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Choi WT, Rabinovitch PS. DNA flow cytometry for detection of genomic instability as a cancer precursor in the gastrointestinal tract. Methods Cell Biol 2024; 186:25-49. [PMID: 38705603 DOI: 10.1016/bs.mcb.2024.02.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2024]
Abstract
One of the earliest applications of flow cytometry was the measurement of DNA content in cells. This method is based on the ability to stain DNA in a stoichiometric manner (i.e., the amount of stain is directly proportional to the amount of DNA within the cell). For more than 40years, a number of studies have consistently demonstrated the utility of DNA flow cytometry as a potential diagnostic and/or prognostic tool in patients with most epithelial tumors, including pre-invasive lesions (such as dysplasia) in the gastrointestinal tract. However, its availability as a clinical test has been limited to few medical centers due to the requirement for fresh tissue in earlier studies and perceived technical demands. However, more recent studies have successfully utilized formalin-fixed paraffin-embedded (FFPE) tissue to generate high-quality DNA content histograms, demonstrating the feasibility of this methodology. This review summarizes step-by-step methods on how to perform DNA flow cytometry using FFPE tissue and analyze DNA content histograms based on the published consensus guidelines in order to assist in the diagnosis and/or risk stratification of many different epithelial tumors, with particular emphasis on dysplasia associated with Barrett's esophagus and inflammatory bowel disease.
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Affiliation(s)
- Won-Tak Choi
- Department of Pathology, University of California at San Francisco, San Francisco, CA, United States.
| | - Peter S Rabinovitch
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, United States
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Cortes-Ciriano I, Steele CD, Piculell K, Al-Ibraheemi A, Eulo V, Bui MM, Chatzipli A, Dickson BC, Borcherding DC, Feber A, Galor A, Hart J, Jones KB, Jordan JT, Kim RH, Lindsay D, Miller C, Nishida Y, Proszek PZ, Serrano J, Sundby RT, Szymanski JJ, Ullrich NJ, Viskochil D, Wang X, Snuderl M, Park PJ, Flanagan AM, Hirbe AC, Pillay N, Miller DT. Genomic Patterns of Malignant Peripheral Nerve Sheath Tumor (MPNST) Evolution Correlate with Clinical Outcome and Are Detectable in Cell-Free DNA. Cancer Discov 2023; 13:654-671. [PMID: 36598417 PMCID: PMC9983734 DOI: 10.1158/2159-8290.cd-22-0786] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 11/09/2022] [Accepted: 12/16/2022] [Indexed: 01/05/2023]
Abstract
Malignant peripheral nerve sheath tumor (MPNST), an aggressive soft-tissue sarcoma, occurs in people with neurofibromatosis type 1 (NF1) and sporadically. Whole-genome and multiregional exome sequencing, transcriptomic, and methylation profiling of 95 tumor samples revealed the order of genomic events in tumor evolution. Following biallelic inactivation of NF1, loss of CDKN2A or TP53 with or without inactivation of polycomb repressive complex 2 (PRC2) leads to extensive somatic copy-number aberrations (SCNA). Distinct pathways of tumor evolution are associated with inactivation of PRC2 genes and H3K27 trimethylation (H3K27me3) status. Tumors with H3K27me3 loss evolve through extensive chromosomal losses followed by whole-genome doubling and chromosome 8 amplification, and show lower levels of immune cell infiltration. Retention of H3K27me3 leads to extensive genomic instability, but an immune cell-rich phenotype. Specific SCNAs detected in both tumor samples and cell-free DNA (cfDNA) act as a surrogate for H3K27me3 loss and immune infiltration, and predict prognosis. SIGNIFICANCE MPNST is the most common cause of death and morbidity for individuals with NF1, a relatively common tumor predisposition syndrome. Our results suggest that somatic copy-number and methylation profiling of tumor or cfDNA could serve as a biomarker for early diagnosis and to stratify patients into prognostic and treatment-related subgroups. This article is highlighted in the In This Issue feature, p. 517.
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Affiliation(s)
- Isidro Cortes-Ciriano
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, United Kingdom
| | - Christopher D. Steele
- Research Department of Pathology, University College London Cancer Institute, Bloomsbury, London, United Kingdom
| | - Katherine Piculell
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts
| | - Alyaa Al-Ibraheemi
- Department of Pathology, Boston Children's Hospital, Boston, Massachusetts
| | - Vanessa Eulo
- Division of Oncology, Department of Internal Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | - Marilyn M. Bui
- Department of Pathology, Moffitt Cancer Center & Research Institute, Tampa, Florida
| | - Aikaterini Chatzipli
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts
| | - Brendan C. Dickson
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Dana C. Borcherding
- Division of Oncology, Departments of Internal Medicine and Pediatrics, Siteman Cancer Center, Washington University School of Medicine, St. Louis, Missouri
| | - Andrew Feber
- Clinical Genomics Translational Research, Institute of Cancer Research, Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Alon Galor
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Jesse Hart
- Department of Pathology, Lifespan Laboratories, Rhode Island Hospital, Providence, Rhode Island
| | - Kevin B. Jones
- Departments of Orthopaedics and Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
| | - Justin T. Jordan
- Pappas Center for Neuro-oncology, Massachusetts General Hospital, Boston, Massachusetts
| | - Raymond H. Kim
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, Sinai Health System, Toronto, Ontario, Canada
- Hospital for Sick Children, University of Toronto, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Daniel Lindsay
- Department of Histopathology, Royal National Orthopaedic Hospital, NHS Trust, Middlesex, United Kingdom
| | - Colin Miller
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, United Kingdom
| | - Yoshihiro Nishida
- Department of Rehabilitation Medicine, Nagoya University Hospital, Nagoya, Aichi, Japan
| | - Paula Z. Proszek
- Clinical Genomics Translational Research, Institute of Cancer Research, Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Jonathan Serrano
- Department of Pathology, New York University Langone Health, Perlmutter Cancer Center, New York City, New York
| | - R. Taylor Sundby
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Jeffrey J. Szymanski
- Division of Cancer Biology, Department of Radiation Oncology, Washington University School of Medicine, St. Louis, Missouri
| | - Nicole J. Ullrich
- Department of Neurology, Boston Children's Hospital, Boston, Massachusetts
| | - David Viskochil
- Division of Medical Genetics, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
| | - Xia Wang
- GeneHome, Department of Individualized Cancer Management, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Matija Snuderl
- Department of Pathology, New York University Langone Health, Perlmutter Cancer Center, New York City, New York
| | - Peter J. Park
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts
| | - Adrienne M. Flanagan
- Research Department of Pathology, University College London Cancer Institute, Bloomsbury, London, United Kingdom
- Department of Histopathology, Royal National Orthopaedic Hospital, NHS Trust, Middlesex, United Kingdom
| | - Angela C. Hirbe
- Division of Oncology, Departments of Internal Medicine and Pediatrics, Siteman Cancer Center, Washington University School of Medicine, St. Louis, Missouri
| | - Nischalan Pillay
- Research Department of Pathology, University College London Cancer Institute, Bloomsbury, London, United Kingdom
- Department of Histopathology, Royal National Orthopaedic Hospital, NHS Trust, Middlesex, United Kingdom
| | - David T. Miller
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts
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Vithayathil M, Modolell I, Ortiz-Fernandez-Sordo J, Oukrif D, Pappas A, Januszewicz W, O'Donovan M, Hadjinicolaou A, Bianchi M, Blasko A, White J, Kaye P, Novelli M, Wernisch L, Ragunath K, di Pietro M. Image-Enhanced Endoscopy and Molecular Biomarkers Vs Seattle Protocol to Diagnose Dysplasia in Barrett's Esophagus. Clin Gastroenterol Hepatol 2022; 20:2514-2523.e3. [PMID: 35183768 DOI: 10.1016/j.cgh.2022.01.060] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 01/21/2022] [Accepted: 01/28/2022] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS Dysplasia in Barrett's esophagus often is invisible on high-resolution white-light endoscopy (HRWLE). We compared the diagnostic accuracy for inconspicuous dysplasia of the combination of autofluorescence imaging (AFI)-guided probe-based confocal laser endomicroscopy (pCLE) and molecular biomarkers vs HRWLE with Seattle protocol biopsies. METHODS Barrett's esophagus patients with no dysplastic lesions were block-randomized to standard endoscopy (HRWLE with the Seattle protocol) or AFI-guided pCLE with targeted biopsies for molecular biomarkers (p53 and cyclin A by immunohistochemistry; aneuploidy by image cytometry), with crossover to the other arm after 6 to 12 weeks. The primary end point was the histologic diagnosis from all study biopsies (trial histology). A sensitivity analysis was performed for overall histology, which included diagnoses within 12 months from the first study endoscopy. Endoscopists were blinded to the referral endoscopy and histology results. The primary outcome was diagnostic accuracy for dysplasia by real-time pCLE vs HRWLE biopsies. RESULTS Of 154 patients recruited, 134 completed both arms. In the primary outcome analysis (trial histology analysis), AFI-guided pCLE had similar sensitivity for dysplasia compared with standard endoscopy (74.3%; 95% CI, 56.7-87.5 vs 80.0%; 95% CI, 63.1-91.6; P = .48). Multivariate logistic regression showed pCLE optical dysplasia, aberrant p53, and aneuploidy had the strongest correlation with dysplasia (secondary outcome). This 3-biomarker panel had higher sensitivity for any grade of dysplasia than the Seattle protocol (81.5% vs 51.9%; P < .001) in the overall histology analysis, but not in the trial histology analysis (91.4% vs 80.0%; P = .16), with an area under the receiver operating curve of 0.83. CONCLUSIONS Seattle protocol biopsies miss dysplasia in approximately half of patients with inconspicuous neoplasia. AFI-guided pCLE has similar accuracy to the current gold standard. The addition of molecular biomarkers could improve diagnostic accuracy.
