1
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Afsari B, Kuo A, Zhang Y, Li L, Lahouel K, Danilova L, Favorov A, Rosenquist TA, Grollman AP, Kinzler KW, Cope L, Vogelstein B, Tomasetti C. Supervised mutational signatures for obesity and other tissue-specific etiological factors in cancer. eLife 2021; 10:61082. [PMID: 33491650 PMCID: PMC7872524 DOI: 10.7554/elife.61082] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 01/24/2021] [Indexed: 12/21/2022] Open
Abstract
Determining the etiologic basis of the mutations that are responsible for cancer is one of the fundamental challenges in modern cancer research. Different mutational processes induce different types of DNA mutations, providing 'mutational signatures' that have led to key insights into cancer etiology. The most widely used signatures for assessing genomic data are based on unsupervised patterns that are then retrospectively correlated with certain features of cancer. We show here that supervised machine-learning techniques can identify signatures, called SuperSigs, that are more predictive than those currently available. Surprisingly, we found that aging yields different SuperSigs in different tissues, and the same is true for environmental exposures. We were able to discover SuperSigs associated with obesity, the most important lifestyle factor contributing to cancer in Western populations.
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Affiliation(s)
- Bahman Afsari
- Division of Biostatistics and Bioinformatics, Department of Oncology, Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Albert Kuo
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, United States
| | - YiFan Zhang
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, United States
| | - Lu Li
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, United States
| | - Kamel Lahouel
- Division of Biostatistics and Bioinformatics, Department of Oncology, Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Ludmila Danilova
- Division of Biostatistics and Bioinformatics, Department of Oncology, Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, United States.,Laboratory of Systems Biology and Computational Genetics, Vavilov Institute of General Genetics, RAS, Moscow, Russian Federation
| | - Alexander Favorov
- Division of Biostatistics and Bioinformatics, Department of Oncology, Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, United States.,Laboratory of Systems Biology and Computational Genetics, Vavilov Institute of General Genetics, RAS, Moscow, Russian Federation
| | | | - Arthur P Grollman
- State University of New York at Stony Brook, Stony Brook, United States
| | - Ken W Kinzler
- Ludwig Center & Howard Hughes Medical Institute, Johns Hopkins Kimmel Cancer Center, Baltimore, United States
| | - Leslie Cope
- Division of Biostatistics and Bioinformatics, Department of Oncology, Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Bert Vogelstein
- Ludwig Center & Howard Hughes Medical Institute, Johns Hopkins Kimmel Cancer Center, Baltimore, United States
| | - Cristian Tomasetti
- Division of Biostatistics and Bioinformatics, Department of Oncology, Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, United States.,Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, United States
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2
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Koenecke A, Powell M, Xiong R, Shen Z, Fischer N, Huq S, Khalafallah AM, Trevisan M, Sparen P, Carrero JJ, Nishimura A, Caffo B, Stuart EA, Bai R, Staedtke V, Thomas DL, Papadopoulos N, Kinzler KW, Vogelstein B, Zhou S, Bettegowda C, Konig MF, Mensh BD, Vogelstein JT, Athey S. Alpha-1 adrenergic receptor antagonists to prevent hyperinflammation and death from lower respiratory tract infection. eLife 2021; 10:61700. [PMID: 34114951 PMCID: PMC8195605 DOI: 10.7554/elife.61700] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Accepted: 05/11/2021] [Indexed: 01/16/2023] Open
Abstract
In severe viral pneumonia, including Coronavirus disease 2019 (COVID-19), the viral replication phase is often followed by hyperinflammation, which can lead to acute respiratory distress syndrome, multi-organ failure, and death. We previously demonstrated that alpha-1 adrenergic receptor (⍺1-AR) antagonists can prevent hyperinflammation and death in mice. Here, we conducted retrospective analyses in two cohorts of patients with acute respiratory distress (ARD, n = 18,547) and three cohorts with pneumonia (n = 400,907). Federated across two ARD cohorts, we find that patients exposed to ⍺1-AR antagonists, as compared to unexposed patients, had a 34% relative risk reduction for mechanical ventilation and death (OR = 0.70, p = 0.021). We replicated these methods on three pneumonia cohorts, all with similar effects on both outcomes. All results were robust to sensitivity analyses. These results highlight the urgent need for prospective trials testing whether prophylactic use of ⍺1-AR antagonists ameliorates lower respiratory tract infection-associated hyperinflammation and death, as observed in COVID-19.
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Affiliation(s)
- Allison Koenecke
- Institute for Computational & Mathematical Engineering, Stanford UniversityStanfordUnited States
| | - Michael Powell
- Department of Biomedical Engineering, Institute for Computational Medicine, The Johns Hopkins UniversityBaltimoreUnited States
| | - Ruoxuan Xiong
- Management Science & Engineering, Stanford UniversityStanfordUnited States
| | - Zhu Shen
- Department of Statistics, Stanford UniversityStanfordUnited States
| | - Nicole Fischer
- The Johns Hopkins University School of MedicineBaltimoreUnited States
| | - Sakibul Huq
- Department of Neurosurgery and Neurology, The Johns Hopkins University School of MedicineBaltimoreUnited States
| | - Adham M Khalafallah
- Department of Neurosurgery and Neurology, The Johns Hopkins University School of MedicineBaltimoreUnited States
| | - Marco Trevisan
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, SwedenSolnaSweden
| | - Pär Sparen
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, SwedenSolnaSweden
| | - Juan J Carrero
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, SwedenSolnaSweden
| | - Akihiko Nishimura
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health at Johns Hopkins UniversityBaltimoreUnited States
| | - Brian Caffo
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health at Johns Hopkins UniversityBaltimoreUnited States
| | - Elizabeth A Stuart
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health at Johns Hopkins UniversityBaltimoreUnited States
| | - Renyuan Bai
- Department of Neurosurgery and Neurology, The Johns Hopkins University School of MedicineBaltimoreUnited States
| | - Verena Staedtke
- Department of Neurosurgery and Neurology, The Johns Hopkins University School of MedicineBaltimoreUnited States
| | - David L Thomas
- The Johns Hopkins University School of MedicineBaltimoreUnited States
| | - Nickolas Papadopoulos
- Ludwig Center, Lustgarten Laboratory, and the Howard Hughes Medical Institute at The Johns Hopkins Kimmel Cancer CenterBaltimoreUnited States
| | - Ken W Kinzler
- Ludwig Center, Lustgarten Laboratory, and the Howard Hughes Medical Institute at The Johns Hopkins Kimmel Cancer CenterBaltimoreUnited States
| | - Bert Vogelstein
- Ludwig Center, Lustgarten Laboratory, and the Howard Hughes Medical Institute at The Johns Hopkins Kimmel Cancer CenterBaltimoreUnited States
| | - Shibin Zhou
- Ludwig Center, Lustgarten Laboratory, and the Howard Hughes Medical Institute at The Johns Hopkins Kimmel Cancer CenterBaltimoreUnited States
| | - Chetan Bettegowda
- The Johns Hopkins University School of MedicineBaltimoreUnited States,Ludwig Center, Lustgarten Laboratory, and the Howard Hughes Medical Institute at The Johns Hopkins Kimmel Cancer CenterBaltimoreUnited States
| | - Maximilian F Konig
- Division of Rheumatology, Department of Medicine, The Johns Hopkins University School of MedicineBaltimoreUnited States
| | - Brett D Mensh
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Joshua T Vogelstein
- Department of Biomedical Engineering, Institute for Computational Medicine, The Johns Hopkins UniversityBaltimoreUnited States,Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health at Johns Hopkins UniversityBaltimoreUnited States
| | - Susan Athey
- Stanford Graduate School of Business, Stanford UniversityStanfordUnited States
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3
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Park S, Chu LC, Fishman EK, Yuille AL, Vogelstein B, Kinzler KW, Horton KM, Hruban RH, Zinreich ES, Fouladi DF, Shayesteh S, Graves J, Kawamoto S. Erratum to "Annotated normal CT data of the abdomen for deep learning: Challenges and strategies for implementation" [Diagn. Interv. Imaging. 101 (2020) 35-44]. Diagn Interv Imaging 2020; 101:427. [PMID: 32446597 DOI: 10.1016/j.diii.2020.04.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- S Park
- The Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University, School of Medicine, 601N. Caroline Street, Baltimore, MD 21287, USA
| | - L C Chu
- The Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University, School of Medicine, 601N. Caroline Street, Baltimore, MD 21287, USA
| | - E K Fishman
- The Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University, School of Medicine, 601N. Caroline Street, Baltimore, MD 21287, USA
| | - A L Yuille
- Department of Computer Science, Johns Hopkins University, School of Arts and Sciences, Baltimore, MD 21218, USA
| | - B Vogelstein
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, School of Medicine, Baltimore, MD 21287, USA; Johns Hopkins University, School of Medicine, Ludwig Center for Cancer Genetics and Therapeutics, Baltimore, MD 21205, USA
| | - K W Kinzler
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, School of Medicine, Baltimore, MD 21287, USA; Johns Hopkins University, School of Medicine, Ludwig Center for Cancer Genetics and Therapeutics, Baltimore, MD 21205, USA
| | - K M Horton
- The Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University, School of Medicine, 601N. Caroline Street, Baltimore, MD 21287, USA
| | - R H Hruban
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University, School of Medicine, Baltimore, MD 21205, USA
| | - E S Zinreich
- The Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University, School of Medicine, 601N. Caroline Street, Baltimore, MD 21287, USA
| | - D F Fouladi
- The Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University, School of Medicine, 601N. Caroline Street, Baltimore, MD 21287, USA
| | - S Shayesteh
- The Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University, School of Medicine, 601N. Caroline Street, Baltimore, MD 21287, USA
| | - J Graves
- The Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University, School of Medicine, 601N. Caroline Street, Baltimore, MD 21287, USA
| | - S Kawamoto
- The Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University, School of Medicine, 601N. Caroline Street, Baltimore, MD 21287, USA.
