1
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Lee S, Bondaruk J, Wang Y, Chen H, Lee JG, Majewski T, Mullen RD, Cogdell D, Chen J, Wang Z, Yao H, Kus P, Jeong J, Lee I, Choi W, Navai N, Guo C, Dinney C, Baggerly K, Mendelsohn C, McConkey D, Behringer RR, Kimmel M, Wei P, Czerniak B. Loss of LPAR6 and CAB39L dysregulates the basal-to-luminal urothelial differentiation program, contributing to bladder carcinogenesis. Cell Rep 2024; 43:114146. [PMID: 38676926 PMCID: PMC11265536 DOI: 10.1016/j.celrep.2024.114146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 02/19/2024] [Accepted: 04/09/2024] [Indexed: 04/29/2024] Open
Abstract
We describe a strategy that combines histologic and molecular mapping that permits interrogation of the chronology of changes associated with cancer development on a whole-organ scale. Using this approach, we present the sequence of alterations around RB1 in the development of bladder cancer. We show that RB1 is not involved in initial expansion of the preneoplastic clone. Instead, we found a set of contiguous genes that we term "forerunner" genes whose silencing is associated with the development of plaque-like field effects initiating carcinogenesis. Specifically, we identified five candidate forerunner genes (ITM2B, LPAR6, MLNR, CAB39L, and ARL11) mapping near RB1. Two of these genes, LPAR6 and CAB39L, are preferentially downregulated in the luminal and basal subtypes of bladder cancer, respectively. Their loss of function dysregulates urothelial differentiation, sensitizing the urothelium to N-butyl-N-(4-hydroxybutyl)nitrosamine-induced cancers, which recapitulate the luminal and basal subtypes of human bladder cancer.
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Affiliation(s)
- Sangkyou Lee
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jolanta Bondaruk
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yishan Wang
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Huiqin Chen
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - June Goo Lee
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Tadeusz Majewski
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Rachel D Mullen
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - David Cogdell
- Department of Neurosurgery, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jiansong Chen
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ziqiao Wang
- Department of Biostatistics, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Hui Yao
- Department of Bioinformatics & Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Pawel Kus
- Department of Systems Biology and Engineering, Silesian University of Technology, Gliwice, Poland
| | - Joon Jeong
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ilkyun Lee
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Woonyoung Choi
- Johns Hopkins Greenberg Bladder Cancer Institute, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Neema Navai
- Department of Urology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Charles Guo
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Colin Dinney
- Department of Urology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Keith Baggerly
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Cathy Mendelsohn
- Department of Urology, Genetics & Development and Pathology, Columbia University, New York, NY 10032, USA
| | - David McConkey
- Johns Hopkins Greenberg Bladder Cancer Institute, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Richard R Behringer
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Marek Kimmel
- Department of Statistics, Rice University, Houston, TX 77005, USA
| | - Peng Wei
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Bogdan Czerniak
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
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Czerniak B, Lee S, Jung SY, Kus P, Bondaruk J, Lee J, Jaksik R, Putluri N, Dinh K, Cogdell D, Chen H, Wang Y, Chen J, Nevai N, Dinney C, Mendelsohn C, McConkey D, Behringer R, Guo C, Wei P, Kimmel M. Inferring Bladder Cancer Evolution from Mucosal field Effects by Whole-Organ Spatial Mutational, Proteomic, and Metabolomic Mapping. RESEARCH SQUARE 2024:rs.3.rs-3994376. [PMID: 38659962 PMCID: PMC11042420 DOI: 10.21203/rs.3.rs-3994376/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Multi-platform mutational, proteomic, and metabolomic spatial mapping was used on the whole-organ scale to identify the molecular evolution of bladder cancer from mucosal field effects. We identified complex proteomic and metabolomic dysregulations in microscopically normal areas of bladder mucosa adjacent to dysplasia and carcinoma in situ. The mutational landscape developed in a background of complex defects of protein homeostasis which included dysregulated nucleocytoplasmic transport, splicesome, ribosome biogenesis, and peroxisome. These changes were combined with altered urothelial differentiation which involved lipid metabolism and protein degradations controlled by PPAR. The complex alterations of proteome were accompanied by dysregulation of gluco-lipid energy-related metabolism. The analysis of mutational landscape identified three types of mutations based on their geographic distribution and variant allele frequencies. The most common were low frequency α mutations restricted to individual mucosal samples. The two other groups of mutations were associated with clonal expansion. The first of this group referred to as β mutations occurred at low frequencies across the mucosa. The second of this group called γ mutations increased in frequency with disease progression. Modeling of the mutations revealed that carcinogenesis may span nearly 30 years and can be divided into dormant and progressive phases. The α mutations developed gradually in the dormant phase. The progressive phase lasted approximately five years and was signified by the advent of β mutations, but it was driven by γ mutations which developed during the last 2-3 years of disease progression to invasive cancer. Our study indicates that the understanding of complex alterations involving mucosal microenvironment initiating bladder carcinogenesis can be inferred from the multi-platform whole-organ mapping.
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Affiliation(s)
| | - Sangkyou Lee
- The University of Texas MD Anderson Cancer Center
| | | | | | | | - June Lee
- The University of Texas MD Anderson Cancer Center
| | | | | | - Khanh Dinh
- Irving Institute for Cancer Dynamics, Columbia University
| | | | - Huiqin Chen
- The University of Texas MD Anderson Cancer Center
| | - Yishan Wang
- The University of Texas MD Anderson Cancer Center
| | | | - Neema Nevai
- The University of Texas MD Anderson Cancer Center
| | - Colin Dinney
- The University of Texas MD Anderson Cancer Center
| | | | - David McConkey
- Johns Hopkins Greenberg Bladder Cancer Institute, Johns Hopkins University
| | | | - Charles Guo
- The University of Texas MD Anderson Cancer Center
| | - Peng Wei
- The University of Texas MD Anderson Cancer Center
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3
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Mendonça V, Pereira Sena P, Evangelista Dos Santos AC, Rodrigues Bonvicino C, Ashton-Prolla P, Epelman S, Ferman SE, Lapunzina P, Nevado J, Grigorovski N, Mattosinho C, Seuànez H, Regla Vargas F. Diverse mutational spectrum in the 13q14 chromosomal region in a Brazilian cohort of retinoblastoma. Exp Eye Res 2022; 224:109211. [PMID: 35985532 DOI: 10.1016/j.exer.2022.109211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 07/19/2022] [Accepted: 08/03/2022] [Indexed: 11/27/2022]
Abstract
Retinoblastoma is a rare childhood tumor caused by the inactivation of both copies of the RB1 gene. Early diagnosis and identification of heritable RB1 mutation carriers can improve the disease outcome and management via genetic counseling. We used the Multiplex Ligation-dependent Probe Amplification (MLPA) method to analyze the RB1 gene and flanking regions in blood samples from 159 retinoblastoma patients previously negative for RB1 point mutations via Sanger sequencing. We detected a wide spectrum of germline chromosomal alterations, ranging from partial loss or duplication of RB1 to large deletions spanning RB1 and adjacent genes. Mutations were validated via karyotyping, fluorescent in situ hybridization (FISH), SNP-arrays (Single Nucleotide Polymorphism-arrays) and/or quantitative relative real-time PCR. Patients with leukocoria as a presenting symptom showed reduced death rate (p = 0.013) and this sign occurred more frequently among carriers of two breakpoints within RB1 (p = 0.05). All unilateral cases presented both breakpoints outside of RB1 (p = 0.0075). Patients with one breakpoint within RB1 were diagnosed at earlier ages (p = 0.017). Our findings characterize the mutational spectrum of a Brazilian cohort of retinoblastoma patients and point to a possible relationship between the mutation breakpoint location and tumor outcome, contributing to a better prospect of the genotype/phenotype correlation and adding to the wide diversity of germline mutations involving RB1 and adjacent regions in retinoblastoma.
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Affiliation(s)
- Vanessa Mendonça
- Genetics Program, Instituto Nacional de Câncer, Rio de Janeiro, Brazil; Genetics Department, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
| | - Priscila Pereira Sena
- Genetics Program, Instituto Nacional de Câncer, Rio de Janeiro, Brazil; Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | | | | | | | - Sidnei Epelman
- Pediatric Oncology Service, Hospital Santa Marcelina, São Paulo, Brazil
| | - Sima Esther Ferman
- Department of Pediatric Oncology, Clinical Division, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | - Pablo Lapunzina
- INGEMM, Hospital La Paz, Universidad de Madrid, Madrid, Spain; CIBERER (Centro de Investigación Médica en Red de Enfermedades Raras), Madrid, Spain; ITHACA-European Reference Network, Hospital La Paz, Madrid, Spain
| | - Julián Nevado
- INGEMM, Hospital La Paz, Universidad de Madrid, Madrid, Spain; CIBERER (Centro de Investigación Médica en Red de Enfermedades Raras), Madrid, Spain; ITHACA-European Reference Network, Hospital La Paz, Madrid, Spain
| | - Nathalia Grigorovski
- Department of Pediatric Oncology, Clinical Division, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | - Clarissa Mattosinho
- Department of Ocular Oncology, Division of Surgery, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | - Hector Seuànez
- Genetics Program, Instituto Nacional de Câncer, Rio de Janeiro, Brazil; Genetics Department, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Fernando Regla Vargas
- Birth Defects Epidemiology Laboratory, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil; Department of Genetics and Molecular Biology, Universidade Federal do Estado do Rio de Janeiro, Rio de Janeiro, Brazil
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4
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Bondaruk J, Jaksik R, Wang Z, Cogdell D, Lee S, Chen Y, Dinh KN, Majewski T, Zhang L, Cao S, Tian F, Yao H, Kuś P, Chen H, Weinstein JN, Navai N, Dinney C, Gao J, Theodorescu D, Logothetis C, Guo CC, Wang W, McConkey D, Wei P, Kimmel M, Czerniak B. The origin of bladder cancer from mucosal field effects. iScience 2022; 25:104551. [PMID: 35747385 PMCID: PMC9209726 DOI: 10.1016/j.isci.2022.104551] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 11/19/2021] [Accepted: 06/02/2022] [Indexed: 12/30/2022] Open
Abstract
Whole-organ mapping was used to study molecular changes in the evolution of bladder cancer from field effects. We identified more than 100 dysregulated pathways, involving immunity, differentiation, and transformation, as initiators of carcinogenesis. Dysregulation of interleukins signified the involvement of inflammation in the incipient phases of the process. An aberrant methylation/expression of multiple HOX genes signified dysregulation of the differentiation program. We identified three types of mutations based on their geographic distribution. The most common were mutations restricted to individual mucosal samples that targeted uroprogenitor cells. Two types of mutations were associated with clonal expansion and involved large areas of mucosa. The α mutations occurred at low frequencies while the β mutations increased in frequency with disease progression. Modeling revealed that bladder carcinogenesis spans 10-15 years and can be divided into dormant and progressive phases. The progressive phase lasted 1-2 years and was driven by β mutations.
