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Martínez-Domínguez SJ, Lanas Á, Domper-Arnal MJ. Esófago de Barrett, hacia la mejora de la práctica clínica. Med Clin (Barc) 2022; 159:92-100. [DOI: 10.1016/j.medcli.2022.02.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 02/07/2022] [Accepted: 02/08/2022] [Indexed: 02/07/2023]
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Paulson TG, Galipeau PC, Oman KM, Sanchez CA, Kuhner MK, Smith LP, Hadi K, Shah M, Arora K, Shelton J, Johnson M, Corvelo A, Maley CC, Yao X, Sanghvi R, Venturini E, Emde AK, Hubert B, Imielinski M, Robine N, Reid BJ, Li X. Somatic whole genome dynamics of precancer in Barrett's esophagus reveals features associated with disease progression. Nat Commun 2022; 13:2300. [PMID: 35484108 PMCID: PMC9050715 DOI: 10.1038/s41467-022-29767-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 03/25/2022] [Indexed: 01/08/2023] Open
Abstract
While the genomes of normal tissues undergo dynamic changes over time, little is understood about the temporal-spatial dynamics of genomes in premalignant tissues that progress to cancer compared to those that remain cancer-free. Here we use whole genome sequencing to contrast genomic alterations in 427 longitudinal samples from 40 patients with stable Barrett’s esophagus compared to 40 Barrett’s patients who progressed to esophageal adenocarcinoma (ESAD). We show the same somatic mutational processes are active in Barrett’s tissue regardless of outcome, with high levels of mutation, ESAD gene and focal chromosomal alterations, and similar mutational signatures. The critical distinction between stable Barrett’s versus those who progress to cancer is acquisition and expansion of TP53−/− cell populations having complex structural variants and high-level amplifications, which are detectable up to six years prior to a cancer diagnosis. These findings reveal the timing of common somatic genome dynamics in stable Barrett’s esophagus and define key genomic features specific to progression to esophageal adenocarcinoma, both of which are critical for cancer prevention and early detection strategies. Barrett’s esophagus is a pre-malignant condition that can progress to esophageal cancer. Here, the authors carry out whole genome sequencing of samples from patients who did or did not progress to cancer and find that mutations in many genes occur regardless of progression status, but also find features associated with progressive disease.
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Affiliation(s)
- Thomas G Paulson
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109-1024, USA.
| | - Patricia C Galipeau
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109-1024, USA
| | - Kenji M Oman
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109-1024, USA
| | - Carissa A Sanchez
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109-1024, USA
| | - Mary K Kuhner
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195-5065, USA.,Brotman Baty Institute for Precision Medicine, Seattle, WA, 98195-5065, USA
| | - Lucian P Smith
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195-5065, USA
| | - Kevin Hadi
- New York Genome Center (NYGC), New York, NY, 10013, USA
| | - Minita Shah
- New York Genome Center (NYGC), New York, NY, 10013, USA
| | - Kanika Arora
- New York Genome Center (NYGC), New York, NY, 10013, USA
| | | | - Molly Johnson
- New York Genome Center (NYGC), New York, NY, 10013, USA
| | - Andre Corvelo
- New York Genome Center (NYGC), New York, NY, 10013, USA
| | - Carlo C Maley
- Arizona Cancer Evolution Center, Biodesign Institute and School of Life Sciences, Arizona State University, Tempe, AZ, 85281, USA
| | - Xiaotong Yao
- New York Genome Center (NYGC), New York, NY, 10013, USA
| | | | | | | | | | - Marcin Imielinski
- New York Genome Center (NYGC), New York, NY, 10013, USA.,Department of Pathology and Laboratory Medicine, Englander Institute for Precision Medicine, Institute for Computational Biomedicine and Meyer Cancer Center, Weill Cornell Medical College, New York, NY, 10065, USA
| | | | - Brian J Reid
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109-1024, USA.,Department of Genome Sciences, University of Washington, Seattle, WA, 98195-5065, USA.,Brotman Baty Institute for Precision Medicine, Seattle, WA, 98195-5065, USA.,Department of Medicine, University of Washington, Seattle, WA, 98195, USA
| | - Xiaohong Li
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109-1024, USA.
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A personalized and dynamic risk estimation model: The new paradigm in Barrett’s esophagus surveillance. PLoS One 2022; 17:e0267503. [PMID: 35476812 PMCID: PMC9045660 DOI: 10.1371/journal.pone.0267503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 04/08/2022] [Indexed: 11/19/2022] Open
Abstract
Objectives The current surveillance strategy in Barrett’s esophagus (BE) uses only histological findings of the last endoscopy to assess neoplastic progression risk. As predictor values vary across endoscopies, single measurements may not be an accurate reflection. Our aim was to explore the value of using longitudinal evolutions (i.e. successive measurements) of histological findings (low-grade dysplasia (LGD)) and immunohistochemical biomarkers (p53 and SOX2) by investigating the association with Barrett’s progression. Methods In this proof-of-principle study of a longitudinal dynamic risk estimation model with a multicenter cohort design, 631 BE patients from 15 Dutch hospitals who were under surveillance were included. Longitudinal dynamic values of LGD, p53, and SOX2 were included in a multivariate joint model to estimate the risk of high-grade dysplasia (HGD)/esophageal adenocarcinoma (EAC). Results Longitudinal evolutions of aberrant expression of p53 (HR 1.26, p<0.01) and SOX2 (HR 1.43, p<0.01) were associated with an increased HGD/EAC risk. We also found weak evidence of an association with the longitudinal evolution of the presence of LGD (HR 1.02, p = 0.12). The performance of the model was good (AUC 0.80–0.88). Using this model, for each future BE patient the probability of aberrant expression of biomarkers based on multiple longitudinal observations can be estimated. This probability is translated in progression risk, expressed as HR. Conclusions This study provides solid ground to further explore a paradigm shift from currently recommended fixed intervals towards personalized surveillance, in which tailored risk estimations and corresponding surveillance intervals can be updated at every FU endoscopy for individual BE patients.
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Zhang CZ, Pellman D. Cancer Genomic Rearrangements and Copy Number Alterations from Errors in Cell Division. ANNUAL REVIEW OF CANCER BIOLOGY 2022. [DOI: 10.1146/annurev-cancerbio-070620-094029] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Analysis of cancer genomes has shown that a large fraction of chromosomal changes originate from catastrophic events including whole-genome duplication, chromothripsis, breakage-fusion-bridge cycles, and chromoplexy. Through sophisticated computational analysis of cancer genomes and experimental recapitulation of these catastrophic alterations, we have gained significant insights into the origin, mechanism, and evolutionary dynamics of cancer genome complexity. In this review, we summarize this progress and survey the major unresolved questions, with particular emphasis on the relative contributions of chromosome fragmentation and DNA replication errors to complex chromosomal alterations.
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Affiliation(s)
- Cheng-Zhong Zhang
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Biomedical Informatics, Blavatnik Institute of Harvard Medical School, Boston, Massachusetts, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - David Pellman
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Cell Biology, Blavatnik Institute of Harvard Medical School, Boston, Massachusetts, USA
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55
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Quante M, Wang TC, Bass AJ. Adenocarcinoma of the oesophagus: is it gastric cancer? Gut 2022; 72:1027-1029. [PMID: 35365571 PMCID: PMC10176420 DOI: 10.1136/gutjnl-2022-327096] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 03/10/2022] [Indexed: 12/14/2022]
Affiliation(s)
- Michael Quante
- Klinik für Innere Medizin II, Universitätsklinikum Freiburg, Freiburg, Germany
| | - Timothy C Wang
- College of Physicians and Surgeons, Division of Digestive and Liver Diseases, Columbia University, New York, New York, USA
| | - Adam J Bass
- Herbert Irving Comprehensive Cancer Center at Columbia University, New York, New York, USA
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Feunteun J, Ostyn P, Delaloge S. TUMOR CELL MALIGNANCY: A COMPLEX TRAIT BUILT THROUGH RECIPROCAL INTERACTIONS BETWEEN TUMORS AND TISSUE-BODY SYSTEM. iScience 2022; 25:104217. [PMID: 35494254 PMCID: PMC9044163 DOI: 10.1016/j.isci.2022.104217] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Since the discovery of oncogenes and tumor suppressor genes in the late past century, cancer research has been overwhelmingly focused on the genetics and biology of tumor cells and hence has addressed mostly cell-autonomous processes with emphasis on traditional driver/passenger genetic models. Nevertheless, over that same period, multiple seminal observations have accumulated highlighting the role of non-cell autonomous effectors in tumor growth and metastasis. However, given that cell autonomous and non-autonomous events are observed together at the time of diagnosis, it is in fact impossible to know whether the malignant transformation is initiated by cell autonomous oncogenic events or by non-cell autonomous conditions generated by alterations of the tissue-body ecosystem. This review aims at addressing this issue by taking the option of defining malignancy as a complex genetic trait incorporating genetically determined reciprocal interactions between tumor cells and tissue-body ecosystem.
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Affiliation(s)
- Jean Feunteun
- INSERM U981, Gustave Roussy, Université Paris-Saclay, Villejuif, France
- UMR 9019, Gustave Roussy, Université Paris-Saclay, Villejuif, France
- Corresponding author
| | - Pauline Ostyn
- UMR 9019, Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | - Suzette Delaloge
- Breast Cancer Group, Gustave Roussy, Université Paris-Saclay, Villejuif, France
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Katz-Summercorn AC, Jammula S, Frangou A, Peneva I, O'Donovan M, Tripathi M, Malhotra S, di Pietro M, Abbas S, Devonshire G, Januszewicz W, Blasko A, Nowicki-Osuch K, MacRae S, Northrop A, Redmond AM, Wedge DC, Fitzgerald RC. Multi-omic cross-sectional cohort study of pre-malignant Barrett's esophagus reveals early structural variation and retrotransposon activity. Nat Commun 2022; 13:1407. [PMID: 35301290 PMCID: PMC8931005 DOI: 10.1038/s41467-022-28237-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 01/14/2022] [Indexed: 12/11/2022] Open
Abstract
Barrett's esophagus is a pre-malignant lesion that can progress to esophageal adenocarcinoma. We perform a multi-omic analysis of pre-cancer samples from 146 patients with a range of outcomes, comprising 642 person years of follow-up. Whole genome sequencing reveals complex structural variants and LINE-1 retrotransposons, as well as known copy number changes, occurring even prior to dysplasia. The structural variant burden captures the most variance across the cohort and genomic profiles do not always match consensus clinical pathology dysplasia grades. Increasing structural variant burden is associated with: high levels of chromothripsis and breakage-fusion-bridge events; increased expression of genes related to cell cycle checkpoint, DNA repair and chromosomal instability; and epigenetic silencing of Wnt signalling and cell cycle genes. Timing analysis reveals molecular events triggering genomic instability with more clonal expansion in dysplastic samples. Overall genomic complexity occurs early in the Barrett's natural history and may inform the potential for cancer beyond the clinically discernible phenotype.