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Affiliation(s)
- Mathew Vithayathil
- Medical Research Council Cancer Unit, University of Cambridge, United Kingdom
| | - Ines Modolell
- Department of Gastroenterology, University Hospital National Health Service Foundation Trust, United Kingdom
| | - Jacobo Ortiz-Fernandez-Sordo
- Nottingham Digestive Diseases Centre, National Institute of Health Research Nottingham Biomedical Research Centre, United Kingdom
| | - Dahmane Oukrif
- Department of Histopathology, University College London Hospital, Longdon, United Kingdom
| | - Apostolos Pappas
- Medical Research Council Cancer Unit, University of Cambridge, United Kingdom
| | - Wladyslaw Januszewicz
- Medical Research Council Cancer Unit, University of Cambridge, United Kingdom; Department of Gastroenterology, Hepatology and Clinical Oncology, Medical Centre for Postgraduate Education, Warsaw, Poland
| | - Maria O'Donovan
- Department of Histopathology, Cambridge University Hospital National Health Service Foundation Trust, United Kingdom
| | - Andreas Hadjinicolaou
- Medical Research Council Cancer Unit, University of Cambridge, United Kingdom; Department of Gastroenterology, University Hospital National Health Service Foundation Trust, United Kingdom
| | - Michele Bianchi
- Medical Research Council Cancer Unit, University of Cambridge, United Kingdom
| | - Adrienn Blasko
- Medical Research Council Cancer Unit, University of Cambridge, United Kingdom
| | - Jonathan White
- Nottingham Digestive Diseases Centre, National Institute of Health Research Nottingham Biomedical Research Centre, United Kingdom
| | - Philip Kaye
- Department of Histopathology, Nottingham University Hospitals National Health Service Trust, University of Nottingham, United Kingdom
| | - Marco Novelli
- Department of Histopathology, University College London Hospital, Longdon, United Kingdom
| | - Lorenz Wernisch
- BIOS Health, Ltd, Cambridge, United Kingdom; Medical Research Council Biostatistics Unit, University of Cambridge, United Kingdom
| | - Krish Ragunath
- Nottingham Digestive Diseases Centre, National Institute of Health Research Nottingham Biomedical Research Centre, United Kingdom
| | - Massimiliano di Pietro
- Medical Research Council Cancer Unit, University of Cambridge, United Kingdom; Department of Gastroenterology, University Hospital National Health Service Foundation Trust, United Kingdom.
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Hadjinicolaou AV, van Munster SN, Achilleos A, Santiago Garcia J, Killcoyne S, Ragunath K, Bergman JJGHM, Fitzgerald RC, di Pietro M. Aneuploidy in targeted endoscopic biopsies outperforms other tissue biomarkers in the prediction of histologic progression of Barrett's oesophagus: A multi-centre prospective cohort study. EBioMedicine 2020; 56:102765. [PMID: 32460165 PMCID: PMC7251385 DOI: 10.1016/j.ebiom.2020.102765] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 04/02/2020] [Accepted: 04/08/2020] [Indexed: 02/08/2023] Open
Abstract
Background The cancer risk in Barrett's oesophagus (BO) is difficult to estimate. Histologic dysplasia has strong predictive power, but can be missed by random biopsies. Other clinical parameters have limited utility for risk stratification. We aimed to assess whether a molecular biomarker panel on targeted biopsies can predict neoplastic progression of BO. Methods 203 patients with BO were tested at index endoscopy for 9 biomarkers (p53 and cyclin A expression; aneuploidy and tetraploidy; CDKN2A (p16), RUNX3 and HPP1 hypermethylation; 9p and 17p loss of heterozygosity) on autofluorescence-targeted biopsies and followed-up prospectively. Data comparing progressors to non-progressors were evaluated by univariate and multivariate analyses using survival curves, Cox-proportional hazards and logistic regression models. Findings 127 patients without high-grade dysplasia (HGD) or oesophageal adenocarcinoma (OAC) at index endoscopy were included, of which 42 had evidence of any histologic progression over time. Aneuploidy was the only predictor of progression from non-dysplastic BO (NDBO) to any grade of neoplasia (p = 0.013) and HGD/OAC (p = 0.002). Aberrant p53 expression correlated with risk of short-term progression within 12 months, with an odds ratio of 6.0 (95% CI: 3.1–11.2). A panel comprising aneuploidy and p53 had an area under the receiving operator characteristics curve of 0.68 (95% CI: 0.59–0.77) for prediction of any progression. Interpretation Aneuploidy is the only biomarker that predicts neoplastic progression of NDBO. Aberrant p53 expression suggests prevalent dysplasia, which might have been missed by random biopsies, and warrants early follow up.
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Affiliation(s)
- Andreas V Hadjinicolaou
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Box 197, Cambridge Biomedical Campus, Cambridge CB2 0XZ, United Kingdom
| | - Sanne N van Munster
- Department of Gastroenterology, Amsterdam University Medical Centre, Meibergdreef 9, 1105 AZ, Amsterdam 22660, the Netherlands
| | - Achilleas Achilleos
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Box 197, Cambridge Biomedical Campus, Cambridge CB2 0XZ, United Kingdom
| | - Jose Santiago Garcia
- Nottingham Digestive Diseases Biomedical Research Centre, Queens Medical Centre Campus, E Floor, West Block, Derby Road, Nottingham NG7 2UH, United Kingdom
| | - Sarah Killcoyne
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Box 197, Cambridge Biomedical Campus, Cambridge CB2 0XZ, United Kingdom; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton CB10 1SD, United Kingdom
| | - Krish Ragunath
- Nottingham Digestive Diseases Biomedical Research Centre, Queens Medical Centre Campus, E Floor, West Block, Derby Road, Nottingham NG7 2UH, United Kingdom
| | - Jacques J G H M Bergman
- Department of Gastroenterology, Amsterdam University Medical Centre, Meibergdreef 9, 1105 AZ, Amsterdam 22660, the Netherlands
| | - Rebecca C Fitzgerald
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Box 197, Cambridge Biomedical Campus, Cambridge CB2 0XZ, United Kingdom
| | - Massimiliano di Pietro
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Box 197, Cambridge Biomedical Campus, Cambridge CB2 0XZ, United Kingdom.
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Duits LC, Lao-Sirieix P, Wolf WA, O’Donovan M, Galeano-Dalmau N, Meijer SL, Offerhaus GJA, Redman J, Crawte J, Zeki S, Pouw RE, Chak A, Shaheen NJ, Bergman JJGHM, Fitzgerald RC. A biomarker panel predicts progression of Barrett's esophagus to esophageal adenocarcinoma. Dis Esophagus 2019; 32:5212855. [PMID: 30496496 PMCID: PMC6303732 DOI: 10.1093/dote/doy102] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Progression from Barrett's esophagus (BE) to esophageal adenocarcinoma (EAC) is uncommon but the consequences are serious. Predictors of progression are essential to optimize resource utilization. This study assessed the utility of a promising panel of biomarkers applicable to routine paraffin embedded biopsies (FFPE) to predict progression of BE to EAC in a large population-based, nested case-control study.We utilized the Amsterdam-based ReBus nested case-control cohort. BE patients who progressed to high-grade dysplasia (HGD)/EAC (n = 130) and BE patients who never progressed (n = 130) were matched on age, sex, length of the BE segment, and duration of endoscopic surveillance. All progressors had minimum 2 years of endoscopic surveillance without HGD/EAC to exclude prevalent neoplasia. We assessed abnormal DNA content, p53, Cyclin A, and Aspergillus oryzae lectin (AOL) in FFPE sections. We performed conditional logistic regression analysis to estimate odds ratio (OR) of progression based on biomarker status.Expert LGD (OR, 8.3; 95% CI, 1.7-41.0), AOL (3 vs. 0 epithelial compartments abnormal; OR, 3.6; 95% CI, 1.2-10.6) and p53 (OR, 2.3; 95% CI, 1.2-4.6) were independently associated with neoplastic progression. Cyclin A did not predict progression and DNA ploidy analysis by image cytometry was unsuccessful in the majority of cases, both were excluded from the multivariate analysis. The multivariable biomarker model had an area under the receiver operating characteristic curve of 0.73.Expert LGD, AOL, and p53 independently predict neoplastic progression in BE patients and are applicable to routine practice. These biomarkers can aid in selecting patients for endoscopic ablation or more intensive surveillance.
