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Koutros S, Kiemeney LA, Pal Choudhury P, Milne RL, Lopez de Maturana E, Ye Y, Joseph V, Florez-Vargas O, Dyrskjøt L, Figueroa J, Dutta D, Giles GG, Hildebrandt MAT, Offit K, Kogevinas M, Weiderpass E, McCullough ML, Freedman ND, Albanes D, Kooperberg C, Cortessis VK, Karagas MR, Johnson A, Schwenn MR, Baris D, Furberg H, Bajorin DF, Cussenot O, Cancel-Tassin G, Benhamou S, Kraft P, Porru S, Carta A, Bishop T, Southey MC, Matullo G, Fletcher T, Kumar R, Taylor JA, Lamy P, Prip F, Kalisz M, Weinstein SJ, Hengstler JG, Selinski S, Harland M, Teo M, Kiltie AE, Tardón A, Serra C, Carrato A, García-Closas R, Lloreta J, Schned A, Lenz P, Riboli E, Brennan P, Tjønneland A, Otto T, Ovsiannikov D, Volkert F, Vermeulen SH, Aben KK, Galesloot TE, Turman C, De Vivo I, Giovannucci E, Hunter DJ, Hohensee C, Hunt R, Patel AV, Huang WY, Thorleifsson G, Gago-Dominguez M, Amiano P, Golka K, Stern MC, Yan W, Liu J, Li SA, Katta S, Hutchinson A, Hicks B, Wheeler WA, Purdue MP, McGlynn KA, Kitahara CM, Haiman CA, Greene MH, Rafnar T, Chatterjee N, Chanock SJ, Wu X, Real FX, Silverman DT, Garcia-Closas M, Stefansson K, Prokunina-Olsson L, Malats N, Rothman N. Genome-wide Association Study of Bladder Cancer Reveals New Biological and Translational Insights. Eur Urol 2023; 84:127-137. [PMID: 37210288 PMCID: PMC10330197 DOI: 10.1016/j.eururo.2023.04.020] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 03/16/2023] [Accepted: 04/19/2023] [Indexed: 05/22/2023]
Abstract
BACKGROUND Genomic regions identified by genome-wide association studies (GWAS) for bladder cancer risk provide new insights into etiology. OBJECTIVE To identify new susceptibility variants for bladder cancer in a meta-analysis of new and existing genome-wide genotype data. DESIGN, SETTING, AND PARTICIPANTS Data from 32 studies that includes 13,790 bladder cancer cases and 343,502 controls of European ancestry were used for meta-analysis. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSES Log-additive associations of genetic variants were assessed using logistic regression models. A fixed-effects model was used for meta-analysis of the results. Stratified analyses were conducted to evaluate effect modification by sex and smoking status. A polygenic risk score (PRS) was generated on the basis of known and novel susceptibility variants and tested for interaction with smoking. RESULTS AND LIMITATIONS Multiple novel bladder cancer susceptibility loci (6p.22.3, 7q36.3, 8q21.13, 9p21.3, 10q22.1, 19q13.33) as well as improved signals in three known regions (4p16.3, 5p15.33, 11p15.5) were identified, bringing the number of independent markers at genome-wide significance (p < 5 × 10-8) to 24. The 4p16.3 (FGFR3/TACC3) locus was associated with a stronger risk for women than for men (p-interaction = 0.002). Bladder cancer risk was increased by interactions between smoking status and genetic variants at 8p22 (NAT2; multiplicative p value for interaction [pM-I] = 0.004), 8q21.13 (PAG1; pM-I = 0.01), and 9p21.3 (LOC107987026/MTAP/CDKN2A; pM-I = 0.02). The PRS based on the 24 independent GWAS markers (odds ratio per standard deviation increase 1.49, 95% confidence interval 1.44-1.53), which also showed comparable results in two prospective cohorts (UK Biobank, PLCO trial), revealed an approximately fourfold difference in the lifetime risk of bladder cancer according to the PRS (e.g., 1st vs 10th decile) for both smokers and nonsmokers. CONCLUSIONS We report novel loci associated with risk of bladder cancer that provide clues to its biological underpinnings. Using 24 independent markers, we constructed a PRS to stratify lifetime risk. The PRS combined with smoking history, and other established risk factors, has the potential to inform future screening efforts for bladder cancer. PATIENT SUMMARY We identified new genetic markers that provide biological insights into the genetic causes of bladder cancer. These genetic risk factors combined with lifestyle risk factors, such as smoking, may inform future preventive and screening strategies for bladder cancer.
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Affiliation(s)
- Stella Koutros
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA.
| | - Lambertus A Kiemeney
- Department for Health Evidence, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Parichoy Pal Choudhury
- Trans-Divisional Research Program, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA; American Cancer Society, Atlanta, GA, USA
| | - Roger L Milne
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Australia; Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Australia; Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Australia
| | - Evangelina Lopez de Maturana
- Genetic and Molecular Epidemiology Group, Spanish National Cancer Research Centre (CNIO) and CIBERONC, Madrid, Spain
| | | | - Vijai Joseph
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Oscar Florez-Vargas
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Lars Dyrskjøt
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Jonine Figueroa
- Usher Institute, University of Edinburgh, Edinburgh, UK; Integrative Tumor Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Diptavo Dutta
- Integrative Tumor Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Graham G Giles
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Australia; Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Australia; Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Australia
| | | | - Kenneth Offit
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | | | | | - Neal D Freedman
- Metabolic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Demetrius Albanes
- Metabolic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Victoria K Cortessis
- Department of Population and Public Health Sciences, Epidemiology and Genetics, University of Southern California, Los Angeles, CA, USA
| | - Margaret R Karagas
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | | | | | - Dalsu Baris
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Helena Furberg
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Dean F Bajorin
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Olivier Cussenot
- Centre de Recherche sur les Pathologies Prostatiques et Urologiques, Paris, France
| | - Geraldine Cancel-Tassin
- Centre de Recherche sur les Pathologies Prostatiques et Urologiques, Paris, France; GRC 5 Predictive Onco-Urology, Sorbonne University, Paris, France
| | - Simone Benhamou
- INSERM U1018, Research Centre on Epidemiology and Population Health, Villejuif, France
| | - Peter Kraft
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Stefano Porru
- Department of Diagnostics and Public Health, Section of Occupational Medicine, University of Verona, Verona, Italy
| | - Angela Carta
- Department of Diagnostics and Public Health, Section of Occupational Medicine, University of Verona, Verona, Italy
| | - Timothy Bishop
- Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
| | - Melissa C Southey
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Australia; Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Australia; Department of Clinical Pathology, The University of Melbourne, Parkville, Australia
| | - Giuseppe Matullo
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Tony Fletcher
- London School of Hygiene and Tropical Medicine, London, UK
| | - Rajiv Kumar
- Division of Functional Genome Analysis, German Cancer Research Center, Heidelberg, Germany
| | - Jack A Taylor
- Epidemiology Branch and Epigenetic and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Philippe Lamy
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Frederik Prip
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Mark Kalisz
- Epithelial Carcinogenesis Group, Spanish National Cancer Research Centre (CNIO) and CIBERONC, Madrid, Spain
| | - Stephanie J Weinstein
- Metabolic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Jan G Hengstler
- Leibniz Research Centre for Working Environment and Human Factors at TU Dortmund (IfADo), Dortmund, Germany
| | - Silvia Selinski
- Leibniz Research Centre for Working Environment and Human Factors at TU Dortmund (IfADo), Dortmund, Germany
| | - Mark Harland
- Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
| | - Mark Teo
- Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
| | - Anne E Kiltie
- Rowett Institute, School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, UK
| | - Adonina Tardón
- Department of Preventive Medicine, Universidad de Oviedo, ISPA and CIBERESP, Spain
| | - Consol Serra
- Center for Research in Occupational Health, Universitat Pompeu Fabra, Hospital del Mar Medical Research Institut, CIBERESP, Barcelona, Spain
| | - Alfredo Carrato
- Department of Medicine, Alcalá University, IRYCIS, CIBERONC, Madrid, Spain
| | | | - Josep Lloreta
- Hospital del Mar, Universitat Pompeu Fabra, Barcelona, Spain
| | - Alan Schned
- Department of Pathology, Dartmouth Medical School, Hanover, NH, USA
| | - Petra Lenz
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Elio Riboli
- School of Public Health, Imperial College London, London, UK
| | - Paul Brennan
- International Agency for Research on Cancer, Lyon, France
| | | | - Thomas Otto
- Department of Urology, Rheinland Klinikum, Lukaskrankenhaus, Neuss, Germany
| | | | - Frank Volkert
- Department of Urology, Evangelic Hospital, Paul Gerhardt Foundation, Lutherstadt Wittenberg, Germany
| | - Sita H Vermeulen
- Department for Health Evidence, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Katja K Aben
- Department for Health Evidence, Radboud University Medical Center, Nijmegen, The Netherlands; Netherlands Comprehensive Cancer Organisation, Utrecht, The Netherlands
| | - Tessel E Galesloot
- Department for Health Evidence, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Constance Turman
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Immaculata De Vivo
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Department of Medicine, Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Edward Giovannucci
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - David J Hunter
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Chancellor Hohensee
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Rebecca Hunt
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Alpa V Patel
- Population Science, American Cancer Society, Atlanta, GA, USA
| | - Wen-Yi Huang
- Metabolic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | | | - Manuela Gago-Dominguez
- Fundación Pública Galega de Medicina Xenómica, Servicio Galego de Saude, Health Research Institute of Santiago de Compostela, Santiago de Compostela, Spain
| | - Pilar Amiano
- Ministry of Health of the Basque Government, Sub Directorate for Public Health and Addictions of Gipuzkoa, San Sebastian, Spain; Biodonostia Health Research Institute, Epidemiology of Chronic and Communicable Diseases Group, San Sebastian, Spain; Spanish Consortium for Research on Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain
| | - Klaus Golka
- Leibniz Research Centre for Working Environment and Human Factors at TU Dortmund (IfADo), Dortmund, Germany
| | - Mariana C Stern
- Department of Population and Public Health Sciences, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Wusheng Yan
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Jia Liu
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Shengchao Alfred Li
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Shilpa Katta
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Amy Hutchinson
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Belynda Hicks
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | | | - Mark P Purdue
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Katherine A McGlynn
- Metabolic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Cari M Kitahara
- Radiation Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Christopher A Haiman
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Mark H Greene
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | | | | | - Stephen J Chanock
- Office of the Director, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Xifeng Wu
- Zhejiang University, Hangzhou, China
| | - Francisco X Real
- Epithelial Carcinogenesis Group, Spanish National Cancer Research Centre (CNIO) and CIBERONC, Madrid, Spain; Departament de Medicina i Ciències de la Vida, Universitat Pompeu Fabra, Barcelona, Spain
| | - Debra T Silverman
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Montserrat Garcia-Closas
- Trans-Divisional Research Program, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | | | - Ludmila Prokunina-Olsson
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Núria Malats
- Genetic and Molecular Epidemiology Group, Spanish National Cancer Research Centre (CNIO) and CIBERONC, Madrid, Spain
| | - Nathaniel Rothman
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
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De Falco F, Cuccaro B, De Tullio R, Alberti A, Cutarelli A, De Carlo E, Roperto S. Possible etiological association of ovine papillomaviruses with bladder tumors in cattle. Virus Res 2023; 328:199084. [PMID: 36878382 DOI: 10.1016/j.virusres.2023.199084] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 02/27/2023] [Accepted: 03/01/2023] [Indexed: 03/08/2023]
Abstract
INTRODUCTION Bladder tumors of cattle are very uncommon accounting from 0.1% to 0.01% of all bovine malignancies. Bladder tumors are common in cattle grazing on bracken fern-infested pasturelands. Bovine papillomaviruses have a crucial role in tumors of bovine urinary bladder. AIM OF THE STUDY To investigate the potential association of ovine papillomavirus (OaPV) infection with bladder carcinogenesis of cattle. METHODS Droplet digital PCR was used to detect and quantify the nucleic acids of OaPVs in bladder tumors of cattle that were collected at public and private slaughterhouses. RESULTS OaPV DNA and RNA were detected and quantified in 10 bladder tumors of cattle that were tested negative for bovine papillomaviruses. The most prevalent genotypes were OaPV1 and OaPV2. OaPV4 was rarely observed. Furthermore, we detected a significant overexpression and hyperphosphorylation of pRb and a significant overexpression and activation of the calpain-1 as well as a significant overexpression of E2F3 and of phosphorylated (activated) PDGFβR in neoplastic bladders in comparison with healthy bladders, which suggests that E2F3 and PDGFβR may play an important role in OaPV-mediated molecular pathways that lead to bladder carcinogenesis. CONCLUSION In all tumors, OaPV RNA could explain the causality of the disease of the urinary bladder. Therefore, persistent infections by OaPVs could be involved in bladder carcinogenesis. Our data showed that there is a possible etiologic association of OaPVs with bladder tumors of cattle.
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Affiliation(s)
- Francesca De Falco
- Dipartimento di Medicina Veterinaria e delle Produzioni Animali, Università degli Studi di Napoli Federico II, Naples, Italy
| | - Bianca Cuccaro
- Dipartimento di Medicina Veterinaria e delle Produzioni Animali, Università degli Studi di Napoli Federico II, Naples, Italy
| | - Roberta De Tullio
- Dipartimento di Medicina Sperimentale (DIMES), Università degli Studi di Genova, Genova, Italy
| | - Alberto Alberti
- Dipartimento di Medicina Veterinaria, Università degli Studi di Sassari, Sassari, Italy
| | - Anna Cutarelli
- Istituto Zooprofilattico Sperimentale del Mezzogiorno, Portici, Naples, Italy
| | - Esterina De Carlo
- Istituto Zooprofilattico Sperimentale del Mezzogiorno, Portici, Naples, Italy
| | - Sante Roperto
- Dipartimento di Medicina Veterinaria e delle Produzioni Animali, Università degli Studi di Napoli Federico II, Naples, Italy.
