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Hayakawa Y, Nakagawa H, Rustgi AK, Que J, Wang TC. Stem cells and origins of cancer in the upper gastrointestinal tract. Cell Stem Cell 2021; 28:1343-1361. [PMID: 34129814 DOI: 10.1016/j.stem.2021.05.012] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The esophagus and stomach, joined by a unique transitional zone, contain actively dividing epithelial stem cells required for organ homeostasis. Upon prolonged inflammation, epithelial cells in both organs can undergo a cell fate switch leading to intestinal metaplasia, predisposing to malignancy. Here we discuss the biology of gastroesophageal stem cells and their role as cells of origin in cancer. We summarize the interactions between the stromal niche and gastroesophageal stem cells in metaplasia and early expansion of mutated stem-cell-derived clones during carcinogenesis. Finally, we review new approaches under development to better study gastroesophageal stem cells and advance the field.
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Affiliation(s)
- Yoku Hayakawa
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, 7-3-1, Hongo, Bunkyoku, Tokyo 113-8655, Japan
| | - Hiroshi Nakagawa
- Division of Digestive and Liver Diseases, Department of Medicine, Columbia University, College of Physicians and Surgeons, 1130 St. Nicholas Avenue, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, 1130 St. Nicholas Avenue, New York, NY 10032, USA
| | - Anil K Rustgi
- Division of Digestive and Liver Diseases, Department of Medicine, Columbia University, College of Physicians and Surgeons, 1130 St. Nicholas Avenue, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, 1130 St. Nicholas Avenue, New York, NY 10032, USA
| | - Jianwen Que
- Division of Digestive and Liver Diseases, Department of Medicine, Columbia University, College of Physicians and Surgeons, 1130 St. Nicholas Avenue, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, 1130 St. Nicholas Avenue, New York, NY 10032, USA; Columbia Center for Human Development, Department of Medicine, Columbia University, College of Physicians and Surgeons, 1130 St. Nicholas Avenue, New York, NY 10032, USA.
| | - Timothy C Wang
- Division of Digestive and Liver Diseases, Department of Medicine, Columbia University, College of Physicians and Surgeons, 1130 St. Nicholas Avenue, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, 1130 St. Nicholas Avenue, New York, NY 10032, USA.
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Stachler MD, Camarda ND, Deitrick C, Kim A, Agoston AT, Odze RD, Hornick JL, Nag A, Thorner AR, Ducar M, Noffsinger A, Lash RH, Redston M, Carter SL, Davison JM, Bass AJ. Detection of Mutations in Barrett's Esophagus Before Progression to High-Grade Dysplasia or Adenocarcinoma. Gastroenterology 2018; 155:156-167. [PMID: 29608884 PMCID: PMC6035092 DOI: 10.1053/j.gastro.2018.03.047] [Citation(s) in RCA: 96] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 03/02/2018] [Accepted: 03/27/2018] [Indexed: 12/11/2022]
Abstract
BACKGROUND & AIMS Barrett's esophagus (BE) is the greatest risk factor for esophageal adenocarcinoma (EAC), but only a small proportion of patients with BE develop cancer. Biomarkers might be able to identify patients at highest risk of progression. We investigated genomic differences in surveillance biopsies collected from patients whose BE subsequently progressed compared to patients whose disease did not progress. METHODS We performed a retrospective case-control study of 24 patients with BE that progressed to high-grade dysplasia (HGD, n = 14) or EAC (n = 10). The control group (n = 73, called non-progressors) comprised patients with BE and at least 5 years of total endoscopic biopsy surveillance without progression to HGD or EAC. From each patient, we selected a single tissue sample obtained more than 1 year before progression (cases) or more than 2 years before the end of follow-up (controls). Pathogenic mutations, gene copy numbers, and ploidy were compared between samples from progressors and non-progressors. RESULTS TP53 mutations were detected in 46% of samples from progressors and 5% of non-progressors. In this case-control sample set, TP53 mutations in BE tissues increased the adjusted risk of progression 13.8-fold (95% confidence interval, 3.2-61.0) (P < .001). We did not observe significant differences in ploidy or copy-number profile between groups. We identified 147 pathogenic mutations in 57 distinct genes-the average number of pathogenic mutations was higher in samples from progressors (n = 2.5) than non-progressors (n = 1.2) (P < .001). TP53 and other somatic mutations were recurrently detected in samples with limited copy-number changes (aneuploidy). CONCLUSIONS In genomic analyses of BE tissues from patients with or without later progression to HGD or EAC, we found significantly higher numbers of TP53 mutations in BE from patients with subsequent progression. These mutations were frequently detected before the onset of dysplasia or substantial changes in copy number.