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Affiliation(s)
- L C Duits
- Amsterdam UMC, University of Amsterdam, Department of Gastroenterology and Hepatology, Amsterdam, the Netherlands
| | - P Lao-Sirieix
- Medical Research Council Cancer Unit, Hutchison-MRC Research Center, University of Cambridge,Cambridge,United Kingdom
| | - W A Wolf
- Center for Esophageal Diseases and Swallowing, Department of Medicine, Division of Gastroenterology, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - M O’Donovan
- Department of Pathology, Cambridge University Hospitals NHS Trust, Cambridge, United Kingdom
| | - N Galeano-Dalmau
- Medical Research Council Cancer Unit, Hutchison-MRC Research Center, University of Cambridge,Cambridge,United Kingdom
| | - S L Meijer
- Department of Pathology, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - G J A Offerhaus
- Department of Pathology, University Medical Center, Utrecht, the Netherlands
| | - J Redman
- Medical Research Council Cancer Unit, Hutchison-MRC Research Center, University of Cambridge,Cambridge,United Kingdom
| | - J Crawte
- Medical Research Council Cancer Unit, Hutchison-MRC Research Center, University of Cambridge,Cambridge,United Kingdom
| | - S Zeki
- Medical Research Council Cancer Unit, Hutchison-MRC Research Center, University of Cambridge,Cambridge,United Kingdom
| | - R E Pouw
- Amsterdam UMC, University of Amsterdam, Department of Gastroenterology and Hepatology, Amsterdam, the Netherlands
| | - A Chak
- Division of Gastroenterology and Liver Disease, Case Western Reserve University, Cleveland, Ohio, USA
| | - N J Shaheen
- Center for Esophageal Diseases and Swallowing, Department of Medicine, Division of Gastroenterology, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - J J G H M Bergman
- Amsterdam UMC, University of Amsterdam, Department of Gastroenterology and Hepatology, Amsterdam, the Netherlands
| | - R C Fitzgerald
- Medical Research Council Cancer Unit, Hutchison-MRC Research Center, University of Cambridge,Cambridge,United Kingdom
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Choi WT, Tsai JH, Rabinovitch PS, Small T, Huang D, Mattis AN, Kakar S. Diagnosis and risk stratification of Barrett's dysplasia by flow cytometric DNA analysis of paraffin-embedded tissue. Gut 2018. [PMID: 28642331 DOI: 10.1136/gutjnl-2017-313815] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
OBJECTIVE The diagnosis of dysplasia in Barrett's oesophagus (BO) can be challenging, and reliable ancillary techniques are not available. This study examines if DNA content abnormality detected by flow cytometry can serve as a diagnostic marker of dysplasia and facilitate risk stratification of low-grade dysplasia (LGD) and indefinite for dysplasia (IND) patients using formalin-fixed paraffin-embedded (FFPE) BO samples with varying degrees of dysplasia. DESIGN DNA flow cytometry was performed on 80 FFPE BO samples with high-grade dysplasia (HGD), 38 LGD, 21 IND and 14 negative for dysplasia (ND). Three to four 60-micron thick sections were cut from each tissue block, and the area of interest was manually dissected. RESULTS DNA content abnormality was identified in 76 HGD (95%), 8 LGD (21.1%), 2 IND (9.5%) and 0 ND samples. As a diagnostic marker of HGD, the estimated sensitivity and specificity of DNA content abnormality were 95% and 85%, respectively. For patients with DNA content abnormality detected at baseline LGD or IND, the univariate HRs for subsequent detection of HGD or oesophageal adenocarcinoma (OAC) were 7.0 and 20.0, respectively (p =<0.001). CONCLUSIONS This study demonstrates the promise of DNA flow cytometry using FFPE tissue in the diagnosis and risk stratification of dysplasia in BO. The presence of DNA content abnormality correlates with increasing levels of dysplasia, as 95% of HGD samples showed DNA content abnormality. DNA flow cytometry also identifies a subset of patients with LGD and IND who are at higher risk for subsequent detection of HGD or OAC.
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Affiliation(s)
- Won-Tak Choi
- Department of Pathology, University of California at San Francisco, San Francisco, California, USA
| | - Jia-Huei Tsai
- Department of Pathology, National Taiwan University Hospital, Taipei, Taiwan
| | | | - Thomas Small
- Department of Pathology, University of Washington, Seattle, Washington, USA
| | - Danning Huang
- Department of Public Health and Preventive Medicine, SUNY Upstate Medical University, Syracuse, New York, USA
| | - Aras N Mattis
- Department of Pathology, University of California at San Francisco, San Francisco, California, USA
| | - Sanjay Kakar
- Department of Pathology, University of California at San Francisco, San Francisco, California, USA
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Ghizoni JS, Sperandio M, Lock C, Odell EW. Image cytometry DNA ploidy analysis: Correlation between two semi-automated methods. Oral Dis 2018; 24:1204-1208. [PMID: 29757479 DOI: 10.1111/odi.12888] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 04/18/2018] [Accepted: 04/29/2018] [Indexed: 11/30/2022]
Abstract
BACKGROUND AND OBJECTIVES Quantitation of cell DNA content, DNA ploidy, has been established as a research and prognostic technique for decades. A variety of instruments have been used although only a few commercially available systems have established quality assurance and published outcome data. The aim of this study was to compare two automated systems. METHODS Nuclear monolayers were obtained from 112 oral biopsies by enzyme digestion and Feulgen staining. These were scanned on both the Fairfield and the Ploidy Work Station (PWS) systems. The overall ploidy diagnosis, number of epithelial nuclei, coefficient of variation (CV) and 5c exceeding rate (5CER) were compared by quantile-quantile plots, t test, Wilcoxon and Spearman's tests. RESULTS The PWS system identified more nuclei (p < 0.0001) at a lower CV (p < 0.0001). Using the PWS system, fewer samples were classified as indeterminate. No difference between 5CER was found between systems (p > 0.54). There was complete concordance between the two systems in terms of DNA ploidy diagnosis. CONCLUSIONS The PWS system is comparable to the Fairfield system for determination of DNA ploidy and has advantages that may lead to improved performance.
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Affiliation(s)
- Janaina S Ghizoni
- Department of Oral Pathology & Medicine, University of South Santa Catarina (UNISUL), Tubarão, Brazil
| | - Marcelo Sperandio
- Department of Oral Pathology & Medicine, Sao Leopoldo Mandic Dental Institute and Research Center, Campinas, Brazil
| | - Claire Lock
- Head and Neck Pathology, Viapath LLC, Guy's Hospital, London, UK
| | - Edward W Odell
- Department of Oral Pathology, King's College London, Guy's Hospital, London, UK
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8
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Kohoutova D, Haidry R, Banks M, Butt MA, Dunn J, Thorpe S, Lovat L. Long-term outcomes of the randomized controlled trial comparing 5-aminolaevulinic acid and Photofrin photodynamic therapy for Barrett's oesophagus related neoplasia. Scand J Gastroenterol 2018; 53:527-532. [PMID: 29161901 DOI: 10.1080/00365521.2017.1403646] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
OBJECTIVE Photodynamic therapy (PDT) was used as therapy for early neoplasia associated with Barrett's oesophagus (BE). This is 5-year follow-up of patients enrolled into randomised controlled trial of 5-aminolaevulinic acid (ALA) vs. Photofrin PDT. METHODS Biopsies were taken from original Barrett's segment during endoscopic follow up using Seattle protocol. Endoscopic mucosal resection (EMR) ± radiofrequency ablation (RFA) was preferred therapy in patients who failed PDT and/or had recurrent neoplasia. RESULTS Fifty eight of 64 patients enrolled in the original trial were followed up including 31 patients treated with ALA PDT (17 patients with ≤6 cm, 14 patients with >6 cm segment of BE) and 27 treated with Photofrin PDT (14 patients with ≤6 cm, 13 patients with >6 cm BE). Initial success was achieved in 65% (20/31) ALA and 48% (13/27) Photofrin patients (p = .289). Thirty five percent patients (7/20) relapsed in ALA group and 54% (7/13) relapsed in Photofrin group (p = .472). At a median follow-up of 67 months, no significant difference was found in long-term complete reversal of intestinal metaplasia (CR-IM) and complete reversal of dysplasia (CR-D) between ALA and Photofrin groups (78% vs. 63%; p = .18; 90% vs. 76%; p = .26). Original length of BE did not alter long-term outcome. Four patients from each group progressed to invasive oesophageal adenocarcinoma. Initial success of ALA PDT was associated with significantly better likelihood of long-term remission (p = .03). CONCLUSIONS Initial response to PDT plays key role in long term outcome. RFA ± EMR have, however, become preferred minimally invasive ablative therapy for BE-related neoplasia due to poor efficacy of PDT.