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Crosstalk of miRNAs with signaling networks in bladder cancer progression: Therapeutic, diagnostic and prognostic functions. Pharmacol Res 2022; 185:106475. [DOI: 10.1016/j.phrs.2022.106475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 09/17/2022] [Accepted: 09/27/2022] [Indexed: 12/24/2022]
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Ognibene M, Cangelosi D, Sorrentino S, Zanardi S, Zara F, Pezzolo A, Parodi S. E2F3 gene expression is a potential negative prognostic marker for localised and MYCN not-amplified neuroblastoma: Results of in silico analysis of 786 samples. Pediatr Blood Cancer 2022; 69:e29800. [PMID: 35652628 DOI: 10.1002/pbc.29800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 04/13/2022] [Accepted: 05/09/2022] [Indexed: 11/06/2022]
Abstract
BACKGROUND Neuroblastoma (NB) is an enigmatic childhood malignancy characterised by a wide range of clinical behaviour. Many potential oncogenes for NB have recently been identified. Among them, E2 transcription factor 3 (E2F3) expression was associated with a poor survival in 134 stage 4S patients, but evidence for other stage groups remains poorly investigated. METHODS We have analysed the expression of E2F3 gene from a database of 786 NB samples. Overall and event-free survivals (EFS) were assessed by the Kaplan-Meier method, splitting the data on the median and tertile expression values. The Cox model was applied to control for the confounding by stage, age and MYCN amplification. Validation was performed by an in silico analysis of an independent cohort of 283 NB patients. Furthermore, an immunofluorescence analysis on 48 formalin-fixed, paraffin-embedded NB specimens was also performed. RESULTS E2F3 overexpression was associated with a poor survival (EFS = 84%, 95% CI: 79%-95%, for low expression levels; EFS = 62%, 95% CI: 56%-68% for middle levels; EFS = 30%, 95% CI: 24%-36%, for high levels, p < .001). This association was confirmed in multivariable analysis and was more evident in patients with MYCN not-amplified and localised stages. Immunofluorescence results and the validation on an independent cohort of NB primary samples confirmed these findings. CONCLUSIONS E2F3 is a new potential prognostic marker in NB with favourable characteristics at diagnosis. Further studies are needed to elucidate the potential role of E2F3 in NB oncogenesis and progression, in order to identify new targets for therapeutic interventions.
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Affiliation(s)
- Marzia Ognibene
- U.O.C. Genetica Medica, IRCCS Istituto Giannina Gaslini, Genova, Italy
| | - Davide Cangelosi
- Unità di Bioinformatica Clinica, Direzione Scientifica, IRCCS Istituto Giannina Gaslini, Genova, Italy
| | - Stefania Sorrentino
- U.O.C. Divisione di Oncologia, IRCCS Istituto Giannina Gaslini, Genova, Italy
| | - Sabrina Zanardi
- U.O.S.I.D. Epidemiologia e Biostatistica, Direzione Scientifica, IRCCS Istituto Giannina Gaslini, Genova, Italy
| | - Federico Zara
- U.O.C. Genetica Medica, IRCCS Istituto Giannina Gaslini, Genova, Italy
| | | | - Stefano Parodi
- Direzione Scientifica, IRCCS Istituto Giannina Gaslini, Genova, Italy
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Abedi Z, MotieGhader H, Hosseini SS, Sheikh Beig Goharrizi MA, Masoudi-Nejad A. mRNA-miRNA bipartite networks reconstruction in different tissues of bladder cancer based on gene co-expression network analysis. Sci Rep 2022; 12:5885. [PMID: 35393513 PMCID: PMC8991185 DOI: 10.1038/s41598-022-09920-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Accepted: 03/24/2022] [Indexed: 12/14/2022] Open
Abstract
Bladder cancer (BC) is one of the most important cancers worldwide, and if it is diagnosed early, its progression in humans can be prevented and long-term survival will be achieved accordingly. This study aimed to identify novel micro-RNA (miRNA) and gene-based biomarkers for diagnosing BC. The microarray dataset of BC tissues (GSE13507) listed in the GEO database was analyzed for this purpose. The gene expression data from three BC tissues including 165 primary bladder cancer (PBC), 58 normal looking-bladder mucosae surrounding cancer (NBMSC), and 23 recurrent non-muscle invasive tumor tissues (RNIT) were used to reconstruct gene co-expression networks. After preprocessing and normalization, deferentially expressed genes (DEGs) were obtained and used to construct the weighted gene co-expression network (WGCNA). Gene co-expression modules and low-preserved modules were extracted among BC tissues using network clustering. Next, the experimentally validated mRNA-miRNA interaction information were used to reconstruct three mRNA-miRNA bipartite networks. Reactome pathway database and Gene ontology (GO) was subsequently performed for the extracted genes of three bipartite networks and miRNAs, respectively. To further analyze the data, ten hub miRNAs (miRNAs with the highest degree) were selected in each bipartite network to reconstruct three bipartite subnetworks. Finally, the obtained biomarkers were comprehensively investigated and discussed in authentic studies. The obtained results from our study indicated a group of genes including PPARD, CST4, CSNK1E, PTPN14, ETV6, and ADRM1 as well as novel miRNAs (e.g., miR-16-5p, miR-335-5p, miR-124-3p, and let-7b-5p) which might be potentially associated with BC and could be a potential biomarker. Afterward, three drug-gene interaction networks were reconstructed to explore candidate drugs for the treatment of BC. The hub miRNAs in the mRNA-miRNA bipartite network played a fundamental role in BC progression; however, these findings need further investigation.
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Affiliation(s)
- Zahra Abedi
- Laboratory of Systems Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Habib MotieGhader
- Department of Biology, Tabriz Branch, Islamic Azad University, Tabriz, Iran.
| | - Sahar Sadat Hosseini
- Laboratory of Systems Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | | | - Ali Masoudi-Nejad
- Laboratory of Systems Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran.
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Nie C, Han J, Bi W, Qiu Z, Chen L, Yu J, Pang R, Liu B, Sheng R, Zhang J. Circular RNA circ_0000644 promotes papillary thyroid cancer progression via sponging miR-1205 and regulating E2F3 expression. Cell Cycle 2021; 21:126-139. [PMID: 34919034 DOI: 10.1080/15384101.2021.2012334] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Abstract
The dysregulation of circular RNAs (circRNAs) facilitates the tumorigenesis of papillary thyroid carcinoma (PTC). This study was targeted at determining the functions and mechanism of circ_0000644 in regulating PTC development. Circ_0000644, microRNA-1205 (miR-1205) and E2F transcription factor 3 (E2F3) expressions were detected by quantitative real-time polymerase chain reaction (qRT-PCR). Actinomycin D (ActD) and Ribonuclease R (RNase R) assays were used to verify the circular characteristic of circ_0000644. After circ_0000644 was knocked down, PTC cell growth, migration, invasion and apoptosis were assessed by cell counting kit-8 (CCK-8) assay, Transwell assay and flow cytometry analysis, respectively. The regulating relationships among circ_0000644, E2F3 and miR-1205 were confirmed through RNA immunoprecipitation (RIP) assay and dual-luciferase reporter assay. Besides, the regulatory effects of circ_0000644 on the protein level of E2F3 was analyzed via Western blot. In PTC, circ_0000644 was highly expressed, and it was located mainly in the cytoplasm, and it had stable structure. The knockdown of circ_0000644 repressed PTC cell growth, migration, and invasion, and facilitated apoptosis. Circ_0000644 could directly interact with miR-1205 to repress the expression of miR-1205, and it served as a miR-1205 sponge to modulate E2F3 expression in PTC cells. Circ_0000644 up-regulates E2F3 expression via sponging miR-1205 to promote PTC progression.
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Affiliation(s)
- Chunlei Nie
- Department of Head and Neck Surgery, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang, China
| | - Jihua Han
- Department of Head and Neck Surgery, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang, China
| | - Wen Bi
- Department of Head and Neck Surgery, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang, China
| | - Zhilin Qiu
- Department of Head and Neck Surgery, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang, China
| | - Lili Chen
- Department of Head and Neck Surgery, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang, China
| | - Jiawei Yu
- Department of Head and Neck Surgery, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang, China
| | - Rui Pang
- Department of Head and Neck Surgery, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang, China
| | - Bo Liu
- Department of Head and Neck Surgery, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang, China
| | - Ruinan Sheng
- Department of Head and Neck Surgery, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang, China
| | - Jiewu Zhang
- Department of Head and Neck Surgery, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang, China
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7
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Zhu Y, Zhou Y, Jiang H, Chen Z, Lu B. Analysis of core genes for colorectal cancer prognosis based on immune and stromal scores. PeerJ 2021; 9:e12452. [PMID: 34820188 PMCID: PMC8607933 DOI: 10.7717/peerj.12452] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 10/18/2021] [Indexed: 01/30/2023] Open
Abstract
Background Colorectal cancer (CRC) is one of the most common malignancies.An early diagnosis and an accurate prognosis are major focuses of CRC research. Tumor microenvironment cells and the extent of infiltrating immune and stromal cells contribute significantly to the tumor prognosis. Methods Immune and stromal scores were calculated based on the ESTIMATE algorithm using the sample expression profile of the The Cancer Genome Atlas (TCGA) database. GSE102479 was used as the validation database. Differentially expressed genes whose expression was significantly associated with the prognosis of CRC patients were identified based on the immune matrix score. Survival analysis was conducted on the union of the differentially expressed genes. A protein–protein interaction (PPI) network was constructed using the STRING database to identify the closely connected modules. To conduct functional enrichment analysis of the relevant genes, GO and KEGG pathway analyses were performed with Cluster Profiler. Pivot analysis of the ncRNAs and TFs was performed by using the RAID2.0 database and TRRUST v2 database. TF-mRNA regulatory relationships were analyzed in the TRRUST V2 database. Hubgene targeting relationships were screened in the TargetScan, miRTarBase and miRDB databases. The SNV data of the hub genes were analyzed by using the R maftools package. A ROC curve was drawn based on the TCGA database. The proportion of immune cells was estimated using CIBERSORT and the LM22 feature matrix. Results The results showed that the matrix score was significantly correlated with colorectal cancer stage T. A total of 789 differentially expressed genes and 121 survival-related prognostic genes were identified. The PPI network showed that 22 core genes were related to the CRC prognosis. Furthermore, four ncRNAs that regulated the core prognosis genes, 11 TFs with regulatory effects on the core prognosis genes, and two drugs, quercetin and pseudoephedrine, that have regulatory effects on colorectal cancer were also identified. Conclusions We obtained a list of tumor microenvironment-related genes for CRC patients. These genes could be useful for determining the prognosis of CRC patients. To confirm the function of these genes, additional experiments are necessary.
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Affiliation(s)
- Yi Zhu
- Department of Gastrointestinal Surgery, The Affiliated Hospital of Jiaxing University, Jiaxing, China
| | - Yuan Zhou
- Department of Gastrointestinal Surgery, The Affiliated Hospital of Jiaxing University, Jiaxing, China
| | - HongGang Jiang
- Department of Gastrointestinal Surgery, The Affiliated Hospital of Jiaxing University, Jiaxing, China
| | - ZhiHeng Chen
- Department of Gastrointestinal Surgery, The Affiliated Hospital of Jiaxing University, Jiaxing, China
| | - BoHao Lu
- Department of Gastrointestinal Surgery, The Affiliated Hospital of Jiaxing University, Jiaxing, China
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8
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CDKAL1 (rs10946398) and TCF7L2 (rs7903146) gene polymorphisms and their association with risk of type-2 diabetes mellitus in population of Uttarakhand, India. Meta Gene 2020. [DOI: 10.1016/j.mgene.2020.100767] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
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9
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Zhang Y, Shao Y, Lv Z, Li C. MiR-210 regulates coelomocyte proliferation through targeting E2F3 in Apostichopus japonicus. FISH & SHELLFISH IMMUNOLOGY 2020; 106:583-590. [PMID: 32835852 DOI: 10.1016/j.fsi.2020.08.036] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 08/14/2020] [Accepted: 08/20/2020] [Indexed: 06/11/2023]
Abstract
MiR-210 plays a crucial role in cell survival, migration, and regeneration in vertebrates. In our previous work, the expression of miR-210 was considerably induced in diseased Apostichopus japonicus with skin ulcer syndrome (SUS). To further explore the mechanism of miR-210 in regulating the SUS, this study identified E2F transcription factor 3 (E2F3), a candidate target of miR-210, from the sea cucumber A. japonicus via RNA-seq and RACE (designated as AjE2F3). A 1992 bp fragment representing the full-length cDNA of AjE2F3 was obtained, which includes an ORF of 1194 bp encoding a polypeptide of 398 amino acids with a molecular weight of 44.43 kDa. Expression profiling analysis suggested that the expression of AjE2F3 decreased while that of miR-210 increased in Vibrio splendidus-challenged sea cucumber coelomocytes. Dual-luciferase reporter assay revealed that miR-210 targeted AjE2F3 via binding to the 3'UTR region from 108 nt to 128 nt. MiR-210 overexpression in cultured coelomocytes repressed AjE2F3 at the mRNA level and reduced cell proliferation in vitro. Consistently, AjE2F3 overexpression significantly promoted coelomocyte proliferation, as assessed by MTT in vitro. Overall, our results indicated that miR-210 can suppress coelomocyte proliferation by targeting AjE2F3 in pathogen-challenged sea cucumbers.
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Affiliation(s)
- Yi Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, PR China
| | - Yina Shao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, PR China
| | - Zhimeng Lv
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, PR China
| | - Chenghua Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, PR China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, PR China.
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10
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Parodi S, Ognibene M, Haupt R, Pezzolo A. The Over-Expression of E2F3 Might Serve as Prognostic Marker for Neuroblastoma Patients with Stage 4S Disease. Diagnostics (Basel) 2020; 10:diagnostics10050315. [PMID: 32429447 PMCID: PMC7277942 DOI: 10.3390/diagnostics10050315] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 05/13/2020] [Accepted: 05/14/2020] [Indexed: 12/27/2022] Open
Abstract
Stage 4S neuroblastoma is a childhood cancer occurring in infants (<12 months at diagnosis) with metastases limited to liver, skin, and bone marrow (<10%). It is associated with an excellent outcome, due to its notable ability to undergo spontaneous regression without any therapeutic intervention. However, a subgroup of patients is doomed to relapse and eventually to die in spite of aggressive therapies. Stage 4S neuroblastoma shows characteristic hypermethylation of genes involved in the telomere maintenance, indicating that the dysregulation of these genes might serve as prognostic marker. The retinoblastoma tumor suppressor protein (RB)-E2F transcription factors pathway is one of the critical tumor-suppressor/oncogene pathways involved in regulating telomerase expression. We have interrogated in silicopublic neuroblastoma databases for regulators involved in the RB-E2F pathway especially for E2F factors themselves, and we identified the E2F transcription factor 3 (E2F3) expression as a potential prognostic marker in stage 4S neuroblastoma. In order to confirm this finding, we screened 38 paraffin-embedded tissue samples stage 4S neuroblastoma for E2F3 protein expression using immunofluorescence, and we observed that augmented expression was strongly associated with impaired event-free survival. These results indicate that E2F3 expression might serve as prognostic marker in patients with stage 4S disease.