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Affiliation(s)
- Matthew D Stachler
- Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, USA,Department of Oncologic Pathology, Dana Farber Cancer Institute, Boston, Massachusetts, USA
| | - Nicholas D Camarda
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA,Eli and Edythe L. Broad Institute, Cambridge, Massachusetts, USA,Department of Molecular Oncology, Dana Farber Cancer Institute, Boston, Massachusetts, USA,Joint Center for Cancer Precision Medicine, Dana Farber Cancer Institute, Boston, Massachusetts, USA
| | - Christopher Deitrick
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Anthony Kim
- Department of Molecular Oncology, Dana Farber Cancer Institute, Boston, Massachusetts, USA
| | - Agoston T Agoston
- Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Robert D Odze
- Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Jason L Hornick
- Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Anwesha Nag
- Center for Cancer Genome Discovery, Dana Farber Cancer Institute, Boston, Massachusetts, USA
| | - Aaron R Thorner
- Center for Cancer Genome Discovery, Dana Farber Cancer Institute, Boston, Massachusetts, USA
| | - Matthew Ducar
- Center for Cancer Genome Discovery, Dana Farber Cancer Institute, Boston, Massachusetts, USA
| | - Amy Noffsinger
- Inform Diagnostics Research Institute, Needham, Massachusetts (AN and MR), Irving, Texas (RHL)
| | - Richard H Lash
- Inform Diagnostics Research Institute, Needham, Massachusetts (AN and MR), Irving, Texas (RHL)
| | - Mark Redston
- Inform Diagnostics Research Institute, Needham, Massachusetts (AN and MR), Irving, Texas (RHL)
| | - Scott L Carter
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA,Eli and Edythe L. Broad Institute, Cambridge, Massachusetts, USA,Department of Molecular Oncology, Dana Farber Cancer Institute, Boston, Massachusetts, USA,Joint Center for Cancer Precision Medicine, Dana Farber Cancer Institute, Boston, Massachusetts, USA
| | - Jon M Davison
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Adam J Bass
- Eli and Edythe L. Broad Institute, Cambridge, Massachusetts; Department of Molecular Oncology, Dana Farber Cancer Institute, Boston, Massachusetts.
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Vora HH, Mehta SV, Shukla SN, Shah PM. No Mutation Detected in Five Hot Spot Codons of the Tp53 Gene by Restriction Site Mutation Analysis in Patients with Carcinoma of the Tongue. Int J Biol Markers 2018; 25:46-51. [DOI: 10.1177/172460081002500107] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The present study evaluated 5 of the 8 main TP53 mutation hot spots in cancer by restriction site mutation analysis and compared the results with p53 protein expression in patients with cancer of the tongue. Tumor samples from 49 patients with tongue cancer were screened for TP53 mutations in exons 5 through 8 by PCR restriction site mutation analysis and for p53 protein expression by immunohistochemistry using the DO-7 antibody. Nuclear accumulation of p53 protein was seen in 22% (11/49) of the tumors, whereas none of the patients exhibited TP53 mutations in exons 5 through 8. The observed data suggest that TP53 mutations alone are not responsible for abnormal accumulation of p53 protein in tobacco-chewing-mediated tongue carcinogenesis.
