1
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Guo CC, Lee S, Lee JG, Chen H, Zaleski M, Choi W, McConkey DJ, Wei P, Czerniak B. Molecular profile of bladder cancer progression to clinically aggressive subtypes. Nat Rev Urol 2024; 21:391-405. [PMID: 38321289 DOI: 10.1038/s41585-023-00847-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/15/2023] [Indexed: 02/08/2024]
Abstract
Bladder cancer is a histologically and clinically heterogenous disease. Most bladder cancers are urothelial carcinomas, which frequently develop distinct histological subtypes. Several urothelial carcinoma histological subtypes, such as micropapillary, plasmacytoid, small-cell carcinoma and sarcomatoid, show highly aggressive behaviour and pose unique challenges in diagnosis and treatment. Comprehensive genomic characterizations of the urothelial carcinoma subtypes have revealed that they probably arise from a precursor subset of conventional urothelial carcinomas that belong to different molecular subtypes - micropapillary and plasmacytoid subtypes develop along the luminal pathway, whereas small-cell and sarcomatoid subtypes evolve along the basal pathway. The subtypes exhibit distinct genomic alterations, but in most cases their biological properties seem to be primarily determined by specific gene expression profiles, including epithelial-mesenchymal transition, urothelial-to-neural lineage plasticity, and immune infiltration with distinct upregulation of immune regulatory genes. These breakthrough studies have transformed our view of bladder cancer histological subtype biology, generated new hypotheses for therapy and chemoresistance, and facilitated the discovery of new therapeutic targets.
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Affiliation(s)
- Charles C Guo
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sangkyou Lee
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - June G Lee
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Huiqin Chen
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Michael Zaleski
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Woonyoung Choi
- Johns Hopkins Greenberg Bladder Cancer Institute, Johns Hopkins University, Baltimore, MD, USA
| | - David J McConkey
- Johns Hopkins Greenberg Bladder Cancer Institute, Johns Hopkins University, Baltimore, MD, USA
| | - Peng Wei
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Bogdan Czerniak
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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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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Bejrananda T, Saetang J, Sangkhathat S. Molecular Subtyping in Muscle-Invasive Bladder Cancer on Predicting Survival and Response of Treatment. Biomedicines 2022; 11:biomedicines11010069. [PMID: 36672577 PMCID: PMC9856180 DOI: 10.3390/biomedicines11010069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 12/19/2022] [Accepted: 12/21/2022] [Indexed: 12/29/2022] Open
Abstract
Molecular classifications for urothelial bladder cancer appear to be promising in disease prognostication and prediction. This study investigated the novel molecular subtypes of muscle invasive bladder cancer (MIBC). Tumor samples and normal tissues of MIBC patients were submitted for transcriptome sequencing. Expression profiles were clustered using K-means clustering and principal component analysis. The molecular subtypes were also applied to The Cancer Genome Atlas (TCGA) dataset and analyzed for clinical outcome correlation. Three molecular subtypes of MIBC were discovered, clusters A, B, and C. The most differentially upregulated genes in cluster A were BDKRB1, EDNRA, AVPR1A, PDGFRB, and TNC, while the most upregulated genes in cluster C were collagen-related genes, PDGFRB, and PRKG1. For cluster B, COL6A3, COL1A2, COL6A2, tenascin C, and fibroblast growth factor 2 were statistically suppressed. When the centroids of clustering on PCA were applied to TCGA data, the clustering significantly predicted survival outcomes. Cluster B had the best overall survival (OS), and cluster C was associated with poor OS but exhibited the best response to perioperative chemotherapy. Among all groups, cluster B had a better pathologic response to neoadjuvant chemotherapy (40%). Based on the results of the present study, the novel clusters of subtype MIBC appear potentially suitable for integration into clinical practice.
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Affiliation(s)
- Tanan Bejrananda
- Department of Surgery, Faculty of Medicine, Prince of Songkla University, Songkhla 90110, Thailand
| | - Jirakrit Saetang
- Department of Surgery, Faculty of Medicine, Prince of Songkla University, Songkhla 90110, Thailand
- International Center of Excellence in Seafood Science and Innovation, Faculty of Agro-Industry, Prince of Songkla University, Songkhla 90112, Thailand
| | - Surasak Sangkhathat
- Department of Surgery, Faculty of Medicine, Prince of Songkla University, Songkhla 90110, Thailand
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Songkhla 90110, Thailand
- Translational Medicine Research Center, Faculty of Medicine, Prince of Songkla University, Songkhla 90110, Thailand
- Correspondence:
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4
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Yu W, Yang MK, Sung DJ, Park TJ, Kim M, Ntigura E, Kim SH, Kim B, Park SW, Bae YM. Differential expression profiles of miRNA in the serum of sarcopenic rats. Biochem Biophys Rep 2022; 30:101251. [PMID: 35313645 PMCID: PMC8933690 DOI: 10.1016/j.bbrep.2022.101251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 03/07/2022] [Accepted: 03/12/2022] [Indexed: 11/30/2022] Open
Abstract
As the geriatric population and life expectancy increase, the interest in preventing geriatric diseases, such as sarcopenia, is increasing. However, the causes of sarcopenia are unclear, and current diagnostic methods for sarcopenia are unreliable. We hypothesized that the changes in the expression of certain miRNAs may be associated with the pathophysiology of sarcopenia. Herein, we analyzed the miRNA expression profiles in the blood of young (3-months-old) healthy rats, old sarcopenic (17-months-old) rats, and age-matched (17-months-old) control rats. The changes in miRNA expression levels were analyzed using Bowtie 2 software. A total of 523 miRNAs were detected in the rat serum. Using scatter plots and clustering heatmap data, we found 130 miRNAs that were differentially expressed in sarcopenic rats (>2-fold change) compared to the expression in young healthy and age-matched control rats. With a threshold of >5-fold change, we identified 14 upregulated miRNAs, including rno-miR-133b-3p, rno-miR-133a-3p, rno-miR-133c, rno-miR-208a-3p, and rno-miR434-5p among others in the serum of sarcopenic rats. A protein network map based on these 14 miRNAs identified the genes involved in skeletal muscle differentiation, among which Notch1, Egr2, and Myocd represented major nodes. The data obtained in this study are potentially useful for the early diagnosis of sarcopenia and for the identification of novel therapeutic targets for the treatment and/or prevention of sarcopenia. Early diagnosis of sarcopenia and discovery of therapeutic targets are necessary. We determined the significantly increased miRNAs in the serum of sarcopenic rats. They include rno-miR-133b-3p, 133a-3p, 133c, 208a-3p, and miR434-5p. Network mapping from the miRNA expression profiles helps identify target proteins. Notch, Egr, and Myocd genes were suggested as targets for sarcopenia treatment.
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Affiliation(s)
- Wonjong Yu
- Department of Physical Therapy, Eulji University, South Korea
| | - Min-kyu Yang
- Department of Physiology, KU Open Innovation Center, Research Institute of Medical Science, Konkuk University School of Medicine, Chungju, South Korea
| | - Dong Jun Sung
- Department of Sport and Health Studies, College of Biomedical and Health Science, Konkuk University, Chungju, Republic of Korea
| | - Tae Jun Park
- Department of Physiology, KU Open Innovation Center, Research Institute of Medical Science, Konkuk University School of Medicine, Chungju, South Korea
| | - Myungchul Kim
- Department of Physical Therapy, Eulji University, South Korea
| | - Eustache Ntigura
- Department of Physiology, KU Open Innovation Center, Research Institute of Medical Science, Konkuk University School of Medicine, Chungju, South Korea
- Department of Preventive and Community Dentistry, School of Dentistry, College of Medicine and Health Sciences, University of Rwanda, Kigali, Rwanda
| | - Sung Hea Kim
- Department of Cardiology, Konkuk University School of Medicine, Seoul, South Korea
| | - Bokyung Kim
- Department of Physiology, KU Open Innovation Center, Research Institute of Medical Science, Konkuk University School of Medicine, Chungju, South Korea
| | - Sang Woong Park
- Department of Emergency Medical Services, Eulji University, South Korea
- Corresponding author.
| | - Young Min Bae
- Department of Physiology, KU Open Innovation Center, Research Institute of Medical Science, Konkuk University School of Medicine, Chungju, South Korea
- Corresponding author.
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5
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Lokeshwar SD, Lopez M, Sarcan S, Aguilar K, Morera DS, Shaheen DM, Lokeshwar BL, Lokeshwar VB. Molecular Oncology of Bladder Cancer from Inception to Modern Perspective. Cancers (Basel) 2022; 14:cancers14112578. [PMID: 35681556 PMCID: PMC9179261 DOI: 10.3390/cancers14112578] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 05/19/2022] [Accepted: 05/20/2022] [Indexed: 02/05/2023] Open
Abstract
Within the last forty years, seminal contributions have been made in the areas of bladder cancer (BC) biology, driver genes, molecular profiling, biomarkers, and therapeutic targets for improving personalized patient care. This overview includes seminal discoveries and advances in the molecular oncology of BC. Starting with the concept of divergent molecular pathways for the development of low- and high-grade bladder tumors, field cancerization versus clonality of bladder tumors, cancer driver genes/mutations, genetic polymorphisms, and bacillus Calmette-Guérin (BCG) as an early form of immunotherapy are some of the conceptual contributions towards improving patient care. Although beginning with a promise of predicting prognosis and individualizing treatments, "-omic" approaches and molecular subtypes have revealed the importance of BC stem cells, lineage plasticity, and intra-tumor heterogeneity as the next frontiers for realizing individualized patient care. Along with urine as the optimal non-invasive liquid biopsy, BC is at the forefront of the biomarker field. If the goal is to reduce the number of cystoscopies but not to replace them for monitoring recurrence and asymptomatic microscopic hematuria, a BC marker may reach clinical acceptance. As advances in the molecular oncology of BC continue, the next twenty-five years should significantly advance personalized care for BC patients.