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Affiliation(s)
- A C Katz-Summercorn
- Medical Research Council Cancer Unit, Hutchison/Medical Research Council Research Centre, University of Cambridge, Cambridge, CB2 0XZ, UK
| | - S Jammula
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
| | - A Frangou
- Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Headington, Oxford, OX3 7BN, UK
- NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headley Way, Headington, Oxford, OX3 9DU, UK
| | - I Peneva
- Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Headington, Oxford, OX3 7BN, UK
- NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headley Way, Headington, Oxford, OX3 9DU, UK
| | - M O'Donovan
- Medical Research Council Cancer Unit, Hutchison/Medical Research Council Research Centre, University of Cambridge, Cambridge, CB2 0XZ, UK
- Department of Histopathology, Addenbrooke's Hospital, Cambridge, CB2 0QQ, UK
| | - M Tripathi
- Medical Research Council Cancer Unit, Hutchison/Medical Research Council Research Centre, University of Cambridge, Cambridge, CB2 0XZ, UK
- Department of Histopathology, Addenbrooke's Hospital, Cambridge, CB2 0QQ, UK
| | - S Malhotra
- Medical Research Council Cancer Unit, Hutchison/Medical Research Council Research Centre, University of Cambridge, Cambridge, CB2 0XZ, UK
- Department of Histopathology, Addenbrooke's Hospital, Cambridge, CB2 0QQ, UK
| | - M di Pietro
- Medical Research Council Cancer Unit, Hutchison/Medical Research Council Research Centre, University of Cambridge, Cambridge, CB2 0XZ, UK
| | - S Abbas
- Medical Research Council Cancer Unit, Hutchison/Medical Research Council Research Centre, University of Cambridge, Cambridge, CB2 0XZ, UK
| | - G Devonshire
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
| | - W Januszewicz
- Medical Research Council Cancer Unit, Hutchison/Medical Research Council Research Centre, University of Cambridge, Cambridge, CB2 0XZ, UK
- Department of Gastroenterology, Hepatology and Clinical Oncology, Centre of Postgraduate Medical Education, Warsaw, Poland
| | - A Blasko
- Medical Research Council Cancer Unit, Hutchison/Medical Research Council Research Centre, University of Cambridge, Cambridge, CB2 0XZ, UK
| | - K Nowicki-Osuch
- Medical Research Council Cancer Unit, Hutchison/Medical Research Council Research Centre, University of Cambridge, Cambridge, CB2 0XZ, UK
| | - S MacRae
- Medical Research Council Cancer Unit, Hutchison/Medical Research Council Research Centre, University of Cambridge, Cambridge, CB2 0XZ, UK
| | - A Northrop
- Medical Research Council Cancer Unit, Hutchison/Medical Research Council Research Centre, University of Cambridge, Cambridge, CB2 0XZ, UK
| | - A M Redmond
- Medical Research Council Cancer Unit, Hutchison/Medical Research Council Research Centre, University of Cambridge, Cambridge, CB2 0XZ, UK
| | - D C Wedge
- Manchester Cancer Research Centre, University of Manchester, Wilmslow Road, Manchester, M20 4GJ, UK
| | - R C Fitzgerald
- Medical Research Council Cancer Unit, Hutchison/Medical Research Council Research Centre, University of Cambridge, Cambridge, CB2 0XZ, UK.
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Zhang X, Wang Y, Meng L. Comparative genomic analysis of esophageal squamous cell carcinoma and adenocarcinoma: New opportunities towards molecularly targeted therapy. Acta Pharm Sin B 2022; 12:1054-1067. [PMID: 35530133 PMCID: PMC9069403 DOI: 10.1016/j.apsb.2021.09.028] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 08/23/2021] [Accepted: 08/27/2021] [Indexed: 12/12/2022] Open
Abstract
Esophageal cancer is one of the most lethal cancers worldwide because of its rapid progression and poor prognosis. Esophageal squamous cell carcinoma (ESCC) and esophageal adenocarcinoma (EAC) are two major subtypes of esophageal cancer. ESCC predominantly affects African and Asian populations, which is closely related to chronic smoking and alcohol consumption. EAC typically arises in Barrett's esophagus with a predilection for Western countries. While surgical operation and chemoradiotherapy have been applied to combat this deadly cancer, molecularly targeted therapy is still at the early stages. With the development of large-scale next-generation sequencing, various genomic alterations in ESCC and EAC have been revealed and their potential roles in the initiation and progression of esophageal cancer have been studied. Potential therapeutic targets have been identified and novel approaches have been developed to combat esophageal cancer. In this review, we comprehensively analyze the genomic alterations in EAC and ESCC and summarize the potential role of the genetic alterations in the development of esophageal cancer. Progresses in the therapeutics based on the different tissue types and molecular signatures have also been reviewed and discussed.
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59
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Frei NF, Stachler MD. Today’s Mistakes and Tomorrow’s Wisdom in Development and Use of Biomarkers for Barrett’s Esophagus. Visc Med 2022; 38:173-181. [DOI: 10.1159/000521706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 12/27/2021] [Indexed: 11/19/2022] Open
Abstract
<b><i>Background:</i></b> A histological diagnosis of dysplasia is our current best predictor of progression in Barrett’s esophagus (BE), the precursor of esophageal adenocarcinoma (EAC). Despite periodic endoscopic surveillance and assessment of dysplastic changes, we fail to identify the majority of those who progress before the development of EAC, whereas the majority of patients undergo endoscopy without showing progression. <b><i>Summary:</i></b> Low-grade dysplasia (LGD), confirmed by expert pathologists, identifies BE patients at higher risk for progression, but the diagnosis of LGD is challenging. Recent research indicates that progression from BE to EAC is heterogeneous and can accelerate via genome doubling and genome catastrophes, resulting in different ways to progression. We identified 3 target areas, which may help to overcome the current lack of an accurate biomarker: (1) the implementation of somatic point mutations, chromosomal alterations, and epigenetic changes (genomics and epigenomics), (2) evaluate and develop biomarkers over space and time, (3) use new sampling methods such as noninvasive self-expandable sponges and endoscopic brushes. This review focus on the state of the art in risk stratifying BE and on recent advances which may overcome the limitations of current strategies. <b><i>Key Messages:</i></b> A panel of clinical factors, genomics, epigenomics, and/or proteomics will most likely lead to an assay that accurately risk stratifies BE patients into low- or high-risk for progression. This biomarker panel needs to be developed and validated in large cohorts containing a sufficient number of progressors, with testing samples over space (spatial distribution) and time (temporal distribution). For implementation in clinical practice, the technique should be affordable and applicable to formalin-fixed paraffin-embedded samples, which represent standard of care.
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Redston M, Noffsinger A, Kim A, Akarca FG, Rara M, Stapleton D, Nowden L, Lash R, Bass AJ, Stachler MD. Abnormal TP53 Predicts Risk of Progression in Patients With Barrett's Esophagus Regardless of a Diagnosis of Dysplasia. Gastroenterology 2022; 162:468-481. [PMID: 34757142 PMCID: PMC9341495 DOI: 10.1053/j.gastro.2021.10.038] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 10/21/2021] [Accepted: 10/24/2021] [Indexed: 02/07/2023]
Abstract
BACKGROUND AND AIMS Barrett's esophagus (BE) is the precursor to esophageal adenocarcinoma. A major challenge is identifying the small group with BE who will progress to advanced disease from the many who will not. Assessment of p53 status has promise as a predictive biomarker, but analytic limitations and lack of validation have precluded its use. The aim of this study was to develop a robust criteria for grading abnormal immunohistochemical (IHC) expression of p53 and to test its utility as a biomarker for progression in BE. METHODS Criteria for abnormal IHC of p53 were developed in BE biopsies and validated with sequencing to assess TP53 mutations. The utility of p53 IHC as a biomarker for progression of BE was tested retrospectively in 561 patients with BE with or without known progression. The findings were prospectively validated in a clinical practice setting in 1487 patients with BE. RESULTS Abnormal p53 IHC highly correlated with TP53 mutation status (90.6% agreement) and was strongly associated with neoplastic progression in the retrospective cohorts, regardless of histologic diagnosis (P < .001). In the retrospective cohort, abnormal p53 was associated with a hazard ratio of 5.03 (95% confidence interval, 3.88-6.5) and a hazard ratio of 5.27 (95% confidence interval, 3.93-7.07) for patients with exclusively nondysplastic disease before progression. In the prospective validation cohort, p53 IHC predicted progression among nondysplastic BE, indefinite for dysplasia, and low-grade dysplasia (P < .001). CONCLUSIONS p53 IHC identifies patients with BE at higher risk of progression, including in patients without evidence of dysplasia. p53 IHC is inexpensive, easily integrated into routine practice, and should be considered in biopsies from all BE patients without high-grade dysplasia or cancer.
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Affiliation(s)
- Mark Redston
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts.
| | | | - Anthony Kim
- Department of Molecular Oncology, Dana Farber Cancer Institute, Boston, Massachusetts
| | - Fahire G. Akarca
- Department of Molecular Oncology, Dana Farber Cancer Institute, Boston, Massachusetts
| | - Marianne Rara
- Department of Pathology, University of California San Francisco, San Francisco, California
| | | | | | | | - Adam J. Bass
- Department of Molecular Oncology, Dana Farber Cancer Institute, Boston, Massachusetts,Eli and Edythe L. Broad Institute, Cambridge, Massachusetts
| | - Matthew D. Stachler
- Department of Pathology, University of California San Francisco, San Francisco, California
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Schmidt M, Hackett RJ, Baker AM, McDonald SAC, Quante M, Graham TA. Evolutionary dynamics in Barrett oesophagus: implications for surveillance, risk stratification and therapy. Nat Rev Gastroenterol Hepatol 2022; 19:95-111. [PMID: 34728819 DOI: 10.1038/s41575-021-00531-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/24/2021] [Indexed: 12/13/2022]
Abstract
Cancer development is a dynamic evolutionary process characterized by marked intratumoural heterogeneity at the genetic, epigenetic and phenotypic levels. Barrett oesophagus, the pre-malignant condition to oesophageal adenocarcinoma (EAC), is an exemplary system to longitudinally study the evolution of malignancy. Evidence has emerged of Barrett oesophagus lesions pre-programmed for progression to EAC many years before clinical detection, indicating a considerable window for therapeutic intervention. In this Review, we explore the mechanisms underlying clonal expansion and contraction that establish the Barrett oesophagus clonal mosaicism over time and space and discuss intrinsic genotypic and extrinsic environmental drivers that direct the evolutionary trajectory of Barrett oesophagus towards a malignant phenotype. We propose that understanding and exploiting the evolutionary dynamics of Barrett oesophagus will identify novel therapeutic targets, improve prognostic tools and offer the opportunity for personalized surveillance programmes geared to prevent progression to EAC.
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Affiliation(s)
- Melissa Schmidt
- Evolution and Cancer Laboratory, Centre for Genomics and Computational Biology, Barts Cancer Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
- Department of Medicine II, Klinikum rechts der Isar, Technical University Munich (TUM), München, Germany
| | - Richard J Hackett
- Clonal Dynamics in Epithelia Group; Centre for Genomics and Computational Biology, Barts Cancer Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Ann-Marie Baker
- Evolution and Cancer Laboratory, Centre for Genomics and Computational Biology, Barts Cancer Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Stuart A C McDonald
- Clonal Dynamics in Epithelia Group; Centre for Genomics and Computational Biology, Barts Cancer Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Michael Quante
- Department of Medicine II, Klinikum rechts der Isar, Technical University Munich (TUM), München, Germany
- Department of Medicine II, Universitaetsklinikum Freiburg, Freiburg, Germany
| | - Trevor A Graham
- Evolution and Cancer Laboratory, Centre for Genomics and Computational Biology, Barts Cancer Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK.
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Mikhael M, Pasha B, Chela H, Tahan V, Daglilar E. Immunological and Metabolic Alterations in Esophageal Cancer. Endocr Metab Immune Disord Drug Targets 2022; 22:579-589. [PMID: 35086463 DOI: 10.2174/1871530322666220127113752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 10/25/2021] [Accepted: 12/02/2021] [Indexed: 12/24/2022]
Abstract
Esophageal cancer is one of the most common types of gastrointestinal malignancies that is encountered. It has a global distribution and affects males and females and is linked to significant morbidity and mortality. The mechanisms underlying pathophysiology are multifactorial and involve the interaction of genetic and environmental factors. This review article describes the immunological and metabolic changes that occur in malignancy of the esophagus.