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4
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Weisberg EM, Chu LC, Park S, Yuille AL, Kinzler KW, Vogelstein B, Fishman EK. Deep lessons learned: Radiology, oncology, pathology, and computer science experts unite around artificial intelligence to strive for earlier pancreatic cancer diagnosis. Diagn Interv Imaging 2019; 101:111-115. [PMID: 31629672 DOI: 10.1016/j.diii.2019.09.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 09/03/2019] [Accepted: 09/17/2019] [Indexed: 10/25/2022]
Affiliation(s)
- E M Weisberg
- The Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins Hospital, 601 North Caroline Street, Baltimore, MD 21287, USA.
| | - L C Chu
- The Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins Hospital, 601 North Caroline Street, Baltimore, MD 21287, USA
| | - S Park
- The Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins Hospital, 601 North Caroline Street, Baltimore, MD 21287, USA
| | - A L Yuille
- Department of Cognitive Science, The Johns Hopkins University, Baltimore, MD, USA
| | - K W Kinzler
- Department of Pharmacology and Molecular Science, Johns Hopkins Hospital, Baltimore, MD, USA
| | - B Vogelstein
- Department of Pathology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins Hospital, Baltimore, MD, USA
| | - E K Fishman
- The Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins Hospital, 601 North Caroline Street, Baltimore, MD 21287, USA
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5
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Eich ML, Rodriguez Pena MDC, Springer S, Taheri D, Tregnago AC, Salles DC, Bezerra SM, Cunha IW, Fujita K, Ertoy D, Bivalacqua TJ, Tomasetti C, Papadopoulos N, Kinzler KW, Vogelstein B, Netto GJ. Incidence and distribution of UroSEEK gene panel in a multi-institutional cohort of bladder urothelial carcinoma. Mod Pathol 2019; 32:1544-1550. [PMID: 31028363 PMCID: PMC6872189 DOI: 10.1038/s41379-019-0276-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 03/22/2019] [Accepted: 03/23/2019] [Indexed: 11/22/2022]
Abstract
Noninvasive approaches for early detection of bladder cancer are actively being investigated. We recently developed a urine- based molecular assay for the detection and surveillance of bladder neoplasms (UroSEEK). UroSEEK is designed to detect alterations in 11 genes that include most common genetic alterations in bladder cancer. In this study, we analyzed 527 cases, including 373 noninvasive and 154 invasive urothelial carcinomas of bladder from transurethral resections or cystectomies performed at four institutions (1991-2016). Two different mutational analysis assays of a representative tumor area were performed: first, a singleplex PCR assay for evaluation of the TERT promoter region (TERTSeqS) and second, a multiplex PCR assay using primers designed to amplify regions of interest of 10 (FGFR3, PIK3CA, TP53, HRAS, KRAS, ERBB2, CDKN2A, MET, MLL, and VHL) genes (UroSeqS). Overall, 92% of all bladder tumors were positive for at least one genetic alteration in the UroSEEK panel. We found TERT promoter mutations in 77% of low-grade noninvasive papillary carcinomas, with a relatively lower incidence of 65% in high-grade noninvasive papillary carcinomas and carcinomas in situ; p = 0.017. Seventy-two percent of pT1 and 63% of muscle-invasive bladder tumors harbored TERT promoter mutations with g.1295228C>T alteration being the most common in all groups. FGFR3 and PIK3CA mutations were more frequent in low-grade noninvasive papillary carcinomas compared with high-grade noninvasive papillary carcinomas and carcinomas in situ (p < 0.0001), while the opposite was true for TP53 (p < 0.0001). Significantly higher rates of TP53 and CDKN2A mutation rates (p = 0.005 and 0.035, respectively) were encountered in muscle-invasive bladder tumors compared with those of pT1 stage. The overwhelming majority of all investigated tumors showed at least one mutation among UroSEEK assay genes, confirming the comprehensive coverage of the panel and supporting its potential utility as a noninvasive urine-based assay.
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Affiliation(s)
- Marie-Lisa Eich
- Department of Pathology, The University of Alabama at Birmingham, Birmingham, AL, United States
| | | | - Simeon Springer
- Howard Hughes Medical Institute, Ludwig Cancer for Cancer Genetics and Therapeutics, Baltimore, United States,Sidney Kimmel Comprehensive Cancer Center, Baltimore, United States
| | - Diana Taheri
- Department of Pathology, Johns Hopkins University, United States,Department of Pathology, Isfahan Kidney Diseases Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | | | | | - Stephania Martins Bezerra
- Department of Pathology, AC Camargo Cancer Center, Sao Paulo, Brazil,Department of Pathology, Rede D’OR-São Luiz, Sao Paulo, Brazil
| | - Isabela W. Cunha
- Department of Pathology, AC Camargo Cancer Center, Sao Paulo, Brazil
| | | | - Dilek Ertoy
- Department of Pathology, Hacettepe University, Ankara, Turkey
| | | | - Cristian Tomasetti
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, United States,Division of Biostatistics and Bioinformatics, Department of Oncology, Sidney Kimmel Cancer Center
| | - Nickolas Papadopoulos
- Howard Hughes Medical Institute, Ludwig Cancer for Cancer Genetics and Therapeutics, Baltimore, United States,Sidney Kimmel Comprehensive Cancer Center, Baltimore, United States
| | - Ken W. Kinzler
- Howard Hughes Medical Institute, Ludwig Cancer for Cancer Genetics and Therapeutics, Baltimore, United States,Sidney Kimmel Comprehensive Cancer Center, Baltimore, United States
| | - Bert Vogelstein
- Howard Hughes Medical Institute, Ludwig Cancer for Cancer Genetics and Therapeutics, Baltimore, United States,Sidney Kimmel Comprehensive Cancer Center, Baltimore, United States
| | - George J. Netto
- Department of Pathology, The University of Alabama at Birmingham, Birmingham, AL, United States
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6
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Lee B, Lipton L, Cohen J, Tie J, Javed AA, Li L, Goldstein D, Burge M, Cooray P, Nagrial A, Tebbutt NC, Thomson B, Nikfarjam M, Harris M, Haydon A, Lawrence B, Tai DWM, Simons K, Lennon AM, Wolfgang CL, Tomasetti C, Papadopoulos N, Kinzler KW, Vogelstein B, Gibbs P. Circulating tumor DNA as a potential marker of adjuvant chemotherapy benefit following surgery for localized pancreatic cancer. Ann Oncol 2019; 30:1472-1478. [PMID: 31250894 PMCID: PMC6771221 DOI: 10.1093/annonc/mdz200] [Citation(s) in RCA: 118] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND In early-stage pancreatic cancer, there are currently no biomarkers to guide selection of therapeutic options. This prospective biomarker trial evaluated the feasibility and potential clinical utility of circulating tumor DNA (ctDNA) analysis to inform adjuvant therapy decision making. MATERIALS AND METHODS Patients considered by the multidisciplinary team to have resectable pancreatic adenocarcinoma were enrolled. Pre- and post-operative samples for ctDNA analysis were collected. PCR-based-SafeSeqS assays were used to identify mutations at codon 12, 13 and 61 of KRAS in the primary pancreatic tumor and to detect ctDNA. Results of ctDNA analysis were correlated with CA19-9, recurrence-free and overall survival (OS). Patient management was per standard of care, blinded to ctDNA data. RESULTS Of 112 patients consented pre-operatively, 81 (72%) underwent resection. KRAS mutations were identified in 91% (38/42) of available tumor samples. Of available plasma samples (N = 42), KRAS mutated ctDNA was detected in 62% (23/37) pre-operative and 37% (13/35) post-operative cases. At a median follow-up of 38.4 months, ctDNA detection in the pre-operative setting was associated with inferior recurrence-free survival (RFS) [hazard ratio (HR) 4.1; P = 0.002)] and OS (HR 4.1; P = 0.015). Detectable ctDNA following curative intent resection was associated with inferior RFS (HR 5.4; P < 0.0001) and OS (HR 4.0; P = 0.003). Recurrence occurred in 13/13 (100%) patients with detectable ctDNA post-operatively, including in seven that received gemcitabine-based adjuvant chemotherapy. CONCLUSION ctDNA studies in localized pancreatic cancer are challenging, with a substantial number of patients not able to undergo resection, not having sufficient tumor tissue for analysis or not completing per protocol sample collection. ctDNA analysis, pre- and/or post-surgery, is a promising prognostic marker. Studies of ctDNA guided therapy are justified, including of treatment intensification strategies for patients with detectable ctDNA post-operatively who appear at very high risk of recurrence despite gemcitabine-based adjuvant therapy.
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Affiliation(s)
- B Lee
- Division of Systems Biology and Personalised Medicine, Walter & Eliza Hall Institute (WEHI), Melbourne; Department of Medical Oncology, Royal Melbourne Hospital, Melbourne; Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne.
| | - L Lipton
- Department of Medical Oncology, Royal Melbourne Hospital, Melbourne; Department of Medical Oncology, Western Health, Melbourne; Department of Medical Oncology, Cabrini Health, Malvern, Australia
| | - J Cohen
- Ludwig Centre and Howard Hughes Medical Institute at Johns Hopkins Kimmel Cancer Centre, Baltimore
| | - J Tie
- Division of Systems Biology and Personalised Medicine, Walter & Eliza Hall Institute (WEHI), Melbourne; Department of Medical Oncology, Royal Melbourne Hospital, Melbourne; Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne; Department of Medical Oncology, Western Health, Melbourne
| | - A A Javed
- Ludwig Centre and Howard Hughes Medical Institute at Johns Hopkins Kimmel Cancer Centre, Baltimore
| | - L Li
- Division of Biostatistics and Bioinformatics, Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, USA
| | - D Goldstein
- Department of Medical Oncology, Prince of Wales Hospital, Randwick
| | - M Burge
- Department of Medical Oncology, Royal Brisbane Hospital, Brisbane
| | - P Cooray
- Department of Medical Oncology, Eastern Health, Melbourne
| | - A Nagrial
- Department of Medical Oncology, Crown Princess Mary Cancer Centre Westmead, Westmead
| | - N C Tebbutt
- Department of Medical Oncology, Olivia Newton-John Cancer and Wellness Centre, Melbourne
| | - B Thomson
- Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne; Department of Surgery, Royal Melbourne Hospital, Melbourne
| | - M Nikfarjam
- Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne; Department of Medical Oncology, Olivia Newton-John Cancer and Wellness Centre, Melbourne
| | - M Harris
- Department of Medical Oncology, Monash Medical Centre, Clayton
| | - A Haydon
- Department of Medical Oncology, Alfred Hospital, Melbourne, Australia
| | - B Lawrence
- Department of Medical Oncology, Auckland City Hospital, Auckland, New Zealand
| | - D W M Tai
- Department of Medical Oncology, National Cancer Centre, Singapore
| | - K Simons
- Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne; Centre for Epidemiology & Biostatistics, University of Melbourne, Melbourne, Australia
| | - A M Lennon
- Ludwig Centre and Howard Hughes Medical Institute at Johns Hopkins Kimmel Cancer Centre, Baltimore
| | - C L Wolfgang
- Ludwig Centre and Howard Hughes Medical Institute at Johns Hopkins Kimmel Cancer Centre, Baltimore
| | - C Tomasetti
- Ludwig Centre and Howard Hughes Medical Institute at Johns Hopkins Kimmel Cancer Centre, Baltimore; Division of Biostatistics and Bioinformatics, Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, USA
| | - N Papadopoulos
- Ludwig Centre and Howard Hughes Medical Institute at Johns Hopkins Kimmel Cancer Centre, Baltimore
| | - K W Kinzler
- Ludwig Centre and Howard Hughes Medical Institute at Johns Hopkins Kimmel Cancer Centre, Baltimore
| | - B Vogelstein
- Ludwig Centre and Howard Hughes Medical Institute at Johns Hopkins Kimmel Cancer Centre, Baltimore
| | - P Gibbs
- Division of Systems Biology and Personalised Medicine, Walter & Eliza Hall Institute (WEHI), Melbourne; Department of Medical Oncology, Royal Melbourne Hospital, Melbourne; Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne; Department of Medical Oncology, Western Health, Melbourne
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7
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Park S, Chu LC, Fishman EK, Yuille AL, Vogelstein B, Kinzler KW, Horton KM, Hruban RH, Zinreich ES, Fouladi DF, Shayesteh S, Graves J, Kawamoto S. Annotated normal CT data of the abdomen for deep learning: Challenges and strategies for implementation. Diagn Interv Imaging 2019; 101:35-44. [PMID: 31358460 DOI: 10.1016/j.diii.2019.05.008] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 05/23/2019] [Accepted: 05/28/2019] [Indexed: 02/08/2023]
Abstract
PURPOSE The purpose of this study was to report procedures developed to annotate abdominal computed tomography (CT) images from subjects without pancreatic disease that will be used as the input for deep convolutional neural networks (DNN) for development of deep learning algorithms for automatic recognition of a normal pancreas. MATERIALS AND METHODS Dual-phase contrast-enhanced volumetric CT acquired from 2005 to 2009 from potential kidney donors were retrospectively assessed. Four trained human annotators manually and sequentially annotated 22 structures in each datasets, then expert radiologists confirmed the annotation. For efficient annotation and data management, a commercial software package that supports three-dimensional segmentation was used. RESULTS A total of 1150 dual-phase CT datasets from 575 subjects were annotated. There were 229 men and 346 women (mean age: 45±12years; range: 18-79years). The mean intra-observer intra-subject dual-phase CT volume difference of all annotated structures was 4.27mL (7.65%). The deep network prediction for multi-organ segmentation showed high fidelity with 89.4% and 1.29mm in terms of mean Dice similarity coefficients and mean surface distances, respectively. CONCLUSIONS A reliable data collection/annotation process for abdominal structures was developed. This process can be used to generate large datasets appropriate for deep learning.