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Affiliation(s)
- Jolanta Bondaruk
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Roman Jaksik
- Department of Systems Biology and Engineering and Biotechnology Centre, Silesian University of Technology, Gliwice, Poland
| | - Ziqiao Wang
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - David Cogdell
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sangkyou Lee
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yujie Chen
- Systems, Synthetic and Physical Biology Program, Rice University, Houston, TX, USA
| | - Khanh Ngoc Dinh
- Department of Statistics and the Irving Institute for Cancer Dynamics, Columbia University, New York, NY, USA
| | - Tadeusz Majewski
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Li Zhang
- Department of Environmental Health, University of Cincinnati, Cincinnati, OH, USA
| | - Shaolong Cao
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Feng Tian
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Hui Yao
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Paweł Kuś
- Department of Systems Biology and Engineering and Biotechnology Centre, Silesian University of Technology, Gliwice, Poland
| | - Huiqin Chen
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - John N. Weinstein
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Neema Navai
- Department of Urology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Colin Dinney
- Department of Urology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jianjun Gao
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, TX, USA
| | - Dan Theodorescu
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai, Los Angeles, CA, USA
| | - Christopher Logothetis
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, TX, USA
| | - Charles C. Guo
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Wenyi Wang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - David McConkey
- Johns Hopkins Greenberg Bladder Cancer Institute, Johns Hopkins University, Baltimore, MD, USA
| | - Peng Wei
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Marek Kimmel
- Department of Statistics, Rice University, Houston, TX, USA
| | - Bogdan Czerniak
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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5
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Di Sciascio L, Ambrosi F, Franceschini T, Giunchi F, Franchini E, Massari F, Bianchi FM, Colecchia M, Fiorentino M, Ricci C. Could double stain for p53/CK20 be a useful diagnostic tool for the appropriate classification of flat urothelial lesions? Pathol Res Pract 2022; 234:153937. [DOI: 10.1016/j.prp.2022.153937] [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: 04/04/2022] [Revised: 04/30/2022] [Accepted: 05/04/2022] [Indexed: 10/18/2022]
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Lokeshwar SD, Lopez M, Sarcan S, Aguilar K, Morera DS, Shaheen DM, Lokeshwar BL, Lokeshwar VB. Molecular Oncology of Bladder Cancer from Inception to Modern Perspective. Cancers (Basel) 2022; 14:cancers14112578. [PMID: 35681556 PMCID: PMC9179261 DOI: 10.3390/cancers14112578] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 05/19/2022] [Accepted: 05/20/2022] [Indexed: 02/05/2023] Open
Abstract
Within the last forty years, seminal contributions have been made in the areas of bladder cancer (BC) biology, driver genes, molecular profiling, biomarkers, and therapeutic targets for improving personalized patient care. This overview includes seminal discoveries and advances in the molecular oncology of BC. Starting with the concept of divergent molecular pathways for the development of low- and high-grade bladder tumors, field cancerization versus clonality of bladder tumors, cancer driver genes/mutations, genetic polymorphisms, and bacillus Calmette-Guérin (BCG) as an early form of immunotherapy are some of the conceptual contributions towards improving patient care. Although beginning with a promise of predicting prognosis and individualizing treatments, "-omic" approaches and molecular subtypes have revealed the importance of BC stem cells, lineage plasticity, and intra-tumor heterogeneity as the next frontiers for realizing individualized patient care. Along with urine as the optimal non-invasive liquid biopsy, BC is at the forefront of the biomarker field. If the goal is to reduce the number of cystoscopies but not to replace them for monitoring recurrence and asymptomatic microscopic hematuria, a BC marker may reach clinical acceptance. As advances in the molecular oncology of BC continue, the next twenty-five years should significantly advance personalized care for BC patients.
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Affiliation(s)
- Soum D. Lokeshwar
- Department of Urology, Yale University School of Medicine, New Haven, CT 06520, USA;
| | - Maite Lopez
- Departments of Biochemistry and Molecular Biology, Medical College of Georgia, Augusta University, 1410 Laney Walker Blvd., Augusta, GA 30912, USA; (M.L.); (S.S.); (K.A.); (D.S.M.)
| | - Semih Sarcan
- Departments of Biochemistry and Molecular Biology, Medical College of Georgia, Augusta University, 1410 Laney Walker Blvd., Augusta, GA 30912, USA; (M.L.); (S.S.); (K.A.); (D.S.M.)
- Department of Urology, University Hospital Schleswig-Holstein, Campus Lübeck, 23562 Lübeck, Germany
| | - Karina Aguilar
- Departments of Biochemistry and Molecular Biology, Medical College of Georgia, Augusta University, 1410 Laney Walker Blvd., Augusta, GA 30912, USA; (M.L.); (S.S.); (K.A.); (D.S.M.)
| | - Daley S. Morera
- Departments of Biochemistry and Molecular Biology, Medical College of Georgia, Augusta University, 1410 Laney Walker Blvd., Augusta, GA 30912, USA; (M.L.); (S.S.); (K.A.); (D.S.M.)
| | - Devin M. Shaheen
- Yale School of Nursing, Yale University, New Haven, CT 06520, USA;
| | - Bal L. Lokeshwar
- Georgia Cancer Center, Medical College of Georgia, Augusta University, 1410 Laney Walker Blvd., Augusta, GA 30912, USA
- Research Service, Charlie Norwood VA Medical Center, Augusta, GA 30904, USA
- Correspondence: (B.L.L.); (V.B.L.)
| | - Vinata B. Lokeshwar
- Departments of Biochemistry and Molecular Biology, Medical College of Georgia, Augusta University, 1410 Laney Walker Blvd., Augusta, GA 30912, USA; (M.L.); (S.S.); (K.A.); (D.S.M.)
- Correspondence: (B.L.L.); (V.B.L.)
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7
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Martins F, Santos I, da Cruz E Silva OAB, Tambaro S, Rebelo S. The role of the integral type II transmembrane protein BRI2 in health and disease. Cell Mol Life Sci 2021; 78:6807-6822. [PMID: 34480585 PMCID: PMC11072861 DOI: 10.1007/s00018-021-03932-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 08/07/2021] [Accepted: 08/26/2021] [Indexed: 10/20/2022]
Abstract
BRI2 is a type II transmembrane protein ubiquitously expressed whose physiological function remains poorly understood. Although several recent important advances have substantially impacted on our understanding of BRI2 biology and function, providing valuable information for further studies on BRI2. These findings have contributed to a better understanding of BRI2 biology and the underlying signaling pathways involved. In turn, these might provide novel insights with respect to neurodegeneration processes inherent to BRI2-related pathologies, namely Familial British and Danish dementias, Alzheimer's disease, ITM2B-related retinal dystrophy, and multiple sclerosis. In this review, we provided a state-of-the-art outline of BRI2 biology, both in physiological and pathological conditions, and discuss the proposed molecular underlying mechanisms. Overall, the BRI2 knowledge here reviewed is of extreme importance and may contribute to propose BRI2 and/or BRI2 proteolytic fragments as novel therapeutic targets for neurodegenerative diseases, such as Alzheimer's disease.
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Affiliation(s)
- Filipa Martins
- Neuroscience and Signaling Laboratory, Institute of Biomedicine (iBiMED), Department of Medical Sciences, University of Aveiro, 3810-193, Aveiro, Portugal.
| | - Isabela Santos
- Neuroscience and Signaling Laboratory, Institute of Biomedicine (iBiMED), Department of Medical Sciences, University of Aveiro, 3810-193, Aveiro, Portugal
| | - Odete A B da Cruz E Silva
- Neuroscience and Signaling Laboratory, Institute of Biomedicine (iBiMED), Department of Medical Sciences, University of Aveiro, 3810-193, Aveiro, Portugal
| | - Simone Tambaro
- Department of Neurobiology, Care Sciences and Society, Division of Neurogeriatrics, Karolinska Institutet, 141 83, Huddinge, Sweden.
| | - Sandra Rebelo
- Neuroscience and Signaling Laboratory, Institute of Biomedicine (iBiMED), Department of Medical Sciences, University of Aveiro, 3810-193, Aveiro, Portugal.
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8
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Linn P, Kohno S, Sheng J, Kulathunga N, Yu H, Zhang Z, Voon D, Watanabe Y, Takahashi C. Targeting RB1 Loss in Cancers. Cancers (Basel) 2021; 13:cancers13153737. [PMID: 34359636 PMCID: PMC8345210 DOI: 10.3390/cancers13153737] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 07/14/2021] [Accepted: 07/21/2021] [Indexed: 12/22/2022] Open
Abstract
Simple Summary Irreversible defects in RB1 tumor suppressor functions often predict poor outcomes in cancer patients. However, the RB1-defecient status can be a benefit as well for them, as it generates a variety of vulnerabilities induced through the upregulation of RB1 targets, relief from functional restrictions due to RB1 binding, presence of genes whose inactivation cause synthetic lethality with RB1 loss, or collateral synthetic lethality owing to simultaneous loss of neighboring genes. Abstract Retinoblastoma protein 1 (RB1) is encoded by a tumor suppressor gene that was discovered more than 30 years ago. Almost all mitogenic signals promote cell cycle progression by braking on the function of RB1 protein through mono- and subsequent hyper-phosphorylation mediated by cyclin-CDK complexes. The loss of RB1 function drives tumorigenesis in limited types of malignancies including retinoblastoma and small cell lung cancer. In a majority of human cancers, RB1 function is suppressed during tumor progression through various mechanisms. The latter gives rise to the acquisition of various phenotypes that confer malignant progression. The RB1-targeted molecules involved in such phenotypic changes are good quarries for cancer therapy. Indeed, a variety of novel therapies have been proposed to target RB1 loss. In particular, the inhibition of a number of mitotic kinases appeared to be synthetic lethal with RB1 deficiency. A recent study focusing on a neighboring gene that is often collaterally deleted together with RB1 revealed a pharmacologically targetable vulnerability in RB1-deficient cancers. Here we summarize current understanding on possible therapeutic approaches targeting functional or genomic aberration of RB1 in cancers.
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Affiliation(s)
- Paing Linn
- Division of Oncology and Molecular Biology, Cancer Research Institute, Kanazawa University, Kanazawa 920-1192, Japan; (P.L.); (S.K.); (J.S.); (N.K.); (H.Y.); (Z.Z.)
- Yangon General Hospital, Yangon, Myanmar
| | - Susumu Kohno
- Division of Oncology and Molecular Biology, Cancer Research Institute, Kanazawa University, Kanazawa 920-1192, Japan; (P.L.); (S.K.); (J.S.); (N.K.); (H.Y.); (Z.Z.)
| | - Jindan Sheng
- Division of Oncology and Molecular Biology, Cancer Research Institute, Kanazawa University, Kanazawa 920-1192, Japan; (P.L.); (S.K.); (J.S.); (N.K.); (H.Y.); (Z.Z.)
| | - Nilakshi Kulathunga
- Division of Oncology and Molecular Biology, Cancer Research Institute, Kanazawa University, Kanazawa 920-1192, Japan; (P.L.); (S.K.); (J.S.); (N.K.); (H.Y.); (Z.Z.)
| | - Hai Yu
- Division of Oncology and Molecular Biology, Cancer Research Institute, Kanazawa University, Kanazawa 920-1192, Japan; (P.L.); (S.K.); (J.S.); (N.K.); (H.Y.); (Z.Z.)
| | - Zhiheng Zhang
- Division of Oncology and Molecular Biology, Cancer Research Institute, Kanazawa University, Kanazawa 920-1192, Japan; (P.L.); (S.K.); (J.S.); (N.K.); (H.Y.); (Z.Z.)
| | - Dominic Voon
- Institute of Frontier Sciences Initiative, Kanazawa University, Kanazawa 920-1192, Japan;
| | | | - Chiaki Takahashi
- Division of Oncology and Molecular Biology, Cancer Research Institute, Kanazawa University, Kanazawa 920-1192, Japan; (P.L.); (S.K.); (J.S.); (N.K.); (H.Y.); (Z.Z.)