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Affiliation(s)
- Stefano Parodi
- U.O. Epidemiologia e Biostatistica, IRCCS Istituto Giannina Gaslini, 16147 Genova, Italy;
- Correspondence: (S.P.); (A.P.); Tel.: +39-010-56363531 (S.P.); Fax: +39-010-3779820 (A.P.)
| | - Marzia Ognibene
- U.O.C. Laboratorio Cellule Staminali Post Natali e Terapie Cellulari, IRCCS Istituto Giannina Gaslini, 16147 Genova, Italy;
| | - Riccardo Haupt
- U.O. Epidemiologia e Biostatistica, IRCCS Istituto Giannina Gaslini, 16147 Genova, Italy;
| | - Annalisa Pezzolo
- U.O.C. Laboratorio Cellule Staminali Post Natali e Terapie Cellulari, IRCCS Istituto Giannina Gaslini, 16147 Genova, Italy;
- Correspondence: (S.P.); (A.P.); Tel.: +39-010-56363531 (S.P.); Fax: +39-010-3779820 (A.P.)
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11
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Guo J, Zhang J, Yang T, Zhang W, Liu M. MiR-22 suppresses the growth and metastasis of bladder cancer cells by targeting E2F3. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2020; 13:587-596. [PMID: 32269700 PMCID: PMC7137025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 01/23/2020] [Indexed: 06/11/2023]
Abstract
Bladder cancer is a common, serious disease worldwide. MicroRNAs (miRNAs) have been reported to participate in the development and progression in many cancers, including bladder cancer. However, the exact roles of miR-22 in bladder cancer process and its underlying mechanism remain largely unknown. The expression levels of miR-22 and E2F3 were analyzed by quantitative real-time polymerase chain reaction (qRT-PCR). Western blot was used to detect the protein levels of E2F3, E-cadherin, N-cadherin, and Vimentin in bladder cancer cells. Cell viability, proliferation, migration, and invasion were determined by 3-(4,5-dimethylthiazol-2-yl)-2,5 diphenyltetrazolium bromide (MTT) assay, colony formation assay, and transwell assay, respectively. The potential binding sites between miR-22 and E2F3 were predicted by TargetScan and verified by luciferase report assay. The expression of miR-22 was downregulated and E2F3 expression was upregulated in bladder cancer tissues and cells. Overexpression of miR-22 or E2F3 knockdown inhibited cell proliferation, migration, invasion, and epithelial-mesenchymal transition (EMT) in bladder cancer cells. In addition, E2F3 was a direct target of miR-22 and its knockdown attenuated the promotion of cell proliferation, migration, invasion, and EMT induced by miR-22 inhibitor in bladder cancer cells. In conclusion, miR-22 suppressed cell proliferation, migration, invasion, and EMT in bladder cancer cells by regulating E2F3 expression, providing a novel avenue for treatment of bladder cancer.
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Affiliation(s)
- Junsheng Guo
- Department of Urology, Affiliated Hospital of Chifeng University Chifeng, Inner Mongolia, China
| | - Jian Zhang
- Department of Urology, Affiliated Hospital of Chifeng University Chifeng, Inner Mongolia, China
| | - Tianxiao Yang
- Department of Urology, Affiliated Hospital of Chifeng University Chifeng, Inner Mongolia, China
| | - Wei Zhang
- Department of Urology, Affiliated Hospital of Chifeng University Chifeng, Inner Mongolia, China
| | - Mingyang Liu
- Department of Urology, Affiliated Hospital of Chifeng University Chifeng, Inner Mongolia, China
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12
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Audenet F, Isharwal S, Cha EK, Donoghue MTA, Drill EN, Ostrovnaya I, Pietzak EJ, Sfakianos JP, Bagrodia A, Murugan P, Dalbagni G, Donahue TF, Rosenberg JE, Bajorin DF, Arcila ME, Hechtman JF, Berger MF, Taylor BS, Al-Ahmadie H, Iyer G, Bochner BH, Coleman JA, Solit DB. Clonal Relatedness and Mutational Differences between Upper Tract and Bladder Urothelial Carcinoma. Clin Cancer Res 2019; 25:967-976. [PMID: 30352907 PMCID: PMC6359971 DOI: 10.1158/1078-0432.ccr-18-2039] [Citation(s) in RCA: 158] [Impact Index Per Article: 31.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 08/20/2018] [Accepted: 10/19/2018] [Indexed: 12/23/2022]
Abstract
PURPOSE To investigate genomic differences between urothelial carcinomas of the upper tract (UTUC) and bladder (UCB), with a focus on defining the clonal relatedness of temporally distinct tumors. EXPERIMENTAL DESIGN We prospectively sequenced tumors and matched germline DNA using targeted next-generation sequencing methods. The cohort included 195 UTUC patients and 454 UCB patients. For a subgroup of 29 patients with UTUC and a history of a subsequent UCB, both tumors were analyzed to assess their clonal relatedness. RESULTS With the progression to higher UTUC clinical state, there were fewer alterations in the RTK/RAS pathway but more alterations in TP53/MDM2. Compared with UCB, TP53, RB1, and ERBB2 were less frequently altered in UTUC (26% vs. 46%, 3% vs. 20%, 8% vs. 19%, respectively; Q < 0.001), whereas FGFR3 and HRAS were more frequently altered (40% vs. 26%, 12% vs. 4%, respectively; Q < 0.001). On the basis of an integrated analysis of tumor mutational burden, MSIsensor score and mutational signature, 7.2% of UTUC tumors were classified as MSI-high/MMR-deficient (MSI-H/dMMR). The risk of bladder recurrence after UTUC was significantly associated with mutations in FGFR3, KDM6A, CCND1, and TP53. Comparison of UCB with corresponding UTUC tumors from the same patient supports their clonal relatedness. CONCLUSIONS UTUC and UCB exhibit significant differences in the prevalence of common genomic alterations. In individual patients with a history of both tumors, UCB and UTUC were always clonally related. Genomic characterization of UTUC provides information regarding the risk of bladder recurrence and can identify tumors associated with Lynch syndrome.
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Affiliation(s)
- François Audenet
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York.
| | - Sumit Isharwal
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Eugene K Cha
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Mark T A Donoghue
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Esther N Drill
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Irina Ostrovnaya
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Eugene J Pietzak
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Aditya Bagrodia
- Department of Urology, UT Southwestern Medical Center, Dallas, Texas
| | - Paari Murugan
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, Minnesota
| | - Guido Dalbagni
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Timothy F Donahue
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jonathan E Rosenberg
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Dean F Bajorin
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Maria E Arcila
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jaclyn F Hechtman
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Michael F Berger
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Barry S Taylor
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Hikmat Al-Ahmadie
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Gopa Iyer
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
- Weil Cornell Medical College, New York, New York
| | - Bernard H Bochner
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
- Weil Cornell Medical College, New York, New York
| | - Jonathan A Coleman
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York.
| | - David B Solit
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York.
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
- Weil Cornell Medical College, New York, New York
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13
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Baek HB, Lombard AP, Libertini SJ, Fernandez-Rubio A, Vinall R, Gandour-Edwards R, Nakagawa R, Vidallo K, Nishida K, Siddiqui S, Wettersten H, Landesman Y, Weiss RH, Ghosh PM, Mudryj M. XPO1 inhibition by selinexor induces potent cytotoxicity against high grade bladder malignancies. Oncotarget 2018; 9:34567-34581. [PMID: 30349650 PMCID: PMC6195388 DOI: 10.18632/oncotarget.26179] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 09/15/2018] [Indexed: 12/28/2022] Open
Abstract
Treatment options for high grade urothelial cancers are limited and have remained largely unchanged for several decades. Selinexor (KPT-330), a first in class small molecule that inhibits the nuclear export protein XPO1, has shown efficacy as a single agent treatment for numerous different malignancies, but its efficacy in limiting bladder malignancies has not been tested. In this study we assessed selinexor-dependent cytotoxicity in several bladder tumor cells and report that selinexor effectively reduced XPO1 expression and limited cell viability in a dose dependent manner. The decrease in cell viability was due to an induction of apoptosis and cell cycle arrest. These results were recapitulated in in vivo studies where selinexor decreased tumor growth. Tumors treated with selinexor expressed lower levels of XPO1, cyclin A, cyclin B, and CDK2 and increased levels of RB and CDK inhibitor p27, a result that is consistent with growth arrest. Cells expressing wildtype RB, a potent tumor suppressor that promotes growth arrest and apoptosis, were most susceptible to selinexor. Cell fractionation and immunofluorescence studies showed that selinexor treatment increased nuclear RB levels and mechanistic studies revealed that RB ablation curtailed the response to the drug. Conversely, limiting CDK4/6 dependent RB phosphorylation by palbociclib was additive with selinexor in reducing bladder tumor cell viability, confirming that RB activity has a role in the response to XPO1 inhibition. These results provide a rationale for XPO1 inhibition as a novel strategy for the treatment of bladder malignancies.
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Affiliation(s)
- Han Bit Baek
- Veterans Affairs-Northern California Health Care System, Mather, CA, USA.,Department of Medical Microbiology and Immunology, University of California Davis, Davis, CA, USA
| | - Alan P Lombard
- Veterans Affairs-Northern California Health Care System, Mather, CA, USA.,Department of Medical Microbiology and Immunology, University of California Davis, Davis, CA, USA.,Biochemistry, Molecular, Cellular, and Developmental Biology Graduate Group and Biotechnology Program, University of California Davis, Davis, CA, USA
| | - Stephen J Libertini
- Veterans Affairs-Northern California Health Care System, Mather, CA, USA.,Department of Medical Microbiology and Immunology, University of California Davis, Davis, CA, USA
| | - Aleida Fernandez-Rubio
- Department of Medical Microbiology and Immunology, University of California Davis, Davis, CA, USA
| | - Ruth Vinall
- California Northstate College of Pharmacy, Elk Grove, CA, USA
| | - Regina Gandour-Edwards
- Department of Pathology and Laboratory Medicine, University of California Davis, Sacramento, CA, USA
| | - Rachel Nakagawa
- Department of Medical Microbiology and Immunology, University of California Davis, Davis, CA, USA
| | - Kathleen Vidallo
- Department of Medical Microbiology and Immunology, University of California Davis, Davis, CA, USA
| | - Kristine Nishida
- Department of Medical Microbiology and Immunology, University of California Davis, Davis, CA, USA
| | - Salma Siddiqui
- Veterans Affairs-Northern California Health Care System, Mather, CA, USA
| | - Hiromi Wettersten
- Department of Internal Medicine, University of California Davis, Davis, CA, USA
| | | | - Robert H Weiss
- Veterans Affairs-Northern California Health Care System, Mather, CA, USA.,Department of Internal Medicine, University of California Davis, Davis, CA, USA
| | - Paramita M Ghosh
- Veterans Affairs-Northern California Health Care System, Mather, CA, USA.,Department of Urology, University of California Davis, Sacramento, CA, USA
| | - Maria Mudryj
- Veterans Affairs-Northern California Health Care System, Mather, CA, USA.,Department of Medical Microbiology and Immunology, University of California Davis, Davis, CA, USA
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14
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Alvarado-Kristensson M. γ-tubulin as a signal-transducing molecule and meshwork with therapeutic potential. Signal Transduct Target Ther 2018; 3:24. [PMID: 30221013 PMCID: PMC6137058 DOI: 10.1038/s41392-018-0021-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 04/23/2018] [Accepted: 05/06/2018] [Indexed: 01/05/2023] Open
Abstract
Knowledge of γ-tubulin is increasing with regard to the cellular functions of this protein beyond its participation in microtubule nucleation. γ-Tubulin expression is altered in various malignancies, and changes in the TUBG1 gene have been found in patients suffering from brain malformations. This review recapitulates the known functions of γ-tubulin in cellular homeostasis and discusses the possible influence of the protein on disease development and cancer.
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Affiliation(s)
- Maria Alvarado-Kristensson
- Molecular Pathology, Department of Translational Medicine, Lund University, Skåne University Hospital, Malmö, 20502 Sweden
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15
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Bellmunt J. Stem-Like Signature Predicting Disease Progression in Early Stage Bladder Cancer. The Role of E2F3 and SOX4. Biomedicines 2018; 6:biomedicines6030085. [PMID: 30072631 PMCID: PMC6164884 DOI: 10.3390/biomedicines6030085] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 07/25/2018] [Accepted: 07/26/2018] [Indexed: 12/21/2022] Open
Abstract
The rapid development of the cancer stem cells (CSC) field, together with powerful genome-wide screening techniques, have provided the basis for the development of future alternative and reliable therapies aimed at targeting tumor-initiating cell populations. Urothelial bladder cancer stem cells (BCSCs) that were identified for the first time in 2009 are heterogenous and originate from multiple cell types; including urothelial stem cells and differentiated cell types—basal, intermediate stratum and umbrella cells Some studies hypothesize that BCSCs do not necessarily arise from normal stem cells but might derive from differentiated progenies following mutational insults and acquisition of tumorigenic properties. Conversely, there is data that normal bladder tissues can generate CSCs through mutations. Prognostic risk stratification by identification of predictive markers is of major importance in the management of urothelial cell carcinoma (UCC) patients. Several stem cell markers have been linked to recurrence or progression. The CD44v8-10 to standard CD44-ratio (total ratio of all CD44 alternative splicing isoforms) in urothelial cancer has been shown to be closely associated with tumor progression and aggressiveness. ALDH1, has also been reported to be associated with BCSCs and a worse prognosis in a large number of studies. UCC include low-grade and high-grade non-muscle invasive bladder cancer (NMIBC) and high-grade muscle invasive bladder cancer (MIBC). Important genetic defects characterize the distinct pathways in each one of the stages and probably grades. As an example, amplification of chromosome 6p22 is one of the most frequent changes seen in MIBC and might act as an early event in tumor progression. Interestingly, among NMIBC there is a much higher rate of amplification in high-grade NMIBC compared to low grade NMIBC. CDKAL1, E2F3 and SOX4 are highly expressed in patients with the chromosomal 6p22 amplification aside from other six well known genes (ID4, MBOAT1, LINC00340, PRL, and HDGFL1). Based on that, SOX4, E2F3 or 6q22.3 amplifications might represent potential targets in this tumor type. Focusing more in SOX4, it seems to exert its critical regulatory functions upstream of the Snail, Zeb, and Twist family of transcriptional inducers of EMT (epithelial–mesenchymal transition), but without directly affecting their expression as seen in several cell lines of the Cancer Cell Line Encyclopedia (CCLE) project. SOX4 gene expression correlates with advanced cancer stages and poor survival rate in bladder cancer, supporting a potential role as a regulator of the bladder CSC properties. SOX4 might serve as a biomarker of the aggressive phenotype, also underlying progression from NMIBC to MIBC. The amplicon in chromosome 6 contains SOX4 and E2F3 and is frequently found amplified in bladder cancer. These genes/amplicons might be a potential target for therapy. As an existing hypothesis is that chromatin deregulation through enhancers or super-enhancers might be the underlying mechanism responsible of this deregulation, a potential way to target these transcription factors could be through epigenetic modifiers.