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Affiliation(s)
- S Park
- The Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University, School of Medicine, 601N. Caroline Street, Baltimore, MD 21287, USA
| | - L C Chu
- The Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University, School of Medicine, 601N. Caroline Street, Baltimore, MD 21287, USA
| | - E K Fishman
- The Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University, School of Medicine, 601N. Caroline Street, Baltimore, MD 21287, USA
| | - A L Yuille
- Department of Computer Science, Johns Hopkins University, School of Arts and Sciences, Baltimore, MD 21218, USA
| | - B Vogelstein
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, School of Medicine, Baltimore, MD 21287, USA; Johns Hopkins University, School of Medicine, Ludwig Center for Cancer Genetics and Therapeutics, Baltimore, MD 21205, USA
| | - K W Kinzler
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, School of Medicine, Baltimore, MD 21287, USA; Johns Hopkins University, School of Medicine, Ludwig Center for Cancer Genetics and Therapeutics, Baltimore, MD 21205, USA
| | - K M Horton
- The Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University, School of Medicine, 601N. Caroline Street, Baltimore, MD 21287, USA
| | - R H Hruban
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University, School of Medicine, Baltimore, MD 21205, USA
| | - E S Zinreich
- The Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University, School of Medicine, 601N. Caroline Street, Baltimore, MD 21287, USA
| | - D F Fouladi
- The Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University, School of Medicine, 601N. Caroline Street, Baltimore, MD 21287, USA
| | - S Shayesteh
- The Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University, School of Medicine, 601N. Caroline Street, Baltimore, MD 21287, USA
| | - J Graves
- The Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University, School of Medicine, 601N. Caroline Street, Baltimore, MD 21287, USA
| | - S Kawamoto
- The Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University, School of Medicine, 601N. Caroline Street, Baltimore, MD 21287, USA.
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8
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Springer SU, Chen CH, Rodriguez Pena MDC, Li L, Douville C, Wang Y, Cohen JD, Taheri D, Silliman N, Schaefer J, Ptak J, Dobbyn L, Papoli M, Kinde I, Afsari B, Tregnago AC, Bezerra SM, VandenBussche C, Fujita K, Ertoy D, Cunha IW, Yu L, Bivalacqua TJ, Grollman AP, Diaz LA, Karchin R, Danilova L, Huang CY, Shun CT, Turesky RJ, Yun BH, Rosenquist TA, Pu YS, Hruban RH, Tomasetti C, Papadopoulos N, Kinzler KW, Vogelstein B, Dickman KG, Netto GJ. Correction: Non-invasive detection of urothelial cancer through the analysis of driver gene mutations and aneuploidy. eLife 2018; 7:43237. [PMID: 30418154 PMCID: PMC6231759 DOI: 10.7554/elife.43237] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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9
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Springer SU, Chen CH, Rodriguez Pena MDC, Li L, Douville C, Wang Y, Cohen JD, Taheri D, Silliman N, Schaefer J, Ptak J, Dobbyn L, Papoli M, Kinde I, Afsari B, Tregnago AC, Bezerra SM, VandenBussche C, Fujita K, Ertoy D, Cunha IW, Yu L, Bivalacqua TJ, Grollman AP, Diaz LA, Karchin R, Danilova L, Huang CY, Shun CT, Turesky RJ, Yun BH, Rosenquist TA, Pu YS, Hruban RH, Tomasetti C, Papadopoulos N, Kinzler KW, Vogelstein B, Dickman KG, Netto GJ. Non-invasive detection of urothelial cancer through the analysis of driver gene mutations and aneuploidy. eLife 2018; 7:32143. [PMID: 29557778 PMCID: PMC5860864 DOI: 10.7554/elife.32143] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 02/19/2018] [Indexed: 12/15/2022] Open
Abstract
Current non-invasive approaches for detection of urothelial cancers are suboptimal. We developed a test to detect urothelial neoplasms using DNA recovered from cells shed into urine. UroSEEK incorporates massive parallel sequencing assays for mutations in 11 genes and copy number changes on 39 chromosome arms. In 570 patients at risk for bladder cancer (BC), UroSEEK was positive in 83% of those who developed BC. Combined with cytology, UroSEEK detected 95% of patients who developed BC. Of 56 patients with upper tract urothelial cancer, 75% tested positive by UroSEEK, including 79% of those with non-invasive tumors. UroSEEK detected genetic abnormalities in 68% of urines obtained from BC patients under surveillance who demonstrated clinical evidence of recurrence. The advantages of UroSEEK over cytology were evident in low-grade BCs; UroSEEK detected 67% of cases whereas cytology detected none. These results establish the foundation for a new non-invasive approach for detection of urothelial cancer.
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Affiliation(s)
- Simeon U Springer
- Howard Hughes Medical Institute, Ludwig Center for Cancer Genetics and Therapeutics, Baltimore, United States.,Sidney Kimmel Comprehensive Cancer Center, Baltimore, United States
| | - Chung-Hsin Chen
- Department of Urology, National Taiwan University Hospital, Taipei, Taiwan
| | - Maria Del Carmen Rodriguez Pena
- Department of Pathology, Johns Hopkins University, Baltimore, United States.,Department of Pathology, University of Alabama at Birmingham, Birmingham, United States
| | - Lu Li
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, United States
| | - Christopher Douville
- Department of Biomedical Engineering, Institute for Computational Medicine, Johns Hopkins University, Baltimore, United States
| | - Yuxuan Wang
- Howard Hughes Medical Institute, Ludwig Center for Cancer Genetics and Therapeutics, Baltimore, United States.,Sidney Kimmel Comprehensive Cancer Center, Baltimore, United States
| | - Joshua David Cohen
- Howard Hughes Medical Institute, Ludwig Center for Cancer Genetics and Therapeutics, Baltimore, United States.,Sidney Kimmel Comprehensive Cancer Center, Baltimore, United States
| | - Diana Taheri
- Department of Pathology, Johns Hopkins University, Baltimore, United States.,Department of Pathology, Isfahan Kidney Diseases Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Natalie Silliman
- Howard Hughes Medical Institute, Ludwig Center for Cancer Genetics and Therapeutics, Baltimore, United States.,Sidney Kimmel Comprehensive Cancer Center, Baltimore, United States
| | - Joy Schaefer
- Howard Hughes Medical Institute, Ludwig Center for Cancer Genetics and Therapeutics, Baltimore, United States.,Sidney Kimmel Comprehensive Cancer Center, Baltimore, United States
| | - Janine Ptak
- Howard Hughes Medical Institute, Ludwig Center for Cancer Genetics and Therapeutics, Baltimore, United States.,Sidney Kimmel Comprehensive Cancer Center, Baltimore, United States
| | - Lisa Dobbyn
- Howard Hughes Medical Institute, Ludwig Center for Cancer Genetics and Therapeutics, Baltimore, United States.,Sidney Kimmel Comprehensive Cancer Center, Baltimore, United States
| | - Maria Papoli
- Howard Hughes Medical Institute, Ludwig Center for Cancer Genetics and Therapeutics, Baltimore, United States.,Sidney Kimmel Comprehensive Cancer Center, Baltimore, United States
| | - Isaac Kinde
- Howard Hughes Medical Institute, Ludwig Center for Cancer Genetics and Therapeutics, Baltimore, United States.,Sidney Kimmel Comprehensive Cancer Center, Baltimore, United States
| | - Bahman Afsari
- Department of Oncology, Johns Hopkins University, Baltimore, United States.,Division of Biostatistics and Bioinformatics, Department of Oncology, Sidney Kimmel Cancer Center, Johns Hopkins School of Medicine, Baltimore, United States
| | - Aline C Tregnago
- Department of Pathology, Johns Hopkins University, Baltimore, United States
| | | | | | | | - Dilek Ertoy
- Department of Pathology, Hacettepe University, Ankara, Turkey
| | - Isabela W Cunha
- Department of Pathology, AC Camargo Cancer Center, Sao Paulo, Brazil
| | - Lijia Yu
- Department of Pathology, University of Alabama at Birmingham, Birmingham, United States
| | | | - Arthur P Grollman
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, United States.,Department of Medicine, Stony Brook University, Stony Brook, United States
| | - Luis A Diaz
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Rachel Karchin
- Department of Biomedical Engineering, Institute for Computational Medicine, Johns Hopkins University, Baltimore, United States.,Department of Oncology, Johns Hopkins University, Baltimore, United States
| | - Ludmila Danilova
- Division of Biostatistics and Bioinformatics, Department of Oncology, Sidney Kimmel Cancer Center, Johns Hopkins School of Medicine, Baltimore, United States.,Department of Pathology, Hacettepe University, Ankara, Turkey
| | - Chao-Yuan Huang
- Department of Urology, National Taiwan University Hospital, Taipei, Taiwan
| | - Chia-Tung Shun
- Department of Forensic Medicine and Pathology, National Taiwan University Hospital, Taipei, Taiwan
| | - Robert J Turesky
- Masonic Cancer Center, University of Minnesota, Minneapolis, United States.,Department of Medicinal Chemistry, University of Minnesota, Minneapolis, United States
| | - Byeong Hwa Yun
- Masonic Cancer Center, University of Minnesota, Minneapolis, United States.,Department of Medicinal Chemistry, University of Minnesota, Minneapolis, United States
| | - Thomas A Rosenquist
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, United States
| | - Yeong-Shiau Pu
- Department of Urology, National Taiwan University Hospital, Taipei, Taiwan
| | - Ralph H Hruban
- Department of Pathology, Johns Hopkins University, Baltimore, United States
| | - Cristian Tomasetti
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, United States.,Division of Biostatistics and Bioinformatics, Department of Oncology, Sidney Kimmel Cancer Center, Johns Hopkins School of Medicine, Baltimore, United States
| | - Nickolas Papadopoulos
- Howard Hughes Medical Institute, Ludwig Center for Cancer Genetics and Therapeutics, Baltimore, United States.,Sidney Kimmel Comprehensive Cancer Center, Baltimore, United States
| | - Ken W Kinzler
- Howard Hughes Medical Institute, Ludwig Center for Cancer Genetics and Therapeutics, Baltimore, United States.,Sidney Kimmel Comprehensive Cancer Center, Baltimore, United States
| | - Bert Vogelstein
- Howard Hughes Medical Institute, Ludwig Center for Cancer Genetics and Therapeutics, Baltimore, United States.,Sidney Kimmel Comprehensive Cancer Center, Baltimore, United States
| | - Kathleen G Dickman
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, United States.,Department of Medicine, Stony Brook University, Stony Brook, United States
| | - George J Netto
- Department of Pathology, Johns Hopkins University, Baltimore, United States.,Department of Pathology, University of Alabama at Birmingham, Birmingham, United States
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10