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Affiliation(s)
- Soum D. Lokeshwar
- Department of Urology, Yale University School of Medicine, New Haven, CT 06520, USA;
| | - Maite Lopez
- Departments of Biochemistry and Molecular Biology, Medical College of Georgia, Augusta University, 1410 Laney Walker Blvd., Augusta, GA 30912, USA; (M.L.); (S.S.); (K.A.); (D.S.M.)
| | - Semih Sarcan
- Departments of Biochemistry and Molecular Biology, Medical College of Georgia, Augusta University, 1410 Laney Walker Blvd., Augusta, GA 30912, USA; (M.L.); (S.S.); (K.A.); (D.S.M.)
- Department of Urology, University Hospital Schleswig-Holstein, Campus Lübeck, 23562 Lübeck, Germany
| | - Karina Aguilar
- Departments of Biochemistry and Molecular Biology, Medical College of Georgia, Augusta University, 1410 Laney Walker Blvd., Augusta, GA 30912, USA; (M.L.); (S.S.); (K.A.); (D.S.M.)
| | - Daley S. Morera
- Departments of Biochemistry and Molecular Biology, Medical College of Georgia, Augusta University, 1410 Laney Walker Blvd., Augusta, GA 30912, USA; (M.L.); (S.S.); (K.A.); (D.S.M.)
| | - Devin M. Shaheen
- Yale School of Nursing, Yale University, New Haven, CT 06520, USA;
| | - Bal L. Lokeshwar
- Georgia Cancer Center, Medical College of Georgia, Augusta University, 1410 Laney Walker Blvd., Augusta, GA 30912, USA
- Research Service, Charlie Norwood VA Medical Center, Augusta, GA 30904, USA
- Correspondence: (B.L.L.); (V.B.L.)
| | - Vinata B. Lokeshwar
- Departments of Biochemistry and Molecular Biology, Medical College of Georgia, Augusta University, 1410 Laney Walker Blvd., Augusta, GA 30912, USA; (M.L.); (S.S.); (K.A.); (D.S.M.)
- Correspondence: (B.L.L.); (V.B.L.)
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6
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Feng C, Pan L, Tang S, He L, Wang X, Tao Y, Xie Y, Lai Z, Tang Z, Wang Q, Li T. Integrative Transcriptomic, Lipidomic, and Metabolomic Analysis Reveals Potential Biomarkers of Basal and Luminal Muscle Invasive Bladder Cancer Subtypes. Front Genet 2021; 12:695662. [PMID: 34484294 PMCID: PMC8415304 DOI: 10.3389/fgene.2021.695662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 06/29/2021] [Indexed: 12/24/2022] Open
Abstract
Muscle invasive bladder cancer (MIBC) is a heterogeneous disease with a high recurrence rate and poor clinical outcomes. Molecular subtype provides a new framework for the study of MIBC heterogeneity. Clinically, MIBC can be classified as basal and luminal subtypes; they display different clinical and pathological characteristics, but the molecular mechanism is still unclear. Lipidomic and metabolomic molecules have recently been considered to play an important role in the genesis and development of tumors, especially as potential biomarkers. Their different expression profiles in basal and luminal subtypes provide clues for the molecular mechanism of basal and luminal subtypes and the discovery of new biomarkers. Herein, we stratified MIBC patients into basal and luminal subtypes using a MIBC classifier based on transcriptome expression profiles. We qualitatively and quantitatively analyzed the lipids and metabolites of basal and luminal MIBC subtypes and identified their differential lipid and metabolite profiles. Our results suggest that free fatty acids (FFAs) and sulfatides (SLs), which are closely associated with immune and stromal cell types, can contribute to the diagnosis of basal and luminal subtypes of MIBC. Moreover, we showed that glycerophosphocholine (GCP)/imidazoles and nucleosides/imidazoles ratios can accurately distinguish the basal and luminal tumors. Overall, by integrating transcriptomic, lipidomic, and metabolomic data, our study reveals specific biomarkers to differentially diagnose basal and luminal MIBC subtypes and may provide a basis for precision therapy of MIBC.
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Affiliation(s)
- Chao Feng
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Nanning, China.,Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Nanning, China.,Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Guangxi Medical University, Nanning, China
| | - Lixin Pan
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Nanning, China.,Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Nanning, China.,Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Guangxi Medical University, Nanning, China
| | - Shaomei Tang
- Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Nanning, China.,Department of Gastroenterology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Liangyu He
- Institute of Urology and Nephrology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China.,Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Nanning, China.,Department of Urology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China.,Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Nanning, China
| | - Xi Wang
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Nanning, China.,Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Nanning, China
| | - Yuting Tao
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Nanning, China.,Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Nanning, China.,Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Guangxi Medical University, Nanning, China
| | - Yuanliang Xie
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Nanning, China.,Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Nanning, China.,Department of Urology, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, China
| | - Zhiyong Lai
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Nanning, China.,Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Nanning, China
| | - Zhong Tang
- School of Information and Management, Guangxi Medical University, Nanning, China
| | - Qiuyan Wang
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Nanning, China.,Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Nanning, China
| | - Tianyu Li
- Institute of Urology and Nephrology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China.,Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Nanning, China.,Department of Urology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China.,Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Nanning, China
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7
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Khan MT, Irlam-Jones JJ, Pereira RR, Lane B, Valentine HR, Aragaki K, Dyrskjøt L, McConkey DJ, Hoskin PJ, Choudhury A, West CML. A miRNA signature predicts benefit from addition of hypoxia-modifying therapy to radiation treatment in invasive bladder cancer. Br J Cancer 2021; 125:85-93. [PMID: 33846523 PMCID: PMC8257670 DOI: 10.1038/s41416-021-01326-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 02/11/2021] [Accepted: 02/19/2021] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND miRNAs are promising biomarkers in oncology as their small size makes them less susceptible to degradation than mRNA in FFPE tissue. We aimed to derive a hypoxia-associated miRNA signature for bladder cancer. METHODS Taqman miRNA array cards identified miRNA seed genes induced under hypoxia in bladder cancer cell lines. A signature was derived using feature selection methods in a TCGA BLCA training data set. miRNA expression data were generated for 190 tumours from the BCON Phase 3 trial and used for independent validation. RESULTS A 14-miRNA hypoxia signature was derived, which was prognostic for poorer overall survival in the TCGA BLCA cohort (n = 403, p = 0.001). Univariable analysis showed that the miRNA signature predicted an overall survival benefit from having carbogen-nicotinamide with radiotherapy (HR = 0.30, 95% CI 0.094-0.95, p = 0.030) and performed similarly to a 24-gene mRNA signature (HR = 0.47, 95% CI 0.24-0.92, p = 0.025). Combining the signatures improved performance (HR = 0.26, 95% CI 0.08-0.82, p = 0.014) with borderline significance for an interaction test (p = 0.065). The interaction test was significant for local relapse-free survival LRFS (p = 0.033). CONCLUSION A 14-miRNA hypoxia signature can be used with an mRNA hypoxia signature to identify bladder cancer patients benefitting most from having carbogen and nicotinamide with radiotherapy.