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Affiliation(s)
- Joaquim Bellmunt
- Department of Medical Oncology, Hospital del Mar, IMIM (PSMAR-Hospital del Mar Research Institute), 08003 Barcelona, Spain.
- Harvard Medical School, Boston, MA 02115, USA.
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16
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Lu Y, Li W. Functional characterization of E2F3b in human HepG2 liver cancer cell line. J Cell Biochem 2017; 119:3429-3439. [PMID: 29135049 DOI: 10.1002/jcb.26513] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 10/03/2017] [Indexed: 12/20/2022]
Abstract
E2F3 is a transcription factor that has been shown to be overexpressed in hepatocellular carcinoma (HCC). It is well-known that the E2F3 gene encodes two proteins E2F3a and E2F3b. Therefore, the functions of the two distinct isoforms need to be clarified separately. To characterize the function of E2F3b in HCC, the effects of ectopic expression of E2F3b on cell proliferation, cell cycle, apoptosis and gene expression were investigated. E2F3b promoted G1/S phase transition and markedly increased cell proliferation, but had minor effect on apoptosis. Microarray analyses identified 366 differentially expressed genes (171 upregulated and 195 downregulated) in E2F3b- overexpressing cells. Differential expression of 16 genes relevant to cell cycle and cell proliferation were further verified by real-time PCR. Six genes, including CDC2, CCNE1, ARF, MAP4K2, MUSK, and PAX2 were confirmed to be upregulated by more than twofold; one gene, CCNA2 was validated to be downregulated by more than twofold. We also confirmed that E2F3b increased the protein levels of both cyclin E and Arf but did not affect cyclin D1 protein. These results suggest that E2F3b functions as an important promoter for cell proliferation and plays important roles in transcriptional regulation in HepG2 liver cancer cells.
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Affiliation(s)
- Yujia Lu
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiaotong University, Shanghai, China
| | - Wei Li
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiaotong University, Shanghai, China
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17
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Bertz S, Eckstein M, Stoehr R, Weyerer V, Hartmann A. Urothelial Bladder Cancer: An Update on Molecular Pathology with Clinical Implications. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.eursup.2017.10.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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18
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The Current Status and Future Role of the Phosphoinositide 3 Kinase/AKT Signaling Pathway in Urothelial Cancer: An Old Pathway in the New Immunotherapy Era. Clin Genitourin Cancer 2017; 16:e269-e276. [PMID: 29199023 DOI: 10.1016/j.clgc.2017.10.011] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 10/13/2017] [Accepted: 10/14/2017] [Indexed: 12/11/2022]
Abstract
The phosphoinositide 3 kinase (PI3K)/protein kinase B (AKT)/mammalian target of rapamycin (mTOR) pathway is a well studied signaling pathway that regulates diverse cellular functions including proliferation, metabolism, and transcription. Aberrant activation of this pathway has been implicated in multiple cancers. Genomic studies have shown that activating mutations in oncogenes as well as inactivating mutations in tumor suppressor genes are present across a variety of malignancies, including urothelial carcinoma. In bladder cancer, up to 40% of tumors exhibit constitutive activation of the PI3K/AKT/mTOR pathway. Current treatments for non-muscle-invasive disease confer a 5-year cancer-specific survival rate as high as 90%. However, patients with muscle-invasive, recurrent, or metastatic disease have a poor prognosis. Although the introduction of immune checkpoint inhibitors is certainly changing the therapeutic landscape and is a great addition to the platinum-based therapy that was the standard of care for the past 3 decades, it is anticipated that a great number of patients would fail to respond or their disease would progress with either chemotherapy or immunotherapy. Therefore, the use of agents that target members of the PI3K/AKT/mTOR pathway represent an attractive, alternative therapeutic strategy for patients with advanced urothelial carcinoma. In this review we describe the pathway, with a focus on the rationale for targeting the PI3K/AKT/mTOR pathway in patients with advanced urothelial carcinoma and considers the challenges that we face from the current clinical trials. Novel agents such as PI3K inhibitors and microRNA inhibitors that target this pathway might lead to durable responses especially when used in combination with chemotherapy or immune checkpoint inhibitors, however, toxicity remains an obstacle. Finally, in this review we discuss the importance of developing biomarkers to help select appropriate patients and identify optimal treatment options.
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Nikitin AG, Potapov VY, Brovkina OI, Koksharova EO, Khodyrev DS, Philippov YI, Michurova MS, Shamkhalova MS, Vikulova OK, Smetanina SA, Suplotova LA, Kononenko IV, Kalashnikov VY, Smirnova OM, Mayorov AY, Nosikov VV, Averyanov AV, Shestakova MV. Association of polymorphic markers of genes FTO, KCNJ11, CDKAL1, SLC30A8, and CDKN2B with type 2 diabetes mellitus in the Russian population. PeerJ 2017; 5:e3414. [PMID: 28717589 PMCID: PMC5511504 DOI: 10.7717/peerj.3414] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Accepted: 05/14/2017] [Indexed: 01/11/2023] Open
Abstract
Background The association of type 2 diabetes mellitus (T2DM) with the KCNJ11, CDKAL1, SLC30A8, CDKN2B, and FTO genes in the Russian population has not been well studied. In this study, we analysed the population frequencies of polymorphic markers of these genes. Methods The study included 862 patients with T2DM and 443 control subjects of Russian origin. All subjects were genotyped for 10 single nucleotide polymorphisms (SNPs) of the genes using real-time PCR (TaqMan assays). HOMA-IR and HOMA-β were used to measure insulin resistance and β-cell secretory function, respectively. Results The analysis of the frequency distribution of polymorphic markers for genes KCNJ11, CDKAL1, SLC30A8 and CDKN2B showed statistically significant associations with T2DM in the Russian population. The association between the FTO gene and T2DM was not statistically significant. The polymorphic markers rs5219 of the KCNJ11 gene, rs13266634 of the SLC30A8 gene, rs10811661 of the CDKN2B gene and rs9465871, rs7756992 and rs10946398 of the CDKAL1 gene showed a significant association with impaired glucose metabolism or impaired β-cell function. Conclusion In the Russian population, genes, which affect insulin synthesis and secretion in the β-cells of the pancreas, play a central role in the development of T2DM.
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Affiliation(s)
- Aleksey G Nikitin
- Federal Research Clinical Center for Specialized Types of Health Care and Medical Technologies of Federal Medical and Biology Agency, Moscow, Russian Federation
| | - Viktor Y Potapov
- Clinic of New Medical Technologies "Archimedes", Moscow, Russian Federation
| | - Olga I Brovkina
- Federal Research Clinical Center for Specialized Types of Health Care and Medical Technologies of Federal Medical and Biology Agency, Moscow, Russian Federation
| | | | - Dmitry S Khodyrev
- Federal Research Clinical Center for Specialized Types of Health Care and Medical Technologies of Federal Medical and Biology Agency, Moscow, Russian Federation
| | | | | | | | - Olga K Vikulova
- Endocrinology Research Centre, Moscow, Russian Federation.,I.M. Sechenov First Moscow State Medical University, Moscow, Russian Federation
| | | | | | - Irina V Kononenko
- Endocrinology Research Centre, Moscow, Russian Federation.,I.M. Sechenov First Moscow State Medical University, Moscow, Russian Federation
| | | | - Olga M Smirnova
- Endocrinology Research Centre, Moscow, Russian Federation.,I.M. Sechenov First Moscow State Medical University, Moscow, Russian Federation
| | - Alexander Y Mayorov
- Endocrinology Research Centre, Moscow, Russian Federation.,I.M. Sechenov First Moscow State Medical University, Moscow, Russian Federation
| | - Valery V Nosikov
- State Research Institute of Genetics and Selection of Industrial Microorganisms, Moscow, Russian Federation
| | - Alexander V Averyanov
- Federal Research Clinical Center for Specialized Types of Health Care and Medical Technologies of Federal Medical and Biology Agency, Moscow, Russian Federation
| | - Marina V Shestakova
- Endocrinology Research Centre, Moscow, Russian Federation.,I.M. Sechenov First Moscow State Medical University, Moscow, Russian Federation
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Zacksenhaus E, Liu J, Jiang Z, Yao Y, Xia L, Shrestha M, Ben-David Y. Transcription Factors in Breast Cancer—Lessons From Recent Genomic Analyses and Therapeutic Implications. CHROMATIN PROTEINS AND TRANSCRIPTION FACTORS AS THERAPEUTIC TARGETS 2017; 107:223-273. [DOI: 10.1016/bs.apcsb.2016.10.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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21
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Khodyrev DS, Nikitin AG, Brovkin AN, Lavrikova EY, Lebedeva NO, Vikulova OK, Shamhalova MS, Shestakova MV, Mayorov MY, Potapov VA, Nosikov VV, Averyanov AV. The analysis of association between type 2 diabetes and polymorphic markers in the CDKAL1 gene and in the HHEX/IDE locus. RUSS J GENET+ 2016. [DOI: 10.1134/s1022795416110065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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22
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Zhang Y, Zhang Z, Li Z, Gong D, Zhan B, Man X, Kong C. MicroRNA-497 inhibits the proliferation, migration and invasion of human bladder transitional cell carcinoma cells by targeting E2F3. Oncol Rep 2016; 36:1293-300. [DOI: 10.3892/or.2016.4923] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2016] [Accepted: 02/14/2016] [Indexed: 11/05/2022] Open
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Truncated Isoforms of lncRNA ANRIL Are Overexpressed in Bladder Cancer, But Do Not Contribute to Repression of INK4 Tumor Suppressors. Noncoding RNA 2015; 1:266-284. [PMID: 29861427 PMCID: PMC5932551 DOI: 10.3390/ncrna1030266] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Revised: 12/06/2015] [Accepted: 12/08/2015] [Indexed: 12/23/2022] Open
Abstract
The INK4/ARF locus at chromosome 9p21 encoding p14ARF, p15INK4B and p16INK4A is a major tumor suppressor locus, constituting an important barrier for tumor growth. It is frequently inactivated in cancers, especially in urothelial carcinoma (UC). In addition to deletions and DNA hypermethylation, further epigenetic mechanisms might underlie its repression. One candidate factor is the long noncoding RNA ANRIL, which recruits Polycomb proteins (PcG) to regulate expression of target genes in cis and trans. We observed ANRIL overexpression in many UC tissues and cell lines mainly resulting from upregulation of 3’-truncated isoforms. However, aberrant ANRIL expression was neither associated with repression of INK4/ARF genes nor with proliferation activity or senescence. We wondered whether truncated ANRIL isoforms exhibit altered properties resulting in loss of function in cis. We excluded delocalization and performed RNA immunoprecipitation demonstrating interaction between full length or truncated ANRIL and PcG protein CBX7, but not SUZ12 of PRC2. Our data indicate that ANRIL in UC cells may not interact with PRC2, which is central for initializing gene repression. Thus, tissue-specific binding activities between ANRIL and PcG proteins may determine the regulatory function of ANRIL. In conclusion, ANRIL does not play a major role in repression of the INK4/ARF locus in UC.
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Shen H, Blijlevens M, Yang N, Frangou C, Wilson KE, Xu B, Zhang Y, Zhang L, Morrison CD, Shepherd L, Hu Q, Zhu Q, Wang J, Liu S, Zhang J. Sox4 Expression Confers Bladder Cancer Stem Cell Properties and Predicts for Poor Patient Outcome. Int J Biol Sci 2015; 11:1363-75. [PMID: 26681916 PMCID: PMC4671994 DOI: 10.7150/ijbs.13240] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 08/28/2015] [Indexed: 12/26/2022] Open
Abstract
Genetic and epigenetic alterations have been identified as to contribute directly or indirectly to the generation of transitional cell carcinoma of the urinary bladder (TCC-UB). We have previously found that amplification of chromosome 6p22 is significantly associated with the muscle-invasive rather than superficial TCC-UB. Here, we demonstrated that Sox4, one of the candidate oncogenes located within the chromosome 6p22 amplicon, confers bladder cancer stem cell (CSC) properties. Down-regulation of Sox4 led to the inhibition of cell migration, colony formation as well as mesenchymal-to-epithelial transition (MET). Interestingly, knockdown of Sox4 also reduced the sphere formation, enriched cell population with high levels of aldehyde dehydrogenase (ALDH high) and tumor formation potential. Using gene expression profiling, we further identified novel Sox4 target genes. Last, immunohistochemistry analysis of human bladder tumor tissue microarrays (TMAs) indicated that high Sox4 expression was correlated with advanced cancer stages and poor survival rate. In summary, our data show that Sox4 is an important regulator of the bladder CSC properties and it may serve as a biomarker of the aggressive phenotype in bladder cancer.