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Affiliation(s)
- Mary Mikhael
- University of Missouri Department of Internal Medicine, Columbia, Missouri, USA
| | - Bilal Pasha
- University of Missouri Department of Internal Medicine, Columbia, Missouri, USA
| | - Harleen Chela
- Division of Gastroenterology and Hepatology,2 Columbia, Missouri, USA
| | - Veysel Tahan
- Division of Gastroenterology and Hepatology,2 Columbia, Missouri, USA
| | - Ebubekir Daglilar
- Division of Gastroenterology and Hepatology,2 Columbia, Missouri, USA
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Whole-genome sequencing reveals the evolutionary trajectory of HBV-related hepatocellular carcinoma early recurrence. Signal Transduct Target Ther 2022; 7:24. [PMID: 35078970 PMCID: PMC8789859 DOI: 10.1038/s41392-021-00838-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Revised: 08/29/2021] [Accepted: 08/31/2021] [Indexed: 11/24/2022] Open
Abstract
Patients with hepatocellular carcinoma (HCC) have poor long-term survival following curative resection because of the high rate of tumor early recurrence. Little is known about the trajectory of genomic evolution from primary to early-recurrent HCC. In this study, we performed whole-genome sequencing (WGS) on 40 pairs of primary and early-recurrent hepatitis B virus (HBV)-related HCC tumors from patients who received curative resection, and from four patients whose primary and recurrent tumor were extensively sampled. We identified two recurrence patterns: de novo recurrence (18/40), which developed genetically independently of the primary tumor and carried different HCC drivers, and ancestral recurrence (22/40), which was clonally related to the primary tumor and progressed more rapidly than de novo recurrence. We found that the recurrence location was predictive of the recurrence pattern: distant recurrence tended to display the de novo pattern, whereas local recurrence tended to display the ancestral pattern. We then uncovered the evolutionary trajectories based on the subclonal architecture, driver-gene mutations, and mutational processes observed in the primary and recurrent tumors. Multi-region WGS demonstrated spatiotemporal heterogeneity and polyclonal, monophyletic dissemination in HCC ancestral recurrence. In addition, we identified recurrence-specific mutations and copy-number gains in BCL9, leading to WNT/β-catenin signaling activation and an immune-excluded tumor microenvironment, which suggests that BCL9 might serve as a new therapeutic target for recurrent HCC. Collectively, our results allow us to view with unprecedented clarity the genomic evolution during HBV-related HCC early recurrence, providing an important molecular foundation for enhanced understanding of HCC with implications for personalized therapy to improve patient survival.
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64
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Busslinger GA. Barrett's esophagus stages: their correlation with SBS17-associated DNA mutations and the identification of histological marker genes. Mol Cell Oncol 2022; 9:2026559. [PMID: 35252552 PMCID: PMC8890392 DOI: 10.1080/23723556.2022.2026559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 12/22/2021] [Accepted: 12/28/2021] [Indexed: 06/14/2023]
Abstract
We have recently reported a correlation between the accumulation of specific T > C and T > G mutations and the chromosomal instability in cells of Barrett's esophagus (BE), which represents a premalignant condition of esophageal adenocarcinoma. Additionally, we identified seven marker genes that facilitate the distinction of individual BE stages by histopathological examination.
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Affiliation(s)
- Georg A. Busslinger
- Division of Gastroenterology and Hepatology, Department of Internal Medicine III, Medical University of Vienna, Vienna, Austria
- Research Center for Molecular Medicine (CeMM) of the Austrian Academy of Sciences, Vienna, Austria
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65
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Choi WT, Lauwers GY, Montgomery EA. Utility of ancillary studies in the diagnosis and risk assessment of Barrett's esophagus and dysplasia. Mod Pathol 2022; 35:1000-1012. [PMID: 35260826 PMCID: PMC9314252 DOI: 10.1038/s41379-022-01056-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 02/09/2022] [Accepted: 02/13/2022] [Indexed: 12/12/2022]
Abstract
Barrett's esophagus (BE) is a major risk factor for the development of esophageal adenocarcinoma (EAC). BE patients undergo periodic endoscopic surveillance with biopsies to detect dysplasia and EAC, but this strategy is imperfect owing to sampling error and inconsistencies in the diagnosis and grading of dysplasia, which may result in an inaccurate diagnosis or risk assessment for progression to EAC. The desire for more accurate diagnosis and better risk stratification has prompted the investigation and development of potential biomarkers that might assist pathologists and clinicians in the management of BE patients, allowing more aggressive endoscopic surveillance and treatment options to be targeted to high-risk individuals, while avoiding frequent surveillance or unnecessary interventions in those at lower risk. It is known that progression of BE to dysplasia and EAC is accompanied by a host of genetic alterations, and that exploration of these markers could be potentially useful to diagnose/grade dysplasia and/or to risk stratify BE patients. Several biomarkers have shown promise in identifying early neoplastic transformation and thus may be useful adjuncts to histologic evaluation. This review provides an overview of some of the currently available biomarkers and assays, including p53 immunostaining, Wide Area Transepithelial Sampling with Three-Dimensional Computer-Assisted Analysis (WATS3D), TissueCypher, mutational load analysis (BarreGen), fluorescence in situ hybridization, and DNA content abnormalities as detected by DNA flow cytometry.
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Affiliation(s)
- Won-Tak Choi
- University of California at San Francisco, Department of Pathology, San Francisco, CA, 94143, USA.
| | - Gregory Y. Lauwers
- grid.468198.a0000 0000 9891 5233H. Lee Moffitt Cancer Center and Research Institute, Department of Pathology, Tampa, FL 33612 USA
| | - Elizabeth A. Montgomery
- grid.26790.3a0000 0004 1936 8606University of Miami Miller School of Medicine, Department of Pathology and Laboratory Medicine, Miami, FL 33136 USA
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66
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Singh H, Seruggia D, Madha S, Saxena M, Nagaraja AK, Wu Z, Zhou J, Huebner AJ, Maglieri A, Wezenbeek J, Hochedlinger K, Orkin SH, Bass AJ, Hornick JL, Shivdasani RA. Transcription factor-mediated intestinal metaplasia and the role of a shadow enhancer. Genes Dev 2021; 36:38-52. [PMID: 34969824 PMCID: PMC8763054 DOI: 10.1101/gad.348983.121] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 12/13/2021] [Indexed: 12/02/2022]
Abstract
Here, Singh et al. show extensive but selective recruitment of intestinal enhancers by CDX2 in gastric cells and that HNF4A-mediated ectopic CDX2 expression in the stomach occurs through a conserved shadow cis-element. These findings identify mechanisms for TF-driven intestinal metaplasia and a likely pathogenic TF hierarchy. Barrett's esophagus (BE) and gastric intestinal metaplasia are related premalignant conditions in which areas of human stomach epithelium express mixed gastric and intestinal features. Intestinal transcription factors (TFs) are expressed in both conditions, with unclear causal roles and cis-regulatory mechanisms. Ectopic CDX2 reprogrammed isogenic mouse stomach organoid lines to a hybrid stomach–intestinal state transcriptionally similar to clinical metaplasia; squamous esophageal organoids resisted this CDX2-mediated effect. Reprogramming was associated with induced activity at thousands of previously inaccessible intestine-restricted enhancers, where CDX2 occupied DNA directly. HNF4A, a TF recently implicated in BE pathogenesis, induced weaker intestinalization by binding a novel shadow Cdx2 enhancer and hence activating Cdx2 expression. CRISPR/Cas9-mediated germline deletion of that cis-element demonstrated its requirement in Cdx2 induction and in the resulting activation of intestinal genes in stomach cells. dCas9-conjugated KRAB repression mapped this activity to the shadow enhancer's HNF4A binding site. Altogether, we show extensive but selective recruitment of intestinal enhancers by CDX2 in gastric cells and that HNF4A-mediated ectopic CDX2 expression in the stomach occurs through a conserved shadow cis-element. These findings identify mechanisms for TF-driven intestinal metaplasia and a likely pathogenic TF hierarchy.
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Affiliation(s)
- Harshabad Singh
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA.,Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Davide Seruggia
- Division of Hematology Oncology, Boston Children's Hospital, Boston, Massachusetts 02215, USA.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Shariq Madha
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Madhurima Saxena
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA.,Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Ankur K Nagaraja
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA.,Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Zhong Wu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Jin Zhou
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Aaron J Huebner
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, Massachusetts, 02114, USA
| | - Adrianna Maglieri
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Juliette Wezenbeek
- Hubretch Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), University Medical Center Utrecht, Utrecht 3584 CT, Netherlands
| | - Konrad Hochedlinger
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, Massachusetts, 02114, USA.,Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, USA
| | - Stuart H Orkin
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA.,Division of Hematology Oncology, Boston Children's Hospital, Boston, Massachusetts 02215, USA.,Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, USA.,Howard Hughes Medical Institute, Boston, Massachusetts 02215, USA
| | - Adam J Bass
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA.,Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Jason L Hornick
- Departments of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Ramesh A Shivdasani
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA.,Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA.,Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, USA
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67
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Maslyonkina KS, Konyukova AK, Alexeeva DY, Sinelnikov MY, Mikhaleva LM. Barrett's esophagus: The pathomorphological and molecular genetic keystones of neoplastic progression. Cancer Med 2021; 11:447-478. [PMID: 34870375 PMCID: PMC8729054 DOI: 10.1002/cam4.4447] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 11/07/2021] [Accepted: 11/09/2021] [Indexed: 02/06/2023] Open
Abstract
Barrett's esophagus is a widespread chronically progressing disease of heterogeneous nature. A life threatening complication of this condition is neoplastic transformation, which is often overlooked due to lack of standardized approaches in diagnosis, preventative measures and treatment. In this essay, we aim to stratify existing data to show specific associations between neoplastic transformation and the underlying processes which predate cancerous transition. We discuss pathomorphological, genetic, epigenetic, molecular and immunohistochemical methods related to neoplasia detection on the basis of Barrett's esophagus. Our review sheds light on pathways of such neoplastic progression in the distal esophagus, providing valuable insight into progression assessment, preventative targets and treatment modalities. Our results suggest that molecular, genetic and epigenetic alterations in the esophagus arise earlier than cancerous transformation, meaning the discussed targets can help form preventative strategies in at-risk patient groups.
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Affiliation(s)
| | | | - Darya Y Alexeeva
- Research Institute of Human Morphology, Moscow, Russian Federation
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68
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Sahgal P, Huffman BM, Patil DT, Chatila WK, Yaeger R, Cleary JM, Sethi NS. Early TP53 Alterations Shape Gastric and Esophageal Cancer Development. Cancers (Basel) 2021; 13:5915. [PMID: 34885025 PMCID: PMC8657039 DOI: 10.3390/cancers13235915] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 11/22/2021] [Accepted: 11/23/2021] [Indexed: 12/14/2022] Open
Abstract
Gastric and esophageal (GE) adenocarcinomas are the third and sixth most common causes of cancer-related mortality worldwide, accounting for greater than 1.25 million annual deaths. Despite the advancements in the multi-disciplinary treatment approaches, the prognosis for patients with GE adenocarcinomas remains poor, with a 5-year survival of 32% and 19%, respectively, mainly due to the late-stage diagnosis and aggressive nature of these cancers. Premalignant lesions characterized by atypical glandular proliferation, with neoplastic cells confined to the basement membrane, often precede malignant disease. We now appreciate that premalignant lesions also carry cancer-associated mutations, enabling disease progression in the right environmental context. A better understanding of the premalignant-to-malignant transition can help us diagnose, prevent, and treat GE adenocarcinoma. Here, we discuss the evidence suggesting that alterations in TP53 occur early in GE adenocarcinoma evolution, are selected for under environmental stressors, are responsible for shaping the genomic mechanisms for pathway dysregulation in cancer progression, and lead to potential vulnerabilities that can be exploited by a specific class of targeted therapy.
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Affiliation(s)
- Pranshu Sahgal
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; (P.S.); (B.M.H.); (J.M.C.)