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Tie J, Kinde I, Wang Y, Wong HL, Roebert J, Christie M, Tacey M, Wong R, Singh M, Karapetis CS, Desai J, Tran B, Strausberg RL, Diaz LA, Papadopoulos N, Kinzler KW, Vogelstein B, Gibbs P. Circulating tumor DNA as an early marker of therapeutic response in patients with metastatic colorectal cancer. Ann Oncol 2015; 26:1715-22. [PMID: 25851626 DOI: 10.1093/annonc/mdv177] [Citation(s) in RCA: 451] [Impact Index Per Article: 50.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 03/20/2015] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Early indicators of treatment response in metastatic colorectal cancer (mCRC) could conceivably be used to optimize treatment. We explored early changes in circulating tumor DNA (ctDNA) levels as a marker of therapeutic efficacy. PATIENTS AND METHODS This prospective study involved 53 mCRC patients receiving standard first-line chemotherapy. Both ctDNA and CEA were assessed in plasma collected before treatment, 3 days after treatment and before cycle 2. Computed tomography (CT) scans were carried out at baseline and 8-10 weeks and were centrally assessed using RECIST v1.1 criteria. Tumors were sequenced using a panel of 15 genes frequently mutated in mCRC to identify candidate mutations for ctDNA analysis. For each patient, one tumor mutation was selected to assess the presence and the level of ctDNA in plasma samples using a digital genomic assay termed Safe-SeqS. RESULTS Candidate mutations for ctDNA analysis were identified in 52 (98.1%) of the tumors. These patient-specific candidate tissue mutations were detectable in the cell-free DNA from the plasma of 48 of these 52 patients (concordance 92.3%). Significant reductions in ctDNA (median 5.7-fold; P < 0.001) levels were observed before cycle 2, which correlated with CT responses at 8-10 weeks (odds ratio = 5.25 with a 10-fold ctDNA reduction; P = 0.016). Major reductions (≥10-fold) versus lesser reductions in ctDNA precycle 2 were associated with a trend for increased progression-free survival (median 14.7 versus 8.1 months; HR = 1.87; P = 0.266). CONCLUSIONS ctDNA is detectable in a high proportion of treatment naïve mCRC patients. Early changes in ctDNA during first-line chemotherapy predict the later radiologic response.
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Affiliation(s)
- J Tie
- Division of Systems Biology and Personalised Medicine, Walter and Eliza Hall Institute of Medical Research, Melbourne Department of Medical Oncology, Western Hospital, Melbourne Department of Medical Oncology, The Royal Melbourne Hospital, Melbourne Faculty of Medicine Dentistry and Health Sciences, The University of Melbourne, Melbourne, Australia
| | - I Kinde
- Ludwig Center for Cancer Genetics and Therapeutics, Howard Hughes Medical Institute at Johns Hopkins Kimmel Cancer Center, Baltimore, USA
| | - Y Wang
- Ludwig Center for Cancer Genetics and Therapeutics, Howard Hughes Medical Institute at Johns Hopkins Kimmel Cancer Center, Baltimore, USA
| | - H L Wong
- Division of Systems Biology and Personalised Medicine, Walter and Eliza Hall Institute of Medical Research, Melbourne Department of Medical Oncology, The Royal Melbourne Hospital, Melbourne Faculty of Medicine Dentistry and Health Sciences, The University of Melbourne, Melbourne, Australia Faculty of Medicine, Nursing and Health Sciences, Monash University, Eastern Health Clinical School, Melbourne
| | | | - M Christie
- Division of Systems Biology and Personalised Medicine, Walter and Eliza Hall Institute of Medical Research, Melbourne Department of Medical Oncology, The Royal Melbourne Hospital, Melbourne Faculty of Medicine Dentistry and Health Sciences, The University of Melbourne, Melbourne, Australia
| | - M Tacey
- Melbourne EpiCentre, Department of Medicine, The University of Melbourne, Melbourne
| | - R Wong
- Faculty of Medicine, Nursing and Health Sciences, Monash University, Eastern Health Clinical School, Melbourne
| | - M Singh
- Andrew Love Cancer Centre, Barwon Health, Geelong
| | - C S Karapetis
- Department of Medical Oncology, Flinders University, Adelaide, Australia
| | - J Desai
- Division of Systems Biology and Personalised Medicine, Walter and Eliza Hall Institute of Medical Research, Melbourne Department of Medical Oncology, The Royal Melbourne Hospital, Melbourne Faculty of Medicine Dentistry and Health Sciences, The University of Melbourne, Melbourne, Australia
| | - B Tran
- Division of Systems Biology and Personalised Medicine, Walter and Eliza Hall Institute of Medical Research, Melbourne Department of Medical Oncology, Western Hospital, Melbourne Department of Medical Oncology, The Royal Melbourne Hospital, Melbourne Faculty of Medicine Dentistry and Health Sciences, The University of Melbourne, Melbourne, Australia
| | | | - L A Diaz
- Ludwig Center for Cancer Genetics and Therapeutics, Howard Hughes Medical Institute at Johns Hopkins Kimmel Cancer Center, Baltimore, USA
| | - N Papadopoulos
- Ludwig Center for Cancer Genetics and Therapeutics, Howard Hughes Medical Institute at Johns Hopkins Kimmel Cancer Center, Baltimore, USA
| | - K W Kinzler
- Ludwig Center for Cancer Genetics and Therapeutics, Howard Hughes Medical Institute at Johns Hopkins Kimmel Cancer Center, Baltimore, USA
| | - B Vogelstein
- Ludwig Center for Cancer Genetics and Therapeutics, Howard Hughes Medical Institute at Johns Hopkins Kimmel Cancer Center, Baltimore, USA
| | - P Gibbs
- Division of Systems Biology and Personalised Medicine, Walter and Eliza Hall Institute of Medical Research, Melbourne Department of Medical Oncology, Western Hospital, Melbourne Department of Medical Oncology, The Royal Melbourne Hospital, Melbourne Faculty of Medicine Dentistry and Health Sciences, The University of Melbourne, Melbourne, Australia Ludwig Institute for Cancer Research, New York, USA Ludwig Institute for Cancer Research, Melbourne, Australia
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11
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12
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Abstract
The finding that individual cancers contain many mutant genes not present in normal tissues has prompted considerable interest in the cancer epitope landscape. To further understand such effects, we applied in silico-based epitope prediction algorithms and high throughput post hoc analysis to identify candidate tumor antigens. Analysis of 1,152 peptides containing missense mutations previously identified in breast and colorectal cancer revealed that individual cancers accumulate on average approximately 10 and approximately 7 novel and unique HLA-A*0201 epitopes, respectively, including genes implicated in the neoplastic process. These data suggest that, with appropriate manipulation of the immune system, tumor cell destruction in situ may provide a polyvalent tumor vaccine without a requirement for knowledge of the targeted antigens.
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Affiliation(s)
- Neil H Segal
- Department of Medicine, Ludwig Center for Cancer Immunotherapy, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA
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13
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Polyak K, Wu TT, Hamilton SR, Kinzler KW, Vogelstein B. Less death in the dying. Cell Death Differ 2006; 4:242-6. [PMID: 16465234 DOI: 10.1038/sj.cdd.4400226] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/1999] [Revised: 08/05/1999] [Accepted: 10/15/1999] [Indexed: 11/10/2022] Open
Abstract
Diseases associated with aging are now the primary causes of death in developed countries. This is in part due to the long recognized exponential association of cancer with age and perhaps to a deterioration of the immune system with advanced age. Both prevention of tumorigenesis and immune function are critically dependent on apoptosis. In this study we examined apoptosis in mice of various age following gamma irradiation. We found a striking age-dependent decrease in radiation-induced apoptosis in splenic lymphocytes but not in colorectal epithelial cells. These observations may therefore provide a clue to the decline of immune function with age.
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Affiliation(s)
- K Polyak
- The Howard Hughes Medical Institute, The Johns Hopkins University School of Medicine, 424. N. Bond St. Baltimore, Maryland 21231, USA
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14
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Dang LH, Bettegowda C, Huso DL, Kinzler KW, Vogelstein B. Combination bacteriolytic therapy for the treatment of experimental tumors. Proc Natl Acad Sci U S A 2001; 98:15155-60. [PMID: 11724950 PMCID: PMC64999 DOI: 10.1073/pnas.251543698] [Citation(s) in RCA: 368] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/12/2001] [Indexed: 11/18/2022] Open
Abstract
Current chemotherapeutic approaches for cancer are in part limited by the inability of drugs to destroy neoplastic cells within poorly vascularized compartments of tumors. We have here systematically assessed anaerobic bacteria for their capacity to grow expansively within avascular compartments of transplanted tumors. Among 26 different strains tested, one (Clostridium novyi) appeared particularly promising. We created a strain of C. novyi devoid of its lethal toxin (C. novyi-NT) and showed that intravenously injected C. novyi-NT spores germinated within the avascular regions of tumors in mice and destroyed surrounding viable tumor cells. When C. novyi-NT spores were administered together with conventional chemotherapeutic drugs, extensive hemorrhagic necrosis of tumors often developed within 24 h, resulting in significant and prolonged antitumor effects. This strategy, called combination bacteriolytic therapy (COBALT), has the potential to add a new dimension to the treatment of cancer.
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Affiliation(s)
- L H Dang
- The Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, The Johns Hopkins School of Medicine, and The Johns Hopkins Oncology Center, Baltimore, MD 21231, USA
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15
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Saha S, Bardelli A, Buckhaults P, Velculescu VE, Rago C, St Croix B, Romans KE, Choti MA, Lengauer C, Kinzler KW, Vogelstein B. A phosphatase associated with metastasis of colorectal cancer. Science 2001; 294:1343-6. [PMID: 11598267 DOI: 10.1126/science.1065817] [Citation(s) in RCA: 479] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
To gain insights into the molecular basis for metastasis, we compared the global gene expression profile of metastatic colorectal cancer with that of primary cancers, benign colorectal tumors, and normal colorectal epithelium. Among the genes identified, the PRL-3 protein tyrosine phosphatase gene was of particular interest. It was expressed at high levels in each of 18 cancer metastases studied but at lower levels in nonmetastatic tumors and normal colorectal epithelium. In 3 of 12 metastases examined, multiple copies of the PRL-3 gene were found within a small amplicon located at chromosome 8q24.3. These data suggest that the PRL-3 gene is important for colorectal cancer metastasis and provide a new therapeutic target for these intractable lesions.