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Affiliation(s)
- Hemangini H. Vora
- Immunohistochemistry and Flow Cytometry Division, The Gujarat Cancer and Research Institute, Ahmedabad, Gujarat
| | - Shalvi V. Mehta
- Immunohistochemistry and Flow Cytometry Division, The Gujarat Cancer and Research Institute, Ahmedabad, Gujarat
| | - Shilin N. Shukla
- Head Department of Medical Oncology Unit III, The Gujarat Cancer and Research Institute, Ahmedabad, Gujarat
| | - Pankaj M. Shah
- The Gujarat Cancer and Research Institute, Ahmedabad, Gujarat - India
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Zhang Y, Calado R, Rao M, Hong JA, Meeker AK, Dumitriu B, Atay S, McCormick PJ, Garfield SH, Wangsa D, Padilla-Nash HM, Burkett S, Zhang M, Kunst TF, Peterson NR, Xi S, Inchauste S, Altorki NK, Casson AG, Beer DG, Harris CC, Ried T, Young NS, Schrump DS. Telomerase variant A279T induces telomere dysfunction and inhibits non-canonical telomerase activity in esophageal carcinomas. PLoS One 2014; 9:e101010. [PMID: 24983628 PMCID: PMC4077737 DOI: 10.1371/journal.pone.0101010] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2013] [Accepted: 06/02/2014] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Although implicated in the pathogenesis of several chronic inflammatory disorders and hematologic malignancies, telomerase mutations have not been thoroughly characterized in human cancers. The present study was performed to examine the frequency and potential clinical relevance of telomerase mutations in esophageal carcinomas. METHODS Sequencing techniques were used to evaluate mutational status of telomerase reverse transcriptase (TERT) and telomerase RNA component (TERC) in neoplastic and adjacent normal mucosa from 143 esophageal cancer (EsC) patients. MTS, flow cytometry, time lapse microscopy, and murine xenograft techniques were used to assess proliferation, apoptosis, chemotaxis, and tumorigenicity of EsC cells expressing either wtTERT or TERT variants. Immunoprecipitation, immunoblot, immunofluorescence, promoter-reporter and qRT-PCR techniques were used to evaluate interactions of TERT and several TERT variants with BRG-1 and β-catenin, and to assess expression of cytoskeletal proteins, and cell signaling. Fluorescence in-situ hybridization and spectral karyotyping techniques were used to examine telomere length and chromosomal stability. RESULTS Sequencing analysis revealed one deletion involving TERC (TERC del 341-360), and two non-synonymous TERT variants [A279T (2 homozygous, 9 heterozygous); A1062T (4 heterozygous)]. The minor allele frequency of the A279T variant was five-fold higher in EsC patients compared to healthy blood donors (p<0.01). Relative to wtTERT, A279T decreased telomere length, destabilized TERT-BRG-1-β-catenin complex, markedly depleted β-catenin, and down-regulated canonical Wnt signaling in cancer cells; these phenomena coincided with decreased proliferation, depletion of additional cytoskeletal proteins, impaired chemotaxis, increased chemosensitivity, and significantly decreased tumorigenicity of EsC cells. A279T expression significantly increased chromosomal aberrations in mouse embryonic fibroblasts (MEFs) following Zeocin™ exposure, as well as Li Fraumeni fibroblasts in the absence of pharmacologically-induced DNA damage. CONCLUSIONS A279T induces telomere dysfunction and inhibits non-canonical telomerase activity in esophageal cancer cells. These findings warrant further analysis of A279T expression in esophageal cancers and premalignant esophageal lesions.