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Affiliation(s)
- Darina Kohoutova
- a Division of Surgery & Interventional Science , University College London , London , UK.,b Division of GI Services , University College London Hospital , London , UK
| | - Rehan Haidry
- a Division of Surgery & Interventional Science , University College London , London , UK.,b Division of GI Services , University College London Hospital , London , UK
| | - Matthew Banks
- a Division of Surgery & Interventional Science , University College London , London , UK.,b Division of GI Services , University College London Hospital , London , UK
| | - Mohammed Adil Butt
- a Division of Surgery & Interventional Science , University College London , London , UK.,b Division of GI Services , University College London Hospital , London , UK
| | - Jason Dunn
- c Guy's and St Thomas' NHS Foundation Trust , London , UK
| | - Sally Thorpe
- b Division of GI Services , University College London Hospital , London , UK
| | - Laurence Lovat
- a Division of Surgery & Interventional Science , University College London , London , UK.,b Division of GI Services , University College London Hospital , London , UK
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Nwachokor J, Tawfik O, Danley M, Mathur S, House J, Sharma P, Christenson LK, Bansal A. Quantitation of spatial and temporal variability of biomarkers for Barrett's Esophagus. Dis Esophagus 2017; 30:1-8. [PMID: 28859356 PMCID: PMC6036660 DOI: 10.1093/dote/dox023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/07/2017] [Accepted: 03/03/2017] [Indexed: 12/11/2022]
Abstract
Chemoprevention and risk-stratification studies in Barrett's esophagus (BE) rely on biomarkers but the variability in their temporal and spatial expression is unknown. If such variability exists, it will impact sampling techniques and sample size calculations. Specimens from three levels of biopsies over two serial endoscopies in nondysplastic BE patients were analyzed for aneuploidy, proliferation markers (Ki67, Mcm2), and cell cycle markers (cyclin A and cyclin D1). A modification of the image cytometry technique, where cytokeratin staining automatically distinguished epithelial and stromal cells, measured aneuploidy on whole tissue sections. Other biomarkers were studied by immunohistochemistry. Coefficient of variability (SD/mean) was calculated; a value <10% indicated low variability. A total of 120 specimens (20 subjects each with three biopsy levels at two time points) from nondysplastic BE patients (71 ± 8.8 years, all Caucasian, 90% males, C5.1M7.5 ± 3.4 cm) were analyzed. The mean interval between endoscopies was 32.8 ± 8.4 months. Aneuploidy had a spatial variability of 6.8% at visit 1 (mean diploid index: 1.1 ± 0.09) and 7.9% at visit 2 (mean diploid index: 1.1 ± 0.06) and a temporal variability of 7.0-8.1% for the three levels. For other biomarkers, the spatial variability ranged from ∼5 to 30% at visit 1 and 11-92% at visit 2 and the temporal variability ranged from 0 to 77%. To conclude, of all the biomarkers, only aneuploidy had both spatial and temporal variability of <10%. Spatial and temporal variability were biomarker dependent and could be as high as 90% even without progression. These data will be useful to design chemoprevention and risk-stratification studies in BE.
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Affiliation(s)
| | - O. Tawfik
- Pathology and Laboratory Medicine, the University of Kansas School of Medicine,The Kansas Cancer Institute, Kansas City, KS
| | - M. Danley
- Pathology and Laboratory Medicine, the University of Kansas School of Medicine
| | - S. Mathur
- Pathology and Laboratory Medicine, the University of Kansas School of Medicine,Department of Pathology and Laboratory Medicine, the Veterans Affairs Medical Center
| | - J. House
- Department of Biostatistics, Saint Lukes Mid-America Heart Institute
| | - P. Sharma
- The Kansas Cancer Institute, Kansas City, KS,Department of Gastroenterology and Hepatology, the Veterans Affairs Medical Center, Kansas City, MO,Departments of Gastroenterology and Hepatology
| | - L. K. Christenson
- Molecular and Integrative Physiology, the University of Kansas Medical Center, Kansas City, KS
| | - A. Bansal
- The Kansas Cancer Institute, Kansas City, KS,Department of Gastroenterology and Hepatology, the Veterans Affairs Medical Center, Kansas City, MO,Departments of Gastroenterology and Hepatology
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10
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Alanazi H, Canul AJ, Garman A, Quimby J, Vasdekis AE. Robust microbial cell segmentation by optical-phase thresholding with minimal processing requirements. Cytometry A 2017; 91:443-449. [PMID: 28371011 PMCID: PMC6585648 DOI: 10.1002/cyto.a.23099] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
High-throughput imaging with single-cell resolution has enabled remarkable discoveries in cell physiology and Systems Biology investigations. A common, and often the most challenging step in all such imaging implementations, is the ability to segment multiple images to regions that correspond to individual cells. Here, a robust segmentation strategy for microbial cells using Quantitative Phase Imaging is reported. The proposed method enables a greater than 99% yeast cell segmentation success rate, without any computationally-intensive, post-acquisition processing. We also detail how the method can be expanded to bacterial cell segmentation with 98% success rates with substantially reduced processing requirements in comparison to existing methods. We attribute this improved performance to the remarkably uniform background, elimination of cell-to-cell and intracellular optical artifacts, and enhanced signal-to-background ratio-all innate properties of imaging in the optical-phase domain. © 2017 International Society for Advancement of Cytometry.
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Affiliation(s)
- H. Alanazi
- Department of PhysicsUniversity of IdahoMoscowIdaho83844
| | - A. J. Canul
- Department of PhysicsUniversity of IdahoMoscowIdaho83844
| | - A. Garman
- Department of PhysicsUniversity of IdahoMoscowIdaho83844
| | - J. Quimby
- Department of PhysicsUniversity of IdahoMoscowIdaho83844
| | - A. E. Vasdekis
- Department of PhysicsUniversity of IdahoMoscowIdaho83844
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11
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Abstract
In The Cancer Genome Atlas the goals were to define how to treat advanced cancers with targeted therapy. However, the challenges facing cancer interception for early detection and prevention include length bias in which current screening and surveillance approaches frequently miss rapidly progressing cancers that then present at advanced stages in the clinic with symptoms (underdiagnosis). In contrast, many early detection strategies detect benign conditions that may never progress to cancer during a lifetime, and the patient dies of unrelated causes (overdiagnosis). This challenge to cancer interception is believed to be due to the speed at which the neoplasm evolves, called length bias sampling; rapidly progressing cancers are missed by current early detection strategies. In contrast, slowly or non-progressing cancers or their precursors are selectively detected. This has led to the concept of cancer interception, which can be defined as active interception of a biological process that drives cancer development before the patient presents in the clinic with an advanced, symptomatic cancer. The solutions needed to advance strategies for cancer interception require assessing the rate at which the cancer evolves over time and space. This is an essential challenge that needs to be addressed by robust study designs including normal and non-progressing controls when known to be appropriate.
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Affiliation(s)
- Brian J. Reid
- Correspondence Address correspondence to: Brian J. Reid, MD, PhD, 1100 Fairview Avenue N, C1-157, PO Box 19024, Seattle, Washington 98109-1024. fax: (206) 667-6192.1100 Fairview Avenue N, C1-157, PO Box 19024SeattleWashington 98109-1024
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12
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Abstract
Gastric cancer (GC) is one of the most common malignant tumors, with high morbidity and mortality. Early detection, diagnosis and treatment are the key to improve the curative effect and prolong the survival of the patients. At present, tumor cell DNA detection technology has been used for the assistant diagnosis of a variety of common tumors and can improve the early detection rate of benign and malignant tumors. In the process of malignant transformation of cells, changes in genetic material such as DNA are earlier than the morphological changes of cells. Therefore, the DNA image cytometry of cells can be used to find early malignant cells with genetic material abnormalities. Being able to detect GC earlier, DNA image cytometry can increase the detection rate of early GC and improve the treatment and prognosis of patients.This article reviews the application of DNA image cytometry in the diagnosis of early GC.
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13
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Abstract
The article by Banerjee and colleagues published in this issue of the journal involving a randomized control prevention trial of ursodeoxycholic acid (UDCA) in Barrett esophagus reported a null outcome despite being well designed and executed. Possible reasons for this null outcome are discussed focusing on use of surrogate endpoints in the trial. The trial is especially topical because it comes at a time when there are calls for a Pre-Cancer Genome Atlas (PCGA) for "understanding the earliest molecular and cellular events associated with cancer initiation…" This commentary discusses current concepts in prevention research including branched evolution that leads to therapeutic resistance. Length bias sampling postulates underdiagnosis is due to rapidly progressing disease that is difficult to detect by screening because it progresses to cancer too rapidly and that overdiagnosis is the result of very slowly or nonprogressing disease that is easy to detect by screening because it persists for a lifetime and the patient dies of unrelated causes. Finally, it also explores study designs, including surrogate endpoints in Barrett esophagus trials, and opportunities and pitfalls for a PCGA in the context of high levels of over and underdiagnosis of Barrett esophagus as well as many other cancers and their precursors. Cancer Prev Res; 9(7); 512-7. ©2016 AACRSee related article by Banerjee, et al., p. 528.
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Affiliation(s)
- Brian J Reid
- Divisions of Human Biology and Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington. Departments of Genome Sciences and Medicine, University of Washington, Seattle, Washington.
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14
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Findlay JM, Middleton MR, Tomlinson I. Genetic Biomarkers of Barrett's Esophagus Susceptibility and Progression to Dysplasia and Cancer: A Systematic Review and Meta-Analysis. Dig Dis Sci 2016; 61:25-38. [PMID: 26445852 PMCID: PMC4700058 DOI: 10.1007/s10620-015-3884-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Accepted: 09/11/2015] [Indexed: 01/01/2023]
Abstract
Barrett's esophagus (BE) is a common and important precursor lesion of esophageal adenocarcinoma (EAC). A third of patients with BE are asymptomatic, and our ability to predict the risk of progression of metaplasia to dysplasia and EAC (and therefore guide management) is limited. There is an urgent need for clinically useful biomarkers of susceptibility to both BE and risk of subsequent progression. This study aims to systematically identify, review, and meta-analyze genetic biomarkers reported to predict both. A systematic review of the PubMed and EMBASE databases was performed in May 2014. Study and evidence quality were appraised using the revised American Society of Clinical Oncology guidelines, and modified Recommendations for Tumor Marker Scores. Meta-analysis was performed for all markers assessed by more than one study. A total of 251 full-text articles were reviewed; 52 were included. A total of 33 germline markers of susceptibility were identified (level of evidence II-III); 17 were included. Five somatic markers of progression were identified; meta-analysis demonstrated significant associations for chromosomal instability (level of evidence II). One somatic marker of progression/relapse following photodynamic therapy was identified. However, a number of failings of methodology and reporting were identified. This is the first systematic review and meta-analysis to evaluate genetic biomarkers of BE susceptibility and risk of progression. While a number of limitations of study quality temper the utility of those markers identified, some-in particular, those identified by genome-wide association studies, and chromosomal instability for progression-appear plausible, although robust validation is required.