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Affiliation(s)
- S Saha
- Howard Hughes Medical Institute, The Oncology Center, Department of Surgery, Johns Hopkins Medical Institutions, Baltimore, MD 21231, USA
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16
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Liu T, Yan H, Kuismanen S, Percesepe A, Bisgaard ML, Pedroni M, Benatti P, Kinzler KW, Vogelstein B, Ponz de Leon M, Peltomäki P, Lindblom A. The role of hPMS1 and hPMS2 in predisposing to colorectal cancer. Cancer Res 2001; 61:7798-802. [PMID: 11691795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
Hereditary nonpolyposis colorectal cancer (HNPCC) is attributable to a deficiency of mismatch repair. Inactivation of DNA mismatch repair underlies the genesis of microsatellite instability in colorectal cancer. Germline mutations in three DNA mismatch repair genes, hMSH2, hMLH1, and hMSH6, have been found to segregate in HNPCC and HNPCC-like families. The two DNA mismatch repair genes hPMS1 and hPMS2 have also been suggested to predispose to HNPCC. In this study, 84 HNPCC and HNPCC-like kindreds without known mutations in the other three known DNA mismatch repair genes were screened for germline mutations in the hPMS1 or hPMS2 gene. No clear-cut pathogenic mutations were identified. Conversion technology was used to detect a large hMSH2 deletion in two affected members of the kindred in which the hPMS1 mutation was originally reported, whereas the hPMS1 mutation was only present in one of these two individuals. Since the hPMS1 and hPMS2 genes were first reported, germline mutations in hPMS2 have been demonstrated primarily in patients with Turcot's syndrome. However, no mutation in any of the two genes has been found to segregate in HNPCC families. Until there is better evidence for an increased colorectal cancer risk associated with germline mutations in these genes, a conservative interpretation of the role of mutations in these genes is advised.
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Affiliation(s)
- T Liu
- Department of Molecular Medicine, Karolinska Institute, S-17176 Stockholm, Sweden
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17
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Abstract
Cell-based screening for novel tumor-specific drugs has been compromised by the lack of appropriate control cells. We describe a strategy for drug screening based on isogenic human cancer cell lines in which key tumorigenic genes have been deleted by targeted homologous recombination. As a test case, a yellow fluorescent protein (YFP) expression vector was introduced into the colon cancer cell line DLD-1, and a blue fluorescent protein (BFP) expression vector was introduced into an isogenic derivative in which the mutant K-Ras allele had been deleted. Co-culture of both cell lines allowed facile screening for compounds with selective toxicity toward the mutant Ras genotype. Among 30,000 compounds screened, a novel cytidine nucleoside analog was identified that displayed selective activity in vitro and inhibited tumor xenografts containing mutant Ras. The present data demonstrate a broadly applicable approach for mining therapeutic agents targeted to the specific genetic alterations responsible for cancer development.
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Affiliation(s)
- C J Torrance
- The Howard Hughes Medical Institute, 1650 Orleans Street, Baltimore, MD 21231, USA
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18
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Buckhaults P, Rago C, St Croix B, Romans KE, Saha S, Zhang L, Vogelstein B, Kinzler KW. Secreted and cell surface genes expressed in benign and malignant colorectal tumors. Cancer Res 2001; 61:6996-7001. [PMID: 11585723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
Abstract
Serial analysis of gene expression was used to identify transcripts encoding secreted or cell surface proteins that were expressed in benign and malignant tumors of the colorectum. A total of 290,394 tags were analyzed from normal, adenomatous, and cancerous colonic epithelium. Of the 21,343 different transcripts observed, 957 were found to be differentially expressed between normal tissue and adenoma or between normal tissue and cancer. Forty-nine transcripts were elevated > or =20-fold in adenomas, 40 transcripts were elevated > or =20-fold in cancers, and 9 transcripts were elevated > or =20-fold in both. Products of six of these nine transcripts (TGFBI, LYS, RDP, MIC-1, REGA, and DEHL) were predicted to be secreted or to reside on the cell surface, and these were analyzed in more detail. The abnormal expression levels predicted by serial analysis of gene expression were confirmed by quantitative PCR analyses of each of these six genes. Moreover, the cell types responsible for the elevated expression were identified by in situ hybridization and by PCR analyses of epithelial cells immunoaffinity purified from primary tumors. This study extends knowledge of the differences in gene expression that underlie various stages of neoplasia and suggests specific diagnostic approaches that may be useful for the early detection of colorectal neoplasia.
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Affiliation(s)
- P Buckhaults
- Howard Hughes Medical Institute, Johns Hopkins Medical Institution, Baltimore, Maryland 21231, USA
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19
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Hwang PM, Bunz F, Yu J, Rago C, Chan TA, Murphy MP, Kelso GF, Smith RA, Kinzler KW, Vogelstein B. Ferredoxin reductase affects p53-dependent, 5-fluorouracil-induced apoptosis in colorectal cancer cells. Nat Med 2001; 7:1111-7. [PMID: 11590433 PMCID: PMC4086305 DOI: 10.1038/nm1001-1111] [Citation(s) in RCA: 335] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Loss of p53 gene function, which occurs in most colon cancer cells, has been shown to abolish the apoptotic response to 5-fluorouracil (5-FU). To identify genes downstream of p53 that might mediate these effects, we assessed global patterns of gene expression following 5-FU treatment of isogenic cells differing only in their p53 status. The gene encoding mitochondrial ferredoxin reductase (protein, FR; gene, FDXR) was one of the few genes significantly induced by p53 after 5-FU treatment. The FR protein was localized to mitochondria and suppressed the growth of colon cancer cells when over-expressed. Targeted disruption of the FDXR gene in human colon cancer cells showed that it was essential for viability, and partial disruption of the gene resulted in decreased sensitivity to 5-FU-induced apoptosis. These data, coupled with the effects of pharmacologic inhibitors of reactive oxygen species, indicate that FR contributes to p53-mediated apoptosis through the generation of oxidative stress in mitochondria.
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Affiliation(s)
- P M Hwang
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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20
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Carson-Walter EB, Watkins DN, Nanda A, Vogelstein B, Kinzler KW, St Croix B. Cell surface tumor endothelial markers are conserved in mice and humans. Cancer Res 2001; 61:6649-55. [PMID: 11559528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
Abstract
We recently identified genes encoding tumor endothelial markers (TEMs) that displayed elevated expression during tumor angiogenesis. From both biological and clinical points of view, TEMs associated with the cell surface membrane are of particular interest. Accordingly, we have further characterized four such genes, TEM1, TEM5, TEM7, and TEM8, all of which contain putative transmembrane domains. TEM5 appears to be a seven-pass transmembrane receptor, whereas TEM1, TEM7, and TEM8 span the membrane once. We identified mouse counterparts of each of these genes, designated mTEM1, mTEM5, mTEM7, and mTEM8. Examination of these mTEMs in mouse tumors, embryos, and adult tissues demonstrated that three of them (mTEM1, mTEM5, and mTEM8) were abundantly expressed in tumor vessels as well as in the vasculature of the developing embryo. Importantly, expression of these mTEMs in normal adult mouse tissues was either undetectable or detected only in a small fraction of the vessels. These results demonstrate conservation of human and mouse tumor angiogenesis at the molecular level and support the idea that tumor angiogenesis largely reflects normal physiological neovasculaturization. The coordinate expression of TEM1, TEM5, and TEM8 on tumor endothelium in humans and mice makes these genes attractive targets for the development of antiangiogenic therapies.
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MESH Headings
- Animals
- Biomarkers, Tumor/genetics
- Colorectal Neoplasms/blood supply
- Endothelium, Vascular/metabolism
- Endothelium, Vascular/physiology
- Gene Expression Regulation, Developmental
- Gene Expression Regulation, Neoplastic
- Humans
- In Situ Hybridization
- Melanoma, Experimental/blood supply
- Membrane Proteins/genetics
- Membrane Proteins/metabolism
- Mice
- Neoplasm Proteins
- Neovascularization, Pathologic/genetics
- Neovascularization, Pathologic/metabolism
- Protein Structure, Tertiary
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Receptors, Cell Surface
- Up-Regulation
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21
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22
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Jallepalli PV, Waizenegger IC, Bunz F, Langer S, Speicher MR, Peters JM, Kinzler KW, Vogelstein B, Lengauer C. Securin is required for chromosomal stability in human cells. Cell 2001; 105:445-57. [PMID: 11371342 DOI: 10.1016/s0092-8674(01)00340-3] [Citation(s) in RCA: 298] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Abnormalities of chromosome number are the most common genetic aberrations in cancer. The mechanisms regulating the fidelity of mitotic chromosome transmission in mammalian cells are therefore of great interest. Here we show that human cells without an hSecurin gene lose chromosomes at a high frequency. This loss was linked to abnormal anaphases during which cells underwent repetitive unsuccessful attempts to segregate their chromosomes. The abnormal mitoses were associated with biochemical defects in the activation of separin, the sister-separating protease, rendering it unable to cleave the cohesin subunit Scc1 efficiently. These results illuminate the function of mammalian securin and show that it is essential for the maintenance of euploidy.
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Affiliation(s)
- P V Jallepalli
- The Johns Hopkins Oncology Center, 1650 Orleans Street, Baltimore, MD 21231, USA
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23
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Dong SM, Traverso G, Johnson C, Geng L, Favis R, Boynton K, Hibi K, Goodman SN, D'Allessio M, Paty P, Hamilton SR, Sidransky D, Barany F, Levin B, Shuber A, Kinzler KW, Vogelstein B, Jen J. Detecting colorectal cancer in stool with the use of multiple genetic targets. J Natl Cancer Inst 2001; 93:858-65. [PMID: 11390535 DOI: 10.1093/jnci/93.11.858] [Citation(s) in RCA: 250] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Colorectal cancer cells are shed into the stool, providing a potential means for the early detection of the disease using noninvasive approaches. Our goal was to develop reliable, specific molecular genetic tests for the detection of colorectal cancer in stool samples. METHODS Stool DNA was isolated from paired stools and primary tumor samples from 51 colorectal cancer patients. Three genetic targets-TP53, BAT26, and K-RAS-were used to detect tumor-associated mutations in the stool prior to or without regard to the molecular analyses of the paired tumors. TP53 gene mutations were detected with a mismatch-ligation assay that detects nine common p53 gene mutations. Deletions within the BAT26 locus were detected by a modified solid-phase minisequencing method. Mutations in codons 12 and 13 of K-RAS were detected with a digital polymerase chain reaction-based method. RESULTS TP53 gene mutations were detected in the tumor DNA of 30 patients, all of whom had the identical TP53 mutation in their stools. Tumors from three patients contained a noninherited deletion at the BAT26 locus, and the same alterations were identified in these patients' stool specimens. Nineteen of 50 tumors tested had a K-RAS mutation; identical mutations were detected in the paired stool DNA samples from eight patients. In no case was a mutation found in stool that was not also present in the primary tumor. Thus, the three genetic markers together detected 36 (71%) of 51 patients (95% confidence interval [CI] = 56% to 83%) with colorectal cancer and 36 (92%) of 39 patients (95% CI = 79% to 98%) whose tumors had an alteration. CONCLUSION We were able to detect the majority of colorectal cancers by analyzing stool DNA for just three genetic markers. Additional work is needed to determine the specificity of these genetic tests for detecting colorectal neoplasia in asymptomatic patients and to more precisely estimate the prevalence of the mutations and sensitivity of the assay.