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Affiliation(s)
- Yuwei Zhang
- Thoracic Surgery Section, Thoracic and GI Oncology Branch; National Cancer Institute, Bethesda, Maryland, United States of America
| | - Rodrigo Calado
- National Heart, Lung, and Blood Institute, Bethesda, Maryland, United States of America
| | - Mahadev Rao
- Thoracic Surgery Section, Thoracic and GI Oncology Branch; National Cancer Institute, Bethesda, Maryland, United States of America
| | - Julie A. Hong
- Thoracic Surgery Section, Thoracic and GI Oncology Branch; National Cancer Institute, Bethesda, Maryland, United States of America
| | - Alan K. Meeker
- Departments of Pathology and Oncology, Johns Hopkins University of Medicine, Baltimore, Maryland, United States of America
| | - Bogdan Dumitriu
- National Heart, Lung, and Blood Institute, Bethesda, Maryland, United States of America
| | - Scott Atay
- Thoracic Surgery Section, Thoracic and GI Oncology Branch; National Cancer Institute, Bethesda, Maryland, United States of America
| | - Peter J. McCormick
- Laboratory of Cellular Oncology, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Susan H. Garfield
- Laboratory of Experimental Carcinogenesis, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Danny Wangsa
- Section of Cancer Genomics, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Hesed M. Padilla-Nash
- Section of Cancer Genomics, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Sandra Burkett
- Comparative Molecular Cytogenetics Core Facility, National Cancer Institute, Frederick, Maryland, United States of America
| | - Mary Zhang
- Thoracic Surgery Section, Thoracic and GI Oncology Branch; National Cancer Institute, Bethesda, Maryland, United States of America
| | - Tricia F. Kunst
- Thoracic Surgery Section, Thoracic and GI Oncology Branch; National Cancer Institute, Bethesda, Maryland, United States of America
| | - Nathan R. Peterson
- National Heart, Lung, and Blood Institute, Bethesda, Maryland, United States of America
| | - Sichuan Xi
- Thoracic Surgery Section, Thoracic and GI Oncology Branch; National Cancer Institute, Bethesda, Maryland, United States of America
| | - Suzanne Inchauste
- Thoracic Surgery Section, Thoracic and GI Oncology Branch; National Cancer Institute, Bethesda, Maryland, United States of America
| | - Nasser K. Altorki
- Department of Thoracic Surgery, Weill Cornell Medical Center, New York, New York, United States of America
| | - Alan G. Casson
- Department of Surgery, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - David G. Beer
- Section of Thoracic Surgery, University of Michigan Medical Center, Ann Arbor, Michigan, United States of America
| | - Curtis C. Harris
- Laboratory of Human Carcinogenesis, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Thomas Ried
- Section of Cancer Genomics, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Neal S. Young
- National Heart, Lung, and Blood Institute, Bethesda, Maryland, United States of America
| | - David S. Schrump
- Thoracic Surgery Section, Thoracic and GI Oncology Branch; National Cancer Institute, Bethesda, Maryland, United States of America
- * E-mail:
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Lisovsky M, Srivastava A. Barrett Esophagus: Evolving Concepts in Diagnosis and Neoplastic Progression. Surg Pathol Clin 2013; 6:475-96. [PMID: 26839097 DOI: 10.1016/j.path.2013.05.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Surgical pathologists need to answer 2 questions when evaluating biopsies from the distal esophagus or gastroesophageal junction in patients with a history of gastroesophageal reflux disease: Are the findings consistent with Barrett esophagus? and Is there any evidence of dysplasia? Pathologists should be well informed about the controversy around the definition of Barrett esophagus and the common pitfalls that lead to a false-positive diagnosis of Barrett esophagus or Barrett esophagus-associated dysplasia. A concise description of distinct morphologic types of dysplasia in Barrett esophagus and a summary of recent data on the natural history of BE are provided in this review.
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Affiliation(s)
- Mikhail Lisovsky
- Department of Pathology, Dartmouth Hitchcock Medical Center, One Medical Center Drive, Lebanon, NH 03756, USA
| | - Amitabh Srivastava
- Department of Pathology, Brigham and Women's Hospital, 75 Francis Street, Boston, MA 02115, USA.
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Abstract
BACKGROUND The p53 gene is the most frequently mutated gene in cancer and accordingly has been the subject of intensive investigation for almost 30 years. Loss of p53 function due to mutations has been unequivocally demonstrated to promote cancer in both humans and in model systems. As a consequence, there exists an enormous body of information regarding the function of normal p53 in biology and the pathobiological consequences of p53 mutation. It has long been recognised that analysis of p53 has considerable potential as a tool for use in both diagnostic and, to a greater extent, prognostic settings and some significant progress has been made in both of these arenas. OBJECTIVE To provide an overview of the biology of p53, particularly in the context of uses of p53 as a diagnostic tool. METHODS A literature review focused upon the methods and uses of p53 analysis in the diagnosis of sporadic cancers, rare genetic disorders and in detection of residual disease. CONCLUSION p53 is currently an essential diagnostic for the rare inherited cancer prone syndrome (Li-Fraumeni) and is an important diagnostic in only a limited number of settings in sporadic disease. Research in specific cancers indicates that the uses of increasingly well informed p53 mutational analysis are likely to expand to other cancers.