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Affiliation(s)
- He Shen
- 1. Department of Cancer Genetics
| | - Maxime Blijlevens
- 1. Department of Cancer Genetics; ; 4. VU medical center, Cancer Center Amsterdam, Laboratory Medical Oncology, De Boelelaan 1118, 1081 HV Amsterdam, The Netherlands
| | - Nuo Yang
- 1. Department of Cancer Genetics
| | | | | | - Bo Xu
- 2. Department of Pathology
| | - Yinglong Zhang
- 1. Department of Cancer Genetics; ; 5. Orthopaedic Oncology Institute, Tangdu Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710032, P.R. China
| | - Lirui Zhang
- 1. Department of Cancer Genetics; ; 6. Department of Gynecology and Obstetrics, The First Affiliated Hospital of Xi'an Jiaotong University School of Medicine, Xi'an, Shaanxi 710061, P.R. China
| | | | - Lori Shepherd
- 3. Center for Biostatistics & Bioinformatics, Roswell Park Cancer Institute, Elm & Carlton Streets, Buffalo NY 14263
| | - Qiang Hu
- 3. Center for Biostatistics & Bioinformatics, Roswell Park Cancer Institute, Elm & Carlton Streets, Buffalo NY 14263
| | - Qianqian Zhu
- 3. Center for Biostatistics & Bioinformatics, Roswell Park Cancer Institute, Elm & Carlton Streets, Buffalo NY 14263
| | - Jianmin Wang
- 3. Center for Biostatistics & Bioinformatics, Roswell Park Cancer Institute, Elm & Carlton Streets, Buffalo NY 14263
| | - Song Liu
- 3. Center for Biostatistics & Bioinformatics, Roswell Park Cancer Institute, Elm & Carlton Streets, Buffalo NY 14263
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Remy E, Rebouissou S, Chaouiya C, Zinovyev A, Radvanyi F, Calzone L. A Modeling Approach to Explain Mutually Exclusive and Co-Occurring Genetic Alterations in Bladder Tumorigenesis. Cancer Res 2015; 75:4042-52. [PMID: 26238783 DOI: 10.1158/0008-5472.can-15-0602] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 06/24/2015] [Indexed: 11/16/2022]
Abstract
Relationships between genetic alterations, such as co-occurrence or mutual exclusivity, are often observed in cancer, where their understanding may provide new insights into etiology and clinical management. In this study, we combined statistical analyses and computational modeling to explain patterns of genetic alterations seen in 178 patients with bladder tumors (either muscle-invasive or non-muscle-invasive). A statistical analysis on frequently altered genes identified pair associations, including co-occurrence or mutual exclusivity. Focusing on genetic alterations of protein-coding genes involved in growth factor receptor signaling, cell cycle, and apoptosis entry, we complemented this analysis with a literature search to focus on nine pairs of genetic alterations of our dataset, with subsequent verification in three other datasets available publicly. To understand the reasons and contexts of these patterns of associations while accounting for the dynamics of associated signaling pathways, we built a logical model. This model was validated first on published mutant mice data, then used to study patterns and to draw conclusions on counter-intuitive observations, allowing one to formulate predictions about conditions where combining genetic alterations benefits tumorigenesis. For example, while CDKN2A homozygous deletions occur in a context of FGFR3-activating mutations, our model suggests that additional PIK3CA mutation or p21CIP deletion would greatly favor invasiveness. Furthermore, the model sheds light on the temporal orders of gene alterations, for example, showing how mutual exclusivity of FGFR3 and TP53 mutations is interpretable if FGFR3 is mutated first. Overall, our work shows how to predict combinations of the major gene alterations leading to invasiveness through two main progression pathways in bladder cancer.
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Affiliation(s)
- Elisabeth Remy
- Aix Marseille Université, CNRS, Centrale Marseille, Marseille, France
| | - Sandra Rebouissou
- Institut Curie, PSL Research University, Paris, France. CNRS, UMR 144, Oncologie Moléculaire, Equipe Labellisée Ligue Contre le Cancer, Institut Curie, Paris, France
| | | | - Andrei Zinovyev
- Institut Curie, PSL Research University, Paris, France. INSERM, U900, Paris, France. Ecole des Mines ParisTech, Fontainebleau, France
| | - François Radvanyi
- Institut Curie, PSL Research University, Paris, France. CNRS, UMR 144, Oncologie Moléculaire, Equipe Labellisée Ligue Contre le Cancer, Institut Curie, Paris, France
| | - Laurence Calzone
- Institut Curie, PSL Research University, Paris, France. INSERM, U900, Paris, France. Ecole des Mines ParisTech, Fontainebleau, France.
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26
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Zehavi L, Schayek H, Jacob-Hirsch J, Sidi Y, Leibowitz-Amit R, Avni D. MiR-377 targets E2F3 and alters the NF-kB signaling pathway through MAP3K7 in malignant melanoma. Mol Cancer 2015; 14:68. [PMID: 25889255 PMCID: PMC4392476 DOI: 10.1186/s12943-015-0338-9] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 03/10/2015] [Indexed: 11/21/2022] Open
Abstract
Background The incidence of cutaneous malignant melanoma continues to rise, and once the disease metastasizes it is almost inevitably fatal. We recently reported that a large miRNAs cluster on human chromosome 14q32, implicated in many types of cancers, is significantly down-regulated in melanoma. miR-377, one of the miRNAs located within this cluster, was studied here. Methods qRT-pCR was used to quantify miR-377 levels in melanoma cell lines and samples. Melanoma cell lines ectopically expressing miR-377 were generated by stable transfection, mRNA expression was assessed using mRNA arrays and protein expression was assessed by Western blot analysis. Potential targets of miR-377 were identified through luciferase reporter assays. Cellular proliferation, migration and soft-agar colony formation were monitored in control and miR-377-expressing cells using cell biology techniques. Results miR-377 is expressed in normal melanocytes but not in melanoma cell lines or samples. Its ectopic stable expression in melanoma cell lines decreased their proliferative and migratory capacity and their colony-forming capability. mRNA arrays of melanoma cells over-expressing miR-377 pointed to several down-regulated mRNAs that have putative binding sites for miR-377 in their 3′UTR, of which both E2F3 and MAP3K7 were found to be direct targets of miR-377. E2F3, a potent transcriptional inducer of cell-cycle progression, was found to be elevated in melanoma cell lines, but decreased following ectopic expression of miR-377. Ectopic miR-377 also led to a decrease in the activity of a reporter plasmid containing three E2F DNA-binding sites linked to a luciferase cDNA sequence, demonstrating that miR-377 down-regulates E2F3-induced transcription. MAP3K7 (known as TAK1), a serine/threonine kinase along the MAPK signaling pathway, was over-expressed in melanoma but decreased following ectopic expression of miR-377. MAP3K7 is involved in the activation of NF-κB. MiR-377 over-expression led to decreased activity of a reporter plasmid containing two NF-κB DNA-binding sites and to decreased output along the NF-kB signaling pathway. Conclusion Our results suggest that miR-377 is an important negative regulator of E2F and MAP3K7/NF-kB signaling pathway in melanoma cells; it is tempting to speculate that its silencing in melanoma promotes the tumorigenic and metastatic potential of the cells through activation of these pathways. Electronic supplementary material The online version of this article (doi:10.1186/s12943-015-0338-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Liron Zehavi
- Center for Cancer Research Sheba Medical Center, Tel Hashomer, Israel. .,Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel.
| | - Hagit Schayek
- Center for Cancer Research Sheba Medical Center, Tel Hashomer, Israel.
| | | | - Yechezkel Sidi
- Center for Cancer Research Sheba Medical Center, Tel Hashomer, Israel. .,Laboratory of Molecular Cell Biology, Center for Cancer Research and Department of Medicine C, Sheba Medical Center, Tel Hashomer, 52621, Israel. .,Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel.
| | - Raya Leibowitz-Amit
- Center for Cancer Research Sheba Medical Center, Tel Hashomer, Israel. .,Institute of Oncology, Sheba Medical Center, Tel Hashomer, 52621, Israel.
| | - Dror Avni
- Center for Cancer Research Sheba Medical Center, Tel Hashomer, Israel. .,Laboratory of Molecular Cell Biology, Center for Cancer Research and Department of Medicine C, Sheba Medical Center, Tel Hashomer, 52621, Israel.
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Knowles MA, Hurst CD. Molecular biology of bladder cancer: new insights into pathogenesis and clinical diversity. Nat Rev Cancer 2015; 15:25-41. [PMID: 25533674 DOI: 10.1038/nrc3817] [Citation(s) in RCA: 812] [Impact Index Per Article: 90.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Urothelial carcinoma of the bladder comprises two long-recognized disease entities with distinct molecular features and clinical outcome. Low-grade non-muscle-invasive tumours recur frequently but rarely progress to muscle invasion, whereas muscle-invasive tumours are usually diagnosed de novo and frequently metastasize. Recent genome-wide expression and sequencing studies identify genes and pathways that are key drivers of urothelial cancer and reveal a more complex picture with multiple molecular subclasses that traverse conventional grade and stage groupings. This improved understanding of molecular features, disease pathogenesis and heterogeneity provides new opportunities for prognostic application, disease monitoring and personalized therapy.
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Affiliation(s)
- Margaret A Knowles
- Section of Experimental Oncology, Leeds Institute of Cancer and Pathology, St James's University Hospital, Beckett Street, Leeds, LS9 7TF, UK
| | - Carolyn D Hurst
- Section of Experimental Oncology, Leeds Institute of Cancer and Pathology, St James's University Hospital, Beckett Street, Leeds, LS9 7TF, UK
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28
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Aftab MN, Dinger ME, Perera RJ. The role of microRNAs and long non-coding RNAs in the pathology, diagnosis, and management of melanoma. Arch Biochem Biophys 2014; 563:60-70. [PMID: 25065585 PMCID: PMC4221535 DOI: 10.1016/j.abb.2014.07.022] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Revised: 07/14/2014] [Accepted: 07/17/2014] [Indexed: 12/21/2022]
Abstract
Melanoma is frequently lethal and its global incidence is steadily increasing. Despite the rapid development of different modes of targeted treatment, durable clinical responses remain elusive. A complete understanding of the molecular mechanisms that drive melanomagenesis is required, both genetic and epigenetic, in order to improve prevention, diagnosis, and treatment. There is increased appreciation of the role of microRNAs (miRNAs) in melanoma biology, including in proliferation, cell cycle, migration, invasion, and immune evasion. Data are also emerging on the role of long non-coding RNAs (lncRNAs), such as SPRY4-IT1, BANCR, and HOTAIR, in melanomagenesis. Here we review the data on the miRNAs and lncRNAs implicated in melanoma biology. An overview of these studies will be useful for providing insights into mechanisms of melanoma development and the miRNAs and lncRNAs that might be useful biomarkers or future therapeutic targets.
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Affiliation(s)
- Muhammad Nauman Aftab
- Sanford-Burnham Medical Research Institute, Orlando, FL 32827, USA; Institute of Industrial Biotechnology, Government College University, Katchery Road, Lahore 54000, Pakistan
| | - Marcel E Dinger
- Garvan Institute of Medical Research and St Vincent's Clinical School, University of New South Wales, Darlinghurst NSW 2010, Australia
| | - Ranjan J Perera
- Sanford-Burnham Medical Research Institute, Orlando, FL 32827, USA.
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Santos M, Martínez-Fernández M, Dueñas M, García-Escudero R, Alfaya B, Villacampa F, Saiz-Ladera C, Costa C, Oteo M, Duarte J, Martínez V, Gómez-Rodriguez MJ, Martín ML, Fernández M, Viatour P, Morcillo MA, Sage J, Castellano D, Rodriguez-Peralto JL, de la Rosa F, Paramio JM. In vivo disruption of an Rb-E2F-Ezh2 signaling loop causes bladder cancer. Cancer Res 2014; 74:6565-6577. [PMID: 25252918 DOI: 10.1158/0008-5472.can-14-1218] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Bladder cancer is a highly prevalent human disease in which retinoblastoma (Rb) pathway inactivation and epigenetic alterations are common events. However, the connection between these two processes is still poorly understood. Here, we show that the in vivo inactivation of all Rb family genes in the mouse urothelium is sufficient to initiate bladder cancer development. The characterization of the mouse tumors revealed multiple molecular features of human bladder cancer, including the activation of E2F transcription factor and subsequent Ezh2 expression and the activation of several signaling pathways previously identified as highly relevant in urothelial tumors. These mice represent a genetically defined model for human high-grade superficial bladder cancer. Whole transcriptional characterizations of mouse and human bladder tumors revealed a significant overlap and confirmed the predominant role for Ezh2 in the downregulation of gene expression programs. Importantly, the increased tumor recurrence and progression in human patients with superficial bladder cancer is associated with increased E2F and Ezh2 expression and Ezh2-mediated gene expression repression. Collectively, our studies provide a genetically defined model for human high-grade superficial bladder cancer and demonstrate the existence of an Rb-E2F-Ezh2 axis in bladder whose disruption can promote tumor development.