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Affiliation(s)
- John M Findlay
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK.
- Oxford OesophagoGastric Centre, Churchill Hospital, Oxford University Hospitals NHS Foundation trust, Oxford, OX3 7LJ, UK.
- NIHR Oxford Biomedical Research Centre, The Joint Research Office, Churchill Hospital, Oxford, OX3 7LE, UK.
| | - Mark R Middleton
- NIHR Oxford Biomedical Research Centre, The Joint Research Office, Churchill Hospital, Oxford, OX3 7LE, UK
- Department of Oncology, Old Road Campus Research Building, University of Oxford, Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - Ian Tomlinson
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
- NIHR Oxford Biomedical Research Centre, The Joint Research Office, Churchill Hospital, Oxford, OX3 7LE, UK
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15
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Revisiting tumour aneuploidy - the place of ploidy assessment in the molecular era. Nat Rev Clin Oncol 2015; 13:291-304. [PMID: 26598944 DOI: 10.1038/nrclinonc.2015.208] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Chromosome instability (CIN) is gaining increasing interest as a central process in cancer. CIN, either past or present, is indicated whenever tumour cells harbour an abnormal quantity of DNA, termed 'aneuploidy'. At present, the most widely used approach to detecting aneuploidy is DNA cytometry - a well-known research assay that involves staining of DNA in the nuclei of cells from a tissue sample, followed by analysis using quantitative flow cytometry or microscopic imaging. Aneuploidy in cancer tissue has been implicated as a predictor of a poor prognosis. In this Review, we have explored this hypothesis by surveying the current landscape of peer-reviewed research in which DNA cytometry has been applied in studies with disease-appropriate clinical follow up. This area of research is broad, however, and we restricted our survey to results published since 2000 relating to seven common epithelial cancers (those of the breast; endometrium, ovary, and uterine cervix; oesophagus; colon and rectum; lung; prostate; and bladder). We placed particular emphasis on results from multivariate analyses to pinpoint situations in which the prognostic value of aneuploidy as a biomarker is strong compared with that of existing indicators, such as clinical stage, histological grade, and specific molecular markers. We summarize the implications of our findings for the prognostic use of ploidy analysis in the clinic and for the theoretical understanding of the role of CIN in carcinogenesis.
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16
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di Pietro M, Bird-Lieberman EL, Liu X, Nuckcheddy-Grant T, Bertani H, O'Donovan M, Fitzgerald RC. Autofluorescence-Directed Confocal Endomicroscopy in Combination With a Three-Biomarker Panel Can Inform Management Decisions in Barrett's Esophagus. Am J Gastroenterol 2015; 110:1549-58. [PMID: 26416188 DOI: 10.1038/ajg.2015.295] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Accepted: 07/16/2015] [Indexed: 02/08/2023]
Abstract
OBJECTIVES Barrett's esophagus (BE) surveillance with white-light endoscopy and quadrantic biopsies (Seattle protocol) is resource intensive and limited by sampling error. Previous work suggests that autofluorescence imaging (AFI) in combination with a molecular panel might reduce the number of biopsies, but this was not sufficiently sensitive for low-grade dysplasia, now a point for endoscopic intervention. Here we used AFI to direct narrow-field imaging tools for real-time optical assessment of dysplasia and biopsies for a biomarker panel. We compared the new diagnostic algorithm with the current standard. METHODS A total of 55 patients with BE were recruited at a single tertiary referral center. Patients underwent high-resolution endoscopy followed by AFI. AFI-targeted areas (n=194) were examined in turn by narrow-band imaging with magnification (NBIz) and probe-based confocal laser endomicroscopy (pCLE). Biopsies were taken from AFI-targeted areas and tested using an established molecular panel comprising aneuploidy plus cyclin A and p53 immunohistochemistry. RESULTS In the per-patient analysis the overall sensitivity and specificity of AFI-targeted pCLE were 100% and 53.6% for high-grade dysplasia/intramucosal cancer and 96.4% and 74.1% for any grade of dysplasia, respectively. NBIz had equal specificity for dysplasia detection (74.1%), but significantly lower sensitivity (57.1%) than pCLE. The time required to perform AFI-targeted pCLE was shorter that that taken by the Seattle protocol (P=0.0004). We found enrichment of molecular abnormalities in areas with optical dysplasia by pCLE (P<0.001), regardless of histologic dysplasia. The addition of the 3-biomarker panel reduced the false positive rate of pCLE by 50%, leading to sensitivity and specificity for any grade of dysplasia of 89.2% and 88.9%, respectively. CONCLUSIONS The combination of pCLE on AFI-targeted areas and a 3-biomarker panel identifies patients with dysplasia.
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Affiliation(s)
| | - Elizabeth L Bird-Lieberman
- MRC Cancer Unit, University of Cambridge, Cambridge, UK.,Translational Gastroenterology Unit, Experimental Medicine Division, John Radcliffe Hospital, Oxford, UK
| | - Xinxue Liu
- MRC Cancer Unit, University of Cambridge, Cambridge, UK
| | | | - Helga Bertani
- Department of Digestive Endoscopy, Nuovo Ospedale Civile S. Agostino, Modena, Italy
| | - Maria O'Donovan
- Department of Histopathology, Cambridge University Hospitals, Cambridge, UK
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17
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Wang Y, McManus DT, Arthur K, Johnston BT, Kennedy AJ, Coleman HG, Murray LJ, Hamilton PW. Whole slide image cytometry: a novel method to detect abnormal DNA content in Barrett's esophagus. J Transl Med 2015; 95:1319-30. [PMID: 26237272 DOI: 10.1038/labinvest.2015.98] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Revised: 06/12/2015] [Accepted: 06/15/2015] [Indexed: 12/20/2022] Open
Abstract
Barrett's esophagus (BE) is a precursor of esophageal adenocarcinoma (EAC). Both low-grade dysplasia (LGD) and high-grade dysplasia (HGD) are associated with an increased risk of progression to EAC. However, histological interpretation and grading of dysplasia (particularly LGD) is subjective and poorly reproducible. This study has combined whole slide imaging with DNA image cytometry to provide a novel method for the detection of abnormal DNA content through image analysis of tissue sections. A total of 20 cases were evaluated, including 8 negative for dysplasia (NFD), 6 LGD, and 6 HGD. Feulgen-stained esophageal sections were scanned in their entirety. Barrett's mucosa was interactively chosen for automatic nuclei segmentation where irrelevant cell types were ignored. The combined DNA content histogram for all nuclei within selected image regions was then obtained. In addition, three histogram measurements were computed, including xER-5C, 2cDI, and DNA-MG. Visual evaluation suggested the shape of DNA content histograms from NFD, LGD, and HGD cases exhibiting identifiable differences. The histogram measurements, xER-5C, 2cDI, and DNA-MG, were shown to be effective in differentiating metaplastic from dysplastic cases with statistical significance. Moreover, they also successfully separated NFD, LGD, and HGD patients with statistical significance. Whole slide image cytometry is a novel and effective method for the detection of abnormal DNA content in BE. Compared with histological review, it is more objective. Compared with flow cytometry and cytology-preparation image cytometry, it is low cost, simple to use, only requires a single 1 μm section, and facilitates selection of tissue and topographical correlation. Whole slide image cytometry can detect differences in DNA content between NFD, LGD, and HGD patients in this cross-sectional study. Abnormal DNA content detection by whole slide image cytometry is a promising biomarker of progression that could affect future diagnostics in BE.
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Affiliation(s)
- Yinhai Wang
- Finland Institute for Molecular Medicine (FIMM), University of Helsinki, Helsinki, Finland
| | - Damian T McManus
- Belfast HSC Trust, Belfast, UK
- Centre for Cancer Research and Cell Biology (CCRCB), Queen's University Belfast, Belfast, UK
| | - Kenneth Arthur
- Centre for Cancer Research and Cell Biology (CCRCB), Queen's University Belfast, Belfast, UK
| | | | | | - Helen G Coleman
- Centre for Public Health, Queen's University Belfast, Belfast, UK
| | - Liam J Murray
- Centre for Public Health, Queen's University Belfast, Belfast, UK
| | - Peter W Hamilton
- Centre for Cancer Research and Cell Biology (CCRCB), Queen's University Belfast, Belfast, UK
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18
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Abstract
Beginning in the 1980s, an alarming rise in the incidence of esophageal adenocarcinoma (EA) led to screening of patients with reflux to detect Barrett's esophagus (BE) and surveillance of BE to detect early EA. This strategy, based on linear progression disease models, resulted in selective detection of BE that does not progress to EA over a lifetime (overdiagnosis) and missed BE that rapidly progresses to EA (underdiagnosis). Here we review the historical thought processes that resulted in this undesired outcome and the transformation in our understanding of genetic and evolutionary principles governing neoplastic progression that has come from application of modern genomic technologies to cancers and their precursors. This new synthesis provides improved strategies for prevention and early detection of EA by addressing the environmental and mutational processes that can determine "windows of opportunity" in time to detect rapidly progressing BE and distinguish it from slowly or nonprogressing BE.