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Affiliation(s)
- Mark T Boyd
- Reader in Molecular Oncology and Director of Laboratories University of Liverpool, p53/MDM2 Research Team, Division of Surgery and Oncology, School of Cancer Studies, 5th Floor, UCD Building, Daulby Street, Liverpool L69 3GA, UK +44 151 706 4185 ; +44 151 706 5826 ;
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Kadam SK, Farmen M, Brandt JT. Quantitative measurement of cell-free plasma DNA and applications for detecting tumor genetic variation and promoter methylation in a clinical setting. J Mol Diagn 2012; 14:346-56. [PMID: 22579630 DOI: 10.1016/j.jmoldx.2012.03.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2010] [Revised: 01/26/2012] [Accepted: 03/15/2012] [Indexed: 12/31/2022] Open
Abstract
An elevated cell-free DNA (cfDNA) level is often reported in patients with advanced cancer and is thought to represent nuclear material from a distant inaccessible tumor. cfDNA can become a valuable source to monitor tumor dynamics and evaluate genetic markers for predictive, prognostic, and diagnostic testing. DNA extraction and quantification were optimized with plasma collected from 20 patients with advanced cancer and 16 healthy controls. Plasma cfDNA from patients with advanced cancer was evaluated for TP53 genetic variation and methylation status of CpG islands in several promoters of known disease-related genes. Tumor biopsy and corresponding plasma specimens were collected from study participants to determine whether the same genetic variations were present in both samples. The cfDNA isolation method provided a lower DNA detection limit of 144 pg, equivalent to DNA from approximately 24 cells. Normal pooled human plasma cfDNA averaged 110 copies/mL of the ACTB gene. Extracted cfDNA was suitable for gene-specific variant detection, sequencing, and promoter methylation analysis. DNA extracted from tumor biopsy and corresponding plasma specimens from two patients with advanced cancer revealed an identical, nonsynonymous variant present in both samples. Immunohistochemical analysis confirmed the TP53 mutant phenotype in the tumor specimens. Quantitative measurement of cfDNA represents a useful biomarker to follow treatment outcome and is a valuable tool with which to characterize specific genetic alterations for both patient selection and personalized treatment.
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Affiliation(s)
- Sunil K Kadam
- Division of Translational Medicine, Lilly Research Laboratories, Eli Lilly & Company, Indianapolis, IN 46285, USA.
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8
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Sonoda R, Naomoto Y, Shirakawa Y, Fujiwara Y, Yamatsuji T, Noma K, Tanabe S, Takaoka M, Gunduz M, Tsujigiwa H, Nagatsuka H, Ohara N, Yoshino T, Takubo K, Vieth M, Tanaka N. Preferential up-regulation of heparanase and cyclooxygenase-2 in carcinogenesis of Barrett's oesophagus and intestinal-type gastric carcinoma. Histopathology 2010; 57:90-100. [PMID: 20653782 DOI: 10.1111/j.1365-2559.2010.03594.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
AIMS Metaplastic changes secondary to chronic inflammation at the gastro-oesophageal junction and at the pyloric antrum are recognized as the premalignant conditions of Barrett's oesophageal adenocarcinoma and intestinal-type gastric carcinoma (GC), respectively. Heparanase (HPSE) and cyclooxygenase (COX)-2 have been proved to play critical roles in inflammation as well as in cancer. The aim was to examine the meaning of their expression in inflammation-related carcinogenesis. METHODS AND RESULTS First, expression of HPSE and COX-2 in 78 clinical tissues of Barrett's oesophagus was examined by immunohistochemistry and in situ hybridization. Their expression was increased during the metaplasia-dysplasia sequence with increased neovascularization. Successively, their expression in Barrett's dysplasia was compared with that of GC (22 cases of diffuse-type and 10 of intestinal-type). Interestingly, the expression pattern in Barrett's dysplasia was similar to that in intestinal-type GC, which mainly arises from chronic inflammation. Furthermore, cultured cell lines isolated from differentiated GC tissues, which are often found to be of intestinal-type, revealed up-regulated mRNA expression of HPSE and COX-2. CONCLUSIONS HPSE and COX-2 are preferentially up-regulated in Barrett's oesophagus and intestinal-type GC. These molecules may play an important role during the development of inflammation-related adenocarcinoma of the upper gastrointestinal tract.