- Correspondence: ; Tel.: +81-76-264-6750; Fax: +81-76-234-4521
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9
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Whole-Organ Genomic Characterization of Mucosal Field Effects Initiating Bladder Carcinogenesis. Cell Rep 2020; 26:2241-2256.e4. [PMID: 30784602 DOI: 10.1016/j.celrep.2019.01.095] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 12/12/2018] [Accepted: 01/25/2019] [Indexed: 12/13/2022] Open
Abstract
We used whole-organ mapping to study the locoregional molecular changes in a human bladder containing multifocal cancer. Widespread DNA methylation changes were identified in the entire mucosa, representing the initial field effect. The field effect was associated with subclonal low-allele frequency mutations and a small number of DNA copy alterations. A founder mutation in the RNA splicing gene, ACIN1, was identified in normal mucosa and expanded clonally with an additional 21 mutations in progression to carcinoma. The patterns of mutations and copy number changes in carcinoma in situ and foci of carcinoma were almost identical, confirming their clonal origins. The pathways affected by the DNA copy alterations and mutations, including the Kras pathway, were preceded by the field changes in DNA methylation, suggesting that they reinforced mechanisms that had already been initiated by methylation. The results demonstrate that DNA methylation can serve as the initiator of bladder carcinogenesis.
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Young FP, Ende D, Epstein RJ. Beyond BCG: the approaching era of personalised bladder-sparing therapies for non-muscle-invasive urothelial cancers. Future Oncol 2019; 15:409-420. [DOI: 10.2217/fon-2018-0565] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Progress in the management of non-muscle invasive bladder cancer has been slow. Despite longstanding use of intravesical therapies (e.g., Bacille Calmette-Guerin; BCG) to complement cystoscopic resection of high-grade lesions, many patients still develop recurrences requiring cystectomy, while others suffer side-effects of BCG without definite benefit. Many questions remain: for example, how many patients receive intravesical prophylaxis without efficacy? Which high-risk patients are best managed with early cystectomy? Could systemic therapies and/or radiotherapy extend bladder preservation times? Such questions may soon be refined by clinicopathologic non-muscle invasive bladder cancer signatures that predict sensitivity to cytotoxic, immune and targeted therapies. Hypothesis-based trials using these signatures should lead to more rational adjuvant treatments, longer bladder preservation times, and better quality of life for patients.
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Affiliation(s)
- Francis P Young
- University of New South Wales Clinical School, St Vincent's Hospital, 390 Victoria St, Darlinghurst 2010, Sydney, Australia
| | - David Ende
- Department of Urologic Surgery, St Vincent's Hospital, 390 Victoria St, Darlinghurst 2010, Sydney, Australia
| | - Richard J Epstein
- University of New South Wales Clinical School, St Vincent's Hospital, 390 Victoria St, Darlinghurst 2010, Sydney, Australia
- The Kinghorn Cancer Centre, Clinical Informatics & Research Centre, St Vincent's Hospital, 370 Victoria St, Darlinghurst 2010, Sydney, Australia
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11
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Abstract
CONTEXT.— Bladder cancer is a heterogeneous disease that exhibits a wide spectrum of clinical and pathologic features. The classification of bladder cancer has been traditionally based on morphologic assessment with the aid of immunohistochemistry. However, recent genomic studies have revealed that distinct alterations of DNA and RNA in bladder cancer may underlie its diverse clinicopathologic features, leading to a novel molecular classification of this common human cancer. OBJECTIVE.— To update recent developments in genomic characterization of bladder cancer, which may shed insights on the molecular mechanisms underlying the origin of bladder cancer, dual-track oncogenic pathways, intrinsic molecular subtyping, and development of histologic variants. DATA SOURCES.— Peer-reviewed literature retrieved from PubMed search and authors' own research. CONCLUSIONS.— Bladder cancer is likely to arise from different uroprogenitor cells through papillary/luminal and nonpapillary/basal tracks. The intrinsic molecular subtypes of bladder cancer referred to as luminal and basal exhibit distinct expression signatures, clinicopathologic features, and sensitivities to standard chemotherapy. Genomic characterization of bladder cancer provides new insights to understanding the biological nature of this complex disease, which may lead to more effective treatment.
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Affiliation(s)
- Charles C Guo
- From the Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston
| | - Bogdan Czerniak
- From the Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston
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12
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Detection of Bladder Cancer in Urine Sediments by a Novel Multicolor Fluorescence In Situ Hybridization (Quartet) Test. Eur Urol Focus 2018; 5:664-675. [PMID: 29428551 DOI: 10.1016/j.euf.2018.01.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 01/12/2018] [Accepted: 01/29/2018] [Indexed: 02/04/2023]
Abstract
BACKGROUND Bladder cancer is among the common human malignancies that show a heavy mutational load and copy number variations of numerous chromosomes, which makes them a target for diagnostic explorations. OBJECTIVE We aimed to design a multicolor fluorescence in situ hybridization (FISH) test referred to as the quartet test for the detection of bladder cancer in urine. DESIGN, SETTING, AND PARTICIPANTS We performed genome-wide copy number variation analysis on cohorts from the University of Texas MD Anderson Cancer Center (n=40) and The Cancer Genome Atlas (n=129), and identified the most frequently amplified chromosomal regions. These data were used to select four of the amplified regions to design a multicolor FISH test, referred to as the quartet test. Assay validation was performed on urine samples from 98 patients with bladder cancer: 56 with low-grade papillary, 42 with high-grade invasive disease, and 48 benign controls. INTERVENTION The quartet test can be used in clinical practice for noninvasive detection of bladder cancer. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS We initially analyzed samples using a fraction of abnormal cell scores and then by the quantitative score, which included not only the proportion of cells with abnormal copy numbers, but also the proportion of cells with numbers of altered copies and degree of amplification. We used receiver operator characteristic (ROC) curves to identify cutoff values for the scores at which performances of sensitivity and specificity were maximized. RESULTS AND LIMITATIONS The copy number status assessed by probes detected in voided urine reflected the amplification status of the primary tumor. An ROC curve summarizing the proportion of assayed cells with any abnormal copy numbers gave specificity of 93.8% and sensitivity of 78.6% using the proportion of cells with abnormal copy numbers. The quantitative score giving extra weight to cells with multiple simultaneous amplifications provided 95.8% specificity and 76.8% sensitivity. Both percentage of abnormal cells and quantitative scores were highly effective for assessing the grade of the tumor. The full spectrum of potential clinical applications was not explored in the current study, and further validation studies are needed. CONCLUSIONS The quartet test shows promising specificity and sensitivity results, but it requires validation on a larger multi-institutional cohort of samples. PATIENT SUMMARY The quartet test can be used for noninvasive detection of bladder cancer in voided urine. It can also be used to assess the grade of the tumor and tumor recurrence as well as post-treatment effects.
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13
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Abstract
DNA mutations are inevitable. Despite proficient DNA repair mechanisms, somatic cells accumulate mutations during development and aging, generating cells with different genotypes within the same individual, a phenomenon known as somatic mosaicism. While the existence of somatic mosaicism has long been recognized, in the last five years, advances in sequencing have provided unprecedented resolution to characterize the extent and nature of somatic genetic variation. Collectively, these new studies are revealing a previously uncharacterized aging phenotype: the accumulation of clones with cancer driver mutations. Here, we summarize the most recent findings, which converge in the novel notion that cancer-associated mutations are prevalent in normal tissue and accumulate with aging.
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Affiliation(s)
- Rosa Ana Risques
- Department of Pathology, University of Washington, Seattle, Washington, United States of America
| | - Scott R. Kennedy
- Department of Pathology, University of Washington, Seattle, Washington, United States of America
- * E-mail:
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14
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Comprehensive multiregional analysis of molecular heterogeneity in bladder cancer. Sci Rep 2017; 7:11702. [PMID: 28916750 PMCID: PMC5600970 DOI: 10.1038/s41598-017-11291-0] [Citation(s) in RCA: 96] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 08/23/2017] [Indexed: 12/15/2022] Open
Abstract
Genetic alterations identified in adjacent normal appearing tissue in bladder cancer patients are indicative of a field disease. Here we assessed normal urothelium transformation and intra-tumour heterogeneity (ITH) in four patients with bladder cancer. Exome sequencing identified private acquired mutations in a lymph node metastasis and local recurrences. Deep re-sequencing revealed presence of at least three and four subclones in two patients with multifocal disease, while no demarcation of subclones was identified in the two patients with unifocal disease. Analysis of adjacent normal urothelium showed low frequency mutations in patients with multifocal disease. Expression profiling showed intra-tumour and intra-patient co-existence of basal- and luminal-like tumour regions, and patients with multifocal disease had a greater degree of genomic and transcriptomic ITH, as well as transformation of adjacent normal cells, compared to patients with unifocal disease. Analysis of the adjacent urothelium may pave the way for therapies targeting the field disease.
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15
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Abstract
Bladder cancer is a highly prevalent disease and is associated with substantial morbidity, mortality and cost. Environmental or occupational exposures to carcinogens, especially tobacco, are the main risk factors for bladder cancer. Most bladder cancers are diagnosed after patients present with macroscopic haematuria, and cases are confirmed after transurethral resection of bladder tumour (TURBT), which also serves as the first stage of treatment. Bladder cancer develops via two distinct pathways, giving rise to non-muscle-invasive papillary tumours and non-papillary (solid) muscle-invasive tumours. The two subtypes have unique pathological features and different molecular characteristics. Indeed, The Cancer Genome Atlas project identified genetic drivers of muscle-invasive bladder cancer (MIBC) as well as subtypes of MIBC with distinct characteristics and therapeutic responses. For non-muscle-invasive bladder cancer (NMIBC), intravesical therapies (primarily Bacillus Calmette-Guérin (BCG)) with maintenance are the main treatments to prevent recurrence and progression after initial TURBT; additional therapies are needed for those who do not respond to BCG. For localized MIBC, optimizing care and reducing morbidity following cystectomy are important goals. In metastatic disease, advances in our genetic understanding of bladder cancer and in immunotherapy are being translated into new therapies.
