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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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Özden-Yılmaz G, Savas B, Bursalı A, Eray A, Arıbaş A, Senturk S, Karaca E, Karakülah G, Erkek-Ozhan S. Differential Occupancy and Regulatory Interactions of KDM6A in Bladder Cell Lines. Cells 2023; 12:cells12060836. [PMID: 36980177 PMCID: PMC10047809 DOI: 10.3390/cells12060836] [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: 12/19/2022] [Revised: 02/16/2023] [Accepted: 03/01/2023] [Indexed: 03/30/2023] Open
Abstract
Epigenetic deregulation is a critical theme which needs further investigation in bladder cancer research. One of the most highly mutated genes in bladder cancer is KDM6A, which functions as an H3K27 demethylase and is one of the MLL3/4 complexes. To decipher the role of KDM6A in normal versus tumor settings, we identified the genomic landscape of KDM6A in normal, immortalized, and cancerous bladder cells. Our results showed differential KDM6A occupancy in the genes involved in cell differentiation, chromatin organization, and Notch signaling depending on the cell type and the mutation status of KDM6A. Transcription factor motif analysis revealed HES1 to be enriched at KDM6A peaks identified in the T24 bladder cancer cell line; moreover, it has a truncating mutation in KDM6A and lacks a demethylase domain. Our co-immunoprecipitation experiments revealed TLE co-repressors and HES1 as potential truncated and wild-type KDM6A interactors. With the aid of structural modeling, we explored how truncated KDM6A could interact with TLE and HES1, as well as RUNX and HHEX transcription factors. These structures provide a solid means of studying the functions of KDM6A independently of its demethylase activity. Collectively, our work provides important contributions to the understanding of KDM6A malfunction in bladder cancer.
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Affiliation(s)
| | - Busra Savas
- Izmir Biomedicine and Genome Center, Inciralti, 35340 Izmir, Turkey
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Inciralti, 35340 Izmir, Turkey
| | - Ahmet Bursalı
- Izmir Biomedicine and Genome Center, Inciralti, 35340 Izmir, Turkey
| | - Aleyna Eray
- Izmir Biomedicine and Genome Center, Inciralti, 35340 Izmir, Turkey
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Inciralti, 35340 Izmir, Turkey
| | - Alirıza Arıbaş
- Izmir Biomedicine and Genome Center, Inciralti, 35340 Izmir, Turkey
| | - Serif Senturk
- Izmir Biomedicine and Genome Center, Inciralti, 35340 Izmir, Turkey
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Inciralti, 35340 Izmir, Turkey
| | - Ezgi Karaca
- Izmir Biomedicine and Genome Center, Inciralti, 35340 Izmir, Turkey
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Inciralti, 35340 Izmir, Turkey
| | - Gökhan Karakülah
- Izmir Biomedicine and Genome Center, Inciralti, 35340 Izmir, Turkey
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Inciralti, 35340 Izmir, Turkey
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Chen J, Wang L, Liu M, Gao G, Zhao W, Fu Q, Wang Y. Implantation of adipose-derived mesenchymal stem cell sheets promotes axonal regeneration and restores bladder function after spinal cord injury. Stem Cell Res Ther 2022; 13:503. [PMID: 36224621 PMCID: PMC9558366 DOI: 10.1186/s13287-022-03188-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Accepted: 09/30/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Cell-based therapy using adipose-derived mesenchymal stem cells (ADSCs) is a promising treatment strategy for neurogenic bladder (NB) associated with spinal cord injury (SCI). However, therapeutic efficacy is low because of inefficient cell delivery. Cell sheets improve the efficacy of cell transplantation. Therefore, this study was conducted to investigate the therapeutic efficacy of transplanting ADSC sheets into an SCI rat model and focused on the function and pathological changes of the bladder. METHODS ADSC sheets were prepared from adipose tissue of Sprague-Dawley (SD) rats using temperature-responsive cell culture dishes. Adult female SD rats were subjected to SCI by transection at the T10 level and administered ADSC sheets or gelatin sponge (the control group). Four and 8 weeks later, in vivo cystometrograms were obtained for voiding function assessment. Rats were sacrificed and the expression of various markers was analyzed in spinal and bladder tissues. RESULTS The number of β-tubulin III-positive axons in the ADSC sheet transplantation group was higher than that in the control group. Conversely, expression of glial fibrillary acidic protein in the ADSC sheet transplantation group was lower than that in the control group. Cystometry showed impairment of the voiding function after SCI, which was improved after ADSC sheet transplantation with increased high-frequency oscillation activity. Furthermore, ADSC sheet transplantation prevented disruption of the bladder urothelium in SCI rats, thereby maintaining the intact barrier. Compared with fibrosis of the bladder wall in the control group, the ADSC sheet transplantation group had normal morphology of the bladder wall and reduced tissue fibrosis as shown by downregulation of type 1 collagen. ADSC sheet transplantation also resulted in strong upregulation of contractile smooth muscle cell (SMC) markers (α-smooth muscle actin and smoothelin) and downregulation of synthetic SMC markers (MYH10 and RBP1). CONCLUSION ADSC sheet transplantation significantly improved voiding function recovery in rats after SCI. ADSC sheet transplantation is a promising cell delivery and treatment option for NB related to SCI.