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Affiliation(s)
- Ryotaro Sonoda
- Department of Gastroenterological Surgery, Transplant, and Surgical Oncology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
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Shuga J, Zeng Y, Novak R, Mathies RA, Hainaut P, Smith MT. Selected technologies for measuring acquired genetic damage in humans. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2010; 51:851-870. [PMID: 20872848 DOI: 10.1002/em.20630] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Technical advances have improved the capacity to detect and quantify genetic variants, providing novel methods for the detection of rare mutations and for better understanding the underlying environmental factors and biological mechanisms contributing to mutagenesis. The polymerase chain reaction (PCR) has revolutionized genetic testing and remains central to many of these new techniques for mutation detection. Millions of genetic variations have been discovered across the genome. These variations include germline mutations and polymorphisms, which are inherited in a Mendelian manner and present in all cells, as well as acquired, somatic mutations that differ widely by type and size [from single-base mutations to whole chromosome rearrangements, and including submicroscopic copy number variations (CNVs)]. This review focuses on current methods for assessing acquired somatic mutations in the genome, and it examines their application in molecular epidemiology and sensitive detection and analysis of disease. Although older technologies have been exploited for detecting acquired mutations in cancer and other disease, the high-throughput and high-sensitivity offered by next-generation sequencing (NGS) systems are transforming the discovery of disease-associated acquired mutations by enabling comparative whole-genome sequencing of diseased and healthy tissues from the same individual. Emerging microfluidic technologies are beginning to facilitate single-cell genetic analysis of target variable regions for investigating cell heterogeneity within tumors as well as preclinical detection of disease. The technologies discussed in this review will significantly expand our knowledge of acquired genetic mutations and causative mechanisms.
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Affiliation(s)
- Joe Shuga
- School of Public Health, University of California, Berkeley, California 94720, USA
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Karaman A, Binici DN, Kabalar ME, Koca T, Dursun H. Genomic instability in patients with Barrett's esophagus. ACTA ACUST UNITED AC 2010; 201:88-93. [DOI: 10.1016/j.cancergencyto.2010.05.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2009] [Revised: 04/08/2010] [Accepted: 05/04/2010] [Indexed: 12/12/2022]
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Meng F, Bermudez E, McKinzie PB, Andersen ME, Clewell HJ, Parsons BL. Measurement of tumor-associated mutations in the nasal mucosa of rats exposed to varying doses of formaldehyde. Regul Toxicol Pharmacol 2010; 57:274-83. [PMID: 20347909 DOI: 10.1016/j.yrtph.2010.03.007] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2009] [Revised: 03/15/2010] [Accepted: 03/17/2010] [Indexed: 01/09/2023]
Abstract
This study examined the potential induction of tumor-associated mutations in formaldehyde-exposed rat nasal mucosa using a sensitive method, allele-specific competitive blocker-PCR (ACB-PCR). Levels of p53 codon 271 CGT to CAT and K-Ras codon 12 GGT to GAT mutations were quantified in nasal mucosa of rats exposed to formaldehyde. In addition, nasal mucosa cell proliferation was monitored because regenerative cell proliferation is considered a key event in formaldehyde-induced carcinogenesis. Male F344 rats (6-7 weeks old, 5 rats/group) were exposed to 0, 0.7, 2, 6, 10, and 15 ppm formaldehyde for 13 weeks (6 h/day, 5 days/week). ACB-PCR was used to determine levels of p53 and K-Ras mutations. Although two of five untreated rats had measureable spontaneous p53 mutant fractions (MFs), most nasal mucosa samples had p53 MFs below 10(-5). All K-Ras MF measurements were below 10(-5). No dose-related increases in p53 or K-Ras MF were observed, even though significant increases in bromodeoxyuridine incorporation demonstrated induced cell proliferation in the 10 and 15 ppm formaldehyde-treatment groups. Therefore, induction of tumor-associated p53 mutation likely occurs after several other key events in formaldehyde-induced carcinogenesis.