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Affiliation(s)
- Mirentxu Santos
- Unidad de Oncología Molecular. CIEMAT (ed70A). Av Complutense 40. 28040 Madrid SPAIN.,Unidad de Oncogenómica. Instituto de Investigación 12 de Octubre i+12, UCM. Av Cordoba s/n. 28041 Madrid SPAIN
| | - Mónica Martínez-Fernández
- Unidad de Oncología Molecular. CIEMAT (ed70A). Av Complutense 40. 28040 Madrid SPAIN.,Unidad de Oncogenómica. Instituto de Investigación 12 de Octubre i+12, UCM. Av Cordoba s/n. 28041 Madrid SPAIN
| | - Marta Dueñas
- Unidad de Oncología Molecular. CIEMAT (ed70A). Av Complutense 40. 28040 Madrid SPAIN.,Unidad de Oncogenómica. Instituto de Investigación 12 de Octubre i+12, UCM. Av Cordoba s/n. 28041 Madrid SPAIN
| | - Ramón García-Escudero
- Unidad de Oncología Molecular. CIEMAT (ed70A). Av Complutense 40. 28040 Madrid SPAIN.,Unidad de Oncogenómica. Instituto de Investigación 12 de Octubre i+12, UCM. Av Cordoba s/n. 28041 Madrid SPAIN
| | - Begoña Alfaya
- Unidad de Oncología Molecular. CIEMAT (ed70A). Av Complutense 40. 28040 Madrid SPAIN
| | - Felipe Villacampa
- Unidad de Uro-Oncología. Hospital Universitario 12 de Octubre. Av Cordoba s/n. 28041 Madrid SPAIN
| | - Cristina Saiz-Ladera
- Unidad de Oncología Molecular. CIEMAT (ed70A). Av Complutense 40. 28040 Madrid SPAIN
| | - Clotilde Costa
- Unidad de Oncología Molecular. CIEMAT (ed70A). Av Complutense 40. 28040 Madrid SPAIN
| | - Marta Oteo
- Unidad de Oncogenómica. Instituto de Investigación 12 de Octubre i+12, UCM. Av Cordoba s/n. 28041 Madrid SPAIN.,Unidad de Aplicaciones Biomédicas y Farmacocinética CIEMAT (ed 12). Av Complutense 40. 28040 Madrid SPAIN
| | - José Duarte
- Unidad de Uro-Oncología. Hospital Universitario 12 de Octubre. Av Cordoba s/n. 28041 Madrid SPAIN
| | - Victor Martínez
- Unidad de Uro-Oncología. Hospital Universitario 12 de Octubre. Av Cordoba s/n. 28041 Madrid SPAIN
| | - Mª José Gómez-Rodriguez
- Unidad de Uro-Oncología. Hospital Universitario 12 de Octubre. Av Cordoba s/n. 28041 Madrid SPAIN
| | - Mª Luisa Martín
- Unidad de Uro-Oncología. Hospital Universitario 12 de Octubre. Av Cordoba s/n. 28041 Madrid SPAIN
| | - Manoli Fernández
- Unidad de Uro-Oncología. Hospital Universitario 12 de Octubre. Av Cordoba s/n. 28041 Madrid SPAIN
| | - Patrick Viatour
- Departments of Pediatrics and Genetics, Stanford University, Stanford, CA 94305, USA
| | - Miguel A Morcillo
- Unidad de Oncogenómica. Instituto de Investigación 12 de Octubre i+12, UCM. Av Cordoba s/n. 28041 Madrid SPAIN.,Unidad de Aplicaciones Biomédicas y Farmacocinética CIEMAT (ed 12). Av Complutense 40. 28040 Madrid SPAIN
| | - Julien Sage
- Departments of Pediatrics and Genetics, Stanford University, Stanford, CA 94305, USA
| | - Daniel Castellano
- Unidad de Uro-Oncología. Hospital Universitario 12 de Octubre. Av Cordoba s/n. 28041 Madrid SPAIN
| | - Jose L Rodriguez-Peralto
- Servicio de Anatomía Patológica. Hospital Universitario 12 de Octubre. Instituto de Investigación 12 de Octubre i+12, UCM. Av Cordoba s/n. 28041 Madrid SPAIN
| | - Federico de la Rosa
- Unidad de Uro-Oncología. Hospital Universitario 12 de Octubre. Av Cordoba s/n. 28041 Madrid SPAIN
| | - Jesús M Paramio
- Unidad de Oncología Molecular. CIEMAT (ed70A). Av Complutense 40. 28040 Madrid SPAIN.,Unidad de Oncogenómica. Instituto de Investigación 12 de Octubre i+12, UCM. Av Cordoba s/n. 28041 Madrid SPAIN
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Shen H, Morrison CD, Zhang J, Underwood W, Yang N, Frangou C, Eng K, Head K, Bollag RJ, Kavuri SK, Rojiani AM, Li Y, Yan L, Hill A, Woloszynska-Read A, Wang J, Liu S, Trump DL, Candace JS. 6p22.3 amplification as a biomarker and potential therapeutic target of advanced stage bladder cancer. Oncotarget 2014; 4:2124-34. [PMID: 24231253 PMCID: PMC3875774 DOI: 10.18632/oncotarget.1485] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Genetic and epigenetic alterations have been identified as to contribute directly or indirectly to the generation of transitional cell carcinoma of the urinary bladder (TCC-UB). In a comparative fashion much less is known about copy number alterations in TCC-UB, but it appears that amplification of chromosome 6p22 is one of the most frequent changes. Using fluorescence in situ hybridization (FISH) analyses, we evaluated chromosomal 6p22 amplification in a large cohort of bladder cancer patients with complete surgical staging and outcome data. We have also used shRNA knockdown candidate oncogenes in the cell based study. We found that amplification of chromosome 6p22.3 is significantly associated with the muscle-invasive transitional cell carcinoma of the urinary bladder (TCC-UB) (22%) in contrast to superficial TCC-UB (9%) (p=7.2-04). The rate of 6p22.3 amplification in pN>1 patients (32%) is more than twice that in pN0 (16%) patients (p=0.05). Interestingly, we found that 6p22.3 amplification is as twice as high (p=0.0201) in African American (AA) than European American (EA) TCC-UB patients. Moreover, we showed that the expression of some candidate genes (E2F3, CDKAL1 and Sox4) in the 6p22.3 region is highly correlated with the chromosomal amplification. In particular, knockdown of E2F3 inhibits cell proliferation in a 6p22.3-dependent manner, whereas knockdown of CDKAL1 and Sox4 has no effect on cell proliferation. Using gene expression profiling, we further identified some common as well as distinctive subset targets of the E2F3 family members. In summary, our data indicate that E2F3 is a key regulator of cell proliferation in a subset of bladder cancer and the 6p22.3 amplicon is a biomarker of aggressive phenotype in this tumor type.
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Affiliation(s)
- He Shen
- Istituto Superiore di Sanità, Rome, Italy
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Retinoblastoma protein (RB) interacts with E2F3 to control terminal differentiation of Sertoli cells. Cell Death Dis 2014; 5:e1274. [PMID: 24901045 PMCID: PMC4611710 DOI: 10.1038/cddis.2014.232] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Revised: 04/08/2014] [Accepted: 04/09/2014] [Indexed: 11/09/2022]
Abstract
The retinoblastoma protein (RB) is essential for normal cell cycle control. RB function depends, at least in part, on interactions with the E2F family of DNA-binding transcription factors (E2Fs). To study the role of RB in the adult testis, a Sertoli cell (SC)-specific Rb knockout mouse line (SC-RbKO) was generated using the Cre/loxP recombination system. SC-RbKO mice exhibited an age-dependent testicular atrophy, impaired fertility, severe SC dysfunction, and spermatogenic defects. Removal of Rb in SC induced aberrant SC cycling, dedifferentiation, and apoptosis. Here we show that E2F3 is the only E2F expressed in mouse SCs and that RB interacts with E2F3 during mouse testicular development. In the absence of RB, the other retinoblastoma family members p107 and p130 began interacting with E2F3 in the adult testes. In vivo silencing of E2F3 partially restored the SC maturation and survival as well as spermatogenesis in the SC-RbKO mice. These results point to RB as a key regulator of SC function in adult mice and that the RB/E2F3 pathway directs SC maturation, cell cycle quiescence, and RB protects SC from apoptosis.
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32
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Wang KL, Mei YY, Cui L, Zhao XX, Li WJ, Gao C, Liu SG, Jiao Y, Liu FF, Wu MY, Ding W, Li ZG. E2F3agene expression has prognostic significance in childhood acute lymphoblastic leukemia. Eur J Haematol 2014; 93:281-9. [PMID: 24758291 DOI: 10.1111/ejh.12341] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/10/2014] [Indexed: 01/27/2023]
Affiliation(s)
- Kai-Ling Wang
- Key Laboratory of Major Diseases in Children (Capital Medical University); Ministry of Education; National Key Discipline of Pediatrics; Ministry of Education; Hematology Center, Beijing Children's Hospital; Capital Medical University; Beijing China
| | - Yan-Yan Mei
- Key Laboratory of Major Diseases in Children (Capital Medical University); Ministry of Education; National Key Discipline of Pediatrics; Ministry of Education; Hematology Center, Beijing Children's Hospital; Capital Medical University; Beijing China
| | - Lei Cui
- Key Laboratory of Major Diseases in Children (Capital Medical University); Ministry of Education; National Key Discipline of Pediatrics; Ministry of Education; Hematology Center, Beijing Children's Hospital; Capital Medical University; Beijing China
| | - Xiao-Xi Zhao
- Key Laboratory of Major Diseases in Children (Capital Medical University); Ministry of Education; National Key Discipline of Pediatrics; Ministry of Education; Hematology Center, Beijing Children's Hospital; Capital Medical University; Beijing China
| | - Wei-Jing Li
- Key Laboratory of Major Diseases in Children (Capital Medical University); Ministry of Education; National Key Discipline of Pediatrics; Ministry of Education; Hematology Center, Beijing Children's Hospital; Capital Medical University; Beijing China
| | - Chao Gao
- Key Laboratory of Major Diseases in Children (Capital Medical University); Ministry of Education; National Key Discipline of Pediatrics; Ministry of Education; Hematology Center, Beijing Children's Hospital; Capital Medical University; Beijing China
| | - Shu-Guang Liu
- Key Laboratory of Major Diseases in Children (Capital Medical University); Ministry of Education; National Key Discipline of Pediatrics; Ministry of Education; Hematology Center, Beijing Children's Hospital; Capital Medical University; Beijing China
| | - Ying Jiao
- Key Laboratory of Major Diseases in Children (Capital Medical University); Ministry of Education; National Key Discipline of Pediatrics; Ministry of Education; Hematology Center, Beijing Children's Hospital; Capital Medical University; Beijing China
| | - Fei-Fei Liu
- Key Laboratory of Major Diseases in Children (Capital Medical University); Ministry of Education; National Key Discipline of Pediatrics; Ministry of Education; Hematology Center, Beijing Children's Hospital; Capital Medical University; Beijing China
| | - Min-Yuan Wu
- Key Laboratory of Major Diseases in Children (Capital Medical University); Ministry of Education; National Key Discipline of Pediatrics; Ministry of Education; Hematology Center, Beijing Children's Hospital; Capital Medical University; Beijing China
| | - Wei Ding
- Department of Medical Genetics; School of Basic Medical Sciences; Capital Medical University; Beijing China
| | - Zhi-Gang Li
- Key Laboratory of Major Diseases in Children (Capital Medical University); Ministry of Education; National Key Discipline of Pediatrics; Ministry of Education; Hematology Center, Beijing Children's Hospital; Capital Medical University; Beijing China
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33
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Kurtyka CA, Chen L, Cress WD. E2F inhibition synergizes with paclitaxel in lung cancer cell lines. PLoS One 2014; 9:e96357. [PMID: 24831239 PMCID: PMC4022639 DOI: 10.1371/journal.pone.0096357] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Accepted: 04/04/2014] [Indexed: 12/22/2022] Open
Abstract
The CDK/Rb/E2F pathway is commonly disrupted in lung cancer, and thus, it is predicted that blocking the E2F pathway would have therapeutic potential. To test this hypothesis, we have examined the activity of HLM006474 (a small molecule pan-E2F inhibitor) in lung cancer cell lines as a single agent and in combination with other compounds. HLM006474 reduces the viability of both SCLC and NSCLC lines with a biological IC50 that varies between 15 and 75 µM, but with no significant difference between the groups. Combination of HLM006474 with cisplatin and gemcitabine demonstrate little synergy; however, HLM006474 synergizes with paclitaxel. Surprisingly, we discovered that brief treatment of cells with HLM006474 led to an increase of E2F3 protein levels (due to de-repression of these promoter sites). Since paclitaxel sensitivity has been shown to correlate with E2F3 levels, we hypothesized that HLM006474 synergy with paclitaxel may be mediated by transient induction of E2F3. To test this, H1299 cells were depleted of E2F3a and E2F3b with siRNA and treated with paclitaxel. Assays of proliferation showed that both siRNAs significantly reduced paclitaxel sensitivity, as expected. Taken together, these results suggest that HLM006474 may have efficacy in lung cancer and may be useful in combination with taxanes.
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Affiliation(s)
- Courtney A. Kurtyka
- Department of Cancer Biology and Evolution, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, United States of America
| | - Lu Chen
- Department of Cancer Biology and Evolution, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, United States of America
| | - W. Douglas Cress
- Department of Cancer Biology and Evolution, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, United States of America
- * E-mail:
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Pinto-Leite R, Carreira I, Melo J, Ferreira SI, Ribeiro I, Ferreira J, Filipe M, Bernardo C, Arantes-Rodrigues R, Oliveira P, Santos L. Genomic characterization of three urinary bladder cancer cell lines: understanding genomic types of urinary bladder cancer. Tumour Biol 2014; 35:4599-617. [PMID: 24459064 DOI: 10.1007/s13277-013-1604-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Accepted: 12/30/2013] [Indexed: 11/25/2022] Open
Abstract
Several genomic regions are frequently altered and associated with the type, stage and progression of urinary bladder cancer (UBC). We present the characterization of 5637, T24 and HT1376 UBC cell lines by karyotyping, fluorescence in situ hybridization (FISH), array comparative genomic hybridization (aCGH) and multiplex ligation-dependent probe amplification (MLPA) analysis. Some cytogenetic anomalies present in UBC were found in the three cell lines, such as chromosome 20 aneuploidy and the loss of 9p21. Some gene loci losses (e.g. CDKN2A) and gains (e.g. HRAS, BCL2L1 and PTPN1) were coincident across all cell lines. Although some significant heterogeneity and complexity were detected between them, their genomic profiles exhibited a similar pattern to UBC. We suggest that 5637 and HT1376 represent the E2F3/RB1 pathway due to amplification of 6p22.3, concomitant with loss of one copy of RB1 and mutation of the remaining copy. The HT1376 presented a 10q deletion involving PTEN region and no alteration of PIK3CA region which, in combination with the inactivation of TP53, bears more invasive and metastatic properties than 5637. The T24 belongs to the alternative pathway of FGFR3/CCND1 by presenting mutated HRAS and over-represented CCND1. These cell lines cover the more frequent subtypes of UBC and are reliable models that can be used, as a group, in preclinical studies.