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Affiliation(s)
- Mairah T. Khan
- grid.5379.80000000121662407Translational Radiobiology Group, Division of Cancer Sciences, University of Manchester, Manchester Academic Health Science Centre, Christie NHS Foundation Trust Hospital, Manchester, UK
| | - Joely J. Irlam-Jones
- grid.5379.80000000121662407Translational Radiobiology Group, Division of Cancer Sciences, University of Manchester, Manchester Academic Health Science Centre, Christie NHS Foundation Trust Hospital, Manchester, UK
| | - Ronnie Rodrigues Pereira
- grid.5379.80000000121662407Translational Oncogenomics, Cancer Research UK Manchester Institute, Oglesby Cancer Research Building, University of Manchester, Manchester, UK
| | - Brian Lane
- grid.5379.80000000121662407Translational Radiobiology Group, Division of Cancer Sciences, University of Manchester, Manchester Academic Health Science Centre, Christie NHS Foundation Trust Hospital, Manchester, UK
| | - Helen R. Valentine
- grid.5379.80000000121662407Translational Radiobiology Group, Division of Cancer Sciences, University of Manchester, Manchester Academic Health Science Centre, Christie NHS Foundation Trust Hospital, Manchester, UK
| | - Kai Aragaki
- grid.21107.350000 0001 2171 9311Greenberg Bladder Cancer Institute, Johns Hopkins University, Baltimore, MD USA
| | - Lars Dyrskjøt
- grid.154185.c0000 0004 0512 597XDepartment of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark ,grid.7048.b0000 0001 1956 2722Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - David J. McConkey
- grid.21107.350000 0001 2171 9311Greenberg Bladder Cancer Institute, Johns Hopkins University, Baltimore, MD USA
| | - Peter J. Hoskin
- grid.5379.80000000121662407Translational Radiobiology Group, Division of Cancer Sciences, University of Manchester, Manchester Academic Health Science Centre, Christie NHS Foundation Trust Hospital, Manchester, UK
| | - Ananya Choudhury
- grid.5379.80000000121662407Translational Radiobiology Group, Division of Cancer Sciences, University of Manchester, Manchester Academic Health Science Centre, Christie NHS Foundation Trust Hospital, Manchester, UK
| | - Catharine M. L. West
- grid.5379.80000000121662407Translational Radiobiology Group, Division of Cancer Sciences, University of Manchester, Manchester Academic Health Science Centre, Christie NHS Foundation Trust Hospital, Manchester, UK
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8
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Measurements Methods for the Development of MicroRNA-Based Tests for Cancer Diagnosis. Int J Mol Sci 2021; 22:ijms22031176. [PMID: 33503982 PMCID: PMC7865473 DOI: 10.3390/ijms22031176] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 01/15/2021] [Accepted: 01/22/2021] [Indexed: 12/19/2022] Open
Abstract
Studies investigating microRNAs as potential biomarkers for cancer, immune-related diseases, or cardiac pathogenic diseases, among others, have exponentially increased in the last years. In particular, altered expression of specific miRNAs correlates with the occurrence of several diseases, making these molecules potential molecular tools for non-invasive diagnosis, prognosis, and response to therapy. Nonetheless, microRNAs are not in clinical use yet, due to inconsistencies in the literature regarding the specific miRNAs identified as biomarkers for a specific disease, which in turn can be attributed to several reasons, including lack of assay standardization and reproducibility. Technological limitations in circulating microRNAs measurement have been, to date, the biggest challenge for using these molecules in clinical settings. In this review we will discuss pre-analytical, analytical, and post-analytical challenges to address the potential technical biases and patient-related parameters that can have an influence and should be improved to translate miRNA biomarkers to the clinical stage. Moreover, we will describe the currently available methods for circulating miRNA expression profiling and measurement, underlining their advantages and potential pitfalls.
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9
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Choi H, Park JY, Bae JH, Tae BS. Current perspectives on novel systemic therapeutic agents beyond immune checkpoint inhibition in metastatic urothelial carcinoma. Transl Cancer Res 2020; 9:6583-6588. [PMID: 35117268 PMCID: PMC8799034 DOI: 10.21037/tcr-20-1262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 04/23/2020] [Indexed: 11/13/2022]
Abstract
Treatment strategies for metastatic urothelial carcinoma (mUC) have evolved dramatically over the last decade. The emergence of immunotherapeutic agents, especially immune checkpoint inhibitors, has been the most significant development. Immunotherapy increased the overall survival rate of patients with mUC and provided a durable response. The success of immune checkpoint inhibitors further led to the development of novel agents that regulate the immune system within the tumor microenvironment. However, despite some success with immune checkpoint inhibitors, researchers are still developing new agents, including small molecule tyrosine kinase inhibitors, mammalian target of rapamycin (mTOR) inhibitors, and novel fusion proteins, tailored for targets other than immune checkpoint inhibitors. Novel treatment strategies are being developed rapidly with ongoing pre-clinical trials. Here, we outline promising new therapies that are expected to improve survival rates for patients with mUC.
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Affiliation(s)
- Hoon Choi
- Department of Urology, Korea University Medical Center, Korea University School of Medicine, Ansan 15355, Korea
| | - Jae Young Park
- Department of Urology, Korea University Medical Center, Korea University School of Medicine, Ansan 15355, Korea
| | - Jae Hyun Bae
- Department of Urology, Korea University Medical Center, Korea University School of Medicine, Ansan 15355, Korea
| | - Bum Sik Tae
- Department of Urology, Korea University Medical Center, Korea University School of Medicine, Ansan 15355, Korea
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10
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Ottley EC, Pell R, Brazier B, Hollidge J, Kartsonaki C, Browning L, O'Neill E, Kiltie AE. Greater utility of molecular subtype rather than epithelial-to-mesenchymal transition (EMT) markers for prognosis in high-risk non-muscle-invasive (HGT1) bladder cancer. J Pathol Clin Res 2020; 6:238-251. [PMID: 32374509 PMCID: PMC7578305 DOI: 10.1002/cjp2.167] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 03/10/2020] [Accepted: 03/20/2020] [Indexed: 01/21/2023]
Abstract
Approximately 75% of bladder cancers are non-muscle invasive (NMIBC). Of these, up to 53% of cases progress to life-threatening muscle-invasive bladder cancer (MIBC). Patients with high-grade stage T1 (HGT1) NMIBC frequently undergo radical cystectomy (RC), although this represents overtreatment for many. Identification of progressors versus non-progressors could spare unnecessary treatment. Recent studies have confirmed that urothelial carcinoma is composed of two main molecular subtypes, basal and luminal, with 12% of basal tumours exhibiting epithelial-to-mesenchymal transition (EMT). Levels of immune cell infiltration have been shown to be subtype-specific. Here, we performed immunohistochemistry (IHC) for 11 antibodies relating to molecular subtypes or EMT in 26 cases of HGT1 urothelial carcinoma cases with 6 matched samples subsequently obtained at cystectomy (n = 6; 1 muscle-invasive, 5 non-muscle-invasive; 3 = pTis, 1 = pT1, 1 = pTa) and at recurrence (n = 2, pT2). RNAScope was also conducted in a subset. Expression patterns in HGT1 specimens versus MIBC (pT2+) were examined, and correlated with disease-specific survival (DSS). Levels of stromal tumour-infiltrating lymphocytes (sTILs) were assessed manually to determine whether lymphocyte infiltration was associated with DSS and whether differences existed between HGT1 and MIBC. Molecular subtype markers demonstrated increased prognostic potential compared to the EMT markers assessed. Increased expression of the luminal markers FOXA1 and SCUBE2, were found to be significantly associated with better DFS. No EMT markers were significantly associated with DFS. In areas of non-invasive papillary urothelial carcinoma, but not invasive carcinoma, sTIL levels were found to be significantly associated with DFS. While differences were observed between HGT1 cases that progressed versus those that did not, a larger cohort study is required for validation of these findings. Taken together, an emphasis on molecular subtype markers, rather than EMT markers, may be preferable when studying biomarkers of HGT1 urothelial carcinoma in the future.
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Affiliation(s)
- Edward C Ottley
- CRUK/MRC Oxford Institute for Radiation OncologyUniversity of OxfordOxfordUK
| | - Robert Pell
- CRUK/MRC Oxford Institute for Radiation OncologyUniversity of OxfordOxfordUK
| | - Benedict Brazier
- CRUK/MRC Oxford Institute for Radiation OncologyUniversity of OxfordOxfordUK
| | - Julianne Hollidge
- Nuffield Department of Surgical SciencesUniversity of OxfordOxfordUK
| | | | - Lisa Browning
- Department of Cellular Pathology, and the NIHR Oxford Biomedical Research CentreJohn Radcliffe HospitalOxfordUK
| | - Eric O'Neill
- CRUK/MRC Oxford Institute for Radiation OncologyUniversity of OxfordOxfordUK
| | - Anne E Kiltie
- CRUK/MRC Oxford Institute for Radiation OncologyUniversity of OxfordOxfordUK
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11
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Han L, Gallan AJ, Steinberg GD, Sweis RF, Paner GP. Morphological correlation of urinary bladder cancer molecular subtypes in radical cystectomies. Hum Pathol 2020; 106:54-61. [PMID: 32987034 DOI: 10.1016/j.humpath.2020.09.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 09/16/2020] [Accepted: 09/21/2020] [Indexed: 12/30/2022]
Abstract
Several molecular subtypes of bladder cancer were identified with differing clinical behavior and responses to platinum-based chemotherapy. But so far, their urothelial histomorphologic features, besides association with some variant histologies, have remained fully undefined. We sought to characterize the histological features of genomically classified bladder cancers more extensively to tumor in radical cystectomy (RC) specimens. Forty-eight bladder cancers submitted to The Cancer Genome Atlas (TCGA) were classified using the BASE47 genomic classifier into luminal subtype (LS) (14 cases), basal subtype (BS) (18 cases), and claudin-low subtype (CLS) (16 cases), and TCGA samples and the corresponding RC specimens were histologically assessed. Marked pleomorphism was more extensive in CLS tumors (87.5% had >15% extent) than in LS tumors (21.4%) (p = 0.0006), whereas the extent in BS tumors was in between LS and CLS tumors. Pleomorphism in distant carcinoma in situ appeared to correlate with that in the main tumor. Ki-67 proliferation was higher in CLS tumors (mean = 61%) than in LS tumors (mean = 29%) or BS (mean = 30%) (p < 0.001). Squamous differentiation was more extensive in BS and CLS tumors (38.2% of BS and CLS tumors versus 7.1% of LS tumors had >30% squamous, p = 0.040). Sarcomatoid change was present in BS and CLS tumors only. The micropapillary variant was identified in LS (3/14) and BS (4/18) tumors only. Histologic features associated with aggressiveness (eg, marked pleomorphism, high proliferation, and sarcomatoid change) are enriched in CLS tumors, correlating with its known poorer outcome that may provide hints in their microscopic distinction. Features more associated with BS than with LS tumors (eg, squamous, marked pleomorphism, and sarcomatoid change) are also identified or enhanced in CLS tumors, supporting the genomic findings suggesting CLS tumor as a hyperbasal form of BS tumor.