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16
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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: 823] [Impact Index Per Article: 91.4] [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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17
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Leblanc R, Peyruchaud O. New insights into the autotaxin/LPA axis in cancer development and metastasis. Exp Cell Res 2014; 333:183-189. [PMID: 25460336 DOI: 10.1016/j.yexcr.2014.11.010] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 11/13/2014] [Indexed: 12/13/2022]
Abstract
Lysophosphatidic acid (LPA) is a simple lipid with a single fatty acyl chain linked to a glycerophosphate backbone. Despite the simplicity of its structure but owing to its interactions with a series of at least six G protein-coupled receptors (LPA1-6), LPA exerts pleiotropic bioactivities including stimulation of proliferation, migration and survival of many cell types. Autotaxin (ATX) is a unique enzyme with a lysophospholipase D (lysoPLD) activity that is responsible for the levels of LPA in the blood circulation. Both LPA receptor family members and ATX/LysoPLD are aberrantly expressed in many human cancers. This review will present the more striking as well as novel experimental evidences using cell lines, cancer mouse models and transgenic animals identifying the roles for ATX and LPA receptors in cancer progression, tumor cell invasion and metastasis.
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Affiliation(s)
- Raphaël Leblanc
- INSERM, UMR1033, UCB Lyon 1, Faculté de Médecine Lyon Est, Lyon, France
| | - Olivier Peyruchaud
- INSERM, UMR1033, UCB Lyon 1, Faculté de Médecine Lyon Est, Lyon, France.
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18
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Atypical spindle cell lipoma: a clinicopathologic, immunohistochemical, and molecular study emphasizing its relationship to classical spindle cell lipoma. Virchows Arch 2014; 465:97-108. [PMID: 24659226 DOI: 10.1007/s00428-014-1568-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2013] [Revised: 01/22/2014] [Accepted: 03/06/2014] [Indexed: 12/16/2022]
Abstract
We studied a series of spindle cell lipomas arising in atypical sites and showing unusual morphologic features (which we called atypical spindle cell lipoma) to assess if these lesions have the same chromosomal alterations as classical spindle cell lipoma but different from those found in atypical lipomatous tumor/well-differentiated liposarcoma. We investigated alterations of different genes in the 13q14 region and the amplification status of the MDM2 and CDK4 genes at 12q14-15 by multiplex ligation-dependent probe amplification (MLPA) and fluorescence in situ hybridization (FISH) analysis. In the atypical spindle cell lipomas, MLPA revealed deletions in the two nearest flanking genes of RB1 (ITM2B and RCBTB2) and in multiple important exons of RB1. In contrast, in classical spindle cell lipomas, a less complex loss of RB1 exons was found but no deletion of ITM2B and RCBTB2. Moreover, MLPA identified a deletion of the DLEU1 gene, a finding which has not been reported earlier. We propose an immunohistochemical panel for lipomatous tumors which comprises of MDM2, CDK4, p16, Rb, which we have found useful in discriminating between atypical or classical spindle cell lipomas and other adipocytic neoplasms, especially atypical lipomatous tumor/well-differentiated liposarcoma. Our findings strengthen the link between atypical spindle cell lipoma and classical spindle cell lipoma, and differentiate them from atypical lipomatous tumor/well-differentiated liposarcoma.
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19
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Apolo AB, Hoffman V, Kaag MG, Latini DM, Lee CT, Rosenberg JE, Knowles M, Theodorescu D, Czerniak BA, Efstathiou JA, Albert ML, Sridhar SS, Margulis V, Matin SF, Galsky MD, Hansel D, Kamat AM, Flaig TW, Smith AB, Messing E, Zipursky Quale D, Lotan Y. Summary of the 8th Annual Bladder Cancer Think Tank: Collaborating to move research forward. Urol Oncol 2014; 33:53-64. [PMID: 25065704 DOI: 10.1016/j.urolonc.2014.06.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2014] [Accepted: 06/23/2014] [Indexed: 02/05/2023]
Abstract
OBJECTIVES The 8th Annual Bladder Cancer Think Tank (BCAN-TT) brought together a multidisciplinary group of clinicians, researchers, and patient advocates in an effort to advance bladder cancer research. METHODS AND MATERIALS With the theme of "Collaborating to Move Research Forward," the meeting included three panel presentations and seven small working groups. RESULTS The panel presentations and interactive discussions focused on three main areas: gender disparities, sexual dysfunction, and targeting novel pathways in bladder cancer. Small working groups also met to identify projects for the upcoming year, including: (1) improving enrollment and quality of clinical trials; (2) collecting data from multiple institutions for future research; (3) evaluating patterns of care for non-muscle-invasive bladder cancer; (4) improving delivery of care for muscle-invasive disease; (5) improving quality of life for survivors; (6) addressing upper tract disease; and (7) examining the impact of health policy changes on research and treatment of bladder cancer. CONCLUSIONS The goal of the BCAN-TT is to advance the care of patients with bladder cancer and to promote collaborative research throughout the year. The meeting provided ample opportunities for collaboration among clinicians from multiple disciplines, patients and patient advocates, and industry representatives.
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Affiliation(s)
- Andrea B Apolo
- Genitourinary Malignancies Branch, National Cancer Institute, Bethesda, MD
| | | | - Matthew G Kaag
- Department of Urology, Penn State Hershey Medical Center, Hershey, PA
| | - David M Latini
- Department of Urology, Baylor College of Medicine, Houston, TX
| | - Cheryl T Lee
- Department of Urology, University of Michigan Health System, Ann Arbor, MI
| | | | - Margaret Knowles
- Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
| | | | | | | | | | - Srikala S Sridhar
- Department of Medical Oncology and Hematology, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Vitaly Margulis
- Department of Urology, University of Texas Southwestern Medical Center, Dallas, TX
| | - Surena F Matin
- Department of Urology, MD Anderson Cancer Center, Houston, TX
| | - Matthew D Galsky
- Department of Medical Oncology, Mount Sinai Hospital, New York, NY
| | - Donna Hansel
- Department of Pathology, University of California, La Jolla, San Diego, CA
| | - Ashish M Kamat
- Department of Urology, MD Anderson Cancer Center, Houston, TX
| | | | - Angela B Smith
- Department of Urology, University of North Carolina, Chapel Hill, NC
| | - Edward Messing
- Department of Urology, University of Rochester Medical Center, Rochester, NY
| | | | - Yair Lotan
- Department of Urology, University of Texas Southwestern Medical Center, Dallas, TX.
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20
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Lee S, Lee I, Jung Y, McConkey D, Czerniak B. In-frame cDNA library combined with protein complementation assay identifies ARL11-binding partners. PLoS One 2012; 7:e52290. [PMID: 23272234 PMCID: PMC3525598 DOI: 10.1371/journal.pone.0052290] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2012] [Accepted: 11/12/2012] [Indexed: 11/20/2022] Open
Abstract
The cDNA expression libraries that produce correct proteins are essential in facilitating the identification of protein-protein interactions. The 5′-untranslated regions (UTRs) that are present in the majority of mammalian and non-mammalian genes are predicted to alter the expression of correct proteins from cDNA libraries. We developed a novel cDNA expression library from which 5′-UTRs were removed using a mixture of polymerase chain reaction primers that complement the Kozak sequences we refer to as an “in-frame cDNA library.” We used this library with the protein complementation assay to identify two novel binding partners for ras-related ADP-ribosylation factor-like 11 (ARL11), cellular retinoic acid binding protein 2 (CRABP2), and phosphoglycerate mutase 1 (PGAM1). Thus, the in-frame cDNA library without 5′-UTRs we describe here increases the chance of correctly identifying protein interactions and will have wide applications in both mammalian and non-mammalian detection systems.
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Affiliation(s)
- Sangkyou Lee
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
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21
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Reis AHO, Vargas FR, Lemos B. More epigenetic hits than meets the eye: microRNAs and genes associated with the tumorigenesis of retinoblastoma. Front Genet 2012; 3:284. [PMID: 23233862 PMCID: PMC3516829 DOI: 10.3389/fgene.2012.00284] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Accepted: 11/21/2012] [Indexed: 12/29/2022] Open
Abstract
Retinoblastoma (RB), a childhood neoplasia of the retinoblasts, can occur unilaterally or bilaterally, with one or multiple foci per eye. RB is associated with somatic loss of function of both alleles of the tumor suppressor gene RB1. Hereditary forms emerge due to germline loss of function mutations in RB1 alleles. RB has long been the prototypic “model” cancer ever since Knudson's “two-hit” hypothesis. However, a simple two-hit model for RB is challenged by an increasing number of studies documenting additional hits that contribute to RB development. Here we review the genetics and epigenetics of RB with a focus on the role of small non-coding RNAs (microRNAs) and on novel findings indicating the relevance of DNA methylation in the development and prognosis of this neoplasia. Studies point to an elaborated landscape of genetic and epigenetic complexity, in which a number of events and pahtways play crucial roles in the origin and prognosis of RB. These include roles for microRNAs, inprinted loci, and parent-of-origin contributions to RB1 regulation and RB progression. This complexity is also manifested in the structure of the RB1 locus itself: it includes numerous repetitive DNA segments and retrotransposon insertion elements, some of which are actively transcribed from the RB1 locus. Altogether, we conclude that RB1 loss of function represents the tip of an iceberg of events that determine RB development, progression, severity, and disease risk. Comprehensive assessment of personalized RB risk will require genetic and epigenetic evaluations beyond RB1 protein coding sequences.