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Affiliation(s)
- Brian J. Reid
- Division of Human Biology, FredHutch, Seattle WA,Division of Public Health Sciences, FredHutch, Seattle WA,Department of Genome Sciences, University of Washington,Department of Medicine, University of Washington,Corresponding author Brian J. Reid, M.D., Ph.D. 1100 Fairview Ave N., C1-157 P.O. Box 19024 Seattle, WA 98109-1024 206-667-4073 (phone) 206-667-6192 (FAX)
| | | | - Xiaohong Li
- Division of Human Biology, FredHutch, Seattle WA
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19
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El Hallani S, Guillaud M, Korbelik J, Marginean EC. Evaluation of Quantitative Digital Pathology in the Assessment of Barrett Esophagus-Associated Dysplasia. Am J Clin Pathol 2015; 144:151-64. [PMID: 26071473 DOI: 10.1309/ajcpk0y1mmfsjdku] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
OBJECTIVES Barrett esophagus (BE) is a precursor lesion that confers an increased risk of esophageal adenocarcinoma. Two issues confront the diagnosis of patients with BE: (1) sampling error at the time of endoscopy and (2) variability among pathologists in grading dysplasia. The purpose of our study was to evaluate quantitative digital pathology (QDP) as a marker of dysplasia and stratification from low-grade to high-grade dysplasia to intramucosal adenocarcinoma in BE. METHODS Sixty-one esophageal biopsy specimens with BE were selected and divided into six groups according to the dysplasia grade. QDP image analysis was carried out by an in-house automated quantitative system on sections. The values of 110 nuclear features that analyze the morphology and chromatin texture were generated for each nucleus. RESULTS A progressive correlation was found between nuclear morphometric features and chromatin features with BE dysplasia. The chromatin texture was the best discriminator of the class diagnosis. There was a significant difference between the chromatin features of isolated low-grade dysplasia vs low-grade dysplasia that was associated with higher grade lesions in other biopsy tissue fragments. CONCLUSIONS QDP is a promising tool in the new era of digital pathology. Pending clinical validation studies, analysis of chromatin texture could contribute to the differential diagnosis of BE class and the detection of concomitant high-grade lesions if not sampled.
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20
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Bansal A, Fitzgerald RC. Biomarkers in Barrett's Esophagus: Role in Diagnosis, Risk Stratification, and Prediction of Response to Therapy. Gastroenterol Clin North Am 2015; 44:373-90. [PMID: 26021200 DOI: 10.1016/j.gtc.2015.02.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Esophageal adenocarcinoma (EAC) has increased dramatically in the past 3 decades, making its precursor lesion Barrett's esophagus (BE) an important clinical problem. Effective interventions are available, but overall outcomes remain unchanged. Most of the BE population remains undiagnosed; most EACs are diagnosed late, and most BE patients will never progress to cancer. These epidemiologic factors make upper endoscopy an inefficient and ineffective strategy for BE diagnosis and risk stratification. In the current review, biomarkers for diagnosis, risk stratification, and predictors of response to therapy in BE are discussed.
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Affiliation(s)
- Ajay Bansal
- Division of Gastroenterology and Hepatology, Department of Veterans Affairs Medical Center and the University of Kansas Medical Center, 4801 East Linwood Boulevard, Kansas City, MO 64128-2295, USA.
| | - Rebecca C Fitzgerald
- MRC Cancer Unit, Hutchison-MRC Research Centre, University of Cambridge, Hills Road, Cambridge CB2 0XZ, UK
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21
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di Pietro M, Boerwinkel DF, Shariff MK, Liu X, Telakis E, Lao-Sirieix P, Walker E, Couch G, Mills L, Nuckcheddy-Grant T, Slininger S, O'Donovan M, Visser M, Meijer SL, Kaye PV, Wernisch L, Ragunath K, Bergman JJGHM, Fitzgerald RC. The combination of autofluorescence endoscopy and molecular biomarkers is a novel diagnostic tool for dysplasia in Barrett's oesophagus. Gut 2015; 64:49-56. [PMID: 24721904 PMCID: PMC4283667 DOI: 10.1136/gutjnl-2013-305975] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
OBJECTIVE Endoscopic surveillance for Barrett's oesophagus (BO) is limited by sampling error and the subjectivity of diagnosing dysplasia. We aimed to compare a biomarker panel on minimal biopsies directed by autofluorescence imaging (AFI) with the standard surveillance protocol to derive an objective tool for dysplasia assessment. DESIGN We performed a cross-sectional prospective study in three tertiary referral centres. Patients with BO underwent high-resolution endoscopy followed by AFI-targeted biopsies. 157 patients completed the biopsy protocol. Aneuploidy/tetraploidy; 9p and 17p loss of heterozygosity; RUNX3, HPP1 and p16 methylation; p53 and cyclin A immunohistochemistry were assessed. Bootstrap resampling was used to select the best diagnostic biomarker panel for high-grade dysplasia (HGD) and early cancer (EC). This panel was validated in an independent cohort of 46 patients. RESULTS Aneuploidy, p53 immunohistochemistry and cyclin A had the strongest association with dysplasia in the per-biopsy analysis and, as a panel, had an area under the receiver operating characteristic curve of 0.97 (95% CI 0.95 to 0.99) for diagnosing HGD/EC. The diagnostic accuracy for HGD/EC of the three-biomarker panel from AFI+ areas was superior to AFI- areas (p<0.001). Compared with the standard protocol, this panel had equal sensitivity for HGD/EC, with a 4.5-fold reduction in the number of biopsies. In an independent cohort of patients, the panel had a sensitivity and specificity for HGD/EC of 100% and 85%, respectively. CONCLUSIONS A three-biomarker panel on a small number of AFI-targeted biopsies provides an accurate and objective diagnosis of dysplasia in BO. The clinical implications have to be studied further.
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Affiliation(s)
| | - David F Boerwinkel
- Department of Gastroenterology, Academic Medical Centre, Amsterdam, The Netherlands
| | | | - Xinxue Liu
- Medical Research Council, Cancer Unit, University of Cambridge, Cambridge, UK
| | | | - Pierre Lao-Sirieix
- Medical Research Council, Cancer Unit, University of Cambridge, Cambridge, UK
| | - Elaine Walker
- Medical Research Council, Cancer Unit, University of Cambridge, Cambridge, UK
| | - George Couch
- Medical Research Council, Cancer Unit, University of Cambridge, Cambridge, UK
| | - Leanne Mills
- Medical Research Council, Cancer Unit, University of Cambridge, Cambridge, UK
| | | | - Susan Slininger
- Digestive Disease Centre, NIHR Biomedical Research Unit, Nottingham University Hospitals NHS trust, Nottingham, UK
| | - Maria O'Donovan
- Medical Research Council, Cancer Unit, University of Cambridge, Cambridge, UK
| | - Mike Visser
- Department of Pathology, Academic Medical Center, Amsterdam, The Netherlands
| | - Sybren L Meijer
- Department of Pathology, Academic Medical Center, Amsterdam, The Netherlands
| | - Philip V Kaye
- Department of Pathology, Nottingham University Hospitals NHS Trust, Nottingham, UK
| | | | - Krish Ragunath
- Digestive Disease Centre, NIHR Biomedical Research Unit, Nottingham University Hospitals NHS trust, Nottingham, UK
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22
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Timmer MR, Brankley SM, Gorospe EC, Sun G, Lutzke LS, Iyer PG, Halling KC, Krishnadath KK, Wang KK. Prediction of response to endoscopic therapy of Barrett's dysplasia by using genetic biomarkers. Gastrointest Endosc 2014; 80:984-91. [PMID: 25085335 PMCID: PMC4311726 DOI: 10.1016/j.gie.2014.06.023] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Accepted: 06/04/2014] [Indexed: 02/06/2023]
Abstract
BACKGROUND Endoscopic therapy for the treatment of high-grade dysplasia (HGD) and intramucosal cancer (IMC) in Barrett's esophagus (BE) may not always result in complete remission of dysplasia (CRD). OBJECTIVE To determine whether genetic alterations in the Barrett's mucosa can predict response to endoscopic therapy. DESIGN Retrospective cohort study. SETTING Tertiary-care institution. PATIENTS Selected patients who underwent endoscopic therapy for BE containing HGD/IMC between 2003 and 2010. INTERVENTIONS Endoscopic therapy combining mucosal resection and different ablation modalities was performed based on patient characteristics, endoscopic findings, and technique evolution. Fluorescence in situ hybridization was used to evaluate genetic alterations on baseline endoscopic cytology brushings by using probes directed to loci 8q24 (MYC), 9p21 (CDKN2A; alias P16), 17q12 (ERBB2; alias Her-2/neu), and 20q13.2 (ZNF217). MAIN OUTCOME MEASUREMENTS Genetic biomarkers predicting achievement of CRD after endoscopic therapy. RESULTS A total of 181 patients were included (145 men; 66 ± 10 years of age). There were 130 patients (72%) who responded to endoscopic therapy with CRD. Multiple gains detected by fluorescence in situ hybridization was found to be a negative predictor (hazard ratio 0.57; 95% confidence interval, 0.40-0.82) after adjusting for potential clinical confounders. Similar results were found when analyses were restricted to patients (n = 66) undergoing radiofrequency ablation (hazard ratio 0.58; 95% confidence interval, 0.31-1.09). LIMITATIONS Retrospective study, heterogeneity of treatment modalities. CONCLUSION Patients with multiple gains detected by brush cytology specimens may have a lower response rate to endoscopic therapy. The presence of multiple gains can be an adjunct to standard histology in prognosticating BE patients with HGD/IMC undergoing endoscopic therapy.