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Affiliation(s)
- Lisa Han
- Department of Pathology, University of Chicago, Chicago, IL, USA
| | - Alexander J Gallan
- Department of Pathology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Gary D Steinberg
- Department of Urology, New York University Langone Health, New York, NY, USA
| | - Randy F Sweis
- Department of Medicine (Hematology-Oncology), University of Chicago, Chicago, IL, USA.
| | - Gladell P Paner
- Department of Pathology, University of Chicago, Chicago, IL, USA; Department of Surgery (Urology), University of Chicago, Chicago, IL, USA.
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12
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Kardoust Parizi M, Margulis V, Compe Rat E, Shariat SF. The value and limitations of urothelial bladder carcinoma molecular classifications to predict oncological outcomes and cancer treatment response: A systematic review and meta-analysis. Urol Oncol 2020; 39:15-33. [PMID: 32900624 DOI: 10.1016/j.urolonc.2020.08.023] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 07/28/2020] [Accepted: 08/10/2020] [Indexed: 01/08/2023]
Abstract
AIM To evaluate the predictive value of molecular subtypes on oncological outcomes and response to cancer treatment in patients with urothelial bladder carcinoma (UBC). MATERIALS AND METHODS A literature search using PubMed, Scopus, and Cochrane Library was conducted on April 2020 to identify relevant studies according to the preferred reporting items for systematic review and meta-analysis guidelines. The pooled overall survival (OS), cancer-specific survival (CSS), and progression-free survival were calculated using a fixed or random effects model. RESULTS We identified 66 studies (including 21,447 molecular subtype records) evaluating the impact of molecular classification on oncologic outcomes in patients with UBC. We found significant association of different molecular subtypes with OS, CSS, progression-free survival, recurrence-free survival, and response to treatment. Totally, 11 studies were included in the meta-analysis. Basal group and NE-like subtypes were associated with worse OS (pooled HR: 1.78, 95%CI: 1.49-2.12, and pooled HR: 2.67, 95%CI: 1.08-6.60, respectively) in patients with muscle invasive bladder cancer. Luminal group was also associated with worse CSS (pooled HR of 3.67, 95%CI: 2.19-6.14). CONCLUSIONS Based on these data, UBC molecular classifications are significant predictors of oncological outcomes and identify patients who are most likely to benefit from intensified or different therapies. The optimal consensus on molecular classification remains to be verified in well-designed prospective studies to allow precise prognostic and predictive value assessment.
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Affiliation(s)
- Mehdi Kardoust Parizi
- Department of Urology, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran; Department of Urology, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Vitaly Margulis
- Department of Urology, University of Texas Southwestern Medical Center, Dallas, TX
| | - Eva Compe Rat
- Department of Pathology, Hôpital Tenon, Assistance Publique-Hôpitaux de Paris, UPMC Paris VI, Paris, France
| | - Shahrokh F Shariat
- Department of Urology, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria; Department of Urology, University of Texas Southwestern Medical Center, Dallas, TX; Departments of Urology, Weill Cornell Medical College, New York, NY; Department of Urology, Second Faculty of Medicine, Charles University, Prag, Czech Republic; Institute for Urology and Reproductive Health, I.M. Sechenov First Moscow State Medical University, Moscow, Russia; Division of Urology, Department of Special Surgery, Jordan University Hospital, The University of Jordan, Amman, Jordan; European Association of Urology Research Foundation, Arnhem, Netherlands.
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13
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Ashrafizadeh M, Hushmandi K, Hashemi M, Akbari ME, Kubatka P, Raei M, Koklesova L, Shahinozzaman M, Mohammadinejad R, Najafi M, Sethi G, Kumar AP, Zarrabi A. Role of microRNA/Epithelial-to-Mesenchymal Transition Axis in the Metastasis of Bladder Cancer. Biomolecules 2020; 10:E1159. [PMID: 32784711 PMCID: PMC7464913 DOI: 10.3390/biom10081159] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 08/03/2020] [Accepted: 08/05/2020] [Indexed: 12/12/2022] Open
Abstract
Bladder cancer (BC) is the 11th most common diagnosed cancer, and a number of factors including environmental and genetic ones participate in BC development. Metastasis of BC cells into neighboring and distant tissues significantly reduces overall survival of patients with this life-threatening disorder. Recently, studies have focused on revealing molecular pathways involved in metastasis of BC cells, and in this review, we focus on microRNAs (miRNAs) and their regulatory effect on epithelial-to-mesenchymal transition (EMT) mechanisms that can regulate metastasis. EMT is a vital process for migration of BC cells, and inhibition of this mechanism restricts invasion of BC cells. MiRNAs are endogenous non-coding RNAs with 19-24 nucleotides capable of regulating different cellular events, and EMT is one of them. In BC cells, miRNAs are able to both induce and/or inhibit EMT. For regulation of EMT, miRNAs affect different molecular pathways such as transforming growth factor-beta (TGF-β), Snail, Slug, ZEB1/2, CD44, NSBP1, which are, discussed in detail this review. Besides, miRNA/EMT axis can also be regulated by upstream mediators such as lncRNAs, circRNAs and targeted by diverse anti-tumor agents. These topics are also discussed here to reveal diverse molecular pathways involved in migration of BC cells and strategies to target them to develop effective therapeutics.
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Affiliation(s)
- Milad Ashrafizadeh
- Department of Basic Science, Faculty of Veterinary Medicine, University of Tabriz, Tabriz 5166616471, Iran;
| | - Kiavash Hushmandi
- Department of Food Hygiene and Quality Control, Division of Epidemiology & Zoonoses, Faculty of Veterinary Medicine, University of Tehran, Tehran 1419963114, Iran;
| | - Mehrdad Hashemi
- Department of Genetics, Faculty of advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran 1916893813, Iran;
| | - Mohammad Esmaeil Akbari
- Cancer Research Center, Shahid Beheshti University of Medical Sciences, Tehran 1989934148, Iran;
| | - Peter Kubatka
- Department of Medical Biology and Division of Oncology—Biomedical Center Martin, Jessenius Faculty of Medicine, Comenius University in Bratislava, 03601 Martin, Slovakia;
| | - Mehdi Raei
- Health Research Center, Life Style Institute, Baqiyatallah University of Medical Sciences, Tehran 1435916471, Iran;
| | - Lenka Koklesova
- Department of Obstetrics and Gynecology, Martin University Hospital and Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, 03601 Martin, Slovakia;
| | - Md Shahinozzaman
- Department of Nutrition and Food Science, University of Maryland, College Park, MD 20742, USA;
| | - Reza Mohammadinejad
- Pharmaceutics Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Kerman 55877577, Iran;
| | - Masoud Najafi
- Radiology and Nuclear Medicine Department, School of Paramedical Sciences, Kermanshah University of Medical Sciences, Kermanshah 6715847141, Iran;
| | - Gautam Sethi
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117600, Singapore;
| | - Alan Prem Kumar
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117600, Singapore;
- Cancer Science Institute of Singapore, Centre for Translational Medicine, 14 Medical Drive, #11-01M, Singapore 117599, Singapore
| | - Ali Zarrabi
- Sabanci University Nanotechnology Research and Application Center (SUNUM), Tuzla, Istanbul 34956, Turkey
- Center of Excellence for Functional Surfaces and Interfaces (EFSUN), Faculty of Engineering and Natural Sciences, Sabanci University, Tuzla, Istanbul 34956, Turkey
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14
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Yang G, Bondaruk J, Cogdell D, Wang Z, Lee S, Lee JG, Zhang S, Choi W, Wang Y, Liang Y, Wang G, Wang Y, Yao H, Dadhania V, Gao J, Logothetis C, Siefker-Radtke A, Kamat A, Dinney C, Theodorescu D, Kimmel M, Wei P, Guo CC, Weinstein JN, McConkey DJ, Czerniak B. Urothelial-to-Neural Plasticity Drives Progression to Small Cell Bladder Cancer. iScience 2020; 23:101201. [PMID: 32521509 PMCID: PMC7286965 DOI: 10.1016/j.isci.2020.101201] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 05/08/2020] [Accepted: 05/22/2020] [Indexed: 12/12/2022] Open
Abstract
We report a comprehensive molecular analysis of 34 cases of small cell carcinoma (SCC) and 84 cases of conventional urothelial carcinoma (UC), with The Cancer Genome Atlas cohort of 408 conventional UC bladder cancers used as the reference. SCCs showed mutational landscapes characterized by nearly uniform inactivation of TP53 and were dominated by Sanger mutation signature 3 associated with loss of BRCA1/2 function. SCCs were characterized by downregulation of luminal and basal markers and were referred to as double-negative. Transcriptome analyses indicated that SCCs displayed lineage plasticity driven by a urothelial-to-neural phenotypic switch with a dysregulated epithelial-to-mesenchymal transition network. SCCs were depleted of immune cells, and expressed high levels of the immune checkpoint receptor, adenosine receptor A2A (ADORA2A), which is a potent inhibitor of immune infiltration. Our observations have important implications for the prognostication and development of more effective therapies for this lethal bladder cancer variant. SCCs show TP53/RB1 loss with mutational signature of BRCA1/2 loss of function SCCs are driven by neural phenotypic switch with dysregulated EMT network SCCs show depleted immune phenotype with upregulation of ADORA2A
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Affiliation(s)
- Guoliang Yang
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jolanta Bondaruk
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - David Cogdell