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Affiliation(s)
- Fanxue Meng
- US Food and Drug Administration, National Center for Toxicological Research, Division of Genetic and Reproductive Toxicology, Jefferson, AR 72079, USA.
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Ivil KD, Jenkins SA, Doak SH, Hawizy AM, Kynaston HG, Parry EM, Jenkins GJS, Parry JM, Stephenson TP. Identification of early p53 mutations in clam ileocystoplasties using restriction site mutation assay. Urology 2007; 70:905-9. [PMID: 17919692 DOI: 10.1016/j.urology.2007.06.1121] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2005] [Revised: 04/18/2007] [Accepted: 06/29/2007] [Indexed: 11/26/2022]
Abstract
OBJECTIVES Because a risk of cancer arising in enterocystoplasties exists, it is necessary to identify which patients are most at risk of tumor formation. The aim of this study was to determine whether rare mutated p53 sequences were more common at the enterovesical anastomosis than in the bladder remnant in patients with a clam ileocystoplasty using the restriction site mutation (RSM) assay. METHODS DNA was extracted from endoscopic biopsies obtained from the ileovesical anastomosis and native bladder remnant (control specimens) of 38 patients with a clam ileocystoplasty. The RSM assay was used to study five known hotspots for mutations of the p53 gene using the restriction enzymes Hha I (codon 175), Taq I (codon 213), Hae III (codon 249/250), and Msp I (codons 248 and 282). The mutational events of p53 were confirmed by sequencing the undigested mutated polymerase chain reaction products identified by RSM analysis. RESULTS We found p53 mutations at the ileovesical anastomosis in 7 of the 38 patients. The mutations were observed at codon 213 (n = 1), codon 248 (n = 3), and codon 250 (n = 3). No p53 mutations were detected in any control specimen. CONCLUSIONS The ileovesical anastomosis is genetically unstable in patients with a clam ileocystoplasty. The p53 mutations identified by the RSM assay at the enterovesical anastomosis could possibly be used as markers of genetic instability to identify patients at risk of developing a tumor. Prospective, randomized longitudinal studies are required to substantiate this hypothesis.
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Affiliation(s)
- Kenneth D Ivil
- Department of Urology, University Hospital of Wales, Cardiff, United Kingdom.
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Gormally E, Caboux E, Vineis P, Hainaut P. Circulating free DNA in plasma or serum as biomarker of carcinogenesis: practical aspects and biological significance. Mutat Res 2007; 635:105-117. [PMID: 17257890 DOI: 10.1016/j.mrrev.2006.11.002] [Citation(s) in RCA: 325] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2006] [Revised: 11/29/2006] [Accepted: 11/29/2006] [Indexed: 12/26/2022]
Abstract
The presence of small amounts of tumor DNA in cell free DNA (CFDNA) circulating in the plasma or serum of cancer patients was first demonstrated 30 years ago. Since then, overall plasma DNA concentration in cancer patients and genetic or epigenetic alterations specific to tumor DNA have been investigated in patients diagnosed with different types of cancer. The proportion of patients with altered CFDNA varies with the pathology and the nature of the marker. However, several studies have reported the presence of altered CFDNA in over 50% of cancer patients, suggesting that this marker may be common and amenable for a variety of clinical and epidemiological studies. Because the mechanisms and timing of CFDNA release in the blood stream are poorly understood, only few studies have addressed the use of CFDNA for early cancer detection or as a biomarker for mutagenesis and tumourigenesis in molecular epidemiology. In this review, we discuss the technical issues involved in obtaining, using and analyzing CFDNA in cancer or healthy subjects. We also summarize the literature available on the mechanisms of CDNA release as well as on cross-sectional or prospective studies aimed at assessing the clinical and biological significance of CFDNA. These studies show that, in some circumstances, CFDNA alterations are detectable ahead of cancer diagnosis, raising the possibility of exploiting them as biomarkers for monitoring cancer occurrence. Testing these hypotheses will require well-designed studies, assessing multiple markers with quantitative and sensitive methods, with adequate follow-up of subjects, and we provide recommendations for the development of such studies.