- Cancer Program, Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Cambridge, MA 02142, USA
- Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - Brandon M. Huffman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; (P.S.); (B.M.H.); (J.M.C.)
| | - Deepa T. Patil
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02215, USA;
| | - Walid K. Chatila
- Tri-Institutional Program in Computational Biology and Medicine, Weill Cornell Medical College, New York, NY 10021, USA;
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Rona Yaeger
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA;
| | - James M. Cleary
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; (P.S.); (B.M.H.); (J.M.C.)
- Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02215, USA
- Gastrointestinal Cancer Center, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Nilay S. Sethi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; (P.S.); (B.M.H.); (J.M.C.)
- Cancer Program, Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Cambridge, MA 02142, USA
- Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02215, USA
- Gastrointestinal Cancer Center, Dana-Farber Cancer Institute, Boston, MA 02215, USA
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69
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Molecular characterization of Barrett's esophagus at single-cell resolution. Proc Natl Acad Sci U S A 2021; 118:2113061118. [PMID: 34795059 PMCID: PMC8617519 DOI: 10.1073/pnas.2113061118] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/05/2021] [Indexed: 02/07/2023] Open
Abstract
Barrett’s esophagus (BE), the premalignant condition of esophageal adenocarcinoma, is categorized into different stages which correlate with the risk of developing carcinoma. We performed single-cell DNA-sequencing experiments with fresh biopsies, which revealed the appearance of a specific T > C and T > G mutational signature, known as COSMIC signature SBS17, in BE cells that are chromosomally unstable. The SBS17-specific mutations were, however, not detected in chromosomally stable BE cells. Additionally, we performed single-cell RNA sequencing experiments which identified seven genes that facilitate the distinction between different BE stages on histological sections. Barrett’s esophagus (BE) is categorized, based on morphological appearance, into different stages, which correlate with the risk of developing esophageal adenocarcinoma. More advanced stages are more likely to acquire chromosomal instabilities, but stage-specific markers remain elusive. Here, we performed single-cell DNA-sequencing experiments (scDNAseq) with fresh BE biopsies. Dysplastic BE cells frequently contained chromosomal instability (CIN) regions, and these CIN cells carried mutations corresponding to the COSMIC mutational signature SBS17, which were not present in biopsy-matched chromosomally stable (CS) cells or patient-matched nondiseased control cells. CS cells were predominantly found in nondysplastic BE biopsies. The single-base substitution (SBS) signatures of all CS BE cells analyzed were indistinguishable from those of nondiseased esophageal or gastric cells. Single-cell RNA-sequencing (scRNAseq) experiments with BE biopsies identified two sets of marker genes which facilitate the distinction between columnar BE epithelium and nondysplastic/dysplastic stages. Moreover, histological validation confirmed a correlation between increased CLDN2 expression and the presence of dysplastic BE stages. Our scDNAseq and scRNAseq datasets, which are a useful resource for the community, provide insight into the mutational landscape and gene expression pattern at different stages of BE development.
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70
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Killcoyne S, Fitzgerald RC. Evolution and progression of Barrett's oesophagus to oesophageal cancer. Nat Rev Cancer 2021; 21:731-741. [PMID: 34545238 DOI: 10.1038/s41568-021-00400-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/12/2021] [Indexed: 02/07/2023]
Abstract
Cancer cells are shaped through an evolutionary process of DNA mutation, cell selection and population expansion. Early steps in this process are driven by a set of mutated driver genes and structural alterations to the genome through copy number gains or losses. Oesophageal adenocarcinoma (EAC) and the pre-invasive tissue, Barrett's oesophagus (BE), provide an ideal example in which to observe and study this evolution. BE displays early genomic instability, specifically in copy number changes that may later be observed in EAC. Furthermore, these early changes result in patterns of progression (that is, 'born bad', gradual or catastrophic) that may help to describe the evolution of EAC. As only a small proportion of patients with BE will go on to develop cancer, a better understanding of these patterns and the resulting genomic changes should improve early detection in EAC and may provide clues for the evolution of cancer more broadly.
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Affiliation(s)
- Sarah Killcoyne
- Medical Research Council Cancer Unit, Hutchison/Medical Research Council Research Centre, University of Cambridge, Cambridge, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Rebecca C Fitzgerald
- Medical Research Council Cancer Unit, Hutchison/Medical Research Council Research Centre, University of Cambridge, Cambridge, UK.
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71
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Salimian KJ, Birkness-Gartman J, Waters KM. The path(ology) from reflux oesophagitis to Barrett oesophagus to oesophageal adenocarcinoma. Pathology 2021; 54:147-156. [PMID: 34711413 DOI: 10.1016/j.pathol.2021.08.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 08/23/2021] [Accepted: 08/23/2021] [Indexed: 02/07/2023]
Abstract
This review seeks to summarise the steps in the path from reflux oesophagitis to Barrett oesophagus to oesophageal adenocarcinoma. The epidemiology, clinical presentation, definitions, pathological features, diagnostic pitfalls, and emerging concepts are reviewed for each entity. The histological features of reflux oesophagitis can be variable and are not specific. Cases of reflux oesophagitis with numerous eosinophils are difficult to distinguish from eosinophilic oesophagitis and other oesophagitides with eosinophils (Crohn's disease, medication effect, and connective tissue disorders). In reflux oesophagitis, the findings are often most pronounced in the distal oesophagus, the eosinophils are randomly distributed throughout the epithelium, and eosinophilic abscesses and degranulated eosinophils are rare. For reflux oesophagitis with prominent lymphocytes, clinical history and ancillary clinical studies are paramount to distinguish reflux oesophagitis from other causes of lymphocytic oesophagitis pattern. For Barrett oesophagus, the definition remains a hotly debated topic for which the requirement for intestinal metaplasia to make the diagnosis is not applied unanimously across the globe. Assessing for dysplasia is a challenging aspect of the histological interpretation that guides clinical management. We describe the histological features that we find useful in making this evaluation. Oesophageal adenocarcinoma has been steadily increasing in incidence and has a poor prognosis. The extent of invasion can be overdiagnosed due to a duplicated muscularis mucosae. We also describe the technical factors that can lead to challenges in distinguishing the mucosal and deep margins of endoscopic resections. Lastly, we give an overview of targeted therapies with emerging importance and the ancillary tests that can identify the cases best suited for each therapy.
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Affiliation(s)
- Kevan J Salimian
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | - Kevin M Waters
- Department of Pathology and Laboratory Medicine, Cedars Sinai Medical Center, Los Angeles, CA, USA.
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72
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Prakadan SM, Alvarez-Breckenridge CA, Markson SC, Kim AE, Klein RH, Nayyar N, Navia AW, Kuter BM, Kolb KE, Bihun I, Mora JL, Bertalan MS, Shaw B, White M, Kaplan A, Stocking JH, Wadsworth MH, Lee EQ, Chukwueke U, Wang N, Subramanian M, Rotem D, Cahill DP, Adalsteinsson VA, Miller JW, Sullivan RJ, Carter SL, Brastianos PK, Shalek AK. Genomic and transcriptomic correlates of immunotherapy response within the tumor microenvironment of leptomeningeal metastases. Nat Commun 2021; 12:5955. [PMID: 34642316 PMCID: PMC8511044 DOI: 10.1038/s41467-021-25860-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Accepted: 08/25/2021] [Indexed: 12/30/2022] Open
Abstract
Leptomeningeal disease (LMD) is a devastating complication of solid tumor malignancies, with dire prognosis and no effective systemic treatment options. Over the past decade, the incidence of LMD has steadily increased due to therapeutics that have extended the survival of cancer patients, highlighting the need for new interventions. To examine the efficacy of immune checkpoint inhibitors (ICI) in patients with LMD, we completed two phase II clinical trials. Here, we investigate the cellular and molecular features underpinning observed patient trajectories in these trials by applying single-cell RNA and cell-free DNA profiling to longitudinal cerebrospinal fluid (CSF) draws from enrolled patients. We recover immune and malignant cell types in the CSF, characterize cell behavior changes following ICI, and identify genomic features associated with relevant clinical phenomena. Overall, our study describes the liquid LMD tumor microenvironment prior to and following ICI treatment and demonstrates clinical utility of cell-free and single-cell genomic measurements for LMD research.
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Affiliation(s)
- Sanjay M Prakadan
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute, Harvard University & Massachusetts Institute of Technology, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Ragon Institute, Harvard University, Massachusetts Institute of Technology, & Massachusetts General Hospital, Cambridge, MA, USA
| | - Christopher A Alvarez-Breckenridge
- Broad Institute, Harvard University & Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Neurosurgery, Harvard Medical School & Massachusetts General Hospital, Boston, MA, USA
| | - Samuel C Markson
- Broad Institute, Harvard University & Massachusetts Institute of Technology, Cambridge, MA, USA
- Division of Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Albert E Kim
- Department of Medicine, Harvard Medical School & Massachusetts General Hospital, Boston, MA, USA
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Robert H Klein
- Broad Institute, Harvard University & Massachusetts Institute of Technology, Cambridge, MA, USA
- Division of Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Naema Nayyar
- Department of Medicine, Harvard Medical School & Massachusetts General Hospital, Boston, MA, USA
| | - Andrew W Navia
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute, Harvard University & Massachusetts Institute of Technology, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Ragon Institute, Harvard University, Massachusetts Institute of Technology, & Massachusetts General Hospital, Cambridge, MA, USA
| | - Benjamin M Kuter
- Department of Medicine, Harvard Medical School & Massachusetts General Hospital, Boston, MA, USA
| | - Kellie E Kolb
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute, Harvard University & Massachusetts Institute of Technology, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Ragon Institute, Harvard University, Massachusetts Institute of Technology, & Massachusetts General Hospital, Cambridge, MA, USA
| | - Ivanna Bihun
- Department of Medicine, Harvard Medical School & Massachusetts General Hospital, Boston, MA, USA
| | - Joana L Mora
- Department of Medicine, Harvard Medical School & Massachusetts General Hospital, Boston, MA, USA
| | - Mia Solana Bertalan
- Department of Medicine, Harvard Medical School & Massachusetts General Hospital, Boston, MA, USA
| | - Brian Shaw
- Department of Medicine, Harvard Medical School & Massachusetts General Hospital, Boston, MA, USA
| | - Michael White
- Department of Medicine, Harvard Medical School & Massachusetts General Hospital, Boston, MA, USA
| | - Alexander Kaplan
- Department of Medicine, Harvard Medical School & Massachusetts General Hospital, Boston, MA, USA
| | - Jackson H Stocking
- Department of Medicine, Harvard Medical School & Massachusetts General Hospital, Boston, MA, USA
| | - Marc H Wadsworth
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute, Harvard University & Massachusetts Institute of Technology, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Ragon Institute, Harvard University, Massachusetts Institute of Technology, & Massachusetts General Hospital, Cambridge, MA, USA
| | - Eudocia Q Lee
- Division of Neuro-Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Ugonma Chukwueke
- Division of Neuro-Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Nancy Wang
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Megha Subramanian
- Department of Medicine, Harvard Medical School & Massachusetts General Hospital, Boston, MA, USA
| | - Denisse Rotem
- Broad Institute, Harvard University & Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Daniel P Cahill
- Department of Neurosurgery, Harvard Medical School & Massachusetts General Hospital, Boston, MA, USA
| | - Viktor A Adalsteinsson
- Broad Institute, Harvard University & Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jeffrey W Miller
- Department of Biostatistics, Harvard TH Chan School of Public Health, Boston, MA, USA
| | - Ryan J Sullivan
- Department of Medicine, Harvard Medical School & Massachusetts General Hospital, Boston, MA, USA
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Scott L Carter
- Broad Institute, Harvard University & Massachusetts Institute of Technology, Cambridge, MA, USA.
- Division of Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Biostatistics, Harvard TH Chan School of Public Health, Boston, MA, USA.
| | - Priscilla K Brastianos
- Broad Institute, Harvard University & Massachusetts Institute of Technology, Cambridge, MA, USA.