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ziqiao Wang
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sangkyou Lee
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - June Goo Lee
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Shizhen Zhang
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Woonyoung Choi
- Johns Hopkins Greenberg Bladder Cancer Institute, Johns Hopkins University, Baltimore, MD, USA
| | - Yan Wang
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yu Liang
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Gang Wang
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ying Wang
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Hui Yao
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Vipulkumar Dadhania
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jianjun Gao
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Christopher Logothetis
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Arlene Siefker-Radtke
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ashish Kamat
- Department of Urology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Colin Dinney
- Department of Urology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Dan Theodorescu
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai, Los Angeles, CA, USA
| | - Marek Kimmel
- Department of Statistics, Rice University, Houston, TX, USA
| | - Peng Wei
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Charles C Guo
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - John N Weinstein
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - David J McConkey
- Johns Hopkins Greenberg Bladder Cancer Institute, Johns Hopkins University, Baltimore, MD, USA
| | - Bogdan Czerniak
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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15
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A Novel Biomarker Based on miRNA to Predict the Prognosis of Muscle-Invasive Bladder Urothelial Carcinoma. JOURNAL OF ONCOLOGY 2019; 2019:2654296. [PMID: 31885571 PMCID: PMC6925814 DOI: 10.1155/2019/2654296] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2019] [Revised: 10/29/2019] [Accepted: 11/20/2019] [Indexed: 01/04/2023]
Abstract
Muscle-invasive bladder urothelial carcinoma (MIBC) is characteristic of high mortality and high recurrence. Distinguishing the prognostic risk of MIBC at the molecular level of miRNA expression is rarely performed and thus of great significance for the management and treatment of MIBC in clinics. Adaptive lasso Cox's proportional hazards model was used to explore the relationship between differential expression miRNAs (DEmiRNAs) and MIBC survival. Furthermore, we evaluated the epithelial-mesenchymal transition (EMT) score and immune infiltration abundance by exploring EMT signature genes and TIMER database, respectively. A total of 8 DEmiRNAs were detected to be associated with the survival rate of MIBC by using the lasso Cox algorithm. Through the linear combination of these 8 DEmiRNAs, we constructed a calculated marker, which could be used to distinguish the prognosis risk in both TCGA dataset (HR = 2.03, 95% CI = (1.47, 2.83)) and independent validation dataset (HR = 7.74, 95% CI = (1.05, 56.93)). Meanwhile, the constructed marker had reasonably high predictive values of the AUC (area under the curve) in the TCGA dataset and validation dataset being 0.73 and 0.63, respectively. In addition, we observed that the expression values of let-7c, miR-100, and miR-145 were associated with EMT score and the abundance of macrophage in tumor tissue as well. This newly identified risk score signature based on the combination of 8 miRNAs could significantly predict the prognostic risk of MIBC and might provide insight into immunotherapy and targeted therapy of MIBC.
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16
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Wong R, Rosser CJ. UroSEEK gene panel for bladder cancer surveillance. Transl Androl Urol 2019; 8:S546-S549. [PMID: 32042643 PMCID: PMC6989847 DOI: 10.21037/tau.2019.12.41] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 12/26/2019] [Indexed: 12/20/2022] Open
Affiliation(s)
- Regan Wong
- Department of Surgery & Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Charles J Rosser
- Department of Surgery & Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
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17
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Prognostic stratification of muscle invasive urothelial carcinomas using limited immunohistochemical panel of Gata3 and cytokeratins 5/6, 14 and 20. Ann Diagn Pathol 2019; 43:151397. [DOI: 10.1016/j.anndiagpath.2019.08.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 07/15/2019] [Accepted: 08/02/2019] [Indexed: 12/12/2022]
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18
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Predicting outcomes in non-muscle invasive (Ta/T1) bladder cancer: the role of molecular grade based on luminal/basal phenotype. Virchows Arch 2019; 475:445-455. [PMID: 31240474 DOI: 10.1007/s00428-019-02593-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 05/14/2019] [Accepted: 06/03/2019] [Indexed: 10/26/2022]
Abstract
Bladder cancer tumors can be divided into two molecular subtypes referred to as luminal or basal. Each subtype may react differently to current chemotherapy or immunotherapy. Likewise, the technology required for comprehensive molecular analysis is expensive and not yet applicable for routine clinical diagnostics. Therefore, it has been suggested that the immunohistochemical expressions of only two markers, luminal (CK20+, CK5/6-) and basal (CK5/6+, CK20-), is sufficient to identify the molecular subtypes of bladder cancer. This would represent a molecular grade that could be used in daily practice. Molecular classification is done using immunohistochemistry to assess luminal-basal phenotype based on tissular expression of CK20 and CK5/6 as surrogate for luminal or basal subtypes, respectively. A series of 147 non-muscle-invasive bladder carcinoma cases was selected, and the tumors were divided into four subgroups based on the presence of CK20 and/or CK5/6, that is, null (CK20-, CK5/6-), mixed (CK20+, CK5/6+), basal (CK20-, CK5/6+), and luminal (CK20+, CK5/6-) categories. Survival analysis was estimated using the Kaplan-Meier method and the log-rank test. Hazard ratios were calculated by Cox multivariate analysis. The molecular grade included cases with null (n = 89), mixed (n = 6), basal (n = 20), and luminal (n = 32) phenotypes with differences in recurrence-free, progression-free and cancer-specific survival associated with molecular-grade categories in patients with low- or high-grade Ta, or high-grade T1 tumors. The multivariate analysis identified the luminal phenotype as a predictor of more aggressive neoplasms. Our findings provide a rationale to investigate luminal and basal subtypes of bladder cancer using two gene expression signatures as surrogate markers and show that non-muscle-invasive bladder carcinoma can be stratified into biologically and clinically different subgroups by using an immunohistochemical classifier.
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19
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Clinical Parameters Outperform Molecular Subtypes for Predicting Outcome in Bladder Cancer: Results from Multiple Cohorts, Including TCGA. J Urol 2019; 203:62-72. [PMID: 31112107 DOI: 10.1097/ju.0000000000000351] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
PURPOSE Studies indicate that molecular subtypes in muscle invasive bladder cancer predict the clinical outcome. We evaluated whether subtyping by a simplified method and established classifications could predict the clinical outcome. MATERIALS AND METHODS We subtyped institutional cohort 1 of 52 patients, including 39 with muscle invasive bladder cancer, an Oncomine™ data set of 151 with muscle invasive bladder cancer and TCGA (The Cancer Genome Atlas) data set of 402 with muscle invasive bladder cancer. Subtyping was done using simplified panels (MCG-1 and MCG-Ext) which included only transcripts common in published studies and were analyzed for predicting metastasis, and cancer specific, overall and recurrence-free survival. TCGA data set was further analyzed using the Lund taxonomy, the Bladder Cancer Molecular Taxonomy Group Consensus and TCGA 2017 mRNA subtype classifications. RESULTS Muscle invasive bladder cancer specimens from cohort 1 and the Oncomine data set showed intratumor heterogeneity for transcript and protein expression. MCG-1 subtypes did not predict the outcome on univariate or Kaplan-Meier analysis. On multivariate analysis N stage (p ≤0.007), T stage (p ≤0.04), M stage (p=0.007) and/or patient age (p=0.01) predicted metastasis, cancer specific and overall survival, and/or the cisplatin based adjuvant chemotherapy response. In TCGA data set publications showed that subtypes risk stratified patients for overall survival. Consistently the MCG-1 and MCG-Ext subtypes were associated with overall but not recurrence-free survival on univariate and Kaplan-Meier analyses. TCGA data set included 21 low grade specimens of the total of 402 and subtypes associated with tumor grade (p=0.005). However, less than 1% of muscle invasive bladder cancer cases are low grade. In only high grade specimens the MCG-1 and MCG-Ext subtypes could not predict overall survival. On univariate analysis subtypes according to the Bladder Cancer Molecular Taxonomy Group Consensus, TCGA 2017 and the Lund taxonomy were associated with tumor grade (p <0.0001) and overall survival (p=0.01 to <0.0001). Regardless of classification, subtypes had about 50% to 60% sensitivity and specificity to predict overall and recurrence-free survival. On multivariate analyses N stage and lymphovascular invasion consistently predicted recurrence-free and overall survival (p=0.039 and 0.003, respectively). CONCLUSIONS Molecular subtypes reflect bladder tumor heterogeneity and are associated with tumor grade. In multiple cohorts and subtyping classifications the clinical parameters outperformed subtypes for predicting the outcome.
