothelial stem cells, are a self-renewing unipotent population, whereas P-cells, a novel urothelial cell type, are progenitors in the embryo, and intermediate cells serve as a progenitor pool in the adult. SUMMARY These findings could have important implications for our understanding of cancer tumorigenesis and could move the fields of regeneration and reconstruction forward.
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Georgopoulos NT, Kirkwood LA, Southgate J. A novel bidirectional positive-feedback loop between Wnt-β-catenin and EGFR-ERK plays a role in context-specific modulation of epithelial tissue regeneration. J Cell Sci 2014; 127:2967-82. [PMID: 24816560 PMCID: PMC4077591 DOI: 10.1242/jcs.150888] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
By operating as both a subunit of the cadherin complex and a key component of Wnt signalling, β-catenin acts as the lynchpin between cell–cell contact and transcriptional regulation of proliferation, coordinating epithelial tissue homeostasis and regeneration. The integration of multiple growth-regulatory inputs with β-catenin signalling has been observed in cancer-derived cells, yet the existence of pathway crosstalk in normal cells is unknown. Using a highly regenerative normal human epithelial culture system that displays contact inhibition, we demonstrate that the receptor tyrosine kinase (RTK)-driven MAPK and Wnt–β-catenin signalling axes form a bidirectional positive-feedback loop to drive cellular proliferation. We show that β-catenin both drives and is regulated by proliferative signalling cues, and its downregulation coincides with the switch from proliferation to contact-inhibited quiescence. We reveal a novel contextual interrelationship whereby positive and negative feedback between three major signalling pathways – EGFR–ERK, PI3K–AKT and Wnt–β-catenin – enable autocrine-regulated tissue homeostasis as an emergent property of physical interactions between cells. Our work has direct implications for normal epithelial tissue homeostasis and provides insight as to how dysregulation of these pathways could drive excessive and sustained cellular growth in disease.
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Affiliation(s)
- Nikolaos T Georgopoulos
- Jack Birch Unit for Molecular Carcinogenesis, Department of Biology, University of York, York YO10 5DD, UK Department of Biological Sciences, School of Applied Sciences, University of Huddersfield, Huddersfield HD1 3DH, UK
| | - Lisa A Kirkwood
- Jack Birch Unit for Molecular Carcinogenesis, Department of Biology, University of York, York YO10 5DD, UK
| | - Jennifer Southgate
- Jack Birch Unit for Molecular Carcinogenesis, Department of Biology, University of York, York YO10 5DD, UK
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