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Affiliation(s)
- Emmanuelle Gormally
- Université Catholique de Lyon, 25 rue du Plat, 69288 Lyon Cedex 02, France; International Agency for Research on Cancer, 150 Cours Albert Thomas, 69372 Lyon Cedex 08, France
| | - Elodie Caboux
- International Agency for Research on Cancer, 150 Cours Albert Thomas, 69372 Lyon Cedex 08, France
| | - Paolo Vineis
- Department of Epidemiology and Public Health, Imperial College of Science, Technology and Medicine, Norfolk Place, W2 1PG London, UK
| | - Pierre Hainaut
- International Agency for Research on Cancer, 150 Cours Albert Thomas, 69372 Lyon Cedex 08, France.
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16
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Novotna K, Trkova M, Pazdro A, Smejkal M, Soukupova A, Kodetova D, Smejkal P, Sedlacek Z. TP53 gene mutations are rare in nondysplastic Barrett's esophagus. Dig Dis Sci 2006; 51:110-3. [PMID: 16416221 DOI: 10.1007/s10620-006-3093-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2005] [Accepted: 03/31/2005] [Indexed: 12/25/2022]
Abstract
In search of potential prognostic markers, we analyzed a large series of tissues of Barrett's esophagus and samples of adenocarcinomas arising in the terrain of Barrett's esophagus for TP53 gene mutations by direct sequencing of exons 5 to 9 of the TP53 gene. While 9 of 21 adenocarcinomas tested (42.9%) contained a TP53 mutation, none of 24 samples from Barrett's esophagus were mutated. This observation suggests that TP53 gene mutation may be a relatively late event in the progression from nondysplastic Barrett's esophagus to adenocarcinoma of esophagus. Therefore, TP53 gene mutations alone are not likely to represent a widely useful prognostic marker of the risk of progression to malignancy, at least not in Barrett's esophagus without dysplasia.
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Affiliation(s)
- Kamila Novotna
- Institute of Biology and Medical Genetics, Charles University Second Medical School, 15006, Prague 5, Czech Republic.
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17
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Doak SH, Jenkins GJS, Parry EM, Griffiths AP, Shah V, Baxter JN, Parry JM. Characterisation of p53 status at the gene, chromosomal and protein levels in oesophageal adenocarcinoma. Br J Cancer 2003; 89:1729-35. [PMID: 14583777 PMCID: PMC2394414 DOI: 10.1038/sj.bjc.6601323] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
p53 mutations and loss of heterozygosity have been commonly associated with oesophageal adenocarcinoma. In this investigation, the p53 status of a Welsh population of Barrett's-associated oesophageal adenocarcinomas were fully characterised at the gene sequence, chromosomal, mRNA and protein levels. In total, 31 tumours were examined for p53 gene sequence mutations using RFLP with sequencing, allelic loss of the gene was characterised by FISH, mRNA expression by p53 pathway signalling arrays and protein levels by p53 immunohistochemistry. In all, 9.6% of adenocarcinomas harboured p53 mutations, 24% displayed p53 allelic loss and 83% exhibited p53 protein accumulation. Point mutations and deletions of the gene did not coexist within the same samples. All samples containing p53 mutations also displayed positive immunostaining; however; in the majority of cases, p53 protein accumulation developed in the absence of mutations. The gene expression analysis demonstrated no differences in p53 and mdm-2 transcription levels between the p53 immunonegative and immunopositive samples, indicating other mechanisms underlie the proteins' overexpression. In conclusion, p53 mutations and deletions do not appear to be frequent events in oesophageal adenocarcinomas; however, abnormal accumulation of the protein is present in a vast majority of cases. P53 gene mutations are not the primary cause of protein overexpression--an alternative mechanism is responsible for the positive p53 immunohistochemistry detected.
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Affiliation(s)
- S H Doak
- Human Molecular Pathology Group, School of Biological Sciences, University of Wales, Swansea SA2 8PP, UK.
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