- Department of Medicine, Harvard Medical School & Massachusetts General Hospital, Boston, MA, USA.
- Massachusetts General Hospital Cancer Center, Boston, MA, USA.
| | - Alex K Shalek
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Broad Institute, Harvard University & Massachusetts Institute of Technology, Cambridge, MA, USA.
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Ragon Institute, Harvard University, Massachusetts Institute of Technology, & Massachusetts General Hospital, Cambridge, MA, USA.
- Division of Health Science & Technology, Harvard Medical School, Cambridge, MA, USA.
- Program in Computational & Systems Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
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Moati E, Taly V, Garinet S, Didelot A, Taieb J, Laurent-Puig P, Zaanan A. Role of Circulating Tumor DNA in Gastrointestinal Cancers: Current Knowledge and Perspectives. Cancers (Basel) 2021; 13:4743. [PMID: 34638228 PMCID: PMC8507552 DOI: 10.3390/cancers13194743] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 09/06/2021] [Accepted: 09/18/2021] [Indexed: 12/21/2022] Open
Abstract
Gastrointestinal (GI) cancers are major health burdens worldwide and biomarkers are needed to improve the management of these diseases along their evolution. Circulating tumor DNA (ctDNA) is a promising non-invasive blood and other bodily-fluid-based biomarker in cancer management that can help clinicians in various cases for the detection, diagnosis, prognosis, monitoring and personalization of treatment in digestive oncology. In addition to the well-studied prognostic role of ctDNA, the main real-world applications appear to be the assessment of minimal residual disease to further guide adjuvant therapy and predict relapse, but also the monitoring of clonal evolution to tailor treatments in metastatic setting. Other challenges such as predicting response to treatment including immune checkpoint inhibitors could also be among the potential applications of ctDNA. Although the level of advancement of ctDNA development in the different tumor localizations is still inhomogeneous, it might be now reliable enough to be soon used in clinical routine for colorectal cancers and shows promising results in other GI cancers.
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Affiliation(s)
- Emilie Moati
- Department of Gastroenterology and Digestive Oncology, Institut du Cancer Paris Carpem, Assistance Publique des Hôpitaux de Paris, European Georges Pompidou Hospital, 75015 Paris, France; (E.M.); (J.T.)
| | - Valerie Taly
- Centre de Recherche des Cordeliers, INSERM UMRS1138, Centre National de la Recherche Scientifique, Sorbonne Université, USPC, Université de Paris, Equipe Labellisée Ligue Nationale Contre le Cancer, CNRS SNC 5096, 75006 Paris, France; (V.T.); (S.G.); (A.D.); (P.L.-P.)
| | - Simon Garinet
- Centre de Recherche des Cordeliers, INSERM UMRS1138, Centre National de la Recherche Scientifique, Sorbonne Université, USPC, Université de Paris, Equipe Labellisée Ligue Nationale Contre le Cancer, CNRS SNC 5096, 75006 Paris, France; (V.T.); (S.G.); (A.D.); (P.L.-P.)
- Department of Biochemistry, Institut du Cancer Paris Carpem, Assistance Publique des Hôpitaux de Paris, European Georges Pompidou Hospital, 75015 Paris, France
| | - Audrey Didelot
- Centre de Recherche des Cordeliers, INSERM UMRS1138, Centre National de la Recherche Scientifique, Sorbonne Université, USPC, Université de Paris, Equipe Labellisée Ligue Nationale Contre le Cancer, CNRS SNC 5096, 75006 Paris, France; (V.T.); (S.G.); (A.D.); (P.L.-P.)
| | - Julien Taieb
- Department of Gastroenterology and Digestive Oncology, Institut du Cancer Paris Carpem, Assistance Publique des Hôpitaux de Paris, European Georges Pompidou Hospital, 75015 Paris, France; (E.M.); (J.T.)
- Centre de Recherche des Cordeliers, INSERM UMRS1138, Centre National de la Recherche Scientifique, Sorbonne Université, USPC, Université de Paris, Equipe Labellisée Ligue Nationale Contre le Cancer, CNRS SNC 5096, 75006 Paris, France; (V.T.); (S.G.); (A.D.); (P.L.-P.)
| | - Pierre Laurent-Puig
- Centre de Recherche des Cordeliers, INSERM UMRS1138, Centre National de la Recherche Scientifique, Sorbonne Université, USPC, Université de Paris, Equipe Labellisée Ligue Nationale Contre le Cancer, CNRS SNC 5096, 75006 Paris, France; (V.T.); (S.G.); (A.D.); (P.L.-P.)
- Department of Biochemistry, Institut du Cancer Paris Carpem, Assistance Publique des Hôpitaux de Paris, European Georges Pompidou Hospital, 75015 Paris, France
| | - Aziz Zaanan
- Department of Gastroenterology and Digestive Oncology, Institut du Cancer Paris Carpem, Assistance Publique des Hôpitaux de Paris, European Georges Pompidou Hospital, 75015 Paris, France; (E.M.); (J.T.)
- Centre de Recherche des Cordeliers, INSERM UMRS1138, Centre National de la Recherche Scientifique, Sorbonne Université, USPC, Université de Paris, Equipe Labellisée Ligue Nationale Contre le Cancer, CNRS SNC 5096, 75006 Paris, France; (V.T.); (S.G.); (A.D.); (P.L.-P.)
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Guccione C, Yadlapati R, Shah S, Knight R, Curtius K. Challenges in Determining the Role of Microbiome Evolution in Barrett's Esophagus and Progression to Esophageal Adenocarcinoma. Microorganisms 2021; 9:2003. [PMID: 34683324 PMCID: PMC8541168 DOI: 10.3390/microorganisms9102003] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 09/15/2021] [Accepted: 09/16/2021] [Indexed: 01/22/2023] Open
Abstract
Esophageal adenocarcinoma (EAC) claims the lives of half of patients within the first year of diagnosis, and its incidence has rapidly increased since the 1970s despite extensive research into etiological factors. The changes in the microbiome within the distal esophagus in modern populations may help explain the growth in cases that other common EAC risk factors together cannot fully explain. The precursor to EAC is Barrett's esophagus (BE), a metaplasia adapted to a reflux-mediated microenvironment that can be challenging to diagnose in patients who do not undergo endoscopic screening. Non-invasive procedures to detect microbial communities in saliva, oral swabs and brushings from the distal esophagus allow us to characterize taxonomic differences in bacterial population abundances within patients with BE versus controls, and may provide an alternative means of BE detection. Unique microbial communities have been identified across healthy esophagus, BE, and various stages of progression to EAC, but studies determining dynamic changes in these communities, including migration from proximal stomach and oral cavity niches, and their potential causal role in cancer formation are lacking. Helicobacter pylori is negatively associated with EAC, and the absence of this species has been implicated in the evolution of chromosomal instability, a main driver of EAC, but joint analyses of microbiome and host genomes are needed. Acknowledging technical challenges, future studies on the prediction of microbial dynamics and evolution within BE and the progression to EAC will require larger esophageal microbiome datasets, improved bioinformatics pipelines, and specialized mathematical models for analysis.
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Affiliation(s)
- Caitlin Guccione
- Division of Biomedical Informatics, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA;
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA 92093, USA;
- Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
| | - Rena Yadlapati
- Division of Gastroenterology, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA; (R.Y.); (S.S.)
| | - Shailja Shah
- Division of Gastroenterology, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA; (R.Y.); (S.S.)
- Veterans Affairs, San Diego Healthcare System, San Diego, CA 92161, USA
| | - Rob Knight
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA 92093, USA;
- Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA 92093, USA
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Kit Curtius
- Division of Biomedical Informatics, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA;
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA 92093, USA;
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75
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Chen ZH, Yan SM, Chen XX, Zhang Q, Liu SX, Liu Y, Luo YL, Zhang C, Xu M, Zhao YF, Huang LY, Liu BL, Xia TL, Xu DZ, Liang Y, Chen YM, Wang W, Yuan SQ, Zhang HZ, Yun JP, Zhai WW, Zeng MS, Bai F, Zhong Q. The genomic architecture of EBV and infected gastric tissue from precursor lesions to carcinoma. Genome Med 2021; 13:146. [PMID: 34493320 PMCID: PMC8422682 DOI: 10.1186/s13073-021-00963-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 08/29/2021] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Epstein-Barr virus (EBV)-associated gastric carcinomas (EBVaGCs) present unique molecular signatures, but the tumorigenesis of EBVaGCs and the role EBV plays during this process remain poorly understood. METHODS We applied whole-exome sequencing, EBV genome sequencing, and whole-genome bisulfite sequencing to multiple samples (n = 123) derived from the same patients (n = 25), which covered saliva samples and different histological stages from morphologically normal epithelial tissues to dysplasia and EBVaGCs. We compared the genomic landscape between EBVaGCs and their precursor lesions and traced the clonal evolution for each patient. We also analyzed genome sequences of EBV from samples of different histological types. Finally, the key molecular events promoting the tumor evolution were demonstrated by MTT, IC50, and colony formation assay in vitro experiments and in vivo xenograft experiments. RESULTS Our analysis revealed increasing mutational burden and EBV load from normal tissues and low-grade dysplasia (LD) to high-grade dysplasia (HD) and EBVaGCs, and oncogenic amplifications occurred late in EBVaGCs. Interestingly, within each patient, EBVaGCs and HDs were monoclonal and harbored single-strain-originated EBV, but saliva or normal tissues/LDs had different EBV strains from that in EBVaGCs. Compared with precursor lesions, tumor cells showed incremental methylation in promotor regions, whereas EBV presented consistent hypermethylation. Dominant alterations targeting the PI3K-Akt and Wnt pathways were found in EBV-infected cells. The combinational inhibition of these two pathways in EBV-positive tumor cells confirmed their synergistic function. CONCLUSIONS We portrayed the (epi) genomic evolution process of EBVaGCs, revealed the extensive genomic diversity of EBV between tumors and normal tissue sites, and demonstrated the synergistic activation of the PI3K and Wnt pathways in EBVaGCs, offering a new potential treatment strategy for this disease.
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Affiliation(s)
- Zhang-Hua Chen
- Biomedical Pioneering Innovation Center (BIOPIC), Integrated Research Building Room 330, School of Life Sciences, Peking University, Yiheyuan Road No.5, Haidian District, Beijing, 100871, China
| | - Shu-Mei Yan
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
- Department of Pathology, Sun Yat-sen University Cancer Centre, Guangzhou, China
| | - Xi-Xi Chen
- Biomedical Pioneering Innovation Center (BIOPIC), Integrated Research Building Room 330, School of Life Sciences, Peking University, Yiheyuan Road No.5, Haidian District, Beijing, 100871, China
| | - Qi Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
- Department of Ultrasound, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, China
- Department of Oncology, Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Shang-Xin Liu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Yang Liu
- Biomedical Pioneering Innovation Center (BIOPIC), Integrated Research Building Room 330, School of Life Sciences, Peking University, Yiheyuan Road No.5, Haidian District, Beijing, 100871, China
| | - Yi-Ling Luo
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Chao Zhang
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, USA
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, New York, USA
| | - Miao Xu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Yi-Fan Zhao
- Biomedical Pioneering Innovation Center (BIOPIC), Integrated Research Building Room 330, School of Life Sciences, Peking University, Yiheyuan Road No.5, Haidian District, Beijing, 100871, China
| | - Li-Yun Huang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
- Department of Pathology, Sun Yat-sen University Cancer Centre, Guangzhou, China
| | - Bin-Liu Liu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Tian-Liang Xia
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Da-Zhi Xu
- Department of Gastric Surgery, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Yao Liang
- Department of Gastric Surgery, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Yong-Ming Chen
- Department of Gastric Surgery, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Wei Wang
- Department of Gastric Surgery, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Shu-Qiang Yuan
- Department of Gastric Surgery, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Hui-Zhong Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
- Department of Pathology, Sun Yat-sen University Cancer Centre, Guangzhou, China
| | - Jing-Ping Yun
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
- Department of Pathology, Sun Yat-sen University Cancer Centre, Guangzhou, China
| | - Wei-Wei Zhai
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Mu-Sheng Zeng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Fan Bai
- Biomedical Pioneering Innovation Center (BIOPIC), Integrated Research Building Room 330, School of Life Sciences, Peking University, Yiheyuan Road No.5, Haidian District, Beijing, 100871, China.