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Affiliation(s)
- Jiasheng Chen
- Department of Urology, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai Eastern Institute of Urologic Reconstruction, Shanghai Jiao Tong University, Shanghai, China
| | - Lin Wang
- Department of Urology, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai Eastern Institute of Urologic Reconstruction, Shanghai Jiao Tong University, Shanghai, China
| | - Meng Liu
- Department of Urology, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai Eastern Institute of Urologic Reconstruction, Shanghai Jiao Tong University, Shanghai, China
| | - Guo Gao
- Key Laboratory for Thin Film and Micro Fabrication of the Ministry of Education, School of Sensing Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Weixin Zhao
- Wake Forest Institute for Regenerative Medicine, Winston Salem, NC, USA
| | - Qiang Fu
- Department of Urology, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai Eastern Institute of Urologic Reconstruction, Shanghai Jiao Tong University, Shanghai, China.
| | - Ying Wang
- Department of Urology, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai Eastern Institute of Urologic Reconstruction, Shanghai Jiao Tong University, Shanghai, China.
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Jackson AR, Narla ST, Bates CM, Becknell B. Urothelial progenitors in development and repair. Pediatr Nephrol 2022; 37:1721-1731. [PMID: 34471946 PMCID: PMC8942604 DOI: 10.1007/s00467-021-05239-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Revised: 07/12/2021] [Accepted: 07/13/2021] [Indexed: 10/20/2022]
Abstract
Urothelium is a specialized multilayer epithelium that lines the urinary tract from the proximal urethra to the kidney. In addition to proliferation and differentiation during development, urothelial injury postnatally triggers a robust regenerative capacity to restore the protective barrier between the urine and tissue. Mounting evidence supports the existence of dedicated progenitor cell populations that give rise to urothelium during development and in response to injury. Understanding the cellular and molecular basis for urothelial patterning and repair will inform tissue regeneration therapies designed to ameliorate a number of structural and functional defects of the urinary tract. Here, we review the current understanding of urothelial progenitors and the signaling pathways that govern urothelial development and repair. While most published studies have focused on bladder urothelium, we also discuss literature on upper tract urothelial progenitors. Furthermore, we discuss evidence supporting existence of context-specific progenitors. This knowledge is fundamental to the development of strategies to regenerate or engineer damaged or diseased urothelium.
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Affiliation(s)
- Ashley R Jackson
- Center for Clinical and Translational Research, The Abigail Wexner Research Institute At Nationwide Children's Hospital, 700 Children's Drive, W308, Columbus, 43205, OH, USA
- Department of Pediatrics, Ohio State University College of Medicine, Columbus, OH, USA
- Division of Nephrology and Hypertension, Nationwide Children's Hospital, Columbus, OH, USA
| | - Sridhar T Narla
- Department of Pediatrics, Division of Nephrology, University of Pittsburgh School of Medicine, Rangos Research Building, 4401 Penn Avenue, Pittsburgh, 15224, PA, USA
| | - Carlton M Bates
- Department of Pediatrics, Division of Nephrology, University of Pittsburgh School of Medicine, Rangos Research Building, 4401 Penn Avenue, Pittsburgh, 15224, PA, USA.