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20
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SIU-ICUD consultation on bladder cancer: basic science. World J Urol 2018; 37:15-29. [PMID: 30547196 DOI: 10.1007/s00345-018-2594-y] [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: 08/23/2018] [Accepted: 11/29/2018] [Indexed: 12/19/2022] Open
Abstract
PURPOSE To provide a condensed summary of the Basic Science chapter that was included in the Third International Consultation on Bladder Cancer. METHODS World bladder cancer basic science experts used the published literature to create summaries of recent progress in their areas of expertise. RESULTS The completion of several large-scale genomics projects coupled with a strong collaborative culture within the research community and the exciting clinical activity of immune checkpoint blockade have combined to transform the bladder cancer research landscape. Bladder cancer molecular subtypes and the presence of specific DNA alterations provide important information about disease heterogeneity that has direct implications for clinical management, and some can be targeted by compounds that are already clinically available. Tests are being developed that can measure many of these alterations non-invasively in peripheral blood or urine, raising confidence that they could be used as biomarkers for surveillance and monitoring the effects of local and systemic therapies. CONCLUSIONS Although the bulk of the mechanistic work lies ahead, the genomics results have created a hypothesis-generating description of bladder cancer heterogeneity that has set the stage for deeper mechanistic studies, and they have already provided us with extremely attractive candidate biomarkers to guide clinical practice. Here, we will summarize the recent progress in basic bladder cancer research and highlight near-term opportunities for the future.
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21
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Abstract
Urothelial malignancies, including carcinomas of the bladder, ureters, and renal pelvis comprised ∼8% of new cancer cases in the USA in 2016. In the metastatic setting, 15% of patients exhibit long-term survival following cisplatin-based chemotherapy and in patients with recurrent disease, response rates to second-line chemotherapy are generally 15%-20% with a 3-month progression-free survival. However, recent advances in immunotherapy represent an opportunity to significantly improve patient outcomes. Moreover, the advent of next-generation sequencing has resulted in both an improved understanding of the fundamental genetic changes that characterize urothelial carcinoma (UC) and identification of several candidate biomarkers of response to various therapies. Incorporation of prospective genotyping into clinical trials will allow for the identification and enrichment of patients most likely to respond to specific targeted therapies and chemotherapy. Combining different therapeutic classes to enhance outcomes is also an area of active research in UC.
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MESH Headings
- Antineoplastic Combined Chemotherapy Protocols/pharmacology
- Antineoplastic Combined Chemotherapy Protocols/therapeutic use
- Biomarkers, Tumor/antagonists & inhibitors
- Biomarkers, Tumor/genetics
- Carcinoma, Transitional Cell/drug therapy
- Carcinoma, Transitional Cell/genetics
- Carcinoma, Transitional Cell/mortality
- Carcinoma, Transitional Cell/pathology
- Clinical Trials as Topic
- Drug Resistance, Neoplasm/drug effects
- Drug Resistance, Neoplasm/genetics
- Gene Expression Profiling
- Gene Expression Regulation, Neoplastic/drug effects
- Gene Expression Regulation, Neoplastic/genetics
- Genotyping Techniques
- High-Throughput Nucleotide Sequencing
- Humans
- Molecular Targeted Therapy/methods
- Mutation Rate
- Progression-Free Survival
- Urologic Neoplasms/drug therapy
- Urologic Neoplasms/genetics
- Urologic Neoplasms/pathology
- Urothelium/pathology
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Affiliation(s)
- G Iyer
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, USA
| | - J E Rosenberg
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, USA.
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22
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Jiang DM, Sridhar SS. Prime time for immunotherapy in advanced urothelial cancer. Asia Pac J Clin Oncol 2018; 14 Suppl 5:24-32. [DOI: 10.1111/ajco.13059] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Di Maria Jiang
- Princess Margaret Cancer Centre; University Health Network; University of Toronto; Toronto Ontario
| | - Srikala S. Sridhar
- Princess Margaret Cancer Centre; University Health Network; University of Toronto; Toronto Ontario
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23
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Gallo Cantafio ME, Grillone K, Caracciolo D, Scionti F, Arbitrio M, Barbieri V, Pensabene L, Guzzi PH, Di Martino MT. From Single Level Analysis to Multi-Omics Integrative Approaches: A Powerful Strategy towards the Precision Oncology. High Throughput 2018; 7:ht7040033. [PMID: 30373182 PMCID: PMC6306876 DOI: 10.3390/ht7040033] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 10/09/2018] [Accepted: 10/22/2018] [Indexed: 02/06/2023] Open
Abstract
Integration of multi-omics data from different molecular levels with clinical data, as well as epidemiologic risk factors, represents an accurate and promising methodology to understand the complexity of biological systems of human diseases, including cancer. By the extensive use of novel technologic platforms, a large number of multidimensional data can be derived from analysis of health and disease systems. Comprehensive analysis of multi-omics data in an integrated framework, which includes cumulative effects in the context of biological pathways, is therefore eagerly awaited. This strategy could allow the identification of pathway-addiction of cancer cells that may be amenable to therapeutic intervention. However, translation into clinical settings requires an optimized integration of omics data with clinical vision to fully exploit precision cancer medicine. We will discuss the available technical approach and more recent developments in the specific field.
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Affiliation(s)
- Maria Eugenia Gallo Cantafio
- Department of Experimental and Clinical Medicine, Magna Graecia University, Salvatore Venuta University Campus, 88100 Catanzaro, Italy.
| | - Katia Grillone
- Department of Experimental and Clinical Medicine, Magna Graecia University, Salvatore Venuta University Campus, 88100 Catanzaro, Italy.
| | - Daniele Caracciolo
- Department of Experimental and Clinical Medicine, Magna Graecia University, Salvatore Venuta University Campus, 88100 Catanzaro, Italy.
| | - Francesca Scionti
- Department of Experimental and Clinical Medicine, Magna Graecia University, Salvatore Venuta University Campus, 88100 Catanzaro, Italy.
| | | | - Vito Barbieri
- Medical Oncology Unit, Mater Domini Hospital, Salvatore Venuta University Campus, 88100 Catanzaro, Italy.
| | - Licia Pensabene
- Department of Medical and Surgical Sciences Pediatric Unit, Magna Graecia University, 88100 Catanzaro, Italy.
| | - Pietro Hiram Guzzi
- Department of Medical and Surgical Sciences, Magna Graecia University, 88100 Catanzaro, Italy.
| | - Maria Teresa Di Martino
- Department of Experimental and Clinical Medicine, Magna Graecia University, Salvatore Venuta University Campus, 88100 Catanzaro, Italy.
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24
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Liu G, Chen Z, Danilova IG, Bolkov MA, Tuzankina IA, Liu G. Identification of miR-200c and miR141-Mediated lncRNA-mRNA Crosstalks in Muscle-Invasive Bladder Cancer Subtypes. Front Genet 2018; 9:422. [PMID: 30323832 PMCID: PMC6172409 DOI: 10.3389/fgene.2018.00422] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 09/10/2018] [Indexed: 11/30/2022] Open
Abstract
Basal and luminal subtypes of muscle-invasive bladder cancer (MIBC) have distinct molecular profiles and heterogeneous clinical behaviors. The interactions between mRNAs and lncRNAs, which might be regulated by miRNAs, have crucial roles in many cancers. However, the miRNA-dependent crosstalk between lncRNA and mRNA in specific MIBC subtypes still remains unclear. In this study, we first classified MIBC into two conservative subtypes using miRNA, mRNA and lncRNA expression data derived from The Cancer Genome Atlas. Then we investigated subtype-related biological pathways and evaluated the subtype classification performance using Decision Trees, Random Forest and eXtreme Gradient Boosting (XGBoost). At last, we explored potential miRNA-mediated lncRNA-mRNA crosstalks based on co-expression analysis. Our results show that: (1) the luminal subtype is primarily characterized by upregulation of metabolism-related pathways while the basal subtype is predominantly characterized by upregulation of epithelial-mesenchymal transition, metastasis, and immune system process-related pathways; (2) the XGBoost prediction model is consistently robust for classification of the molecular subtypes of MIBC across four datasets (The area under the ROC curve > 0.9); (3) the expression levels of the molecules in the miR-200c and miR141-mediated lncRNA-mRNA crosstalks differ considerably between the two subtypes and have close relationships with the prognosis of MIBC. The miR-200c and miR-141-dependent mRNA-lncRNA crosstalks might be of great significance in tumorigenesis and tumor progression and may serve as the novel prognostic predictors and classification markers of MIBC subtypes.