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Affiliation(s)
- Adriana H O Reis
- Genetics Program, Instituto Nacional de Câncer Rio de Janeiro, Brazil
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22
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Jacobs KB, Yeager M, Zhou W, Wacholder S, Wang Z, Rodriguez-Santiago B, Hutchinson A, Deng X, Liu C, Horner MJ, Cullen M, Epstein CG, Burdett L, Dean MC, Chatterjee N, Sampson J, Chung CC, Kovaks J, Gapstur SM, Stevens VL, Teras LT, Gaudet MM, Albanes D, Weinstein SJ, Virtamo J, Taylor PR, Freedman ND, Abnet CC, Goldstein AM, Hu N, Yu K, Yuan JM, Liao L, Ding T, Qiao YL, Gao YT, Koh WP, Xiang YB, Tang ZZ, Fan JH, Aldrich MC, Amos C, Blot WJ, Bock CH, Gillanders EM, Harris CC, Haiman CA, Henderson BE, Kolonel LN, Le Marchand L, McNeill LH, Rybicki BA, Schwartz AG, Signorello LB, Spitz MR, Wiencke JK, Wrensch M, Wu X, Zanetti KA, Ziegler RG, Figueroa JD, Garcia-Closas M, Malats N, Marenne G, Prokunina-Olsson L, Baris D, Schwenn M, Johnson A, Landi MT, Goldin L, Consonni D, Bertazzi PA, Rotunno M, Rajaraman P, Andersson U, Freeman LEB, Berg CD, Buring JE, Butler MA, Carreon T, Feychting M, Ahlbom A, Gaziano JM, Giles GG, Hallmans G, Hankinson SE, Hartge P, Henriksson R, Inskip PD, Johansen C, Landgren A, McKean-Cowdin R, Michaud DS, Melin BS, Peters U, Ruder AM, Sesso HD, Severi G, Shu XO, Visvanathan K, White E, Wolk A, Zeleniuch-Jacquotte A, Zheng W, Silverman DT, Kogevinas M, Gonzalez JR, Villa O, Li D, Duell EJ, Risch HA, Olson SH, Kooperberg C, Wolpin BM, Jiao L, Hassan M, Wheeler W, Arslan AA, Bas Bueno-de-Mesquita H, Fuchs CS, Gallinger S, Gross MD, Holly EA, Klein AP, LaCroix A, Mandelson MT, Petersen G, Boutron-Ruault MC, Bracci PM, Canzian F, Chang K, Cotterchio M, Giovannucci EL, Goggins M, Bolton JAH, Jenab M, Khaw KT, Krogh V, Kurtz RC, McWilliams RR, Mendelsohn JB, Rabe KG, Riboli E, Tjønneland A, Tobias GS, Trichopoulos D, Elena JW, Yu H, Amundadottir L, Stolzenberg-Solomon RZ, Kraft P, Schumacher F, Stram D, Savage SA, Mirabello L, Andrulis IL, Wunder JS, García AP, Sierrasesúmaga L, Barkauskas DA, Gorlick RG, Purdue M, Chow WH, Moore LE, Schwartz KL, Davis FG, Hsing AW, Berndt SI, Black A, Wentzensen N, Brinton LA, Lissowska J, Peplonska B, McGlynn KA, Cook MB, Graubard BI, Kratz CP, Greene MH, Erickson RL, Hunter DJ, Thomas G, Hoover RN, Real FX, Fraumeni JF, Caporaso NE, Tucker M, Rothman N, Pérez-Jurado LA, Chanock SJ. Detectable clonal mosaicism and its relationship to aging and cancer. Nat Genet 2012; 44:651-8. [PMID: 22561519 PMCID: PMC3372921 DOI: 10.1038/ng.2270] [Citation(s) in RCA: 448] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2011] [Accepted: 04/09/2012] [Indexed: 12/14/2022]
Abstract
In an analysis of 31,717 cancer cases and 26,136 cancer-free controls from 13 genome-wide association studies, we observed large chromosomal abnormalities in a subset of clones in DNA obtained from blood or buccal samples. We observed mosaic abnormalities, either aneuploidy or copy-neutral loss of heterozygosity, of >2 Mb in size in autosomes of 517 individuals (0.89%), with abnormal cell proportions of between 7% and 95%. In cancer-free individuals, frequency increased with age, from 0.23% under 50 years to 1.91% between 75 and 79 years (P = 4.8 × 10(-8)). Mosaic abnormalities were more frequent in individuals with solid tumors (0.97% versus 0.74% in cancer-free individuals; odds ratio (OR) = 1.25; P = 0.016), with stronger association with cases who had DNA collected before diagnosis or treatment (OR = 1.45; P = 0.0005). Detectable mosaicism was also more common in individuals for whom DNA was collected at least 1 year before diagnosis with leukemia compared to cancer-free individuals (OR = 35.4; P = 3.8 × 10(-11)). These findings underscore the time-dependent nature of somatic events in the etiology of cancer and potentially other late-onset diseases.
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Affiliation(s)
- Kevin B Jacobs
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
- Core Genotyping Facility, SAIC-Frederick, Inc., NCI-Frederick, Frederick, Maryland, USA
| | - Meredith Yeager
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
- Core Genotyping Facility, SAIC-Frederick, Inc., NCI-Frederick, Frederick, Maryland, USA
| | - Weiyin Zhou
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
- Core Genotyping Facility, SAIC-Frederick, Inc., NCI-Frederick, Frederick, Maryland, USA
| | - Sholom Wacholder
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Zhaoming Wang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
- Core Genotyping Facility, SAIC-Frederick, Inc., NCI-Frederick, Frederick, Maryland, USA
| | - Benjamin Rodriguez-Santiago
- Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, E-08003 Barcelona, Spain
- Quantitative Genomic Medicine Laboratory, qGenomics, E-08003 Barcelona, Spain
| | - Amy Hutchinson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
- Core Genotyping Facility, SAIC-Frederick, Inc., NCI-Frederick, Frederick, Maryland, USA
| | - Xiang Deng
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
- Core Genotyping Facility, SAIC-Frederick, Inc., NCI-Frederick, Frederick, Maryland, USA
| | - Chenwei Liu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
- Core Genotyping Facility, SAIC-Frederick, Inc., NCI-Frederick, Frederick, Maryland, USA
| | - Marie-Josephe Horner
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Michael Cullen
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
- Core Genotyping Facility, SAIC-Frederick, Inc., NCI-Frederick, Frederick, Maryland, USA
| | - Caroline G Epstein
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Laurie Burdett
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
- Core Genotyping Facility, SAIC-Frederick, Inc., NCI-Frederick, Frederick, Maryland, USA
| | - Michael C Dean
- Laboratory of Experimental Immunology, Center for Cancer Research, NCI- Frederick, Frederick, MD, USA
| | - Nilanjan Chatterjee
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Joshua Sampson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Charles C Chung
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Joseph Kovaks
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Susan M Gapstur
- Epidemiology Research Program, American Cancer Society, Atlanta, Georgia, USA
| | - Victoria L Stevens
- Epidemiology Research Program, American Cancer Society, Atlanta, Georgia, USA
| | - Lauren T Teras
- Epidemiology Research Program, American Cancer Society, Atlanta, Georgia, USA
| | - Mia M Gaudet
- Epidemiology Research Program, American Cancer Society, Atlanta, Georgia, USA
| | - Demetrius Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Stephanie J Weinstein
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Jarmo Virtamo
- Department of Chronic Disease Prevention, National Institute for Health and Welfare, Helsinki, Finland
| | - Philip R Taylor
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Neal D Freedman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Christian C Abnet
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Alisa M Goldstein
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Nan Hu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Kai Yu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Jian-Min Yuan
- Department of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, MN, USA
- University of Pittsburgh Cancer Institute, Pittsburgh, PA, USA
| | - Linda Liao
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Ti Ding
- Shanxi Cancer Hospital, Taiyuan, Shanxi, People’s Republic of China
| | - You-Lin Qiao
- Department of Epidemiology, Cancer Institute (Hospital), Chinese Academy of Medical Sciences, Beijing, People’s Republic of China
| | - Yu-Tang Gao
- Shanghai Cancer Institute, Shanghai, People’s Republic of China
| | - Woon-Puay Koh
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
| | - Yong-Bing Xiang
- Shanghai Cancer Institute, Shanghai, People’s Republic of China
| | - Ze-Zhong Tang
- Shanxi Cancer Hospital, Taiyuan, Shanxi, People’s Republic of China
| | - Jin-Hu Fan
- Department of Epidemiology, Cancer Institute (Hospital), Chinese Academy of Medical Sciences, Beijing, People’s Republic of China
| | - Melinda C Aldrich
- Department of Thoracic Surgery, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
- Division of Epidemiology in the Department of Medicine, Vanderbilt Epidemiology Center,Nashville, Tennessee,USA
| | - Christopher Amos
- Department of Epidemiology, Division of Cancer Prevention and Population Sciences, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - William J Blot
- Division of Epidemiology in the Department of Medicine, Vanderbilt Epidemiology Center,Nashville, Tennessee,USA
- International Epidemiology Institute, Rockville, Maryland 20850, USA
| | - Cathryn H Bock
- Karmanos Cancer Institute, Wayne State University, Detroit, Michigan, USA
- Department of Oncology, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Elizabeth M Gillanders
- Division of Cancer Control and Population Sciences, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Curtis C Harris
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Christopher A Haiman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California/Norris Comprehensive Cancer Center, Los Angeles, California 90033, USA
| | - Brian E Henderson
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California/Norris Comprehensive Cancer Center, Los Angeles, California 90033, USA
| | - Laurence N Kolonel
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, Hawaii 96813, USA
| | - Loic Le Marchand
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, Hawaii 96813, USA
| | - Lorna H McNeill
- Department of Health Disparities Research, Division of Office of the Vice-President, Cancer Prevention and Population Sciences, The University of Texas MD Anderson Cancer Center, Houston, Texas , USA
- Center for Community Engaged Translational Research , Duncan Family Institute, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Benjamin A Rybicki
- Department of Public Health Sciences, Henry Ford Hospital, Detroit, Michigan 48202, USA
| | - Ann G Schwartz
- Karmanos Cancer Institute, Wayne State University, Detroit, Michigan, USA
- Department of Oncology, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Lisa B Signorello
- Division of Epidemiology in the Department of Medicine, Vanderbilt Epidemiology Center,Nashville, Tennessee,USA
- International Epidemiology Institute, Rockville, Maryland 20850, USA
- Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee 37203,USA
| | - Margaret R Spitz
- Dan L Duncan Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - John K Wiencke
- Department of Neurological Surgery, University of California San Francisco , San Francisco, California 94158, USA
| | - Margaret Wrensch
- Department of Neurological Surgery, University of California San Francisco , San Francisco, California 94158, USA
| | - Xifeng Wu
- Department of Epidemiology, Division of Cancer Prevention and Population Sciences, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Krista A Zanetti
- Division of Cancer Control and Population Sciences, National Cancer Institute, Bethesda, Maryland 20892, USA
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Regina G Ziegler
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Jonine D Figueroa
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Montserrat Garcia-Closas
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | - Nuria Malats
- Genetics and Molecular Epidemiology Group, Centro Nacional de Investigaciones Oncológicas (CNIO), Madrid, Spain
| | - Gaelle Marenne
- Genetics and Molecular Epidemiology Group, Centro Nacional de Investigaciones Oncológicas (CNIO), Madrid, Spain
| | | | - Dalsu Baris
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | | | | | - Maria Teresa Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Lynn Goldin
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Dario Consonni
- Department of Occupational and Environmental Health , University of Milan, Milan, 20122, Italy
- Unit of Epidemiology, Fondazione Istituto di Ricevero e Cura a Carattere Scientifico (IRCCS), Ospedale Maggiore Policlinico, Mangiagalli e Regina Elena, Milan, 20122, Italy
| | - Pier Alberto Bertazzi
- Department of Occupational and Environmental Health , University of Milan, Milan, 20122, Italy
- Unit of Epidemiology, Fondazione Istituto di Ricevero e Cura a Carattere Scientifico (IRCCS), Ospedale Maggiore Policlinico, Mangiagalli e Regina Elena, Milan, 20122, Italy
| | - Melissa Rotunno
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Preetha Rajaraman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Ulrika Andersson
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
| | - Laura E Beane Freeman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Christine D Berg
- Clinical and Translational Epidemiology Branch, Division of Cancer Control and Population Sciences, National Cancer Institute, Bethesda, MD, USA
| | - Julie E Buring
- Department of Ambulatory Care and Prevention, Harvard Medical School, Boston, MA, USA
- Division of Preventive Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Mary A Butler
- National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Cincinnati, OH, USA
| | - Tania Carreon
- National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Cincinnati, OH, USA
| | - Maria Feychting
- Division of Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Anders Ahlbom
- Division of Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - J Michael Gaziano
- Division of Preventive Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Division of Aging, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Massachusetts Veteran’s Epidemiology, Research and Information Center, Geriatric Research Education and Clinical Center, VA Boston Healthcare System, Boston, MA, USA