- Division of Nephrology, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, USA.
| | - Brian Becknell
- Center for Clinical and Translational Research, The Abigail Wexner Research Institute At Nationwide Children's Hospital, 700 Children's Drive, W308, Columbus, 43205, OH, USA.
- Department of Pediatrics, Ohio State University College of Medicine, Columbus, OH, USA.
- Division of Nephrology and Hypertension, Nationwide Children's Hospital, Columbus, OH, USA.
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Wiessner GB, Plumber SA, Xiang T, Mendelsohn CL. Development, regeneration and tumorigenesis of the urothelium. Development 2022; 149:dev198184. [PMID: 35521701 PMCID: PMC10656457 DOI: 10.1242/dev.198184] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The urothelium of the bladder functions as a waterproof barrier between tissue and outflowing urine. Largely quiescent during homeostasis, this unique epithelium rapidly regenerates in response to bacterial or chemical injury. The specification of the proper cell types during development and injury repair is crucial for tissue function. This Review surveys the current understanding of urothelial progenitor populations in the contexts of organogenesis, regeneration and tumorigenesis. Furthermore, we discuss pathways and signaling mechanisms involved in urothelial differentiation, and consider the relevance of this knowledge to stem cell biology and tissue regeneration.
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Affiliation(s)
- Gregory B. Wiessner
- Departments of Urology, Genetics and Development, Pathology and Cell Biology, Columbia Stem Cell Initiative and Institute of Human Nutrition, Columbia University, New York, NY 10032, USA
- Institute of Human Nutrition, Columbia University, New York, NY 10032, USA
| | - Sakina A. Plumber
- Departments of Urology, Genetics and Development, Pathology and Cell Biology, Columbia Stem Cell Initiative and Institute of Human Nutrition, Columbia University, New York, NY 10032, USA
| | - Tina Xiang
- Departments of Urology, Genetics and Development, Pathology and Cell Biology, Columbia Stem Cell Initiative and Institute of Human Nutrition, Columbia University, New York, NY 10032, USA
| | - Cathy L. Mendelsohn
- Departments of Urology, Genetics and Development, Pathology and Cell Biology, Columbia Stem Cell Initiative and Institute of Human Nutrition, Columbia University, New York, NY 10032, USA
- Institute of Human Nutrition, Columbia University, New York, NY 10032, USA
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Kanaki Z, Voutsina A, Markou A, Pateras IS, Potaris K, Avgeris M, Makrythanasis P, Athanasiadis EI, Vamvakaris I, Patsea E, Vachlas K, Lianidou E, Georgoulias V, Kotsakis A, Klinakis A. Generation of Non-Small Cell Lung Cancer Patient-Derived Xenografts to Study Intratumor Heterogeneity. Cancers (Basel) 2021; 13:cancers13102446. [PMID: 34070013 PMCID: PMC8157865 DOI: 10.3390/cancers13102446] [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: 04/05/2021] [Revised: 05/12/2021] [Accepted: 05/13/2021] [Indexed: 12/25/2022] Open
Abstract
Simple Summary It is widely thought that tumors are composed of different subpopulations of cancer cells carrying genetic alterations with some of them being common among all cells while others are unique for each subpopulation. This variable genetic profile of tumor cells is a component of what is collectively described as intratumor heterogeneity (ITH). Surviving the immune system and therapies, and establishing metastases are forces of natural selection that act upon ITH and drive tumor evolution and, eventually, the clinical presentation of patients. The aim of this prospective study was to investigate ITH in early-stage operable non-small cell lung cancer. We directly grafted human tumors in immunosuppressed mice and compared the genetic profile of the tumors grown in mice with that of the original human tumors. We identified clinical factors that affected the ability of human tumors to grow as mouse xenografts. Abstract Recent advances in sequencing technologies have allowed the in-depth molecular study of tumors, even at the single cell level. Sequencing efforts have uncovered a previously unappreciated heterogeneity among tumor cells, which has been postulated to be the driving force of tumor evolution and to facilitate recurrence, metastasis, and drug resistance. In the current study, focused on early-stage operable non-small cell lung cancer, we used tumor growth in patient-derived xenograft (PDX) models in mice as a fast-forward tumor evolution process to investigate the molecular characteristics of tumor cells that grow in mice, as well as the parameters that affect the grafting efficiency. We found that squamous cell carcinomas grafted significantly more efficiently compared with adenocarcinomas. Advanced stage, patient age and primary tumor size were positively correlated with grafting. Additionally, we isolated and characterized circulating tumor cells (CTC) from patients’ peripheral blood and found that the presence of CTCs expressing epithelial-to-mesenchymal (EMT) markers correlated with the grafting potential. Interestingly, exome sequencing of the PDX tumor identified genetic alterations in DNA repair and genome integrity genes that were under-represented in the human primary counterpart. In conclusion, through the generation of a PDX biobank of NSCLC, we identified the clinical and molecular properties of tumors that affected growth in mice.