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Affiliation(s)
- Guojun Liu
- Institute of Natural Sciences and Mathematics, Ural Federal University, Yekaterinburg, Russia
| | - Zihao Chen
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Irina G Danilova
- Institute of Natural Sciences and Mathematics, Ural Federal University, Yekaterinburg, Russia
| | - Mikhail A Bolkov
- Institute of Immunology and Physiology, Ural Branch of the Russian Academy of Sciences, Yekaterinburg, Russia
| | - Irina A Tuzankina
- Institute of Immunology and Physiology, Ural Branch of the Russian Academy of Sciences, Yekaterinburg, Russia
| | - Guoqing Liu
- School of Life Sciences and Technology, Inner Mongolia University of Science and Technology, Baotou, China
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25
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Lee E, Collazo-Lorduy A, Castillo-Martin M, Gong Y, Wang L, Oh WK, Galsky MD, Cordon-Cardo C, Zhu J. Identification of microR-106b as a prognostic biomarker of p53-like bladder cancers by ActMiR. Oncogene 2018; 37:5858-5872. [PMID: 29970902 PMCID: PMC6212417 DOI: 10.1038/s41388-018-0367-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 04/24/2018] [Accepted: 05/13/2018] [Indexed: 12/18/2022]
Abstract
Bladder cancers can be categorized into subtypes according to gene expression patterns. P53-like muscle-invasive bladder cancers are generally resistant to cisplatin-based chemotherapy, but exhibit heterogeneous clinical outcomes with a prognosis intermediate to that of the luminal and basal subtypes. The optimal approach to p53-like tumors remains poorly defined and better means to risk-stratify such tumors and identification of novel therapeutic targets is urgently needed. MicroRNAs (miRNAs) play a key role in cancer, both in tumorigenesis and tumor progression. In the past few years, miRNA expression signatures have been reported as prognostic biomarkers in different tumor types including bladder cancer. However, miRNA’s expression does not always correlate well with its activity. We previously developed ActMiR, a computational method for explicitly inferring miRNA activities. We applied ActMiR to The Cancer Genome Atlas (TCGA) bladder cancer data set and identified the activities of miR-106b-5p and miR-532-3p as potential prognostic markers of the p53-like subtype, and validated them in three independent bladder cancer data sets. Especially, higher miR-106b-5p activity was consistently associated with better survival in these data sets. Furthermore, we experimentally validated causal relationships between miR-106-5p and its predicted target genes in p53-like cell line HT1197. HT1197 cells treated with the miR-106b-5p-specific inhibitor were more invasive while cells treated with the miR-106b-5p-specific mimic were less invasive than corresponding controls. Altogether, our results suggest that miR-106b-5p activity can categorize p53-like bladder tumors into more and less-favorable prognostic groups, which provides critical information for personalizing treatment option for p53-like bladder cancers.
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Affiliation(s)
- Eunjee Lee
- Department of Genetics and Genomic Sciences, New York, NY, USA.,Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Sema4, a Mount Sinai venture, Stamford, CT, USA
| | - Ana Collazo-Lorduy
- Departments of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Mireia Castillo-Martin
- Departments of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Pathology, Champalimaud Centre for the Unknown, Lisbon, Portugal
| | - Yixuan Gong
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Li Wang
- Department of Genetics and Genomic Sciences, New York, NY, USA.,Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Sema4, a Mount Sinai venture, Stamford, CT, USA
| | - William K Oh
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Matthew D Galsky
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Carlos Cordon-Cardo
- Departments of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jun Zhu
- Department of Genetics and Genomic Sciences, New York, NY, USA. .,Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA. .,Sema4, a Mount Sinai venture, Stamford, CT, USA. .,The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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26
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Poirion OB, Chaudhary K, Garmire LX. Deep Learning data integration for better risk stratification models of bladder cancer. AMIA JOINT SUMMITS ON TRANSLATIONAL SCIENCE PROCEEDINGS. AMIA JOINT SUMMITS ON TRANSLATIONAL SCIENCE 2018; 2017:197-206. [PMID: 29888072 PMCID: PMC5961799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
We propose an unsupervised multi-omics integration pipeline, using deep-learning autoencoder algorithm, to predict the survival subtypes in bladder cancer (BC). We used TCGA dataset comprising mRNA, miRNA and methylation to infer two survival subtypes. We then constructed a supervised classification model to predict the survival subgroups of any new individual sample. Our training data gave two subgroups with significant survival differences (p-value=8e-4), where high-risk survival subgroup was enriched with KRT6/14 overexpression and PI3K-Akt pathways. We tested the robustness of model by randomly splitting the main dataset into multiple training and test folds, which gave overall significant p-values. Then, we successfully inferred the subtypes for a subset of samples kept as test dataset (p-value=0.03). We further applied our pipeline to predict the survival subgroups from another validation dataset with miRNA data (p-value=0.02). Conclusively, present pipeline is an effective approach to infer the survival subtype of a new sample, exemplified by BC.
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Affiliation(s)
- Olivier B Poirion
- Epidemiology Program, University of Hawaii Cancer Center Honolulu, HI 96813, USA
- These authors contributed equally to the work
| | - Kumardeep Chaudhary
- Epidemiology Program, University of Hawaii Cancer Center Honolulu, HI 96813, USA
- These authors contributed equally to the work
| | - Lana X Garmire
- Epidemiology Program, University of Hawaii Cancer Center Honolulu, HI 96813, USA
- Molecular Biosciences and Bioengineering Graduate Program, University of Hawaii at Manoa, Honolulu, HI 96822, USA
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27
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Barth I, Schneider U, Grimm T, Karl A, Horst D, Gaisa NT, Knüchel R, Garczyk S. Progression of urothelial carcinoma in situ of the urinary bladder: a switch from luminal to basal phenotype and related therapeutic implications. Virchows Arch 2018; 472:749-758. [PMID: 29654370 PMCID: PMC5978840 DOI: 10.1007/s00428-018-2354-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Revised: 03/13/2018] [Accepted: 04/02/2018] [Indexed: 01/03/2023]
Abstract
The stratification of bladder cancer into luminal and basal tumors has recently been introduced as a novel prognostic system in patient cohorts of muscle-invasive bladder cancer or high-grade papillary carcinomas. Using a representative immunohistochemistry panel, we analyzed luminal and basal marker expression in a large case series (n = 156) of urothelial carcinoma in situ (CIS), a precancerous lesion that frequently progresses to muscle-invasive disease. The majority of CIS cases was characterized by a positivity for luminal markers (aberrant cytokeratin (CK) 20 85% (132/156), GATA3 median Remmele score (score of staining intensity (0-3) multiplied with percentage of positive cells (0-4)): 12, estrogen receptor (ER) β Remmele score > 2: 88% (138/156), human epidermal growth factor receptor 2 (Her2) Dako score 3+ 32% (50/156), Her2 Dako score 2+ 33% (51/156)), and marginal expression of basal markers (CK5/6+ 2% (3/156), CK14+ 1% (2/156)). To further investigate phenotypic stability during disease progression, we compared 48 pairs of CIS and invasive tumors from the same biopsy. A highly significant loss of luminal marker expression (p < 0.001) was observed in the course of progression whereas an increase of basal marker expression (p < 0.01) was noted in the invasive compartment. Importantly, 91% of CIS cases demonstrated a positivity for at least one of the two predictive markers Her2 and ERβ, indicating that the analysis of Her2 and ERβ may help to identify CIS-patient subgroups prone to more efficient targeted treatment strategies. Larger prospective and biomarker-embedded clinical trials are needed to confirm and validate our preliminary findings.
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Affiliation(s)
- Isabella Barth
- Institute of Pathology, University Hospital RWTH Aachen, Pauwelsstrasse 30, 52074, Aachen, Germany
| | - Ursula Schneider
- Institute of Pathology, University Hospital RWTH Aachen, Pauwelsstrasse 30, 52074, Aachen, Germany
| | - Tobias Grimm
- Department of Urology, LMU Munich University, Munich, Marchioninistraße 15, 81377, Munich, Germany
| | - Alexander Karl
- Department of Urology, LMU Munich University, Munich, Marchioninistraße 15, 81377, Munich, Germany
| | - David Horst
- Institute of Pathology, LMU Munich University, Munich, Thalkirchner Str. 36, 80337, Munich, Germany
| | - Nadine T Gaisa
- Institute of Pathology, University Hospital RWTH Aachen, Pauwelsstrasse 30, 52074, Aachen, Germany
| | - Ruth Knüchel
- Institute of Pathology, University Hospital RWTH Aachen, Pauwelsstrasse 30, 52074, Aachen, Germany.
| | - Stefan Garczyk
- Institute of Pathology, University Hospital RWTH Aachen, Pauwelsstrasse 30, 52074, Aachen, Germany
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28
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Wach S, Weigelt K, Michalke B, Lieb V, Stoehr R, Keck B, Hartmann A, Wullich B, Taubert H, Chaudhri A. Diagnostic potential of major and trace elements in the serum of bladder cancer patients. J Trace Elem Med Biol 2018; 46:150-155. [PMID: 29413105 DOI: 10.1016/j.jtemb.2017.12.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 12/22/2017] [Accepted: 12/27/2017] [Indexed: 12/17/2022]
Abstract
Major and trace elements may play a role in the diagnosis of diseases. In this study, we investigated the concentration of 26 major and trace elements in the serum by inductively coupled plasma (ICP) - optical emission spectrometry (OES) and ICP-sector field-mass spectrometry (sf-MS). We analyzed the serum from a discovery cohort of 6 bladder cancer (BCa) patients and 12 healthy controls as well as from a validation cohort of 21 BCa patients, 29 non-tumor bladder patients (with acute and chronic inflammation) and 18 healthy controls. Patients were recruited after written consent was obtained at one medical center. Serum was prepared from peripheral blood prior to surgical treatment. Differences in the levels of major and trace elements were determined by a nonparametric Mann-Whitney test and Kruskal-Wallis statistics. In the discovery cohort, we measured significantly increased levels of calcium, mercury, potassium, lithium, nickel, phosphorus and strontium and a significantly decreased level of sodium in BCa patients compared with healthy controls. These findings were reassessed in our validation cohort. We measured significantly increased levels of boron, calcium, cadmium, copper, chromium, lead, lithium, potassium, magnesium, nickel, sulfur, strontium, titan, vanadium and zinc and significantly decreased levels of iron and molybdenum. When we studied the concordance for the discovery and validation cohorts, concentrations of five elements were detected as significantly increased in BCa patients compared with healthy controls: calcium, lithium, potassium, nickel, and strontium. Interestingly, the levels of three elements (calcium, potassium and strontium) were also significantly increased in non-tumor bladder patients compared with healthy controls. But no element was significantly altered between non-tumor bladder patients and BCa patients. In summary, we suggest that determination of the elements calcium, lithium, nickel and strontium in the serum could be a new and promising tool for the early diagnosis of BCa.