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Affiliation(s)
- Rosário Pinto-Leite
- Cytogenetic Laboratory, Department of Human Genetics, Hospital Center of Trás-os-Montes and Alto Douro, Vila Real, Portugal
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Selective roles of E2Fs for ErbB2- and Myc-mediated mammary tumorigenesis. Oncogene 2013; 34:119-28. [PMID: 24276244 PMCID: PMC4032808 DOI: 10.1038/onc.2013.511] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Revised: 10/23/2013] [Accepted: 10/25/2013] [Indexed: 11/08/2022]
Abstract
Previous studies have demonstrated that cyclin D1, an upstream regulator of the Rb/E2F pathway, is an essential component of the ErbB2/Ras (but not the Wnt/Myc) oncogenic pathway in the mammary epithelium. However, the role of specific E2fs for ErbB2/Ras-mediated mammary tumorigenesis remains unknown. Here, we show that in the majority of mouse and human primary mammary carcinomas with ErbB2/HER2 overexpression, E2f3a is up-regulated, raising the possibility that E2F3a is a critical effector of the ErbB2 oncogenic signaling pathway in the mammary gland. We examined the consequence of ablating individual E2fs in mice on ErbB2-triggered mammary tumorigenesis in comparison to a comparable Myc-driven mammary tumor model. We found that loss of E2f1 or E2f3 led to a significant delay in tumor onset in both oncogenic models, whereas loss of E2f2 accelerated mammary tumorigenesis driven by Myc-overexpression. Furthermore, southern blot analysis of final tumors derived from conditionally deleted E2f3(-/loxP) mammary glands revealed that there is a selection against E2f3(-/-) cells from developing mammary carcinomas, and that such selection pressure is higher in the presence of ErbB2 activation than in the presence of Myc activation. Taken together, our data suggest oncogenic activities of E2F1 and E2F3 in ErbB2- or Myc-triggered mammary tumorigenesis, and a tumor suppressor role of E2F2 in Myc-mediated mammary tumorigenesis.
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An Q, Wang Y, An R, Li Y, Yao T, Zhai B, Sun X. Association of E2F3 expression with clinicopathological features of Wilms' tumors. J Pediatr Surg 2013; 48:2187-93. [PMID: 24210184 DOI: 10.1016/j.jpedsurg.2013.05.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Revised: 05/07/2013] [Accepted: 05/08/2013] [Indexed: 10/26/2022]
Abstract
PURPOSE The transcription factor E2F3 plays an important role in controlling cell cycle progression and proliferation, and is overexpressed in various human cancers. The present study was undertaken to examine the expression of E2F3 and investigate its relevance in clinical and pathological features of pediatric Wilms' tumors. METHODS Twenty-six Wilms' tumor samples collected at the First Affiliated Hospital of Harbin Medical University underwent immunohistochemical staining for E2F3 protein expression by measuring the percentage of E2F3-positive cells and integrated optical density (IOD), and quantitative real-time polymerase chain reaction (qRT-PCR) for E2F3 mRNA expression. RESULTS The expression of E2F3 protein and mRNA was detectable in all the Wilms' tumor samples with big variations (The average percentage of positive cells was 30.2%±23.5%, range 0.3%-75.6%; average IOD was 6.61×10(4)±3.92×10(4), range 2.32×10(4)-13.84×10(4); average relative mRNA unit was 0.54±0.38, range 0.03-1.31), but not in fetal kidney tissues. Wilms' tumors with aggressive features, such as higher stage, unfavorable histology and higher risk level, expressed higher levels of E2F3 protein and mRNA. CONCLUSIONS The preliminary data indicate that E2F3 is frequently expressed in pediatric Wilms' tumors examined in the present study. E2F3 expression may be associated with Wilms' tumors, particularly those that have more aggressive features. However, further studies are needed to validate these pilot observations and to clarify the functional and mechanistic significance of this association.
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Affiliation(s)
- Qun An
- Department of Pediatric Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin 150001, China
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37
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López V, González-Peramato P, Suela J, Serrano A, Algaba F, Cigudosa JC, Vidal A, Bellmunt J, Heredero O, Sánchez-Carbayo M. Identification of prefoldin amplification (1q23.3-q24.1) in bladder cancer using comparative genomic hybridization (CGH) arrays of urinary DNA. J Transl Med 2013; 11:182. [PMID: 23914742 PMCID: PMC3750577 DOI: 10.1186/1479-5876-11-182] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2013] [Accepted: 06/27/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Array-CGH represents a comprehensive tool to discover genomic disease alterations that could potentially be applied to body fluids. In this report, we aimed at applying array-CGH to urinary samples to characterize bladder cancer. METHODS Urinary DNA from bladder cancer patients and controls were hybridized on 44K oligonucleotide arrays. Validation analyses of identified regions and candidates included fluorescent in situ hybridization (FISH) and immunohistochemistry in an independent set of bladder tumors spotted on custom-made tissue arrays (n = 181). RESULTS Quality control of array-CGH provided high reproducibility in dilution experiments and when comparing reference pools. The most frequent genomic alterations (minimal recurrent regions) among bladder cancer urinary specimens included gains at 1q and 5p, and losses at 10p and 11p. Supervised hierarchical clustering identified the gain at 1q23.3-q24.1 significantly correlated to stage (p = 0.011), and grade (p = 0.002). The amplification and overexpression of Prefoldin (PFND2), a selected candidate mapping to 1q23.3-q24.1, correlated to increasing stage and tumor grade by means of custom-designed and optimized FISH (p = 0.013 and p = 0.023, respectively), and immunohistochemistry (p ≤0.0005 and p = 0.011, respectively), in an independent set of bladder tumors included in tissue arrays. Moreover, PFND2 overexpression was significantly associated with poor disease-specific survival (p ≤0.0005). PFND2 was amplified and overexpressed in bladder tumors belonging to patients providing urinary specimens where 1q23.3q24.1 amplification was detected by array-CGH. CONCLUSIONS Genomic profiles of urinary DNA mirrowed bladder tumors. Molecular profiling of urinary DNA using array-CGH contributed to further characterize genomic alterations involved in bladder cancer progression. PFND2 was identified as a tumor stratification and clinical outcome prognostic biomarker for bladder cancer patients.
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Affiliation(s)
- Virginia López
- Tumor Markers Group, Molecular Pathology Program, Spanish National Cancer Center, Melchor Fernandez Almagro 3, Madrid E-28029, Spain
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Di Fiore R, D'Anneo A, Tesoriere G, Vento R. RB1 in cancer: different mechanisms of RB1 inactivation and alterations of pRb pathway in tumorigenesis. J Cell Physiol 2013; 228:1676-87. [PMID: 23359405 DOI: 10.1002/jcp.24329] [Citation(s) in RCA: 131] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2012] [Accepted: 01/15/2013] [Indexed: 12/14/2022]
Abstract
Loss of RB1 gene is considered either a causal or an accelerating event in retinoblastoma. A variety of mechanisms inactivates RB1 gene, including intragenic mutations, loss of expression by methylation and chromosomal deletions, with effects which are species-and cell type-specific. RB1 deletion can even lead to aneuploidy thus greatly increasing cancer risk. The RB1gene is part of a larger gene family that includes RBL1 and RBL2, each of the three encoding structurally related proteins indicated as pRb, p107, and p130, respectively. The great interest in these genes and proteins springs from their ability to slow down neoplastic growth. pRb can associate with various proteins by which it can regulate a great number of cellular activities. In particular, its association with the E2F transcription factor family allows the control of the main pRb functions, while the loss of these interactions greatly enhances cancer development. As RB1 gene, also pRb can be functionally inactivated through disparate mechanisms which are often tissue specific and dependent on the scenario of the involved tumor suppressors and oncogenes. The critical role of the context is complicated by the different functions played by the RB proteins and the E2F family members. In this review, we want to emphasize the importance of the mechanisms of RB1/pRb inactivation in inducing cancer cell development. The review is divided in three chapters describing in succession the mechanisms of RB1 inactivation in cancer cells, the alterations of pRb pathway in tumorigenesis and the RB protein and E2F family in cancer.
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Affiliation(s)
- Riccardo Di Fiore
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, Polyclinic, University of Palermo, Palermo, Italy
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Eriksson P, Aine M, Sjödahl G, Staaf J, Lindgren D, Höglund M. Detailed Analysis of Focal Chromosome Arm 1q and 6p Amplifications in Urothelial Carcinoma Reveals Complex Genomic Events on 1q, and SOX4 as a Possible Auxiliary Target on 6p. PLoS One 2013; 8:e67222. [PMID: 23825644 PMCID: PMC3688975 DOI: 10.1371/journal.pone.0067222] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2012] [Accepted: 05/20/2013] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Urothelial carcinoma shows frequent amplifications at 6p22 and 1q21-24. The main target gene at 6p22 is believed to be E2F3, frequently co-amplified with CDKAL1 and SOX4. There are however reports on 6p22 amplifications that do not include E2F3. Previous analyses have identified frequent aberrations occurring at 1q21-24. However, due to complex rearrangements it has been difficult to identify specific 1q21-24 target regions and genes. METHODS We selected 29 cases with 6p and 37 cases with 1q focal genomic amplifications from 261 cases of urothelial carcinoma analyzed by array-CGH for high resolution zoom-in oligonucleotide array analyses. Genomic analyses were combined with gene expression data and genomic sequence analyses to characterize and fine map 6p22 and 1q21-24 amplifications. RESULTS We show that the most frequently amplified gene at 6p22 is SOX4 and that SOX4 can be amplified and overexpressed without the E2F3 or CDKAL1 genes being included in the amplicon. Hence, our data point to SOX4 as an auxiliary amplification target at 6p22. We further show that at least three amplified regions are observed at 1q21-24. Copy number data, combined with gene expression data, highlighted BCL9 and CHD1L as possible targets in the most proximal region and MCL1, SETDB1, and HIF1B as putative targets in the middle region, whereas no obvious targets could be determined in the most distal amplicon. We highlight enrichment of G4 quadruplex sequence motifs and a high number of intraregional sequence duplications, both known to contribute to genomic instability, as prominent features of the 1q21-24 region. CONCLUSIONS Our detailed analyses of the 6p22 amplicon suggest SOX4 as an auxiliary target gene for amplification. We further demonstrate three separate target regions for amplification at 1q21-24 and identified BCL9, CHD1L, and MCL1, SETDB1, and HIF1B as putative target genes within these regions.
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Affiliation(s)
- Pontus Eriksson
- Department of Oncology, Clinical Sciences, Skåne University Hospital, Lund University, Lund Sweden
| | - Mattias Aine
- Department of Oncology, Clinical Sciences, Skåne University Hospital, Lund University, Lund Sweden
| | - Gottfrid Sjödahl
- Department of Oncology, Clinical Sciences, Skåne University Hospital, Lund University, Lund Sweden
| | - Johan Staaf
- Department of Oncology, Clinical Sciences, Skåne University Hospital, Lund University, Lund Sweden
- CREATE Health Strategic Center for Translational Cancer Research, Lund University, Lund, Sweden
| | - David Lindgren
- Center for Molecular Pathology, Department of Laboratory Medicine, Skåne University Hospital, Lund University, Malmö, Sweden
| | - Mattias Höglund
- Department of Oncology, Clinical Sciences, Skåne University Hospital, Lund University, Lund Sweden
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Christova N, Tuleva B, Kril A, Georgieva M, Konstantinov S, Terziyski I, Nikolova B, Stoineva I. Chemical structure and in vitro antitumor activity of rhamnolipids from Pseudomonas aeruginosa BN10. Appl Biochem Biotechnol 2013; 170:676-89. [PMID: 23604971 DOI: 10.1007/s12010-013-0225-z] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2011] [Accepted: 04/07/2013] [Indexed: 11/28/2022]
Abstract
A newly isolated indigenous strain BN10 identified as Pseudomonas aeruginosa was found to produce glycolipid (i.e., rhamnolipid-type) biosurfactants. Two representative rhamnolipidic fractions, RL-1 and RL-2, were separated on silica gel columns and their chemical structure was elucidated by a combination of nuclear magnetic resonance and mass spectroscopy. Subsequently, their cytotoxic effect on cancer cell lines HL-60, BV-173, SKW-3, and JMSU-1 was investigated. RL-1 was superior in terms of potency, causing 50 % inhibition of cellular viability at lower concentrations, as compared to RL-2. Furthermore, the results from fluorescent staining analysis demonstrated that RL-1 inhibited proliferation of BV-173 pre-B human leukemia cells by induction of apoptotic cell death. These findings suggest that RL-1 could be of potential for application in biomedicine as a new and promising therapeutic agent.
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Affiliation(s)
- Neli Christova
- Institute of Microbiology, Bulgarian Academy of Sciences, Acad. G. Bonchev str., bl 26, 1113 Sofia, Bulgaria
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Chekaluk Y, Wu CL, Rosenberg J, Riester M, Dai Q, Lin S, Guo Y, McDougal WS, Kwiatkowski DJ. Identification of nine genomic regions of amplification in urothelial carcinoma, correlation with stage, and potential prognostic and therapeutic value. PLoS One 2013; 8:e60927. [PMID: 23593348 PMCID: PMC3617176 DOI: 10.1371/journal.pone.0060927] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Accepted: 03/04/2013] [Indexed: 12/16/2022] Open
Abstract
We performed a genome wide analysis of 164 urothelial carcinoma samples and 27 bladder cancer cell lines to identify copy number changes associated with disease characteristics, and examined the association of amplification events with stage and grade of disease. Multiplex inversion probe (MIP) analysis, a recently developed genomic technique, was used to study 80 urothelial carcinomas to identify mutations and copy number changes. Selected amplification events were then analyzed in a validation cohort of 84 bladder cancers by multiplex ligation-dependent probe assay (MLPA). In the MIP analysis, 44 regions of significant copy number change were identified using GISTIC. Nine gene-containing regions of amplification were selected for validation in the second cohort by MLPA. Amplification events at these 9 genomic regions were found to correlate strongly with stage, being seen in only 2 of 23 (9%) Ta grade 1 or 1–2 cancers, in contrast to 31 of 61 (51%) Ta grade 3 and T2 grade 2 cancers, p<0.001. These observations suggest that analysis of genomic amplification of these 9 regions might help distinguish non-invasive from invasive urothelial carcinoma, although further study is required. Both MIP and MLPA methods perform well on formalin-fixed paraffin-embedded DNA, enhancing their potential clinical use. Furthermore several of the amplified genes identified here (ERBB2, MDM2, CCND1) are potential therapeutic targets.