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Affiliation(s)
- S M Dong
- Division of Head and Neck Cancer Research, Department of Otolaryngology-Head and Neck Surgery, The Johns Hopkins Medical School, The Johns Hopkins University, Baltimore, MD, USA
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24
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Bardelli A, Cahill DP, Lederer G, Speicher MR, Kinzler KW, Vogelstein B, Lengauer C. Carcinogen-specific induction of genetic instability. Proc Natl Acad Sci U S A 2001; 98:5770-5. [PMID: 11296254 PMCID: PMC33288 DOI: 10.1073/pnas.081082898] [Citation(s) in RCA: 125] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
It has been proposed recently that the type of genetic instability in cancer cells reflects the selection pressures exerted by specific carcinogens. We have tested this hypothesis by treating immortal, genetically stable human cells with representative carcinogens. We found that cells resistant to the bulky-adduct-forming agent 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP) exhibited a chromosomal instability (CIN), whereas cells resistant to the methylating agent N-methyl-N'-nitro-N-nitrosoguanidine (MNNG) exhibited a microsatellite instability (MIN) associated with mismatch repair defects. Conversely, we found that cells purposely made into CIN cells are resistant to PhIP, whereas MIN cells are resistant to MNNG. These data demonstrate that exposure to specific carcinogens can indeed select for tumor cells with distinct forms of genetic instability and vice versa.
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Affiliation(s)
- A Bardelli
- The Johns Hopkins Oncology Center, Howard Hughes Medical Institute, and Graduate Program in Human Genetics and Molecular Biology, 1650 Orleans Street, Baltimore, MD 21231, USA
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25
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Zhang L, Yu J, Willson JK, Markowitz SD, Kinzler KW, Vogelstein B. Short mononucleotide repeat sequence variability in mismatch repair-deficient cancers. Cancer Res 2001; 61:3801-5. [PMID: 11325855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
Abstract
Mismatch repair-deficient cancers are characterized by widespread insertions and deletions in microsatellite sequences, including those comprised of mononucleotide repeats. Such alterations have been observed in relatively short mononucleotide tracts in several genes and often are interpreted to indicate that the affected genes normally act as tumor suppressors. To aid in the interpretation of such changes, we have systematically assessed their frequency within transcribed regions of the genome that are unlikely to play a tumorigenic role. The advent of the complete human genomic sequences of chromosome 22 allowed us to select 29 genes for this analysis, spaced at approximately 1-Mb intervals. Each of the selected genes had an (A)(8) or a (G)(8) tract deep within intronic sequences that was not included in the processed transcript. Surprisingly, we found that there was substantial variation in the prevalence of mutations among these tracts. Some tracts were altered in < 5% of the mismatch repair-deficient cancers studied, whereas other tracts were altered in nearly half of the cancers. In particular, (G)(8) tracts were considerably more prone to mutation than (A)(8) tracts, and the sequences or chromatin structures surrounding the mononucleotide tracts seemed to affect their mutability significantly.
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Affiliation(s)
- L Zhang
- Johns Hopkins Oncology Center, Baltimore, Maryland 21231, USA
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26
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Sparks AB, Peterson SN, Bell C, Loftus BJ, Hocking L, Cahill DP, Frassica FJ, Streeten EA, Levine MA, Fraser CM, Adams MD, Broder S, Venter JC, Kinzler KW, Vogelstein B, Ralston SH. Mutation screening of the TNFRSF11A gene encoding receptor activator of NF kappa B (RANK) in familial and sporadic Paget's disease of bone and osteosarcoma. Calcif Tissue Int 2001; 68:151-5. [PMID: 11351498 DOI: 10.1007/s002230001211] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Paget's disease of bone (PDB) is a common disorder characterized by focal areas of increased and disorganized osteoclastic bone resorption, leading to bone pain, deformity, pathological fracture, and an increased risk of osteosarcoma. Genetic factors play an important role in the pathogenesis of Paget's disease. In some families, the disease has been found to be linked to a susceptibility locus on chromosome 18q21-22, which also contains the gene responsible for familial expansile osteolysis (FEO)--a rare bone dysplasia with many similarities to Paget's disease. Insertion mutations of the TNFRSF11A gene encoding Receptor Activator of NF kappa B (RANK) have recently been found to be responsible for FEO and rare cases of early onset familial Paget's disease. Loss of heterozygosity (LOH) affecting the PDB/FEO critical region has also been described in osteosarcomas suggesting that TNFRSF11A might also be involved in the development of osteosarcoma. In order to investigate the possible role of TNFRSF11A in the pathogenesis of Paget's disease and osteosarcoma, we conducted mutation screening of the TNFRSF11A gene in patients with familial and sporadic Paget's disease as well as DNA extracted from Pagetic bone lesions, an osteosarcoma arising in Pagetic bone and six osteosarcoma cell lines. No specific abnormalities of the TNFRSF11A gene were identified in a Pagetic osteosarcoma, the osteosarcoma cell lines, DNA extracted from Pagetic bone lesions, or DNA extracted from peripheral blood in patients with familial or sporadic Paget's disease including several individuals with early onset Paget's disease. These data indicate that TNFRSF11A mutations contribute neither to the vast majority of cases of sporadic or familial PDB, nor to the development of osteosarcoma.
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Affiliation(s)
- A B Sparks
- Molecular Genetics Laboratory, Johns Hopkins Oncology Center, Baltimore, MD, USA
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27
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Abstract
Through global profiling of genes that were expressed soon after p53 expression, we identified a novel gene termed PUMA (p53 upregulated modulator of apoptosis). The protein encoded by PUMA was found to be exclusively mitochondrial and to bind to Bcl-2 and Bcl-X(L) through a BH3 domain. Exogenous expression of PUMA resulted in an extremely rapid and profound apoptosis that occurred much earlier than that resulting from exogenous expression of p53. Based on its unique expression patterns, p53 dependence, and biochemical properties, PUMA may be a direct mediator of p53-associated apoptosis.
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Affiliation(s)
- J Yu
- The Johns Hopkins Oncology Center, The Johns Hopkins Medical Institutions, Baltimore, Maryland 21231, USA
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28
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Thiagalingam S, Laken S, Willson JK, Markowitz SD, Kinzler KW, Vogelstein B, Lengauer C. Mechanisms underlying losses of heterozygosity in human colorectal cancers. Proc Natl Acad Sci U S A 2001; 98:2698-702. [PMID: 11226302 PMCID: PMC30201 DOI: 10.1073/pnas.051625398] [Citation(s) in RCA: 163] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/28/2000] [Indexed: 12/11/2022] Open
Abstract
Losses of heterozygosity are the most common molecular genetic alteration observed in human cancers. However, there have been few systematic studies to understand the mechanism(s) responsible for losses of heterozygosity in such tumors. Here we report a detailed investigation of the five chromosomes lost most frequently in human colorectal cancers. A total of 10,216 determinations were made with 88 microsatellite markers, revealing 245 chromosomal loss events. The mechanisms of loss were remarkably chromosome-specific. Some chromosomes displayed complete loss such as that predicted to result from mitotic nondisjunction. However, more than half of the losses were associated with losses of only part of a chromosome rather than a whole chromosome. Surprisingly, these losses were due largely to structural alterations rather than to mitotic recombination, break-induced replication, or gene conversion, suggesting novel mechanisms for the generation of much of the aneuploidy in this common tumor type.
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Affiliation(s)
- S Thiagalingam
- Oncology Center, Program in Molecular Biology, Johns Hopkins University School of Medicine, 1650 Orleans Street, Baltimore, MD 21231, USA
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29
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Abstract
Peroxisome proliferator-activated receptors (PPARs) are nuclear hormone receptors that have been implicated in a variety of biologic processes. The PPARdelta isotype was recently proposed as a downstream target of the adenomatous polyposis coli (APC)/beta-catenin pathway in colorectal carcinogenesis. To evaluate its role in tumorigenesis, a PPARdelta null cell line was created by targeted homologous recombination. When inoculated as xenografts in nude mice, PPARdelta -/- cells exhibited a decreased ability to form tumors compared with PPARdelta +/- and wild-type controls. These data suggest that suppression of PPARdelta expression contributes to the growth-inhibitory effects of the APC tumor suppressor.
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Affiliation(s)
- B H Park
- Johns Hopkins Oncology Center and Howard Hughes Medical Institute, 1650 Orleans Street, Room 590, Baltimore, MD 21231, USA
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30
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Shih IM, Wang TL, Traverso G, Romans K, Hamilton SR, Ben-Sasson S, Kinzler KW, Vogelstein B. Top-down morphogenesis of colorectal tumors. Proc Natl Acad Sci U S A 2001; 98:2640-5. [PMID: 11226292 PMCID: PMC30191 DOI: 10.1073/pnas.051629398] [Citation(s) in RCA: 253] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
One of the fundamental tenets of oncology is that tumors arise from stem cells. In the colon, stem cells are thought to reside at the base of crypts. In the early stages of tumorigenesis, however, dysplastic cells are routinely found at the luminal surface of the crypts whereas the cells at the bases of these same crypts appear morphologically normal. To understand this discrepancy, we evaluated the molecular characteristics of cells isolated from the bases and orifices of the same crypts in small colorectal adenomas. We found that the dysplastic cells at the tops of the crypts often exhibited genetic alterations of adenomatous polyposis coli (APC) and neoplasia-associated patterns of gene expression. In contrast, cells located at the base of these same crypts did not contain such alterations and were not clonally related to the contiguous transformed cells above them. These results imply that development of adenomatous polyps proceeds through a top-down mechanism. Genetically altered cells in the superficial portions of the mucosae spread laterally and downward to form new crypts that first connect to preexisting normal crypts and eventually replace them.