- Beijing Advanced Innovation Center for Genomics (ICG), Peking University, Beijing, China.
| | - Qian Zhong
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China.
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76
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Tokunaga M, Okimoto K, Akizue N, Ishikawa K, Hirotsu Y, Amemiya K, Ota M, Matsusaka K, Nishimura M, Matsushita K, Ishikawa T, Nagashima A, Shiratori W, Kaneko T, Oura H, Kanayama K, Ohta Y, Taida T, Saito K, Matsumura T, Chiba T, Mochizuki H, Arai M, Kato J, Ikeda JI, Omata M, Kato N. Genetic profiles of Barrett's esophagus and esophageal adenocarcinoma in Japanese patients. Sci Rep 2021; 11:17671. [PMID: 34480065 PMCID: PMC8417273 DOI: 10.1038/s41598-021-97249-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 08/17/2021] [Indexed: 11/10/2022] Open
Abstract
The genetic characteristics of Barrett’s esophagus (BE) and esophageal adenocarcinoma (EAC) in the Japanese population is unclear. This study aims to investigate the genetic characteristics from nondysplastic BE (NDBE) to early EAC in Japan. Clinical information was collected. Moreover, the genetic profile of NDBE without concurrent dysplasia, early EAC, and surrounding BE were also investigated using endoscopic biopsy samples and formalin-fixed, paraffin-embedded specimens from Japanese patients by targeted next-generation sequencing. Immunohistochemical staining for p53 was also performed for EAC lesions. Targeted NGS was performed for 33 cases with 77 specimens. No significant difference exists in the NDBE group between the number of putative drivers per lesion in the short-segment Barrett’s esophagus (SSBE) and long-segment Barrett’s esophagus (LSBE) [0 (range, 0–1) vs. 0 (range, 0–1). p = 1.00]. TP53 putative drivers were found in two patients (16.7%) with nondysplastic SSBE. TP53 was the majority of putative drivers in both BE adjacent to EAC and EAC, accounting for 66.7% and 66.7%, respectively. More putative drivers per lesion were found in the EAC than in the NDBE group [1 (range, 0–3) vs. 0 (range, 0–1). p < 0.01]. The genetic variants of TP53 in the Japanese early EAC were similar to those in western countries. However, TP53 putative drivers were detected even in Japanese patients with nondysplastic SSBE. This is significant because such nondysplastic SSBE might have higher risk of progressing to high-grade dysplasia or EAC. The risks of progression may not be underestimated and appropriate follow-ups may be necessary even in patients with SSBE. Trial registration: This study was registered at the University Hospital Medical Information Network (UMIN000034247).
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Affiliation(s)
- Mamoru Tokunaga
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, Inohana 1-8-1, Chiba, 260-8670, Japan
| | - Kenichiro Okimoto
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, Inohana 1-8-1, Chiba, 260-8670, Japan.
| | - Naoki Akizue
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, Inohana 1-8-1, Chiba, 260-8670, Japan
| | - Kentaro Ishikawa
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, Inohana 1-8-1, Chiba, 260-8670, Japan
| | - Yosuke Hirotsu
- Genome Analysis Center, Yamanashi Prefectural Central Hospital, Yamanashi, Japan
| | - Kenji Amemiya
- Genome Analysis Center, Yamanashi Prefectural Central Hospital, Yamanashi, Japan
| | - Masayuki Ota
- Department of Molecular Pathology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Keisuke Matsusaka
- Department of Molecular Pathology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Motoi Nishimura
- Division of Laboratory Medicine, Chiba University Hospital, Chiba, Japan
| | | | - Tsubasa Ishikawa
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, Inohana 1-8-1, Chiba, 260-8670, Japan
| | - Ariki Nagashima
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, Inohana 1-8-1, Chiba, 260-8670, Japan
| | - Wataru Shiratori
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, Inohana 1-8-1, Chiba, 260-8670, Japan
| | - Tatsuya Kaneko
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, Inohana 1-8-1, Chiba, 260-8670, Japan
| | - Hirotaka Oura
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, Inohana 1-8-1, Chiba, 260-8670, Japan
| | - Kengo Kanayama
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, Inohana 1-8-1, Chiba, 260-8670, Japan
| | - Yuki Ohta
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, Inohana 1-8-1, Chiba, 260-8670, Japan
| | - Takashi Taida
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, Inohana 1-8-1, Chiba, 260-8670, Japan
| | - Keiko Saito
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, Inohana 1-8-1, Chiba, 260-8670, Japan
| | - Tomoaki Matsumura
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, Inohana 1-8-1, Chiba, 260-8670, Japan
| | - Tetsuhiro Chiba
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, Inohana 1-8-1, Chiba, 260-8670, Japan
| | - Hitoshi Mochizuki
- Genome Analysis Center, Yamanashi Prefectural Central Hospital, Yamanashi, Japan
| | - Makoto Arai
- Department of Medicine and Clinical Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Jun Kato
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, Inohana 1-8-1, Chiba, 260-8670, Japan
| | - Jun-Ichiro Ikeda
- Department of Molecular Pathology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Masao Omata
- Genome Analysis Center, Yamanashi Prefectural Central Hospital, Yamanashi, Japan.,The University of Tokyo, Tokyo, Japan
| | - Naoya Kato
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, Inohana 1-8-1, Chiba, 260-8670, Japan
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Hoppe S, Jonas C, Wenzel MC, Velazquez Camacho O, Arolt C, Zhao Y, Büttner R, Quaas A, Plum PS, Hillmer AM. Genomic and Transcriptomic Characteristics of Esophageal Adenocarcinoma. Cancers (Basel) 2021; 13:cancers13174300. [PMID: 34503107 PMCID: PMC8428370 DOI: 10.3390/cancers13174300] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 08/20/2021] [Accepted: 08/22/2021] [Indexed: 12/28/2022] Open
Abstract
Simple Summary Cancer of the esophagus is a deadly disease. There are two main subtypes, adenocarcinoma and squamous cell carcinoma, with adenocarcinoma of the esophagus (EAC) being more common in Western countries. Barrett’s esophagus (BE) describes a change in the esophageal surface near the stomach in response to reflux of gastric acid into the esophagus. BE increases the risk of developing EAC, and the incidence of EAC has risen dramatically over recent decades. One likely reason for the poor prognosis of EAC is based on the fact that each tumor has many genes affected by mutations, and most of these genes differ across patients, hampering the efficacy of therapies that target specific cancer driver proteins. In this review, we provide an overview of the gene mutations and gene activity changes in EAC and how these features can be used to divide patients into groups that might have different clinical characteristics. Abstract Esophageal adenocarcinoma (EAC) is a deadly disease with limited options for targeted therapy. With the help of next-generation sequencing studies over the last decade, we gained an understanding of the genomic architecture of EAC. The tumor suppressor gene TP53 is mutated in 70 to 80% of tumors followed by genomic alterations in CDKN2A, KRAS, ERBB2, ARID1A, SMAD4 and a long tail of less frequently mutated genes. EAC is characterized by a high burden of point mutations and genomic rearrangements, resulting in amplifications and deletions of genomic regions. The genomic complexity is likely hampering the efficacy of targeted therapies. Barrett’s esophagus (BE), a metaplastic response of the esophagus to gastro-esophageal reflux disease, is the main risk factor for the development of EAC. Almost all EACs are derived from BE. The sequence from BE to EAC provides an opportunity to study the genomic evolution towards EAC. While the overlap of point mutations between BE and EAC within the same patient is, at times, surprisingly low, there is a correlation between the complexity of the genomic copy number profile and the development of EAC. Transcriptomic analyses separated EAC into a basal and a classical subtype, with the basal subtype showing a higher level of resistance to chemotherapy. In this review, we provide an overview of the current knowledge of the genomic and transcriptomic characteristics of EAC and their relevance for the development of the disease and patient care.
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Affiliation(s)
- Sascha Hoppe
- Institute of Pathology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany; (S.H.); (C.J.); (M.C.W.); (O.V.C.); (C.A.); (R.B.); (A.Q.); (P.S.P.)
| | - Christoph Jonas
- Institute of Pathology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany; (S.H.); (C.J.); (M.C.W.); (O.V.C.); (C.A.); (R.B.); (A.Q.); (P.S.P.)
| | - Marten Christian Wenzel
- Institute of Pathology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany; (S.H.); (C.J.); (M.C.W.); (O.V.C.); (C.A.); (R.B.); (A.Q.); (P.S.P.)
| | - Oscar Velazquez Camacho
- Institute of Pathology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany; (S.H.); (C.J.); (M.C.W.); (O.V.C.); (C.A.); (R.B.); (A.Q.); (P.S.P.)
| | - Christoph Arolt
- Institute of Pathology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany; (S.H.); (C.J.); (M.C.W.); (O.V.C.); (C.A.); (R.B.); (A.Q.); (P.S.P.)
| | - Yue Zhao
- Department of General, Visceral, Cancer and Transplantation Surgery, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany;
| | - Reinhard Büttner
- Institute of Pathology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany; (S.H.); (C.J.); (M.C.W.); (O.V.C.); (C.A.); (R.B.); (A.Q.); (P.S.P.)
| | - Alexander Quaas
- Institute of Pathology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany; (S.H.); (C.J.); (M.C.W.); (O.V.C.); (C.A.); (R.B.); (A.Q.); (P.S.P.)
| | - Patrick Sven Plum
- Institute of Pathology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany; (S.H.); (C.J.); (M.C.W.); (O.V.C.); (C.A.); (R.B.); (A.Q.); (P.S.P.)
- Department of General, Visceral, Cancer and Transplantation Surgery, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany;
| | - Axel Maximilian Hillmer
- Institute of Pathology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany; (S.H.); (C.J.); (M.C.W.); (O.V.C.); (C.A.); (R.B.); (A.Q.); (P.S.P.)
- Center for Molecular Medicine Cologne, University of Cologne, 50931 Cologne, Germany
- Correspondence:
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McShane R, Arya S, Stewart AJ, Caie P, Bates M. Prognostic features of the tumour microenvironment in oesophageal adenocarcinoma. Biochim Biophys Acta Rev Cancer 2021; 1876:188598. [PMID: 34332022 DOI: 10.1016/j.bbcan.2021.188598] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 07/26/2021] [Accepted: 07/26/2021] [Indexed: 12/12/2022]
Abstract
Oesophageal adenocarcinoma (OAC) is a disease with an incredibly poor survival rate and a complex makeup. The growth and spread of OAC tumours are profoundly influenced by their surrounding microenvironment and the properties of the tumour itself. Constant crosstalk between the tumour and its microenvironment is key to the survival of the tumour and ultimately the death of the patient. The tumour microenvironment (TME) is composed of a complex milieu of cell types including cancer associated fibroblasts (CAFs) which make up the tumour stroma, endothelial cells which line blood and lymphatic vessels and infiltrating immune cell populations. These various cell types and the tumour constantly communicate through environmental cues including fluctuations in pH, hypoxia and the release of mitogens such as cytokines, chemokines and growth factors, many of which help promote malignant progression. Eventually clusters of tumour cells such as tumour buds break away and spread through the lymphatic system to nearby lymph nodes or enter the circulation forming secondary metastasis. Collectively, these factors need to be considered when assessing and treating patients clinically. This review aims to summarise the ways in which these various factors are currently assessed and how they relate to patient treatment and outcome at an individual level.