| | - Graham G Giles
- Cancer Epidemiology Centre, The Cancer Council of Victoria, Melbourne, Australia
- Centre for Molecular, Environmental, Genetic, and Analytic Epidemiology, University of Melbourne, Melbourne, Australia
| | - Goran Hallmans
- Department of Public Health and Clinical Medicine, Umeå University, Umeå, Sweden
| | - Susan E Hankinson
- Channing Laboratory, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Patricia Hartge
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Roger Henriksson
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
- Department of Oncology, Karolinska University Hospital, SE-171 76 Stockholm, Sweden
| | - Peter D Inskip
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | | | - Annelie Landgren
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Roberta McKean-Cowdin
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California/Norris Comprehensive Cancer Center, Los Angeles, California 90033, USA
| | - Dominique S Michaud
- Division of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
- Department of Epidemiology, Division of Biology and Medicine, Brown University, Providence, RI, USA
| | - Beatrice S Melin
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
| | - Ulrike Peters
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Avima M Ruder
- National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Cincinnati, OH, USA
| | - Howard D Sesso
- Division of Preventive Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Gianluca Severi
- Cancer Epidemiology Centre, The Cancer Council of Victoria, Melbourne, Australia
- Centre for Molecular, Environmental, Genetic, and Analytic Epidemiology, University of Melbourne, Melbourne, Australia
| | - Xiao-Ou Shu
- Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee 37203,USA
| | - Kala Visvanathan
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Emily White
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Alicja Wolk
- Division of Nutritional Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Anne Zeleniuch-Jacquotte
- Division of Epidemiology, Department of Environmental Medicine, NYU School of Medicine, New York, NY
| | - Wei Zheng
- Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee 37203,USA
| | - Debra T Silverman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Manolis Kogevinas
- National School of Public Health, Athens, Greece
- Centro de Investigacion Biomedica en Red Epidemiologia y Slaud Publica (CIBERESP), Barcelona
| | - Juan R Gonzalez
- Centre for Research in Environmental Epidemiology (CREAL), Barcelona, Spain
- Centro de Investigacion Biomedica en Red Epidemiologia y Slaud Publica (CIBERESP), Barcelona
| | - Olaya Villa
- Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, E-08003 Barcelona, Spain
- Quantitative Genomic Medicine Laboratory, qGenomics, E-08003 Barcelona, Spain
| | - Donghui Li
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Eric J Duell
- Catalan Institute of Oncology (ICO), Institut d’Investigació Biomèdica de Bellvitge (IDIBELL ), Barcelona, Spain
| | - Harvey A Risch
- Yale University School of Public Health, New Haven, CT, USA
| | - Sara H Olson
- Department of Epidemiology and Biostatistics, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Brian M Wolpin
- Channing Laboratory, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Li Jiao
- Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Manal Hassan
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | - Alan A Arslan
- Department of Obstetrics and Gynecology, New York University School of Medicine, New York, NY, USA
- New York University Cancer Institute, New York, NY, USA
| | - H Bas Bueno-de-Mesquita
- Department of Gastroenterology and Hepatology, University Medical Center Utrecht, Utrecht, The Netherlands
- National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Charles S Fuchs
- Channing Laboratory, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Steven Gallinger
- Fred. A. Litwin Centre for Cancer Genetics, Samuel Lunenfeld Research Institute, Toronto, Ontario, Canada
| | - Myron D Gross
- Department of Laboratory Medicine and Pathology, School of Medicine, University of Minnesota, Minneapolis, MN, USA
| | - Elizabeth A Holly
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - Alison P Klein
- Department of Oncology, the Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Andrea LaCroix
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Margaret T Mandelson
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Group Health Center for Health Studies, Seattle, WA, USA
| | - Gloria Petersen
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Marie-Christine Boutron-Ruault
- Institut National de la Santé et de la Recherche Médicale (INSERM), Paris-Sud University, Institut Gustave-Roussy, Villejuif, France
| | - Paige M Bracci
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - Federico Canzian
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Kenneth Chang
- Comprehensive Digestive Disease Center, University of California, Irvine Medical Center, Orange, CA, USA
| | - Michelle Cotterchio
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
| | - Edward L Giovannucci
- Channing Laboratory, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Department of Epidemiology, Harvard School of Public Health, Boston, MA, USA
- Department of Nutrition, Harvard School of Public Health, Boston, MA, USA
| | - Michael Goggins
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
- Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Judith A Hoffman Bolton
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Mazda Jenab
- International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | - Kay-Tee Khaw
- Department of Public Health and Primary Care, Clinical Gerontology, Addenbrooke’s Hospital, University of Cambridge, Cambridge, UK
| | - Vittorio Krogh
- Nutritional Epidemiology Unit, Fondazione Istituto Di Ricovero e Cura a Carattere Scientifico (IRCCS), Istituto Nazionale dei Tumori, Milan, Italy
| | - Robert C Kurtz
- Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | | | - Julie B Mendelsohn
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Kari G Rabe
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Elio Riboli
- Division of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
| | - Anne Tjønneland
- Institute of Cancer Epidemiology, Danish Cancer Society, Copenhagen, Denmark
| | - Geoffrey S Tobias
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Dimitrios Trichopoulos
- Department of Epidemiology, Harvard School of Public Health, Boston, MA, USA
- Bureau of Epidemiologic Research, Academy of Athens, Athens, Greece
| | - Joanne W Elena
- Clinical and Translational Epidemiology Branch, Division of Cancer Control and Population Sciences, National Cancer Institute, Bethesda, MD, USA
| | - Herbert Yu
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, Hawaii 96813, USA
| | - Laufey Amundadottir
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | | | - Peter Kraft
- Channing Laboratory, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Department of Epidemiology, Harvard School of Public Health, Boston, MA, USA
| | - Fredrick Schumacher
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California/Norris Comprehensive Cancer Center, Los Angeles, California 90033, USA
| | - Daniel Stram
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California/Norris Comprehensive Cancer Center, Los Angeles, California 90033, USA
| | - Sharon A Savage
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Lisa Mirabello
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Irene L Andrulis
- Fred. A. Litwin Centre for Cancer Genetics, Samuel Lunenfeld Research Institute, Toronto, Ontario, Canada
- Mount Sinai Hospital Christopher Sharp Centre for Surgery and Oncology, Toronto, Ontario, Canada
| | - Jay S Wunder
- Fred. A. Litwin Centre for Cancer Genetics, Samuel Lunenfeld Research Institute, Toronto, Ontario, Canada
- Mount Sinai Hospital Christopher Sharp Centre for Surgery and Oncology, Toronto, Ontario, Canada
| | - Ana Patiño García
- Department of Pediatrics, Clínica Universidad de Navarra, E31080 Pamplona, Spain
| | - Luis Sierrasesúmaga
- Department of Pediatrics, Clínica Universidad de Navarra, E31080 Pamplona, Spain
| | - Donald A Barkauskas
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California/Norris Comprehensive Cancer Center, Los Angeles, California 90033, USA
| | - Richard G Gorlick
- Department of Molecular Pharmacology , Albert Einstein College of Medicine of Yeshiva University, Bronx, NY, USA
- Department of Pediatrics, Albert Einstein College of Medicine of Yeshiva University, Bronx, NY, USA
| | - Mark Purdue
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Wong-Ho Chow
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Lee E Moore
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Kendra L Schwartz
- Department of Family Medicine and Public Health Sciences, Wayne State University, MI, USA
| | - Faith G Davis
- Division of Epidemiology and Biostatistics, School of Public Health, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Ann W Hsing
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Sonja I Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Amanda Black
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Nicolas Wentzensen
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Louise A Brinton
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Jolanta Lissowska
- Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland
| | | | - Katherine A McGlynn
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Michael B Cook
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Barry I Graubard
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Christian P Kratz
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
- Zentrum für Kinderheilkunde und Jugendmedizin, Klinik für Pädiatrische Hämatologie und Onkologie, Medizinische Hochschule Hannover, Hannover, Germany
| | - Mark H Greene
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | | | - David J Hunter
- Channing Laboratory, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Department of Epidemiology, Harvard School of Public Health, Boston, MA, USA
| | - Gilles Thomas
- Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Robert N Hoover
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Francisco X Real
- Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, E-08003 Barcelona, Spain
- Epithelial Carcinogenesis Group, Centro Nacional de Investigaciones Oncológicas (CNIO), Madrid, Spain
| | - Joseph F Fraumeni
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Neil E Caporaso
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Margaret Tucker
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Nathaniel Rothman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Luis A Pérez-Jurado
- Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, E-08003 Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), E-08003 Barcelona, Spain
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
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Abstract
Lysophosphatidic acid (LPA; monoacyl-glycerol-3-phosphate) is a lipid mediator that functions as a mitogen and motility factor for many cell types. LPA signals through six specific G protein-coupled receptors, named LPA(1-6), which trigger both overlapping and distinct signaling pathways. LPA is produced from extracellular lysophosphatidylcholine by a secreted lysophospholipase D, named autotaxin (ATX), originally identified as an "autocrine motility factor" for tumor cells. ATX-LPA signaling is vital for embryonic development and promotes tumor formation, angiogenesis, and experimental metastasis in mice. Elevated expression of ATX and/or aberrant expression of LPA receptors are found in several human malignancies, while loss of LPA(6) function has been implicated in bladder cancer. In this review, we summarize our present understanding of ATX and LPA receptor signaling in cancer.
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Affiliation(s)
- Anna J S Houben
- Division of Cell Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
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Mutoh T, Rivera R, Chun J. Insights into the pharmacological relevance of lysophospholipid receptors. Br J Pharmacol 2012; 165:829-44. [PMID: 21838759 PMCID: PMC3312481 DOI: 10.1111/j.1476-5381.2011.01622.x] [Citation(s) in RCA: 114] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2011] [Revised: 07/22/2011] [Accepted: 07/23/2011] [Indexed: 12/22/2022] Open
Abstract
The discovery of lysophospholipid (LP) 7-transmembrane, G protein-coupled receptors (GPCRs) that began in the 1990s, together with research into the functional roles of the major LPs known as lysophosphatidic acid (LPA) and sphingosine 1-phosphate (S1P), have opened new research avenues into their biological processes and mechanisms. Major examples of LP signalling effects include embryogenesis, nervous system development, vascular development, uterine implantation, immune cell trafficking, and inflammatory reactions. LP signalling also influences the pathophysiology of many diseases including cancer, autoimmune and inflammatory diseases, which indicate that LP receptors may be attractive targets for pharmacological therapies. A key example of such a therapeutic agent is the S1P receptor modulator FTY720, which upon phosphorylation and continued drug exposure, acts as an S1P receptor functional antagonist. This compound (also known as fingolimod or Gilenya) has recently been approved by the FDA for the treatment of relapsing forms of multiple sclerosis. Continued basic and translational research on LP signalling should provide novel insights into both basic biological mechanisms, as well as novel therapeutic approaches to combat a range of human diseases.