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Affiliation(s)
- I M Shih
- The Howard Hughes Medical Institute, Johns Hopkins Oncology Center, Johns Hopkins Medical Institutions, Baltimore, MD 21231, USA
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31
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Shih IM, Zhou W, Goodman SN, Lengauer C, Kinzler KW, Vogelstein B. Evidence that genetic instability occurs at an early stage of colorectal tumorigenesis. Cancer Res 2001; 61:818-22. [PMID: 11221861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
Abstract
Chromosomal instability is believed to be a common feature of most human tumors, but the stage at which such instability originates has not been defined. At the molecular level, chromosomal instability is characterized by allelic imbalance (AI), representing losses or gains of defined chromosomal regions. We have assessed AI in early colorectal tumors using newly developed methods for assessing AI in complex cell populations. A total of 32 adenomas of average size (2 mm; range, 1-3 mm) were studied. AI of chromosome 5q markers occurred in 55% of tumors analyzed, consistent with a gatekeeping role of the adenomatous polyposis coli tumor suppressor gene located at chromosomal position 5q21. AI was also detected in each of the other four chromosomes tested. The fractions of adenomas with AI of chromosomes 1p, 8p, 15q, and 18q were 10,19, 28, and 28%, respectively. Over 90% of the tumors exhibited AI of at least one chromosome, and 67% had allelic imbalance of a chromosome other than 5q. These findings demonstrate that AI is a common event, even in very small tumors, and suggest that chromosomal instability occurs very early during colorectal neoplasia.
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Affiliation(s)
- I M Shih
- Johns Hopkins Oncology Center, Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, Maryland 21231, USA
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32
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Zhou W, Galizia G, Lieto E, Goodman SN, Romans KE, Kinzler KW, Vogelstein B, Choti MA, Montgomery EA. Counting alleles reveals a connection between chromosome 18q loss and vascular invasion. Nat Biotechnol 2001; 19:78-81. [PMID: 11135558 DOI: 10.1038/83572] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The analysis of loss of heterozygosity (LOH) is perhaps the most widely used technique in cancer genetics. In primary tumors, however, the analysis of LOH is fraught with technical problems that have limited its reproducibility and interpretation. In particular, tumors are mixtures of neoplastic and nonneoplastic cells, and the DNA from the nonneoplastic cells can mask LOH. We here describe a new experimental approach, involving two components, to overcome these problems. First, a form of digital PCR was employed to directly count, one by one, the number of each of the two alleles in tumor samples. Second, Bayesian-type likelihood methods were used to measure the strength of the evidence for the allele distribution being different from normal. This approach imparts a rigorous statistical basis to LOH analyses, and should be able to provide more reliable information than heretofore possible in LOH studies of diverse tumor types.
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Affiliation(s)
- W Zhou
- Molecular Genetics Laboratory, Johns Hopkins Oncology Center, Baltimore, MD 21231, USA
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33
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Fink SP, Swinler SE, Lutterbaugh JD, Massagué J, Thiagalingam S, Kinzler KW, Vogelstein B, Willson JK, Markowitz S. Transforming growth factor-beta-induced growth inhibition in a Smad4 mutant colon adenoma cell line. Cancer Res 2001; 61:256-60. [PMID: 11196171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
Abstract
Transforming growth factor-beta (TGF-beta) inhibits growth and induces apoptosis of colon epithelial cells. Binding of TGF-beta to its receptor induces phosphorylation of the Smad proteins Smad2 and Smad3, which then form heteromeric complexes with Smad4, translocate to the nucleus, and activate gene transcription. Smad4 function has been considered an obligate requirement for TGF-beta signaling, and Smad4 mutations present in some cancers have been considered sufficient to inactivate TGF-beta signaling. In this work, we describe studies with a nontransformed human colon epithelial cell line that is mutant for Smad4 but remains growth-inhibited by TGF-beta. The colon cell line VACO-235 has lost one of its Smad4 alleles via a chromosome 18q deletion. The remaining allele bears two missense point mutations located in regions important for Smad4 trimer formation, which is thought necessary for Smad4 function. As expected, pSBE4-BV/Luc, a Smad4-activated transcriptional reporter, was inactive in VACO-235. Nonetheless, VACO-235 demonstrated 80% growth inhibition in response to TGF-beta, as well as retention of some TGF-beta-mediated activation of the p3TP-Lux transcriptional reporter. Transient transfection of the VACO-235 Smad4 mutant allele into a Smad4-null cell line confirmed that this allele is functionally inactive as assayed by both the pSBE4-BV and p3TP-Lux reporters. The simplest explanation of these results is that there is a non-Smad4-dependent pathway for TGF-beta-mediated signaling and growth inhibition in VACO-235 cells.
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Affiliation(s)
- S P Fink
- Howard Hughes Medical Institute, Case Western Reserve University and University Hospitals of Cleveland, Ohio 44106, USA
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34
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Abstract
To assess the role of BAX in drug-induced apoptosis in human colorectal cancer cells, we generated cells that lack functional BAX genes. Such cells were partially resistant to the apoptotic effects of the chemotherapeutic agent 5-fluorouracil, but apoptosis was not abolished. In contrast, the absence of BAX completely abolished the apoptotic response to the chemopreventive agent sulindac and other nonsteroidal anti-inflammatory drugs (NSAIDs). NSAIDs inhibited the expression of the antiapoptotic protein Bcl-XL, resulting in an altered ratio of BAX to Bcl-XL and subsequent mitochondria-mediated cell death. These results establish an unambiguous role for BAX in apoptotic processes in human epithelial cancers and may have implications for cancer chemoprevention strategies.
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Affiliation(s)
- L Zhang
- Howard Hughes Medical Institute, Oncology Center, and Program in Human Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
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35
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Abstract
Methods of comprehensive gene expression analysis have traditionally been limited to analysing bulk tissue or millions of cells. New modifications of serial analysis of gene expression (SAGE) have now permitted the analysis of gene expression in cell subpopulations or microanatomic structures, providing access to unexplored transcriptomes of normal and disease biology.
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Affiliation(s)
- V E Velculescu
- Johns Hopkins Oncology Center, Johns Hopkins University School of Medicine, 1650 Orleans St., Baltimore MD 21231, USA.
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36
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Affiliation(s)
- H Yan
- Howard Hughes Medical Institute and the Johns Hopkins Oncology Center, Baltimore, MD 21231, USA
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37
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Torrance CJ, Jackson PE, Montgomery E, Kinzler KW, Vogelstein B, Wissner A, Nunes M, Frost P, Discafani CM. Combinatorial chemoprevention of intestinal neoplasia. Nat Med 2000; 6:1024-8. [PMID: 10973323 DOI: 10.1038/79534] [Citation(s) in RCA: 345] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
A combination of two drugs afforded remarkable protection from intestinal neoplasia in APC(Min/+) mice, a murine model of human familial adenomatous polyposis (FAP). One of the drugs was sulindac, a prototypical non-steroidal anti-inflammatory drug with established chemopreventative activity. The second drug was EKI-569, a newly developed, irreversible inhibitor of the epidermal growth factor receptor kinase. Although 100% of the untreated APC(Min/+) mice developed approximately 20 polyps, nearly half the mice treated with these two agents developed no polyps at all. These results suggest a powerful strategy for the chemoprevention of human colonic neoplasia.
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Affiliation(s)
- C J Torrance
- The Howard Hughes Medical Institute and The Johns Hopkins Oncology Center, Baltimore, Maryland 21231, USA
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38
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St Croix B, Rago C, Velculescu V, Traverso G, Romans KE, Montgomery E, Lal A, Riggins GJ, Lengauer C, Vogelstein B, Kinzler KW. Genes expressed in human tumor endothelium. Science 2000; 289:1197-202. [PMID: 10947988 DOI: 10.1126/science.289.5482.1197] [Citation(s) in RCA: 1353] [Impact Index Per Article: 56.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
To gain a molecular understanding of tumor angiogenesis, we compared gene expression patterns of endothelial cells derived from blood vessels of normal and malignant colorectal tissues. Of over 170 transcripts predominantly expressed in the endothelium, 79 were differentially expressed, including 46 that were specifically elevated in tumor-associated endothelium. Several of these genes encode extracellular matrix proteins, but most are of unknown function. Most of these tumor endothelial markers were expressed in a wide range of tumor types, as well as in normal vessels associated with wound healing and corpus luteum formation. These studies demonstrate that tumor and normal endothelium are distinct at the molecular level, a finding that may have significant implications for the development of anti-angiogenic therapies.
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MESH Headings
- Biomarkers, Tumor
- Cell Separation
- Cells, Cultured
- Colon/blood supply
- Colon/metabolism
- Colorectal Neoplasms/blood supply
- Colorectal Neoplasms/genetics
- Colorectal Neoplasms/metabolism
- Colorectal Neoplasms/pathology
- Corpus Luteum/blood supply
- Corpus Luteum/metabolism
- Endothelium, Vascular/cytology
- Endothelium, Vascular/metabolism
- Endothelium, Vascular/pathology
- Extracellular Matrix Proteins/genetics
- Female
- Gene Expression
- Gene Expression Profiling
- Humans
- Intestinal Mucosa/blood supply
- Intestinal Mucosa/cytology
- Intestinal Mucosa/pathology
- Neoplasms/blood supply
- Neoplasms/genetics
- Neoplasms/metabolism
- Neovascularization, Pathologic/genetics
- Neovascularization, Physiologic/genetics
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Rectum/blood supply
- Rectum/metabolism
- Tumor Cells, Cultured
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Affiliation(s)
- B St Croix
- Johns Hopkins Oncology Center, Howard Hughes Medical Institute, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
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39
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Flatt PM, Polyak K, Tang LJ, Scatena CD, Westfall MD, Rubinstein LA, Yu J, Kinzler KW, Vogelstein B, Hill DE, Pietenpol JA. p53-dependent expression of PIG3 during proliferation, genotoxic stress, and reversible growth arrest. Cancer Lett 2000; 156:63-72. [PMID: 10840161 DOI: 10.1016/s0304-3835(00)00441-9] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The p53-inducible gene 3 (PIG3) was recently identified in a screen for genes induced by p53 before the onset of apoptosis. PIG3 shares significant homology with oxidoreductases from several species. In this study, PIG3-specific antibodies were used to analyze cellular PIG3 protein levels under control and genotoxic stress conditions. PIG3 protein was localized to the cytoplasm and induced in primary, non-transformed, and transformed cell cultures after exposure to genotoxic agents. The induction of PIG3 was p53-dependent and occurred with delayed kinetics as compared with other p53 downstream targets, such as p21 and MDM2. Using a p53-inducible cell model system, in which p53-mediated growth arrest is reversible, we found that PIG3 levels were increased during p53-mediated growth arrest. Interestingly, elevated levels of PIG3 were maintained in cells that resumed cycling in the absence of ectopic p53 expression, suggesting that PIG3 is a long-lived reporter, which may be useful for detecting transient activation of p53.