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Affiliation(s)
- Margriet R. Timmer
- Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First Street SW, Rochester, Minnesota 55905, United States,Department of Gastroenterology and Hepatology, Academic Medical Center, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
| | - Shannon M. Brankley
- Department of Laboratory Medicine, Mayo Clinic, 200 First Street SW Rochester, Minnesota 55905, United States
| | - Emmanuel C. Gorospe
- Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First Street SW, Rochester, Minnesota 55905, United States
| | - Gang Sun
- Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First Street SW, Rochester, Minnesota 55905, United States
| | - Lori S. Lutzke
- Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First Street SW, Rochester, Minnesota 55905, United States
| | - Prasad G. Iyer
- Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First Street SW, Rochester, Minnesota 55905, United States
| | - Kevin C. Halling
- Department of Laboratory Medicine, Mayo Clinic, 200 First Street SW Rochester, Minnesota 55905, United States
| | - Kausilia K. Krishnadath
- Department of Gastroenterology and Hepatology, Academic Medical Center, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
| | - Kenneth K. Wang
- Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First Street SW, Rochester, Minnesota 55905, United States
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Fouad YM, Mostafa I, Yehia R, El-Khayat H. Biomarkers of Barrett's esophagus. World J Gastrointest Pathophysiol 2014; 5:450-456. [PMID: 25400988 PMCID: PMC4231509 DOI: 10.4291/wjgp.v5.i4.450] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/28/2013] [Revised: 07/02/2014] [Accepted: 07/17/2014] [Indexed: 02/06/2023] Open
Abstract
Barrett’s esophagus is the strongest risk for esophageal adenocarcinoma (EAC). Metaplasia in patients with BE may progress to dysplasia and then invasive carcinoma. Well-defined diagnostic, progressive, predictive, and prognostic biomarkers are needed to identify the presence of the disease, estimate the risk of malignant transformation, and predict the therapeutic outcome and survival of EAC patients. There are many predictive and prognostic markers that lack substantial validation, and do not allow stratification of patients with gastroesophageal reflux disease in clinical practice for outcome and effectiveness of therapy. In this short review we summarize the current knowledge regarding possible biomarkers, focusing on the pathophysiologic mechanisms to improve prognostic and therapeutic approaches.
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24
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Hamilton PW, Bankhead P, Wang Y, Hutchinson R, Kieran D, McArt DG, James J, Salto-Tellez M. Digital pathology and image analysis in tissue biomarker research. Methods 2014; 70:59-73. [PMID: 25034370 DOI: 10.1016/j.ymeth.2014.06.015] [Citation(s) in RCA: 124] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Revised: 06/26/2014] [Accepted: 06/27/2014] [Indexed: 12/14/2022] Open
Abstract
Digital pathology and the adoption of image analysis have grown rapidly in the last few years. This is largely due to the implementation of whole slide scanning, advances in software and computer processing capacity and the increasing importance of tissue-based research for biomarker discovery and stratified medicine. This review sets out the key application areas for digital pathology and image analysis, with a particular focus on research and biomarker discovery. A variety of image analysis applications are reviewed including nuclear morphometry and tissue architecture analysis, but with emphasis on immunohistochemistry and fluorescence analysis of tissue biomarkers. Digital pathology and image analysis have important roles across the drug/companion diagnostic development pipeline including biobanking, molecular pathology, tissue microarray analysis, molecular profiling of tissue and these important developments are reviewed. Underpinning all of these important developments is the need for high quality tissue samples and the impact of pre-analytical variables on tissue research is discussed. This requirement is combined with practical advice on setting up and running a digital pathology laboratory. Finally, we discuss the need to integrate digital image analysis data with epidemiological, clinical and genomic data in order to fully understand the relationship between genotype and phenotype and to drive discovery and the delivery of personalized medicine.
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Affiliation(s)
- Peter W Hamilton
- Centre for Cancer Research & Cell Biology, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7BL, Northern Ireland, United Kingdom.
| | - Peter Bankhead
- Centre for Cancer Research & Cell Biology, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7BL, Northern Ireland, United Kingdom
| | - Yinhai Wang
- Centre for Cancer Research & Cell Biology, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7BL, Northern Ireland, United Kingdom
| | - Ryan Hutchinson
- Centre for Cancer Research & Cell Biology, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7BL, Northern Ireland, United Kingdom
| | - Declan Kieran
- Centre for Cancer Research & Cell Biology, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7BL, Northern Ireland, United Kingdom
| | - Darragh G McArt
- Centre for Cancer Research & Cell Biology, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7BL, Northern Ireland, United Kingdom
| | - Jacqueline James
- Centre for Cancer Research & Cell Biology, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7BL, Northern Ireland, United Kingdom
| | - Manuel Salto-Tellez
- Centre for Cancer Research & Cell Biology, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7BL, Northern Ireland, United Kingdom
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25
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di Pietro M, Alzoubaidi D, Fitzgerald RC. Barrett's esophagus and cancer risk: how research advances can impact clinical practice. Gut Liver 2014; 8:356-70. [PMID: 25071900 PMCID: PMC4113043 DOI: 10.5009/gnl.2014.8.4.356] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Accepted: 04/15/2014] [Indexed: 12/18/2022] Open
Abstract
Barrett’s esophagus (BE) is the only known precursor to esophageal adenocarcinoma (EAC), whose incidence has increased sharply in the last 4 decades. The annual conversion rate of BE to cancer is significant, but small. The identification of patients at a higher risk of cancer therefore poses a clinical conundrum. Currently, endoscopic surveillance is recommended in BE patients, with the aim of diagnosing either dysplasia or cancer at early stages, both of which are curable with minimally invasive endoscopic techniques. There is a large variation in clinical practice for endoscopic surveillance, and dysplasia as a marker of increased risk is affected by sampling error and high interobserver variability. Screening programs have not yet been formally accepted, mainly due to the economic burden that would be generated by upper gastrointestinal endoscopy. Screening programs have not yet been formally accepted, mainly due to the economic burden that would be generated by widespread indication to upper gastrointestinal endoscopy. In fact, it is currently difficult to formulate an accurate algorithm to confidently target the population at risk, based on the known clinical risk factors for BE and EAC. This review will focus on the clinical and molecular factors that are involved in the development of BE and its conversion to cancer and on how increased knowledge in these areas can improve the clinical management of the disease.
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Affiliation(s)
| | - Durayd Alzoubaidi
- Department of Gastroenterology, Basildon and Thurrock University Hospital, Basildon, UK
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26
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Agarwal N, Biancardi AM, Patten FW, Reeves AP, Seibel EJ. Three-dimensional DNA image cytometry by optical projection tomographic microscopy for early cancer diagnosis. J Med Imaging (Bellingham) 2014; 1:017501. [PMID: 26158032 DOI: 10.1117/1.jmi.1.1.017501] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2014] [Revised: 04/18/2014] [Accepted: 05/20/2014] [Indexed: 12/29/2022] Open
Abstract
Aneuploidy is typically assessed by flow cytometry (FCM) and image cytometry (ICM). We used optical projection tomographic microscopy (OPTM) for assessing cellular DNA content using absorption and fluorescence stains. OPTM combines some of the attributes of both FCM and ICM and generates isometric high-resolution three-dimensional (3-D) images of single cells. Although the depth of field of the microscope objective was in the submicron range, it was extended by scanning the objective's focal plane. The extended depth of field image is similar to a projection in a conventional x-ray computed tomography. These projections were later reconstructed using computed tomography methods to form a 3-D image. We also present an automated method for 3-D nuclear segmentation. Nuclei of chicken, trout, and triploid trout erythrocyte were used to calibrate OPTM. Ratios of integrated optical densities extracted from 50 images of each standard were compared to ratios of DNA indices from FCM. A comparison of mean square errors with thionin, hematoxylin, Feulgen, and SYTOX green was done. Feulgen technique was preferred as it showed highest stoichiometry, least variance, and preserved nuclear morphology in 3-D. The addition of this quantitative biomarker could further strengthen existing classifiers and improve early diagnosis of cancer using 3-D microscopy.
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Affiliation(s)
- Nitin Agarwal
- University of Washington , Human Photonics Laboratory, Department of Bioengineering, 204 Fluke Hall, Seattle, Washington 98195
| | - Alberto M Biancardi
- Cornell University , Vision & Image Analysis Group, School of Electrical and Computer Engineering, 392 Rhodes Hall, Ithaca, New York 14850
| | | | - Anthony P Reeves
- Cornell University , Vision & Image Analysis Group, School of Electrical and Computer Engineering, 392 Rhodes Hall, Ithaca, New York 14850
| | - Eric J Seibel
- University of Washington , Human Photonics Laboratory, Department of Mechanical Engineering, P.O. Box 352600, Seattle, Washington 98195
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Weaver JMJ, Ross-Innes CS, Fitzgerald RC. The '-omics' revolution and oesophageal adenocarcinoma. Nat Rev Gastroenterol Hepatol 2014; 11:19-27. [PMID: 23982683 DOI: 10.1038/nrgastro.2013.150] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Oesophageal adenocarcinoma (OAC) is the eighth most common cancer type worldwide with a dismal 5-year survival. Barrett oesophagus, the replacement of the normal squamous epithelia with glandular cells, is the first step in the pathway towards OAC. Although most patients with OAC present de novo, the presence of the easily detectable OAC precursor lesion, Barrett oesophagus, enables the possibility of early detection of high-risk patients who are more likely to progress. Currently, identification of high-risk patients depends on histopathological assessment of dysplasia with no regards to molecular pathogenesis. In the future, screening and risk stratification initiatives for Barrett oesophagus that incorporate molecular profiles might permit improved early diagnosis and intervention strategies with the possibility of preventing OAC. For the majority of patients presenting de novo at an advanced stage, combining so-called -omics datasets with current clinical staging algorithms might enable OACs to be better classified according to distinct molecular programmes, thereby leading to better targeted treatment strategies as well as cancer monitoring regimes. This Review discusses how the latest advances in -omics technologies have improved our understanding of the development and biology of OAC, and how this development might alter patient management in the future.