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Affiliation(s)
| | - Swati Arya
- School of Medicine, University of St Andrews, Fife, UK
| | | | - Peter Caie
- School of Medicine, University of St Andrews, Fife, UK
| | - Mark Bates
- Department of Surgery, Trinity Translational Medicine Institute, St. James's Hospital, Dublin 8, Ireland; Trinity St James's Cancer Institute, St James's Hospital, Dublin 8, Ireland.
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Abstract
Upper gastroesophageal carcinomas consist of cancers arising from the esophagus and stomach. Squamous cell carcinomas and adenocarcinomas are seen in the esophagus and despite arising from the same organ have different biology. Gastric adenocarcinomas are categorized into 4 molecular subtypes: high Epstein-Barr virus load, microsatellite unstable cancers, chromosomal unstable (CIN) cancers, and genomically stable cancers. Genomically stable gastric cancers correlate highly with histologically defined diffuse-type cancers. Esophageal carcinomas and CIN gastric cancers often are driven by high-level amplifications of oncogenes and contain a high degree of intratumoral heterogeneity. Targeted therapeutics is an active area of research for gastroesophageal cancers.
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Affiliation(s)
- Matthew D Stachler
- Department of Pathology, University of California San Francisco, 513 Parnassus Avenue HSW450B, San Francisco, CA 94143, USA.
| | - Ramon U Jin
- Section of Hematology/Oncology, Department of Medicine, Baylor College of Medicine, 7200 Cambridge Street, Suite 7B, MS: BCM904, Houston, TX 77030, USA
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80
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Scott SJ, Li X, Jammula S, Devonshire G, Lindon C, Fitzgerald RC, D'Avino PP. Evidence that polyploidy in esophageal adenocarcinoma originates from mitotic slippage caused by defective chromosome attachments. Cell Death Differ 2021; 28:2179-2193. [PMID: 33649470 PMCID: PMC8257792 DOI: 10.1038/s41418-021-00745-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 01/22/2021] [Accepted: 01/28/2021] [Indexed: 01/19/2023] Open
Abstract
Polyploidy is present in many cancer types and is increasingly recognized as an important factor in promoting chromosomal instability, genome evolution, and heterogeneity in cancer cells. However, the mechanisms that trigger polyploidy in cancer cells are largely unknown. In this study, we investigated the origin of polyploidy in esophageal adenocarcinoma (EAC), a highly heterogenous cancer, using a combination of genomics and cell biology approaches in EAC cell lines, organoids, and tumors. We found the EAC cells and organoids present specific mitotic defects consistent with problems in the attachment of chromosomes to the microtubules of the mitotic spindle. Time-lapse analyses confirmed that EAC cells have problems in congressing and aligning their chromosomes, which can ultimately culminate in mitotic slippage and polyploidy. Furthermore, whole-genome sequencing, RNA-seq, and quantitative immunofluorescence analyses revealed alterations in the copy number, expression, and cellular distribution of several proteins known to be involved in the mechanics and regulation of chromosome dynamics during mitosis. Together, these results provide evidence that an imbalance in the amount of proteins implicated in the attachment of chromosomes to spindle microtubules is the molecular mechanism underlying mitotic slippage in EAC. Our findings that the likely origin of polyploidy in EAC is mitotic failure caused by problems in chromosomal attachments not only improves our understanding of cancer evolution and diversification, but may also aid in the classification and treatment of EAC and possibly other highly heterogeneous cancers.
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Affiliation(s)
- Stacey J Scott
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Xiaodun Li
- Medical Research Council Cancer Unit, Hutchison/Medical Research Council Research Centre, University of Cambridge, Cambridge, UK
| | - Sriganesh Jammula
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Ginny Devonshire
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Catherine Lindon
- Department of Pharmacology, University of Cambridge, Cambridge, UK
| | - Rebecca C Fitzgerald
- Medical Research Council Cancer Unit, Hutchison/Medical Research Council Research Centre, University of Cambridge, Cambridge, UK
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81
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Genomic instability signals offer diagnostic possibility in early cancer detection. Trends Genet 2021; 37:966-972. [PMID: 34218956 DOI: 10.1016/j.tig.2021.06.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 06/07/2021] [Accepted: 06/08/2021] [Indexed: 12/12/2022]
Abstract
Emerging evidence from the large numbers of cancer genomes analyzed in recent years indicates that chromosomal instability (CI), a well-established hallmark of cancer cells, is detectable in precancerous lesions. In this opinion, we discuss the association of this instability with tumor progression and cancer risk. We highlight the opportunity that early genomic instability presents for the diagnosis of esophageal adenocarcinoma (EAC) and its precancerous lesion, Barrett's esophagus (BE). With a growing body of evidence suggesting that only a small pool of cancer-related genes are involved in early tumor development, we argue that general genomic instability may hold greater diagnostic potential for early cancer detection as opposed to the identification of individual mutational biomarkers.
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82
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McKay RR, Kwak L, Crowdis JP, Sperger JM, Zhao SG, Xie W, Werner L, Lis RT, Zhang Z, Wei XX, Lang JM, Van Allen EM, Bhatt RS, Yu EY, Nelson PS, Bubley GJ, Montgomery RB, Taplin ME. Phase II Multicenter Study of Enzalutamide in Metastatic Castration-Resistant Prostate Cancer to Identify Mechanisms Driving Resistance. Clin Cancer Res 2021; 27:3610-3619. [PMID: 33849963 PMCID: PMC8254786 DOI: 10.1158/1078-0432.ccr-20-4616] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 02/23/2021] [Accepted: 04/09/2021] [Indexed: 12/15/2022]
Abstract
PURPOSE Enzalutamide is a second-generation androgen receptor (AR) inhibitor that has improved overall survival (OS) in metastatic castration-resistant prostate cancer (CRPC). However, nearly all patients develop resistance. We designed a phase II multicenter study of enzalutamide in metastatic CRPC incorporating tissue and blood biomarkers to dissect mechanisms driving resistance. PATIENTS AND METHODS Eligible patients with metastatic CRPC underwent a baseline metastasis biopsy and then initiated enzalutamide 160 mg daily. A repeat metastasis biopsy was obtained at radiographic progression from the same site when possible. Blood for circulating tumor cell (CTC) analysis was collected at baseline and progression. The primary objective was to analyze mechanisms of resistance in serial biopsies. Whole-exome sequencing was performed on tissue biopsies. CTC samples underwent RNA sequencing. RESULTS A total of 65 patients initiated treatment, of whom 22 (33.8%) had received prior abiraterone. Baseline biopsies were enriched for alterations in AR (mutations, amplifications) and tumor suppression genes (PTEN, RB1, and TP53), which were observed in 73.1% and 92.3% of baseline biopsies, respectively. Progression biopsies revealed increased AR amplifications (64.7% at progression vs. 53.9% at baseline) and BRCA2 alterations (64.7% at progression vs. 38.5% at baseline). Genomic analysis of baseline and progression CTC samples demonstrated increased AR splice variants, AR-regulated genes, and neuroendocrine markers at progression. CONCLUSIONS Our results demonstrate that a large proportion of enzalutamide-treated patients have baseline and progression alterations in the AR pathway and tumor suppressor genes. We demonstrate an increased number of BRCA2 alterations post-enzalutamide, highlighting the importance of serial tumor sampling in CRPC.
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Affiliation(s)
- Rana R McKay
- University of California San Diego, San Diego, California
- Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Lucia Kwak
- Dana-Farber Cancer Institute, Boston, Massachusetts
| | | | - Jamie M Sperger
- Carbone Cancer Center, University of Wisconsin-Madison, Madison, Wisconsin
| | - Shuang G Zhao
- Carbone Cancer Center, University of Wisconsin-Madison, Madison, Wisconsin
| | - Wanling Xie
- Dana-Farber Cancer Institute, Boston, Massachusetts
| | | | - Rosina T Lis
- Dana-Farber Cancer Institute, Boston, Massachusetts
| | | | - Xiao X Wei
- Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Joshua M Lang
- Carbone Cancer Center, University of Wisconsin-Madison, Madison, Wisconsin
| | | | - Rupal S Bhatt
- Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - Evan Y Yu
- University of Washington, Seattle, Washington
- Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Peter S Nelson
- University of Washington, Seattle, Washington
- Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Glenn J Bubley
- Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - R Bruce Montgomery
- University of Washington, Seattle, Washington
- Fred Hutchinson Cancer Research Center, Seattle, Washington
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83
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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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84
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Jabbour SK, Williams TM, Sayan M, Miller ED, Ajani JA, Chang AC, Coleman N, El-Rifai W, Haddock M, Ilson D, Jamorabo D, Kunos C, Lin S, Liu G, Prasanna PG, Rustgi AK, Wong R, Vikram B, Ahmed MM. Potential Molecular Targets in the Setting of Chemoradiation for Esophageal Malignancies. J Natl Cancer Inst 2021; 113:665-679. [PMID: 33351071 PMCID: PMC8600025 DOI: 10.1093/jnci/djaa195] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 10/03/2020] [Accepted: 11/30/2020] [Indexed: 11/14/2022] Open
Abstract
Although the development of effective combined chemoradiation regimens for esophageal cancers has resulted in statistically significant survival benefits, the majority of patients treated with curative intent develop locoregional and/or distant relapse. Further improvements in disease control and survival will require the development of individualized therapy based on the knowledge of host and tumor genomics and potentially harnessing the host immune system. Although there are a number of gene targets that are amplified and proteins that are overexpressed in esophageal cancers, attempts to target several of these have not proven successful in unselected patients. Herein, we review our current state of knowledge regarding the molecular pathways implicated in esophageal carcinoma, and the available agents for targeting these pathways that may rationally be combined with standard chemoradiation, with the hope that this commentary will guide future efforts of novel combinations of therapy.
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Affiliation(s)
- Salma K Jabbour
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ, USA
| | - Terence M Williams
- Department of Radiation Oncology, The Ohio State University, Columbus, OH, USA
- Department of Radiation Oncology, City of Hope National Medical Center, Duarte, CA, USA
| | - Mutlay Sayan
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ, USA
| | - Eric D Miller
- Department of Radiation Oncology, The Ohio State University, Columbus, OH, USA
| | - Jaffer A Ajani
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Andrew C Chang
- Department of Surgery, University of Michigan, Ann Arbor, MI, USA
- Department of Surgery, Section of Thoracic Surgery, University of Michigan, Ann Arbor, MI, USA
| | - Norman Coleman
- National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Wael El-Rifai
- Department of Surgery, Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL, USA
- Department of Veterans Affairs, Miami Healthcare System, Miami, FL, USA
| | - Michael Haddock
- Department of Radiation Oncology, Mayo Clinic, Rochester, MN, USA
| | - David Ilson
- Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | | | - Charles Kunos
- Investigational Drug Branch, Cancer Therapy Evaluation Program, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Steven Lin
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Geoffrey Liu
- Division of Medical Oncology, Princess Margaret Cancer Centre, Toronto, Canada
| | - Pataje G Prasanna
- Radiation Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Anil K Rustgi
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA
| | - Rosemary Wong
- Radiation Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Bhadrasain Vikram
- Radiation Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Mansoor M Ahmed
- Radiation Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
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85
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De A, Zhou J, Liu P, Huang M, Gunewardena S, Mathur SC, Christenson LK, Sharma M, Zhang Q, Bansal A. Forkhead box F1 induces columnar phenotype and epithelial-to-mesenchymal transition in esophageal squamous cells to initiate Barrett's like metaplasia. J Transl Med 2021; 101:745-759. [PMID: 33495575 PMCID: PMC9296259 DOI: 10.1038/s41374-021-00534-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 12/22/2020] [Accepted: 12/28/2020] [Indexed: 11/08/2022] Open
Abstract
Multiple genome-wide association studies (GWAS) have linked Forkhead Box F1 (FOXF1) to Barrett's esophagus (BE). Understanding whether FOXF1 is involved in initiation of Barrett's metaplasia could allow FOXF1 to be used for risk stratification and for therapy. Two-dimensional cell cultures and three-dimensional organoid cultures and well-annotated human biopsies were used to determine the role of FOXF1 in BE pathogenesis. Multiple established esophageal squamous and BE cell lines were tested in gain- and loss-of-function studies. Initiation of a BE-like metaplastic change was evaluated by measuring characteristic cytokeratins and global gene expression profiling and by culturing organoids. Epithelial-mesenchymal transition (EMT) was evaluated by immunostaining for E-cadherin, vimentin and Snail, and by cell motility assay. Columnar esophageal epithelium of BE patients exhibited higher expression of FOXF1 compared to normal squamous esophageal epithelium of GERD patients (P < 0.001). Acidic bile salts induced nuclear FOXF1 in esophageal squamous cells. FOXF1 overexpression in normal esophageal squamous cells: (a) increased columnar cytokeratins and decreased squamous cytokeratins, (b) converted squamous organoids to glandular organoids, and (c) switched global gene profiles to resemble that of human BE epithelium (P = 2.1685e - 06 for upregulated genes and P = 8.3378e - 09 for downregulated genes). FOXF1 inhibition in BE cell lines led to loss of BE differentiation markers, CK7, and mucin 2. Also, FOXF1 induced EMT and promoted cell motility in normal esophageal squamous epithelial cells. FOXF1-induced genes mapped to pathways such as Cancer, Cellular Assembly and Organization, DNA Replication, Recombination, and Repair. In conclusion, FOXF1 promotes a BE-like columnar phenotype and cell motility in esophageal squamous epithelial cells, which may have a critical role in BE development. FOXF1 should be studied further as a biomarker for BE and as a target for BE treatment.