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Affiliation(s)
- P M Flatt
- Department of Biochemistry, Center in Molecular Toxicology, and the Vanderbilt-Ingram Cancer Center, 652 Medical Research Building II, Vanderbilt University School of Medicine, 2220 Pierce Avenue, Nashville, TN 37232-6305, Nashville, USA
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40
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Chan TA, Hwang PM, Hermeking H, Kinzler KW, Vogelstein B. Cooperative effects of genes controlling the G(2)/M checkpoint. Genes Dev 2000; 14:1584-8. [PMID: 10887152 PMCID: PMC316737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
It is believed that multiple effectors independently control the checkpoints permitting transitions between cell cycle phases. However, this has not been rigorously demonstrated in mammalian cells. The p53-induced genes p21 and 14-3-3sigma are each required for the G(2) arrest and allow a specific test of this fundamental tenet. We generated human cells deficient in both p21 and 14-3-3sigma and determined whether the double knockout was more sensitive to DNA damage than either single knockout. p21(-/-) 14-3-3sigma(-/-) cells were significantly more sensitive to DNA damage or to the exogenous expression of p53 than cells lacking only p21 or only 14-3-3sigma. Thus, p21 and 14-3-3sigma play distinct but complementary roles in the G(2)/M checkpoint, and help explain why genes at the nodal points of growth arrest pathways, like p53, are the targets of mutation in cancer cells.
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Affiliation(s)
- T A Chan
- Howard Hughes Medical Institute and Johns Hopkins Oncology Center, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
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41
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Shih IM, Torrance C, Sokoll LJ, Chan DW, Kinzler KW, Vogelstein B. Assessing tumors in living animals through measurement of urinary beta-human chorionic gonadotropin. Nat Med 2000; 6:711-4. [PMID: 10835692 DOI: 10.1038/76299] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
MESH Headings
- Animals
- Biomarkers, Tumor/therapeutic use
- Biomarkers, Tumor/urine
- Chorionic Gonadotropin, beta Subunit, Human/genetics
- Chorionic Gonadotropin, beta Subunit, Human/therapeutic use
- Chorionic Gonadotropin, beta Subunit, Human/urine
- Female
- Genetic Engineering
- Humans
- Melanoma, Experimental/genetics
- Melanoma, Experimental/physiopathology
- Melanoma, Experimental/therapy
- Melanoma, Experimental/urine
- Mice
- Mice, Inbred BALB C
- Mice, Inbred C57BL
- Transfection
- Tumor Cells, Cultured
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Affiliation(s)
- I M Shih
- The Johns Hopkins Oncology Center, Johns Hopkins Medical Institutions, Baltimore, Maryland 21231, USA
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42
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Rhee I, Jair KW, Yen RW, Lengauer C, Herman JG, Kinzler KW, Vogelstein B, Baylin SB, Schuebel KE. CpG methylation is maintained in human cancer cells lacking DNMT1. Nature 2000; 404:1003-7. [PMID: 10801130 DOI: 10.1038/35010000] [Citation(s) in RCA: 305] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Hypermethylation is associated with the silencing of tumour susceptibility genes in several forms of cancer; however, the mechanisms responsible for this aberrant methylation are poorly understood. The prototypic DNA methyltransferase, DNMT1, has been widely assumed to be responsible for most of the methylation of the human genome, including the abnormal methylation found in cancers. To test this hypothesis, we disrupted the DNMT1 gene through homologous recombination in human colorectal carcinoma cells. Here we show that cells lacking DNMT1 exhibited markedly decreased cellular DNA methyltransferase activity, but there was only a 20% decrease in overall genomic methylation. Although juxtacentromeric satellites became significantly demethylated, most of the loci that we analysed, including the tumour suppressor gene p16INK4a, remained fully methylated and silenced. These results indicate that DNMT1 has an unsuspected degree of regional specificity in human cells and that methylating activities other than DNMT1 can maintain the methylation of most of the genome.
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Affiliation(s)
- I Rhee
- The Johns Hopkins Oncology Center, and Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, USA
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43
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Shih IM, Yu J, He TC, Vogelstein B, Kinzler KW. The beta-catenin binding domain of adenomatous polyposis coli is sufficient for tumor suppression. Cancer Res 2000; 60:1671-6. [PMID: 10749138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Inactivation of the adenomatous polyposis coli (APC) gene is a critical event in the development of human colorectal cancers. At the biochemical level, several functions have been assigned to the multidomain APC protein, but the cellular effects of APC expression and how they relate to its biochemical functions are less well defined. To address these issues, we generated a recombinant adenovirus (Ad-CBR) that constitutively expresses the central third of APC, which includes all of the known beta-catenin binding repeats. When expressed in colon cancer cells, Ad-CBR blocked the nuclear translocation of beta-catenin and inhibited beta-catenin/Tcf-4-mediated transactivation. Accordingly, expression of endogenous targets of the APC/beta-catenin/Tcf-4 pathway was down-regulated. Ad-CBR infection of colorectal cancer cell lines with mutant APC but wild-type beta-catenin resulted in substantial growth arrest followed by apoptosis. These effects were attenuated in lines with wild-type APC but with mutated beta-catenin. These findings suggest that the beta-catenin-binding domain in the central third of APC is sufficient for its tumor suppressor activity.
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Affiliation(s)
- I M Shih
- Johns Hopkins Oncology Center, Baltimore, Maryland 21231, USA
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44
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Abstract
Genetic instability has long been hypothesized to be a cardinal feature of cancer. Recent work has strengthened the proposal that mutational alterations conferring instability occur early during tumour formation. The ensuing genetic instability drives tumour progression by generating mutations in oncogenes and tumour-suppressor genes. These mutant genes provide cancer cells with a selective growth advantage, thereby leading to the clonal outgrowth of a tumour. Here, we discuss the role of genetic instability in tumour formation and outline future work necessary to substantiate the genetic instability hypothesis.
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Affiliation(s)
- D P Cahill
- Program in Human Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
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45
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Hermeking H, Rago C, Schuhmacher M, Li Q, Barrett JF, Obaya AJ, O'Connell BC, Mateyak MK, Tam W, Kohlhuber F, Dang CV, Sedivy JM, Eick D, Vogelstein B, Kinzler KW. Identification of CDK4 as a target of c-MYC. Proc Natl Acad Sci U S A 2000; 97:2229-34. [PMID: 10688915 PMCID: PMC15783 DOI: 10.1073/pnas.050586197] [Citation(s) in RCA: 362] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The prototypic oncogene c-MYC encodes a transcription factor that can drive proliferation by promoting cell-cycle reentry. However, the mechanisms through which c-MYC achieves these effects have been unclear. Using serial analysis of gene expression, we have identified the cyclin-dependent kinase 4 (CDK4) gene as a transcriptional target of c-MYC. c-MYC induced a rapid increase in CDK4 mRNA levels through four highly conserved c-MYC binding sites within the CDK4 promoter. Cell-cycle progression is delayed in c-MYC-deficient RAT1 cells, and this delay was associated with a defect in CDK4 induction. Ectopic expression of CDK4 in these cells partially alleviated the growth defect. Thus, CDK4 provides a direct link between the oncogenic effects of c-MYC and cell-cycle regulation.
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Affiliation(s)
- H Hermeking
- Howard Hughes Medical Institute, The Johns Hopkins Oncology Center, The Johns Hopkins University School of Medicine, 424 North Bond Street, Baltimore, MD 21231, USA
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46
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Yan H, Papadopoulos N, Marra G, Perrera C, Jiricny J, Boland CR, Lynch HT, Chadwick RB, de la Chapelle A, Berg K, Eshleman JR, Yuan W, Markowitz S, Laken SJ, Lengauer C, Kinzler KW, Vogelstein B. Conversion of diploidy to haploidy. Nature 2000; 403:723-4. [PMID: 10693791 DOI: 10.1038/35001659] [Citation(s) in RCA: 149] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- H Yan
- Howard Hughes Medical Institute, The Oncology Center, Department of Mathematical Sciences, The Johns Hopkins University, Baltimore, Maryland 21231, USA
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47
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Abstract
Sequence-specific transactivation by p53 is essential to its role as a tumor suppressor. A modified tetracycline-inducible system was established to search for transcripts that were activated soon after p53 induction. Among 9,954 unique transcripts identified by serial analysis of gene expression, 34 were increased more than 10-fold; 31 of these had not previously been known to be regulated by p53. The transcription patterns of these genes, as well as previously described p53-regulated genes, were evaluated and classified in a panel of widely studied colorectal cancer cell lines. "Class I" genes were uniformly induced by p53 in all cell lines; "class II" genes were induced in a subset of the lines; and "class III" genes were not induced in any of the lines. These genes were also distinguished by the timing of their induction, their induction by clinically relevant chemotherapeutic agents, the absolute requirement for p53 in this induction, and their inducibility by p73, a p53 homolog. The results revealed substantial heterogeneity in the transcriptional responses to p53, even in cells derived from a single epithelial cell type, and pave the way to a deeper understanding of p53 tumor suppressor action.
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Affiliation(s)
- J Yu
- Graduate Program in Human Genetics, The Johns Hopkins University, Baltimore, MD 21205, USA
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48
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Velculescu VE, Madden SL, Zhang L, Lash AE, Yu J, Rago C, Lal A, Wang CJ, Beaudry GA, Ciriello KM, Cook BP, Dufault MR, Ferguson AT, Gao Y, He TC, Hermeking H, Hiraldo SK, Hwang PM, Lopez MA, Luderer HF, Mathews B, Petroziello JM, Polyak K, Zawel L, Kinzler KW. Analysis of human transcriptomes. Nat Genet 1999; 23:387-8. [PMID: 10581018 DOI: 10.1038/70487] [Citation(s) in RCA: 506] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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49
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Cahill DP, Kinzler KW, Vogelstein B, Lengauer C. Genetic instability and darwinian selection in tumours. Trends Cell Biol 1999; 9:M57-60. [PMID: 10611684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
Genetic instability has long been hypothesized to be a cardinal feature of cancer. Recent work has strengthened the proposal that mutational alterations conferring instability occur early during tumour formation. The ensuing genetic instability drives tumour progression by generating mutations in oncogenes and tumour-suppressor genes. These mutant genes provide cancer cells with a selective growth advantage, thereby leading to the clonal outgrowth of a tumour. Here, we discuss the role of genetic instability in tumour formation and outline future work necessary to substantiate the genetic instability hypothesis.
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Affiliation(s)
- D P Cahill
- Program in Human Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
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50
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Lal A, Lash AE, Altschul SF, Velculescu V, Zhang L, McLendon RE, Marra MA, Prange C, Morin PJ, Polyak K, Papadopoulos N, Vogelstein B, Kinzler KW, Strausberg RL, Riggins GJ. A public database for gene expression in human cancers. Cancer Res 1999; 59:5403-7. [PMID: 10554005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/14/2023]
Abstract
A public database, SAGEmap, was created as a component of the Cancer Genome Anatomy Project to provide a central location for depositing, retrieving, and analyzing human gene expression data. This database uses serial analysis of gene expression to quantify transcript levels in both malignant and normal human tissues. By accessing SAGEmap (http://www.ncbi.nlm.nih.gov/SAGE) the user can compare transcript populations between any of the posted libraries. As an initial demonstration of the database's utility, gene expression in human glioblastomas was compared with that of normal brain white matter. Of the 47,174 unique transcripts expressed in these two tissues, 471 (1.0%) were differentially expressed by more than 5-fold (P<0.001). Classification of these genes revealed functions consistent with the biological properties of glioblastomas, in particular: angiogenesis, transcription, and cell cycle related genes.
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Affiliation(s)
- A Lal
- Department of Pathology, Duke University Medical Center, Durham, North Carolina 27710, USA
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