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Affiliation(s)
- Jamie M J Weaver
- MRC Cancer Cell Unit, Hutchison/MRC Research Centre, Hills Road, Cambridge CB2 0XZ, UK
| | - Caryn S Ross-Innes
- MRC Cancer Cell Unit, Hutchison/MRC Research Centre, Hills Road, Cambridge CB2 0XZ, UK
| | - Rebecca C Fitzgerald
- MRC Cancer Cell Unit, Hutchison/MRC Research Centre, Hills Road, Cambridge CB2 0XZ, UK
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GERD-Barrett-Adenocarcinoma: Do We Have Suitable Prognostic and Predictive Molecular Markers? Gastroenterol Res Pract 2013; 2013:643084. [PMID: 23573078 PMCID: PMC3615572 DOI: 10.1155/2013/643084] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/21/2013] [Accepted: 02/18/2013] [Indexed: 02/07/2023] Open
Abstract
Due to unfavorable lifestyle habits (unhealthy diet and tobacco abuse) the incidence of gastroesophageal reflux disease (GERD) in western countries is increasing. The GERD-Barrett-Adenocarcinoma sequence currently lacks well-defined diagnostic, progressive, predictive, and prognostic biomarkers (i) providing an appropriate screening method identifying the presence of the disease, (ii) estimating the risk of evolving cancer, that is, the progression from Barrett's esophagus (BE) to esophageal adenocarcinoma (EAC), (iii) predicting the response to therapy, and (iv) indicating an overall survival—prognosis for EAC patients. Based on histomorphological findings, detailed screening and therapeutic guidelines have been elaborated, although epidemiological studies could not support the postulated increasing progression rates of GERD to BE and EAC. Additionally, proposed predictive and prognostic markers are rather heterogeneous by nature, lack substantial proofs, and currently do not allow stratification of GERD patients for progression, outcome, and therapeutic effectiveness in clinical practice. The aim of this paper is to discuss the current knowledge regarding the GERD-BE-EAC sequence mainly focusing on the disputable and ambiguous status of proposed biomarkers to identify promising and reliable markers in order to provide more detailed insights into pathophysiological mechanisms and thus to improve prognostic and predictive therapeutic approaches.
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di Pietro M, Fitzgerald RC. Screening and risk stratification for Barrett's esophagus: how to limit the clinical impact of the increasing incidence of esophageal adenocarcinoma. Gastroenterol Clin North Am 2013; 42:155-73. [PMID: 23452636 DOI: 10.1016/j.gtc.2012.11.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Barrett's esophagus (BE) and gastroesophageal reflux disease are the strongest risk factors for esophageal adenocarcinoma. To reduce the clinical impact of this disease, endoscopic screening to detect BE has been proposed and nonendoscopic diagnostic techniques are under investigation. Because screening would result in new diagnoses of BE and additional costs related to endoscopic surveillance, novel tools for risk stratification are also warranted. Dysplasia is the gold standard for risk stratification. Molecular biomarkers may provide a more objective and reproducible estimation of the individual risk, and further prospective studies are required as a prelude to introducing biomarkers into routine clinical practice.
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Bird-Lieberman EL, Dunn JM, Coleman HG, Lao-Sirieix P, Oukrif D, Moore CE, Varghese S, Johnston BT, Arthur K, McManus DT, Novelli MR, O'Donovan M, Cardwell CR, Lovat LB, Murray LJ, Fitzgerald RC. Population-based study reveals new risk-stratification biomarker panel for Barrett's esophagus. Gastroenterology 2012; 143:927-35.e3. [PMID: 22771507 DOI: 10.1053/j.gastro.2012.06.041] [Citation(s) in RCA: 134] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2012] [Revised: 06/20/2012] [Accepted: 06/22/2012] [Indexed: 12/17/2022]
Abstract
BACKGROUND & AIMS The risk of progression of Barrett's esophagus (BE) to esophageal adenocarcinoma (EAC) is low and difficult to calculate. Accurate tools to determine risk are needed to optimize surveillance and intervention. We assessed the ability of candidate biomarkers to predict which cases of BE will progress to EAC or high-grade dysplasia and identified those that can be measured in formalin-fixed tissues. METHODS We analyzed data from a nested case-control study performed using the population-based Northern Ireland BE Register (1993-2005). Cases who progressed to EAC (n = 89) or high-grade dysplasia ≥ 6 months after diagnosis with BE were matched to controls (nonprogressors, n = 291), for age, sex, and year of BE diagnosis. Established biomarkers (abnormal DNA content, p53, and cyclin A expression) and new biomarkers (levels of sialyl Lewis(a), Lewis(x), and Aspergillus oryzae lectin [AOL] and binding of wheat germ agglutinin) were assessed in paraffin-embedded tissue samples from patients with a first diagnosis of BE. Conditional logistic regression analysis was applied to assess odds of progression for patients with dysplastic and nondysplastic BE, based on biomarker status. RESULTS Low-grade dysplasia and all biomarkers tested, other than Lewis(x), were associated with risk of EAC or high-grade dysplasia. In backward selection, a panel comprising low-grade dysplasia, abnormal DNA ploidy, and AOL most accurately identified progressors and nonprogressors. The adjusted odds ratio for progression of patients with BE with low-grade dysplasia was 3.74 (95% confidence interval, 2.43-5.79) for each additional biomarker and the risk increased by 2.99 for each additional factor (95% confidence interval, 1.72-5.20) in patients without dysplasia. CONCLUSIONS Low-grade dysplasia, abnormal DNA ploidy, and AOL can be used to identify patients with BE most likely to develop EAC or high-grade dysplasia.
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Varghese S, Lao-Sirieix P, Fitzgerald RC. Identification and clinical implementation of biomarkers for Barrett's esophagus. Gastroenterology 2012; 142:435-441.e2. [PMID: 22266150 DOI: 10.1053/j.gastro.2012.01.013] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Sibu Varghese
- MRC Cancer Cell Unit, Hutchison-MRC Research Centre, Cambridge, UK
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Comparison of nuclear texture analysis and image cytometric DNA analysis for the assessment of dysplasia in Barrett's oesophagus. Br J Cancer 2011; 105:1218-23. [PMID: 21934680 PMCID: PMC3208493 DOI: 10.1038/bjc.2011.353] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Background: Dysplasia is a marker of cancer risk in Barrett's oesophagus (BO), but this risk is variable and diagnosis is subject to inter-observer variability. Cancer risk in BO is increased when chromosomal instability is present. Nucleotyping (NT) is a new method that uses high-resolution digital images of nuclei to assess chromatin organisation both quantitatively and qualitatively. We aimed to evaluate NT as a marker of dysplasia in BO and compare with image cytometric DNA analysis (ICM). Methods: In all, 120 patients with BO were studied. The non-dysplastic group (n=60) had specialised intestinal metaplasia only on two consecutive endoscopies after 51 months median follow-up (IQR=25–120 months). The dysplastic group (n=60) had high-grade dysplasia or carcinoma in situ. The two groups were then randomly assigned to a training set and a blinded test set in a 1 : 1 ratio. Image cytometric DNA analysis and NT was then carried out on Feulgen-stained nuclear monolayers. Results: The best-fit model for NT gave a correct classification rate (CCR) for the training set of 83%. The test set was then analysed using the same textural features and yielded a CCR of 78%. Image cytometric DNA analysis alone yielded a CCR of 73%. The combination of ICM and NT yielded a CCR of 84%. Conclusion: Nucleotyping differentiates dysplastic and non-dysplastic BO, with a greater sensitivity than ICM. A combination score based on both techniques performed better than either test in isolation. These data demonstrate that NT/ICM on nuclear monolayers is a very promising single platform test of genomic instability, which may aid pathologists in the diagnosis of dysplasia and has potential as a biomarker in BO.
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Abstract
Barrett's esophagus is an acquired metaplastic abnormality in which the normal stratified squamous epithelium lining of the esophagus is replaced by an intestinal-like columnar epithelium. While in itself a benign and asymptomatic disorder, the clinical importance of this relatively common condition relates to its role as a precursor lesion to esophageal adenocarcinoma, the incidence of which has dramatically increased in Western populations in recent years. Although known to arise as a consequence of chronic gastroesophageal reflux, the cellular and molecular mechanisms underlying development Barrett's esophagus and its progression to cancer remain unclear.
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Affiliation(s)
- Wayne A Phillips
- Division of Cancer Surgery, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.
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