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Affiliation(s)
- Tetsuji Mutoh
- Department of Molecular Biology, Dorris Neuroscience Center, The Scripps Research InstituteLa Jolla, CA, USA
- Gunma Kokusai AcademyGunma, Japan
| | - Richard Rivera
- Department of Molecular Biology, Dorris Neuroscience Center, The Scripps Research InstituteLa Jolla, CA, USA
| | - Jerold Chun
- Department of Molecular Biology, Dorris Neuroscience Center, The Scripps Research InstituteLa Jolla, CA, USA
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25
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Katkoori VR, Shanmugam C, Jia X, Vitta SP, Sthanam M, Callens T, Messiaen L, Chen D, Zhang B, Bumpers HL, Samuel T, Manne U. Prognostic significance and gene expression profiles of p53 mutations in microsatellite-stable stage III colorectal adenocarcinomas. PLoS One 2012; 7:e30020. [PMID: 22276141 PMCID: PMC3261849 DOI: 10.1371/journal.pone.0030020] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2011] [Accepted: 12/12/2011] [Indexed: 12/15/2022] Open
Abstract
Although the prognostic value of p53 abnormalities in Stage III microsatellite stable (MSS) colorectal cancers (CRCs) is known, the gene expression profiles specific to the p53 status in the MSS background are not known. Therefore, the current investigation has focused on identification and validation of the gene expression profiles associated with p53 mutant phenotypes in MSS Stage III CRCs. Genomic DNA extracted from 135 formalin-fixed paraffin-embedded tissues, was analyzed for microsatellite instability (MSI) and p53 mutations. Further, mRNA samples extracted from five p53-mutant and five p53-wild-type MSS-CRC snap-frozen tissues were profiled for differential gene expression by Affymetrix Human Genome U133 Plus 2.0 arrays. Differentially expressed genes were further validated by the high-throughput quantitative nuclease protection assay (qNPA), and confirmed by quantitative real-time polymerase chain reaction (qRT-PCR) and by immunohistochemistry (IHC). Survival rates were estimated by Kaplan-Meier and Cox regression analyses. A higher incidence of p53 mutations was found in MSS (58%) than in MSI (30%) phenotypes. Both univariate (log-rank, P = 0.025) and multivariate (hazard ratio, 2.52; 95% confidence interval, 1.25-5.08) analyses have demonstrated that patients with MSS-p53 mutant phenotypes had poor CRC-specific survival when compared to MSS-p53 wild-type phenotypes. Gene expression analyses identified 84 differentially expressed genes. Of 49 down-regulated genes, LPAR6, PDLIM3, and PLAT, and, of 35 up-regulated genes, TRIM29, FUT3, IQGAP3, and SLC6A8 were confirmed by qNPA, qRT-PCR, and IHC platforms. p53 mutations are associated with poor survival of patients with Stage III MSS CRCs and p53-mutant and wild-type phenotypes have distinct gene expression profiles that might be helpful in identifying aggressive subsets.
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Affiliation(s)
- Venkat R. Katkoori
- Department of Pathology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Chandrakumar Shanmugam
- Department of Pathology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Xu Jia
- Department of Pathology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Swaroop P. Vitta
- Department of Pathology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Meenakshi Sthanam
- Department of Pathology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Tom Callens
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Ludwine Messiaen
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Dongquan Chen
- Division of Preventive Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Bin Zhang
- Department of Biostatistics, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Harvey L. Bumpers
- Department of Surgery, Morehouse School of Medicine, Atlanta, Georgia, United States of America
| | - Temesgen Samuel
- Department of Pathology, Tuskegee University, Tuskegee, Alabama, United States of America
| | - Upender Manne
- Department of Pathology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- UAB Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
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26
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Chun J, Hla T, Lynch KR, Spiegel S, Moolenaar WH. International Union of Basic and Clinical Pharmacology. LXXVIII. Lysophospholipid receptor nomenclature. Pharmacol Rev 2010; 62:579-87. [PMID: 21079037 PMCID: PMC2993255 DOI: 10.1124/pr.110.003111] [Citation(s) in RCA: 246] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Lysophospholipids are cell membrane-derived lipids that include both glycerophospholipids such as lysophosphatidic acid (LPA) and sphingoid lipids such as sphingosine 1-phosphate (S1P). These and related molecules can function in vertebrates as extracellular signals by binding and activating G protein-coupled receptors. There are currently five LPA receptors, along with a proposed sixth (LPA₁-LPA₆), and five S1P receptors (S1P₁-S1P₅). A remarkably diverse biology and pathophysiology has emerged since the last review, driven by cloned receptors and targeted gene deletion ("knockout") studies in mice, which implicate receptor-mediated lysophospholipid signaling in most organ systems and multiple disease processes. The entry of various lysophospholipid receptor modulatory compounds into humans through clinical trials is ongoing and may lead to new medicines that are based on this signaling system. This review incorporates IUPHAR Nomenclature Committee guidelines in updating the nomenclature for lysophospholipid receptors ( http://www.iuphar-db.org/DATABASE/FamilyMenuForward?familyId=36).
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Affiliation(s)
- Jerold Chun
- Department of Molecular Biology, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA 92037, USA.
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McConkey DJ, Lee S, Choi W, Tran M, Majewski T, Lee S, Siefker-Radtke A, Dinney C, Czerniak B. Molecular genetics of bladder cancer: Emerging mechanisms of tumor initiation and progression. Urol Oncol 2010; 28:429-40. [PMID: 20610280 DOI: 10.1016/j.urolonc.2010.04.008] [Citation(s) in RCA: 150] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2010] [Revised: 04/15/2010] [Accepted: 04/26/2010] [Indexed: 02/08/2023]
Abstract
Urothelial cancer has served as one of the most important sources of information about the mutational events that underlie the development of human solid malignancies. Although "field effects" that affect the entire bladder mucosa appear to initiate disease, tumors develop along 2 distinct biological "tracks" that present vastly different challenges for clinical management. Recent whole genome methodologies have facilitated even more rapid progress in the identification of the molecular mechanisms involved in bladder cancer initiation and progression. Specifically, whole organ mapping combined with high resolution, high throughput SNP analyses have identified a novel class of candidate tumor suppressors ("forerunner genes") that localize near more familiar tumor suppressors but are disrupted at an earlier stage of cancer development. Furthermore, whole genome comparative genomic hybridization (CGH) and mRNA expression profiling have demonstrated that the 2 major subtypes of urothelial cancer (papillary/superficial and non-papillary/muscle-invasive) are truly distinct molecular entities, and in recent work our group has discovered that muscle-invasive tumors express molecular markers characteristic of a developmental process known as "epithelial-to-mesenchymal transition" (EMT). Emerging evidence indicates that urothelial cancers contain subpopulations of tumor-initiating cells ("cancer stem cells") but the phenotypes of these cells in different tumors are heterogeneous, raising questions about whether or not the 2 major subtypes of cancer share a common precursor. This review will provide an overview of these new insights and discuss priorities for future investigation.
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Affiliation(s)
- David J McConkey
- Department of Urology, University of Texas M. D. Anderson Cancer Center, Houston, TX 77030, USA.
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Rodríguez-Santiago B, Malats N, Rothman N, Armengol L, Garcia-Closas M, Kogevinas M, Villa O, Hutchinson A, Earl J, Marenne G, Jacobs K, Rico D, Tardón A, Carrato A, Thomas G, Valencia A, Silverman D, Real FX, Chanock SJ, Pérez-Jurado LA. Mosaic uniparental disomies and aneuploidies as large structural variants of the human genome. Am J Hum Genet 2010; 87:129-38. [PMID: 20598279 DOI: 10.1016/j.ajhg.2010.06.002] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2010] [Revised: 05/28/2010] [Accepted: 06/08/2010] [Indexed: 10/19/2022] Open
Abstract
Mosaicism is defined as the coexistence of cells with different genetic composition within an individual, caused by postzygotic somatic mutation. Although somatic mosaicism for chromosomal abnormalities is a well-established cause of developmental and somatic disorders and has also been detected in different tissues, its frequency and extent in the adult normal population are still unknown. We provide here a genome-wide survey of mosaic genomic variation obtained by analyzing Illumina 1M SNP array data from blood or buccal DNA samples of 1991 adult individuals from the Spanish Bladder Cancer/EPICURO genome-wide association study. We found mosaic abnormalities in autosomes in 1.7% of samples, including 23 segmental uniparental disomies, 8 complete trisomies, and 11 large (1.5-37 Mb) copy-number variants. Alterations were observed across the different autosomes with recurrent events in chromosomes 9 and 20. No case-control differences were found in the frequency of events or the percentage of cells affected, thus indicating that most rearrangements found are not central to the development of bladder cancer. However, five out of six events tested were detected in both blood and bladder tissue from the same individual, indicating an early developmental origin. The high cellular frequency of the anomalies detected and their presence in normal adult individuals suggest that this type of mosaicism is a widespread phenomenon in the human genome. Somatic mosaicism should be considered in the expanding repertoire of inter- and intraindividual genetic variation, some of which may cause somatic human diseases but also contribute to modifying inherited disorders and/or late-onset multifactorial traits.
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Urothelial dysplasia and other flat lesions of the urinary bladder: clinicopathologic and molecular features. Hum Pathol 2010; 41:155-62. [DOI: 10.1016/j.humpath.2009.07.002] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/28/2009] [Revised: 07/02/2009] [Accepted: 07/09/2009] [Indexed: 11/19/2022]
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Abstract
It has become increasingly evident that the study of DNA is inadequate to explain many, if not most, aspects of the development and progression of neoplastic lesions from pre-invasive lesions to metastasis. Thus, the term "genetic" can no longer refer to just the study of the genome. Much of the action in genetic research now shifts to the methods by which the pre-mRNA from one gene is processed to yield multiple different proteins, different quantities of the same protein as well as other forms of regulating RNA. Thus, the age of post-transcriptional processing and epigenetic control of the transfer of information from the genome has arrived. The mechanisms of post-transcriptional processing and epigenetic control that must be characterized in greater detail including alternate splicing, regulation of mRNA degradation, RNA regulatory factors including those factors which extensively edit mRNAs, control of translation, and control of protein stability and degradation. This chapter reviews many of the processes that control information from the genome to proteins and how these factors lead from less than 40,000 genes to more than an order of magnitude increase more proteins which actually control the phenotypes of cells - normal or neoplastic. It is usually the products of genes (e.g., mRNA, microRNA and proteins) that are the molecular markers that will control translational research and ultimately, individualized (personal) medical approaches to disease. This chapter emphasizes how the process of neoplasia "hijacks" the normal processes of cellular operations, especially those processes that are important in the normal development of the organisms - including proliferation, cellular death, angiogenesis, cellular mobility and invasion, and immunoregulation to ensure neoplastic development, survival and progression. This chapter reviews the wide range of processes controlling the information that flows from the genome to proteins and emphasizes how molecular steps in pure processes can be used as biomarkers to study prevention, treatment and/or management of diseases.
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Affiliation(s)
- Sudhir Srivastava
- National Cancer Institute, National Institutes of Health, Bethesda MD, USA.