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Affiliation(s)
- Zoi Kanaki
- Center for Basic Research, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece; (Z.K.); (A.V.); (P.M.)
| | - Alexandra Voutsina
- Center for Basic Research, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece; (Z.K.); (A.V.); (P.M.)
| | - Athina Markou
- Analysis of Circulating Tumor Cells Lab, Lab of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, 15771 Athens, Greece; (A.M.); (E.L.)
| | - Ioannis S. Pateras
- Department of Histology and Embryology, School of Medicine, National and Kapodistrian University of Athens, 11527 Athens, Greece;
| | - Konstantinos Potaris
- Department of Thoracic Surgery, Sotiria Hospital for Chest Diseases, 11527 Athens, Greece; (K.P.); (K.V.)
| | - Margaritis Avgeris
- Laboratory of Clinical Biochemistry–Molecular Diagnostics, Second Department of Pediatrics, School of Medicine, National and Kapodistrian University of Athens, “P. & A. Kyriakou” Children’s Hospital, 11527 Athens, Greece;
| | - Periklis Makrythanasis
- Center for Basic Research, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece; (Z.K.); (A.V.); (P.M.)
| | | | - Ioannis Vamvakaris
- Pathology Department, Athens Chest Hospital “Sotiria”, 11527 Athens, Greece;
| | - Eleni Patsea
- Department of Pathology, Metropolitan Hospital, 18547 Cholargos, Greece;
| | - Konstantinos Vachlas
- Department of Thoracic Surgery, Sotiria Hospital for Chest Diseases, 11527 Athens, Greece; (K.P.); (K.V.)
| | - Evi Lianidou
- Analysis of Circulating Tumor Cells Lab, Lab of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, 15771 Athens, Greece; (A.M.); (E.L.)
| | | | - Athanasios Kotsakis
- Department of Medical Oncology, General University Hospital of Larissa, 41110 Larissa, Greece;
| | - Apostolos Klinakis
- Center for Basic Research, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece; (Z.K.); (A.V.); (P.M.)
- Correspondence:
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Ferreira A, Aster JC. Notch signaling in cancer: Complexity and challenges on the path to clinical translation. Semin Cancer Biol 2021; 85:95-106. [PMID: 33862222 DOI: 10.1016/j.semcancer.2021.04.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Revised: 03/29/2021] [Accepted: 04/11/2021] [Indexed: 12/22/2022]
Abstract
Notch receptors participate in a conserved pathway in which ligands expressed on neighboring cells trigger a series of proteolytic cleavages that allow the intracellular portion of the receptor to travel to the nucleus and form a short-lived transcription complex that turns on target gene expression. The directness and seeming simplicity of this signaling mechanism belies the complexity of the outcomes of Notch signaling in normal cells, which are highly context and dosage dependent. This complexity is reflected in the diverse roles of Notch in cancers of various types, in which Notch may be oncogenic or tumor suppressive and may have a wide spectrum of effects on tumor cells and stromal elements. This review provides an overview of the roles of Notch in cancer and discusses challenges to clinical translation of Notch targeting agents as well as approaches that may overcome these hurdles.
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Affiliation(s)
- Antonio Ferreira
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, 75 Francis Street, Boston, MA, 02115, United States
| | - Jon C Aster
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, 75 Francis Street, Boston, MA, 02115, United States.
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