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Affiliation(s)
- Yvonne Chekaluk
- Division of Translational Medicine, Brigham and Women's Hospital, Boston, Massachusetts, United States of America
| | - Chin-Lee Wu
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Jonathan Rosenberg
- Division of Genitourinary Oncology, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
| | - Markus Riester
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, and Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Qishan Dai
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Sharron Lin
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Yanan Guo
- Division of Translational Medicine, Brigham and Women's Hospital, Boston, Massachusetts, United States of America
| | - W. Scott McDougal
- Department of Urology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- * E-mail: (DJK); (WSM)
| | - David J. Kwiatkowski
- Division of Translational Medicine, Brigham and Women's Hospital, Boston, Massachusetts, United States of America
- * E-mail: (DJK); (WSM)
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Niini T, Scheinin I, Lahti L, Savola S, Mertens F, Hollmén J, Böhling T, Kivioja A, Nord KH, Knuutila S. Homozygous deletions of cadherin genes in chondrosarcoma—an array comparative genomic hybridization study. Cancer Genet 2012; 205:588-93. [DOI: 10.1016/j.cancergen.2012.09.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2012] [Revised: 09/26/2012] [Accepted: 09/27/2012] [Indexed: 12/11/2022]
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43
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Vimala K, Sundarraj S, Sujitha MV, Kannan S. Curtailing overexpression of E2F3 in breast cancer using siRNA (E2F3)-based gene silencing. Arch Med Res 2012; 43:415-22. [PMID: 22960857 DOI: 10.1016/j.arcmed.2012.08.009] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2011] [Accepted: 08/06/2012] [Indexed: 12/24/2022]
Abstract
BACKGROUND AND AIMS The E2F3 transcription factor claims its role in controlling cell cycle progression. As reported earlier, nuclear E2F3 overexpression leads to development of bladder and prostate cancer in humans. Accordingly, the present investigation has been designed to assess to what extent E2F3 would be overexpressed in breast cancer. The aim of this study was to emphasize that the levels of E2F3 are increased in breast cancer and highlights the efficacy of siRNA targeted to E2F3. METHODS To investigate the expression level of E2F3 and the progression of breast tumors, quantitative real-time PCR analysis was carried out. Western blotting analysis was performed to measure its counterparts, namely, E2F3a and E2F3b. RESULTS In the novel axis of E2F3, a large set of 11 breast cancer cell lines were identified to have the property of overexpression. Furthermore, the small interfering RNA (siRNA) developed against E2F3 significantly blocked the expression of the E2F3 in the selected breast cancer cell lines. Thus, the present findings authenticate the efficiency of siRNA (E2F3) to fight against breast cancer; hence, the siRNA mediated E2F3 gene silencing knockdown the E2F3. CONCLUSIONS This in vitro study demonstrates that E2F3 is a newly identified diagnostic and potential therapeutic target in breast cancer. Outcomes of this study affirm that siRNA for E2F3 facilitates the silencing of E2F3 overexpression and fights against breast cancer. Therefore, it plays a vital role as an alternative for diagnosis and clinical outcome for the treatment of breast cancer.
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Affiliation(s)
- Karuppaiya Vimala
- Proteomics and Molecular Cell Physiology Laboratory, Department of Zoology, School of Life Sciences, Bharathiar University, Coimbatore, TN 641046, India
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Lindgren D, Sjödahl G, Lauss M, Staaf J, Chebil G, Lövgren K, Gudjonsson S, Liedberg F, Patschan O, Månsson W, Fernö M, Höglund M. Integrated genomic and gene expression profiling identifies two major genomic circuits in urothelial carcinoma. PLoS One 2012; 7:e38863. [PMID: 22685613 PMCID: PMC3369837 DOI: 10.1371/journal.pone.0038863] [Citation(s) in RCA: 149] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2012] [Accepted: 05/13/2012] [Indexed: 11/29/2022] Open
Abstract
Similar to other malignancies, urothelial carcinoma (UC) is characterized by specific recurrent chromosomal aberrations and gene mutations. However, the interconnection between specific genomic alterations, and how patterns of chromosomal alterations adhere to different molecular subgroups of UC, is less clear. We applied tiling resolution array CGH to 146 cases of UC and identified a number of regions harboring recurrent focal genomic amplifications and deletions. Several potential oncogenes were included in the amplified regions, including known oncogenes like E2F3, CCND1, and CCNE1, as well as new candidate genes, such as SETDB1 (1q21), and BCL2L1 (20q11). We next combined genome profiling with global gene expression, gene mutation, and protein expression data and identified two major genomic circuits operating in urothelial carcinoma. The first circuit was characterized by FGFR3 alterations, overexpression of CCND1, and 9q and CDKN2A deletions. The second circuit was defined by E3F3 amplifications and RB1 deletions, as well as gains of 5p, deletions at PTEN and 2q36, 16q, 20q, and elevated CDKN2A levels. TP53/MDM2 alterations were common for advanced tumors within the two circuits. Our data also suggest a possible RAS/RAF circuit. The tumors with worst prognosis showed a gene expression profile that indicated a keratinized phenotype. Taken together, our integrative approach revealed at least two separate networks of genomic alterations linked to the molecular diversity seen in UC, and that these circuits may reflect distinct pathways of tumor development.
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Affiliation(s)
- David Lindgren
- Department of Molecular Pathology, Lund University, Malmö, Sweden
| | - Gottfrid Sjödahl
- Canceromics Branch, Department of Oncology, Lund University, Lund, Sweden
| | - Martin Lauss
- Canceromics Branch, Department of Oncology, Lund University, Lund, Sweden
| | - Johan Staaf
- Canceromics Branch, Department of Oncology, Lund University, Lund, Sweden
| | - Gunilla Chebil
- Department of Oncology, Lund University, Skåne University Hospital, Lund, Sweden
| | - Kristina Lövgren
- Department of Oncology, Lund University, Skåne University Hospital, Lund, Sweden
| | | | | | - Oliver Patschan
- Department of Urology, Skåne University Hospital, Malmö, Sweden
| | - Wiking Månsson
- Department of Urology, Skåne University Hospital, Malmö, Sweden
| | - Mårten Fernö
- Department of Oncology, Lund University, Skåne University Hospital, Lund, Sweden
| | - Mattias Höglund
- Canceromics Branch, Department of Oncology, Lund University, Lund, Sweden
- * E-mail:
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Abstract
Osteosarcoma is a primary bone malignancy with a particularly high incidence rate in children and adolescents relative to other age groups. The etiology of this often aggressive cancer is currently unknown, because complicated structural and numeric genomic rearrangements in cancer cells preclude understanding of tumour development. In addition, few consistent genetic changes that may indicate effective molecular therapeutic targets have been reported. However, high-resolution techniques continue to improve knowledge of distinct areas of the genome that are more commonly associated with osteosarcomas. Copy number gains at chromosomes 1p, 1q, 6p, 8q, and 17p as well as copy number losses at chromosomes 3q, 6q, 9, 10, 13, 17p, and 18q have been detected by numerous groups, but definitive oncogenes or tumour suppressor genes remain elusive with respect to many loci. In this paper, we examine studies of the genetics of osteosarcoma to comprehensively describe the heterogeneity and complexity of this cancer.
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Rebouissou S, Hérault A, Letouzé E, Neuzillet Y, Laplanche A, Ofualuka K, Maillé P, Leroy K, Riou A, Lepage ML, Vordos D, de la Taille A, Denoux Y, Sibony M, Guyon F, Lebret T, Benhamou S, Allory Y, Radvanyi F. CDKN2A
homozygous deletion is associated with muscle invasion in FGFR3
-mutated urothelial bladder carcinoma. J Pathol 2012; 227:315-24. [DOI: 10.1002/path.4017] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2011] [Revised: 02/20/2012] [Accepted: 02/24/2012] [Indexed: 11/06/2022]
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Libertini SJ, Chen H, al-Bataina B, Koilvaram T, George M, Gao AC, Mudryj M. The interleukin 6 receptor is a direct transcriptional target of E2F3 in prostate tumor derived cells. Prostate 2012; 72:649-60. [PMID: 21837779 DOI: 10.1002/pros.21468] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/13/2011] [Accepted: 07/05/2011] [Indexed: 01/09/2023]
Abstract
BACKGROUND The E2F/RB pathway is frequently disrupted in multiple human cancers. E2F3 levels are elevated in prostate tumors and E2F3 overexpression independently predicts clinical outcome. The goals of this study were to identify direct transcriptional targets of E2F3 in prostate tumor derived cells. METHODS Expression array studies identified the interleukin 6 receptor (IL-6R) as an E2F3 target. E2F3-dependent expression of IL-6R was analyzed by real time PCR and Western immunoblot analysis in several cell lines. Chromatin immunoprecipitation (ChIP) and IL-6R-luciferase reporter plasmid studies were used to characterize the IL-6R promoter. RESULTS Expression array studies identified genes that were regulated by E2F3 in prostate tumor derived cell lines. The network most significantly associated with E2F3-regulated transcripts was cytokine signaling and the IL-6R was a component of several of the most prominent E2F3-regulated pathways. The transcriptional regulation of IL-6R by E2F3 knockdown was validated in several prostate tumor-derived cell lines at the RNA level and protein level. The IL-6R regulatory region containing ChIP-identified E2F3 binding sites was cloned into a reporter and co-transfected with an E2F3a expression plasmid. The luciferase assay showed that E2F3a transactivated the IL-6R promoter in a dose dependent manner. The functional consequence of IL-6R decrease was a reduction in the levels of ERK1/2 phosphorylation, indicating that IL-6R initiated signaling was altered. CONCLUSION These studies connect the E2F and IL-6 signaling cascade, thus providing the mechanistic link between two major regulatory networks that are perturbed during prostate tumorigenesis.
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Affiliation(s)
- Stephen J Libertini
- Veterans Affairs-Northern California Health Care System, Mather, California, USA
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Miles WO, Tschöp K, Herr A, Ji JY, Dyson NJ. Pumilio facilitates miRNA regulation of the E2F3 oncogene. Genes Dev 2012; 26:356-68. [PMID: 22345517 DOI: 10.1101/gad.182568.111] [Citation(s) in RCA: 121] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
E2F transcription factors are important regulators of cell proliferation and are frequently dysregulated in human malignancies. To identify novel regulators of E2F function, we used Drosophila as a model system to screen for mutations that modify phenotypes caused by reduced levels of dE2F1. This screen identified components of the Pumilio translational repressor complex (Pumilio, Nanos, and Brain tumor) as suppressors of dE2F1-RNAi phenotypes. Subsequent experiments provided evidence that Pumilio complexes repress dE2F1 levels and that this mechanism of post-transcriptional regulation is conserved in human cells. The human Pumilio homologs Pum 1 and Pum 2 repress the translation of E2F3 by binding to the E2F3 3' untranslated region (UTR) and also enhance the activity of multiple E2F3 targeting microRNAs (miRNAs). E2F3 is an oncogene with strong proliferative potential and is regularly dysregulated or overexpressed in cancer. Interestingly, Pumilio/miRNA-mediated regulation of E2F3 is circumvented in cancer cells in several different ways. Bladder carcinomas selectively down-regulate miRNAs that cooperate with Pumilio to target E2F3, and multiple tumor cell lines shorten the 3' end of the E2F3 mRNA, removing the Pumilio regulatory elements. These studies suggest that Pumilio-miRNA repression of E2F3 translation provides an important level of E2F regulation that is frequently abrogated in cancer cells.
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Affiliation(s)
- Wayne O Miles
- Massachusetts General Hospital Cancer Center, Laboratory of Molecular Oncology, Harvard Medical School, Charlestown, 02129, USA
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Varanasi L, Do PM, Goluszko E, Martinez LA. Rad18 is a transcriptional target of E2F3. Cell Cycle 2012; 11:1131-41. [PMID: 22391204 DOI: 10.4161/cc.11.6.19558] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The E2F family of transcription factors responds to a variety of intracellular and extracellular signals and, as such, are key regulators of cell growth, differentiation and cell death. The cellular response to DNA damage is a multistep process generally involving the initial detection of DNA damage, propagation of signals via posttranslational modifications (e.g., phosphorylation and ubiquitination) and, finally, the implementation of a response. We have previously reported that E2F3 can be induced by DNA damage, and that it plays an important role in DNA damage-induced apoptosis. Here, we demonstrate that E2F3 knockdown compromises two canonical DNA damage modification events, the ubiquitination of H2AX and PCNA. We find that the defect in these posttranscriptional modifications after E2F3 knockdown is due to reduced expression of important DNA damage responsive ubiquitin ligases. We characterized the regulation of one of these ligases, Rad18, and we demonstrated that E2F3 associates with the Rad18 promoter and directly controls its activity. Furthermore, we find that ectopic expression of Rad18 is sufficient to rescue the PCNA ubiquitination defect resulting from E2F3 knockdown. Our study reveals a novel facet of E2F3's control of the DNA damage response.
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Affiliation(s)
- Lakshman Varanasi
- Department of Biochemistry and University of Mississippi Cancer Institute, University of Mississippi Medical Center, Jackson, MS, USA
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Noguchi S, Mori T, Otsuka Y, Yamada N, Yasui Y, Iwasaki J, Kumazaki M, Maruo K, Akao Y. Anti-oncogenic microRNA-203 induces senescence by targeting E2F3 protein in human melanoma cells. J Biol Chem 2012; 287:11769-77. [PMID: 22354972 DOI: 10.1074/jbc.m111.325027] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
MicroRNAs regulate gene expression by repressing translation or directing sequence-specific degradation of their complementary mRNA. We recently reported that miR-203 is down-regulated, and its exogenous expression inhibits cell growth in canine oral malignant melanoma tissue specimens as well as in canine and human malignant melanoma cells. A microRNA target database predicted E2F3 and ZBP-89 as putative targets of microRNA-203 (miR-203). The expression levels of E2F3a, E2F3b, and ZBP-89 were markedly up-regulated in human malignant melanoma Mewo cells compared with those in human epidermal melanocytes. miR-203 significantly suppressed the luciferase activity of reporter plasmids containing the 3'-UTR sequence of either E2F3 or ZBP-89 complementary to miR-203. The ectopic expression of miR-203 in melanoma cells reduced the levels of E2F3a, E2F3b, and ZBP-89 protein expression. At the same time, miR-203 induced cell cycle arrest and senescence phenotypes, such as elevated expression of hypophosphorylated retinoblastoma and other markers for senescence. Silencing of E2F3, but not of ZBP-89, inhibited cell growth and induced cell cycle arrest and senescence. These results demonstrate a novel role for miR-203 as a tumor suppressor acting by inducing senescence in melanoma cells.
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Affiliation(s)
- Shunsuke Noguchi
- United Graduate School of Veterinary Sciences, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
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