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Affiliation(s)
- Sven Wach
- Dept. of Urology and Pediatric Urology, University Hospital Erlangen, Friedrich Alexander-University Erlangen-Nürnberg, Krankenhausstr. 12, D- 91054 Erlangen, Germany; Bridge Consortium e.V., Germany
| | - Katrin Weigelt
- Dept. of Urology and Pediatric Urology, University Hospital Erlangen, Friedrich Alexander-University Erlangen-Nürnberg, Krankenhausstr. 12, D- 91054 Erlangen, Germany
| | - Bernhard Michalke
- Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Analytical BioGeoChemistry, Ingolstaedter Landstr. 1, D-85764 Neuherberg, Germany.
| | - Verena Lieb
- Dept. of Urology and Pediatric Urology, University Hospital Erlangen, Friedrich Alexander-University Erlangen-Nürnberg, Krankenhausstr. 12, D- 91054 Erlangen, Germany
| | - Robert Stoehr
- Institute of Pathology, University Hospital Erlangen, Friedrich Alexander-University Erlangen-Nürnberg, Krankenhausstr. 8-10, D-91054 Erlangen, Germany; Bridge Consortium e.V., Germany
| | - Bastian Keck
- Dept. of Urology and Pediatric Urology, University Hospital Erlangen, Friedrich Alexander-University Erlangen-Nürnberg, Krankenhausstr. 12, D- 91054 Erlangen, Germany; Bridge Consortium e.V., Germany
| | - Arndt Hartmann
- Institute of Pathology, University Hospital Erlangen, Friedrich Alexander-University Erlangen-Nürnberg, Krankenhausstr. 8-10, D-91054 Erlangen, Germany; Bridge Consortium e.V., Germany
| | - Bernd Wullich
- Dept. of Urology and Pediatric Urology, University Hospital Erlangen, Friedrich Alexander-University Erlangen-Nürnberg, Krankenhausstr. 12, D- 91054 Erlangen, Germany; Bridge Consortium e.V., Germany
| | - Helge Taubert
- Dept. of Urology and Pediatric Urology, University Hospital Erlangen, Friedrich Alexander-University Erlangen-Nürnberg, Krankenhausstr. 12, D- 91054 Erlangen, Germany; Bridge Consortium e.V., Germany
| | - Anwar Chaudhri
- Institute for Surface Science and Corrosion, Department of Materials Science, Friedrich Alexander-University Erlangen-Nürnberg, Martensstraße 7, D-91058 Erlangen, Germany
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29
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Giridhar KV, Kohli M. Management of Muscle-Invasive Urothelial Cancer and the Emerging Role of Immunotherapy in Advanced Urothelial Cancer. Mayo Clin Proc 2017; 92:1564-1582. [PMID: 28982487 DOI: 10.1016/j.mayocp.2017.07.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Revised: 07/19/2017] [Accepted: 07/24/2017] [Indexed: 12/21/2022]
Abstract
The incidence of bladder cancer has increased in the past decade, and mortality from bladder cancer remains a substantial public health burden. After 3 decades of minimal progress in the treatment of advanced-stage disease, recent advances in the genomic characterization of urothelial cancer and breakthroughs in bladder cancer therapeutics have rejuvenated the field. This review highlights the landmark clinical trials of chemotherapy in both the neoadjuvant and advanced or metastatic urothelial carcinoma settings. We describe treatment paradigms for multimodal treatment of locally advanced bladder cancer, including discussion on bladder preservation strategies. Lastly, we discuss novel immunomodulatory, targeted, and combination therapies in development for the treatment of advanced urothelial carcinoma.
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Affiliation(s)
- Karthik V Giridhar
- Division of Medical Oncology, Department of Oncology, Mayo Clinic, Rochester, MN
| | - Manish Kohli
- Division of Medical Oncology, Department of Oncology, Mayo Clinic, Rochester, MN.
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30
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Detassis S, Grasso M, Del Vescovo V, Denti MA. microRNAs Make the Call in Cancer Personalized Medicine. Front Cell Dev Biol 2017; 5:86. [PMID: 29018797 PMCID: PMC5614923 DOI: 10.3389/fcell.2017.00086] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 09/08/2017] [Indexed: 12/13/2022] Open
Abstract
Since their discovery and the advent of RNA interference, microRNAs have drawn enormous attention because of their ubiquitous involvement in cellular pathways from life to death, from metabolism to communication. It is also widely accepted that they possess an undeniable role in cancer both as tumor suppressors and tumor promoters modulating cell proliferation and migration, epithelial-mesenchymal transition and tumor cell invasion and metastasis. Moreover, microRNAs can even affect the tumor surrounding environment influencing angiogenesis and immune system activation and recruitment. The tight association of microRNAs with several cancer-related processes makes them undoubtedly connected to the effect of specific cancer drugs inducing either resistance or sensitization. In this context, personalized medicine through microRNAs arose recently with the discovery of single nucleotide polymorphisms in the target binding sites, in the sequence of the microRNA itself or in microRNA biogenesis related genes, increasing risk, susceptibility and progression of multiple types of cancer in different sets of the population. The depicted scenario implies that the overall variation displayed by these small non-coding RNAs have an impact on patient-specific pharmacokinetics and pharmacodynamics of cancer drugs, pushing on a rising need of personalized treatment. Indeed, microRNAs from either tissues or liquid biopsies are also extensively studied as valuable biomarkers for disease early recognition, progression and prognosis. Despite microRNAs being intensively studied in recent years, a comprehensive review describing these topics all in one is missing. Here we report an up-to-date and critical summary of microRNAs as tools for better understanding personalized cancer biogenesis, evolution, diagnosis and treatment.
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Affiliation(s)
| | | | | | - Michela A. Denti
- Laboratory of RNA Biology and Biotechnology, Centre for Integrative Biology, University of TrentoTrento, Italy
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31
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Zhang ZC, Liu JX, Shao ZW, Pu FF, Wang BC, Wu Q, Zhang YK, Zeng XL, Guo XD, Yang SH, He TC. In vitro effect of microRNA-107 targeting Dkk-1 by regulation of Wnt/β-catenin signaling pathway in osteosarcoma. Medicine (Baltimore) 2017; 96:e7245. [PMID: 28682874 PMCID: PMC5502147 DOI: 10.1097/md.0000000000007245] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND The aim of the study was to explore the effects of microRNA-107 (miR-107) by targeting Dkk-1 on osteosarcoma (OS) via the Wnt/β-catenin signaling pathway. METHODS OS and adjacent tissues were collected from 67 patients diagnosed with OS. Expressions of miR-107, Dkk-1, LRP5, β-catenin, and c-Myc were detected by the quantitative real-time polymerase chain reaction (qRT-PCR) and Western blotting. The dual-luciferase reporter gene assay was performed to observe the relationship between miR-107 and Dkk-1.Transfected cells were divided into different investigating groups designated as Inhibitor, Mimic, siRNA, Inhibitor + siRNA, negative control (NC), and blank groups. qRT-PCR and Western blotting were used to detect expressions of miR-107, Dkk-1, β-catenin, Bcl-2, c-Myc, Caspase-3, and PARP. Cell counting kit-8 (CCK-8), flow cytometry (FCM), colony-formation efficiency (CFE), and subcutaneous tumorigenicity assays were all utilized for to determine cell proliferation, apoptosis, colony-forming, and tumorigenic abilities. RESULTS Dkk-1 is the target gene of miR-107. Decreased expressions of miR-107, LRP5, β-catenin, and c-Myc, and increased expressions of Dkk-1 were found in OS tissues. The Mimic and siRNA groups exhibited decreased proliferation rates, colony-forming abilities, and tumorigenicity and increased apoptosis rates, whereas the inhibitor group showed opposite trends when compared to the blank group. On the other hand, expressions of miR-107, LRP5, β-catenin, c-Myc, Caspase-3, and PARP were all elevated in the mimic group, whereas expressions of Dkk-1 and Bcl-2 were reduced; opposite trends were observed in the inhibitor group. CONCLUSION We conclude that miR-107 is likely to inhibit the occurrence and development of OS by down-regulating Dkk-1 via the Wnt/β-catenin signaling pathway, providing us with a new therapeutic target for the treatment of OS.
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Affiliation(s)
- Zhi-Cai Zhang
- Department of Orthopedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P.R. China
| | - Jian-Xiang Liu
- Department of Orthopedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P.R. China
| | - Zeng-Wu Shao
- Department of Orthopedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P.R. China
| | - Fei-Fei Pu
- Department of Orthopedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P.R. China
| | - Bai-Chuan Wang
- Department of Orthopedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P.R. China
| | - Qiang Wu
- Department of Orthopedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P.R. China
| | - Yu-Kun Zhang
- Department of Orthopedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P.R. China
| | - Xian-Lin Zeng
- Department of Orthopedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P.R. China
| | - Xiao-Dong Guo
- Department of Orthopedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P.R. China
| | - Shu-Hua Yang
- Department of Orthopedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P.R. China
| | - Tong-Chuan He
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery, The University of Chicago Medical Center, Chicago, IL
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