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Abstract
Invasive tumors (cancers or malignant lesions) typically develop in the setting in which there is the presence of putative non-invasive lesions and the development of these non-invasive lesions frequently precedes the development of cancers. For some organs, such as the oral cavity, cervix and skin, the respective putative pre-invasive lesions can be observed over time and documented to progress to invasive lesions. However, for less readily observable lesions, such as those of the prostate, the progression of the pre-invasive lesions, e.g., prostatic intraepithelial neoplasia (PIN) and prostatic proliferative inflammatory atrophy (PIA) to prostatic cancer are more difficult to document. Thus, for most organ systems, specific pre-invasive neoplastic lesions have been proposed based upon the apparent observations of one or more of the following: 1) microinvasive disease developing from a pre-invasive neoplastic lesion, 2) the general association of the pre-invasive lesion with invasive lesions, 3) the subsequent development of invasive lesions following diagnosis of the pre-invasive lesion, 4) correlations of the molecular features of the putative pre-invasive lesion with the matching invasive lesions, and 5) reductions in the rate of cancer following removal of the pre-invasive lesion. When there are mixtures of pre-invasive lesions with actual cancers in the same case, some of the above specific associations are more difficult to make. Several terms have been used to describe pre-invasive lesions, many of which are now less useful as our knowledge of these lesions increases. It is now commonly accepted that these lesions are a features of the spectrum of neoplastic development and most are accepted as ``neoplastic lesions'' with associated molecular features, even though they may be reversible even if they have mutations in suppressor genes (e.g., p53) or are associated with viral etiologies (e.g., cervical intraepithelial neoplasia). The overall term, "pre-invasive neoplasia", seems to best describe these putative pre-invasive lesions. Thus, terms such as incipient neoplasia should be abandoned. The term "intra-epithelial neoplasia" with an associated grade, which has been developed for pre-invasive neoplastic lesions of the cervix, i.e. cervical intraepithelial neoplasia (CIN), seems to be a terminology that adds consistency across epithelial organs. Thus, adoption of these terms for the additional organ sites of pancreas (PanIN) and prostate (PIN) seems accepted. Less descriptive terms such as the degrees of dysplasia of the oral cavity and bronchopulmonary system and actinic keratosis and Bowen's disease of the skin might be better designated as oral intraepithelial neoplasia (OIN), pulmonary intraepithelial neoplasia (PulIN) and dermal intraepithelial neoplasia (DIN). The etiology of pre-invasive neoplasia is the etiology of the matching cancers. Some obvious initiating factors include exposure to the whole range of ionizing and non-ionizing radiation, tobacco abuse and a broad range of other carcinogens (e.g., benzene). A frequent initiation factor is the setting of long standing continuing damage, inflammation and repair (LOCDIR) which leads to early molecular features associated with neoplasia after about one year. An excellent example of this is ulcerative colitis (UC) in which dysregulation of microsatellite repair enzymes have been documented one year following diagnosis of UC. While the nomenclature, description, diagnosis and etiology of pre-invasive neoplasia has advanced, approaches to therapy of such lesions have not progressed adequately even though it has been identified that, for example, removal of polyps periodically from the colorectum, DCIS from the breast, and high grade CIN from the cervix, results in a reduction in the development of cancers of the colorectum, breast, and cervix, respectively. With the development of more molecularly targeted therapy with fewer side effects, preventive therapies may be more successfully targeted to pre-invasive neoplastic lesions.
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Affiliation(s)
- William E Grizzle
- Department of Pathology, Division of Anatomic Pathology, University of Alabama at Birmingham, Birmingham, AL, USA.
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O'Neal J, Gao F, Hassan A, Monahan R, Barrios S, Kilimann MW, Lee I, Chng WJ, Vij R, Tomasson MH. Neurobeachin (NBEA) is a target of recurrent interstitial deletions at 13q13 in patients with MGUS and multiple myeloma. Exp Hematol 2009; 37:234-44. [PMID: 19135901 DOI: 10.1016/j.exphem.2008.10.014] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2008] [Revised: 09/17/2008] [Accepted: 10/15/2008] [Indexed: 01/10/2023]
Abstract
OBJECTIVE Chromosome 13 deletions (del[13]), detected by metaphase cytogenetics, predict poor outcomes in multiple myeloma (MM), but the gene(s) responsible have not been conclusively identified. We sought to identify tumor-suppressor genes on chromosome 13 using a novel array comparative genomic hybridization (aCGH) strategy. MATERIALS AND METHODS We identified DNA copy number losses on chromosome 13 using genomic DNA isolated from CD138-enriched bone marrow cells (tumor) from 20 patients with MM, monoclonal gammopathy of undetermined significance, or amyloidosis. We used matched skin biopsy (germline) genomic DNA to control for copy number polymorphisms and a novel aCGH array dedicated to chromosome 13 to map somatic DNA gains and losses at ultra-high resolution (>385,000 probes; median probe spacing 60 bp). We analyzed microarray expression data from an additional 262 patient samples both with and without del[13]. RESULTS Two distinct minimally deleted regions at 13q14 and 13q13 were defined that affected the RB1 and NBEA genes, respectively. RB1 is a canonical tumor suppressor previously implicated in MM. NBEA is implicated in membrane trafficking in neurons, protein kinase A binding, and has no known role in cancer. Noncoding RNAs on chromosome 13 were not affected by interstitial deletions. Both the RB1 and NBEA genes were deleted in 40% of cases (8 of 20; 5 patients with del[13] detected by traditional methods and 3 patients with interstitial deletions detected by aCGH). Forty-one additional MM patient samples were used for complete exonic sequencing of RB1, but no somatic mutations were found. Along with RB1, NBEA gene expression was significantly reduced in cases with del[13]. CONCLUSIONS The NBEA gene at 13q13, and its expression are frequently disrupted in MM. Additional studies are warranted to evaluate the role of NBEA as a novel candidate tumor-suppressor gene.
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Affiliation(s)
- Julie O'Neal
- Department of Internal Medicine, Division of Oncology, Washington University, Siteman Cancer Center, St Louis, MO, USA
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Majewski T, Lee S, Jeong J, Yoon DS, Kram A, Kim MS, Tuziak T, Bondaruk J, Lee S, Park WS, Tang KS, Chung W, Shen L, Ahmed SS, Johnston DA, Grossman HB, Dinney CP, Zhou JH, Harris RA, Snyder C, Filipek S, Narod SA, Watson P, Lynch HT, Gazdar A, Bar-Eli M, Wu XF, McConkey DJ, Baggerly K, Issa JP, Benedict WF, Scherer SE, Czerniak B. Understanding the development of human bladder cancer by using a whole-organ genomic mapping strategy. J Transl Med 2008; 88:694-721. [PMID: 18458673 PMCID: PMC2849658 DOI: 10.1038/labinvest.2008.27] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
The search for the genomic sequences involved in human cancers can be greatly facilitated by maps of genomic imbalances identifying the involved chromosomal regions, particularly those that participate in the development of occult preneoplastic conditions that progress to clinically aggressive invasive cancer. The integration of such regions with human genome sequence variation may provide valuable clues about their overall structure and gene content. By extension, such knowledge may help us understand the underlying genetic components involved in the initiation and progression of these cancers. We describe the development of a genome-wide map of human bladder cancer that tracks its progression from in situ precursor conditions to invasive disease. Testing for allelic losses using a genome-wide panel of 787 microsatellite markers was performed on multiple DNA samples, extracted from the entire mucosal surface of the bladder and corresponding to normal urothelium, in situ preneoplastic lesions, and invasive carcinoma. Using this approach, we matched the clonal allelic losses in distinct chromosomal regions to specific phases of bladder neoplasia and produced a detailed genetic map of bladder cancer development. These analyses revealed three major waves of genetic changes associated with growth advantages of successive clones and reflecting a stepwise conversion of normal urothelial cells into cancer cells. The genetic changes map to six regions at 3q22-q24, 5q22-q31, 9q21-q22, 10q26, 13q14, and 17p13, which may represent critical hits driving the development of bladder cancer. Finally, we performed high-resolution mapping using single nucleotide polymorphism markers within one region on chromosome 13q14, containing the model tumor suppressor gene RB1, and defined a minimal deleted region associated with clonal expansion of in situ neoplasia. These analyses provided new insights on the involvement of several non-coding sequences mapping to the region and identified novel target genes, termed forerunner (FR) genes, involved in early phases of cancer development.
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Affiliation(s)
- Tadeusz Majewski
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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Abstract
Bladder cancer, arising from the transitional cells of the mucosal urothelium, may present as a noninvasive, papillary tumor protruding from the mucosal surface, or as a solid, nonpapillary tumor that invades the bladder wall and has a high propensity for metastasis. The nonpapillary tumors originate from in situ dysplasia. The most common environmental risk for bladder cancer is active smoking; occupational exposure to arsenic or other carcinogens is also a risk factor. A possible familial component to bladder cancer has been described. Conventional models of carcinogenesis suppose the existence of successive mutation events within a specific cell clone, enabling its eventual escape from regulation of cell division and maintenance of genomic integrity. Important new information has emerged from whole-organ mapping of the mucosal genome in bladders resected for invasive cancer (Majewski et al, Lab Invest; published online 5 May 2008). Mapping of genetic hits across the entire mucosa demonstrates genetic alterations in six chromosomal regions, not only in mucosal regions of evident dysplasia, but also in morphologically normal mucosa. These clonally expanded regions cover vast expanses of the bladder surface, as a 'first wave' of pre-neoplasia. Target genes in these regions are termed 'forerunner genes' (FR genes), based on the concept that these genes enable the initial clonal expansion of in situ urothelial neoplasia. Extensive further analysis of human populations with urothelial cancer implicates genetic polymorphisms in one of these genes, P2RY5, as being present in a familial cluster of cancers of multiple organs, and as imparting risk for development of bladder cancer in active smokers. P2RY5 is a gene encoded within intron 17 of RB1, a prototypic tumor suppressor gene whose expression is lost at a later stage of bladder carcinogenesis. Alterations of the FR gene status provide a novel opportunity to screen individuals at risk for the earliest stage of bladder pre-neoplasia and represent attractive targets for therapeutic and chemopreventive interventions. These findings support the hypothesis that bladder carcinogenesis is initiated by clonal expansion of genetically altered but histologically normal cells that cover broad expanses of the mucosa. Effort must now be given to identifying the biological function of these novel FR genes.
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Shimomura Y, Wajid M, Ishii Y, Shapiro L, Petukhova L, Gordon D, Christiano AM. Disruption of P2RY5, an orphan G protein-coupled receptor, underlies autosomal recessive woolly hair. Nat Genet 2008; 40:335-9. [PMID: 18297072 DOI: 10.1038/ng.100] [Citation(s) in RCA: 155] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2007] [Accepted: 01/28/2008] [Indexed: 11/09/2022]
Abstract
The genetic determinants of hair texture in humans are largely unknown. Several human syndromes exist in which woolly hair comprises a part of the phenotype; however, simple autosomal recessive inheritance of isolated woolly hair has only rarely been reported. To identify a gene involved in controlling hair texture, we performed genetic linkage analysis in six families of Pakistani origin with autosomal recessive woolly hair (ARWH; OMIM 278150). All six families showed linkage to chromosome 13q14.2-14.3 (Z = 17.97). In all cases, we discovered pathogenic mutations in P2RY5, which encodes a G protein-coupled receptor and is a nested gene residing within intron 17 of the retinoblastoma 1 (RB1) gene. P2RY5 is expressed in both Henle's and Huxley's layers of the inner root sheath of the hair follicle. Our findings indicate that disruption of P2RY5 underlies ARWH and, more broadly, uncover a new gene involved in determining hair texture in humans.
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Affiliation(s)
- Yutaka Shimomura
- Department of Dermatology, Columbia University, College of Physicians & Surgeons, 630 West 168th Street, VC15 204a, New York, New York 10032, USA
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