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Affiliation(s)
- Alok De
- Midwest Veterans' Biomedical Research Foundation (MVBRF), Kansas City, MO, USA
- Kansas City VA Medical Center, Kansas City, MO, USA
| | - Jianping Zhou
- Midwest Veterans' Biomedical Research Foundation (MVBRF), Kansas City, MO, USA
- Kansas City VA Medical Center, Kansas City, MO, USA
| | - Pi Liu
- Department of Medicine, Center for Esophageal Diseases, Baylor University Medical Center and Center for Esophageal Research, Baylor Scott & White Research Institute, Dallas, TX, 75246, USA
| | - Manling Huang
- Department of Medicine, Center for Esophageal Diseases, Baylor University Medical Center and Center for Esophageal Research, Baylor Scott & White Research Institute, Dallas, TX, 75246, USA
| | - Sumedha Gunewardena
- Department of Molecular and Integrative Physiology, The University of Kansas Medical Center, Kansas City, KS, USA
| | - Sharad C Mathur
- Department of Pathology and Laboratory Medicine, Veterans Affairs Medical Center, Kansas City, MO, USA
- The University of Kansas Medical Center, Kansas City, KS, USA
| | - Lane K Christenson
- Department of Molecular and Integrative Physiology, The University of Kansas Medical Center, Kansas City, KS, USA
| | - Mukut Sharma
- Midwest Veterans' Biomedical Research Foundation (MVBRF), Kansas City, MO, USA
- Research and Development Service, Kansas City Veterans Affairs Medical Center, Kansas City, MO, USA
| | - Qiuyang Zhang
- Department of Medicine, Center for Esophageal Diseases, Baylor University Medical Center and Center for Esophageal Research, Baylor Scott & White Research Institute, Dallas, TX, 75246, USA.
| | - Ajay Bansal
- Division of Gastroenterology and Hepatology, The University of Kansas Medical Center, Kansas City, KS, USA.
- Division of Gastroenterology and Hepatology, Veterans Affairs Medical Center, Kansas City, MO, USA.
- The University of Kansas Cancer Center, Kansas City, KS, USA.
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86
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Kumar S, Buon L, Talluri S, Roncador M, Liao C, Zhao J, Shi J, Chakraborty C, Gonzalez G, Tai YT, Prabhala R, Samur MK, Munshi NC, Shammas MA. Integrated genomics and comprehensive validation reveal drivers of genomic evolution in esophageal adenocarcinoma. Commun Biol 2021; 4:617. [PMID: 34031527 PMCID: PMC8144613 DOI: 10.1038/s42003-021-02125-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 04/16/2021] [Indexed: 12/13/2022] Open
Abstract
Esophageal adenocarcinoma (EAC) is associated with a marked genomic instability, which underlies disease progression and development of resistance to treatment. In this study, we used an integrated genomics approach to identify a genomic instability signature. Here we show that elevated expression of this signature correlates with poor survival in EAC as well as three other cancers. Knockout and overexpression screens establish the relevance of these genes to genomic instability. Indepth evaluation of three genes (TTK, TPX2 and RAD54B) confirms their role in genomic instability and tumor growth. Mutational signatures identified by whole genome sequencing and functional studies demonstrate that DNA damage and homologous recombination are common mechanisms of genomic instability induced by these genes. Our data suggest that the inhibitors of TTK and possibly other genes identified in this study have potential to inhibit/reduce growth and spontaneous as well as chemotherapy-induced genomic instability in EAC and possibly other cancers. Subodh Kumar et al. identify a gene signature correlated with genomic instability and poor survival in esophageal adenocarcinoma (EAC), using a combination of integrative genomic analysis of patient data and laboratory validation in cell line models and mice. They find that inhibitors of some of the identified proteins, including TTK, could be used to reduce genomic evolution as well as inhibit growth of EAC cells.
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Affiliation(s)
- Subodh Kumar
- Dana Farber Cancer Institute, Boston, MA, USA.,Veterans Administration Healthcare System, Boston, MA, USA
| | - Leutz Buon
- Dana Farber Cancer Institute, Boston, MA, USA
| | - Srikanth Talluri
- Dana Farber Cancer Institute, Boston, MA, USA.,Veterans Administration Healthcare System, Boston, MA, USA
| | | | - Chengcheng Liao
- Dana Farber Cancer Institute, Boston, MA, USA.,Veterans Administration Healthcare System, Boston, MA, USA
| | - Jiangning Zhao
- Dana Farber Cancer Institute, Boston, MA, USA.,Veterans Administration Healthcare System, Boston, MA, USA
| | - Jialan Shi
- Dana Farber Cancer Institute, Boston, MA, USA.,Veterans Administration Healthcare System, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | | | - Gabriel Gonzalez
- Veterans Administration Healthcare System, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Yu-Tzu Tai
- Dana Farber Cancer Institute, Boston, MA, USA
| | - Rao Prabhala
- Dana Farber Cancer Institute, Boston, MA, USA.,Veterans Administration Healthcare System, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | | | - Nikhil C Munshi
- Dana Farber Cancer Institute, Boston, MA, USA.,Veterans Administration Healthcare System, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Masood A Shammas
- Dana Farber Cancer Institute, Boston, MA, USA. .,Veterans Administration Healthcare System, Boston, MA, USA.
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87
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Liu M, Chen J, Wang X, Wang C, Zhang X, Xie Y, Zuo Z, Ren J, Zhao Q. MesKit: a tool kit for dissecting cancer evolution of multi-region tumor biopsies through somatic alterations. Gigascience 2021; 10:6279596. [PMID: 34018555 PMCID: PMC8138830 DOI: 10.1093/gigascience/giab036] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 03/23/2021] [Accepted: 04/23/2021] [Indexed: 11/17/2022] Open
Abstract
Background Multi-region sequencing (MRS) has been widely used to analyze intra-tumor heterogeneity (ITH) and cancer evolution. However, comprehensive analysis of mutational data from MRS is still challenging, necessitating complicated integration of a plethora of computational and statistical approaches. Findings Here, we present MesKit, an R/Bioconductor package that can assist in characterizing genetic ITH and tracing the evolutionary history of tumors based on somatic alterations detected by MRS. MesKit provides a wide range of analysis and visualization modules, including ITH evaluation, metastatic route inference, and mutational signature identification. In addition, MesKit implements an auto-layout algorithm to generate phylogenetic trees based on somatic mutations. The application of MesKit for 2 reported MRS datasets of hepatocellular carcinoma and colorectal cancer identified known heterogeneous features and evolutionary patterns, together with potential driver events during cancer evolution. Conclusions In summary, MesKit is useful for interpreting ITH and tracing evolutionary trajectory based on MRS data. MesKit is implemented in R and available at https://bioconductor.org/packages/MesKit under the GPL v3 license.
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Affiliation(s)
- Mengni Liu
- School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China.,State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, 651 E Dongfeng Road, Guangzhou, Guangdong 510060, China
| | - Jianyu Chen
- School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China
| | - Xin Wang
- School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China
| | - Chengwei Wang
- School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China
| | - Xiaolong Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, 651 E Dongfeng Road, Guangzhou, Guangdong 510060, China
| | - Yubin Xie
- School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China
| | - Zhixiang Zuo
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, 651 E Dongfeng Road, Guangzhou, Guangdong 510060, China
| | - Jian Ren
- School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China.,State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, 651 E Dongfeng Road, Guangzhou, Guangdong 510060, China
| | - Qi Zhao
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, 651 E Dongfeng Road, Guangzhou, Guangdong 510060, China
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88
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Hibino S, Kawazoe T, Kasahara H, Itoh S, Ishimoto T, Sakata-Yanagimoto M, Taniguchi K. Inflammation-Induced Tumorigenesis and Metastasis. Int J Mol Sci 2021; 22:ijms22115421. [PMID: 34063828 PMCID: PMC8196678 DOI: 10.3390/ijms22115421] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 05/07/2021] [Accepted: 05/11/2021] [Indexed: 02/07/2023] Open
Abstract
Inflammation, especially chronic inflammation, plays a pivotal role in tumorigenesis and metastasis through various mechanisms and is now recognized as a hallmark of cancer and an attractive therapeutic target in cancer. In this review, we discuss recent advances in molecular mechanisms of how inflammation promotes tumorigenesis and metastasis and suppresses anti-tumor immunity in various types of solid tumors, including esophageal, gastric, colorectal, liver, and pancreatic cancer as well as hematopoietic malignancies.
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Affiliation(s)
- Sana Hibino
- Research Center for Advanced Science and Technology, Department of Inflammology, The University of Tokyo, Tokyo 153-0041, Japan;
| | - Tetsuro Kawazoe
- Department of Microbiology and Immunology, Keio University School of Medicine, Tokyo 160-8582, Japan;
- Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan;
| | - Hidenori Kasahara
- National Center for Global Health and Medicine, Department of Stem Cell Biology, Research Institute, Tokyo 162-8655, Japan;
- Division of Hematology, Department of Medicine, Keio University School of Medicine, Tokyo 160-8582, Japan
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA
| | - Shinji Itoh
- Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan;
| | - Takatsugu Ishimoto
- Gastrointestinal Cancer Biology, International Research Center of Medical Sciences (IRCMS), Kumamoto University, Kumamoto 860-0811, Japan;
| | | | - Koji Taniguchi
- Department of Microbiology and Immunology, Keio University School of Medicine, Tokyo 160-8582, Japan;
- Department of Pathology, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Sapporo 060-8638, Japan
- Correspondence: ; Tel.: +81-11-706-5050
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89
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Lonie JM, Barbour AP, Dolcetti R. Understanding the immuno-biology of oesophageal adenocarcinoma: Towards improved therapeutic approaches. Cancer Treat Rev 2021; 98:102219. [PMID: 33993033 DOI: 10.1016/j.ctrv.2021.102219] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 04/30/2021] [Accepted: 05/05/2021] [Indexed: 12/12/2022]
Abstract
With an incidence that is constantly rising, oesophageal adenocarcinoma (OAC) is becoming an increasing health burden worldwide. Although significant advances in treatment regimens have improved patient outcomes, survival rates for this deadly cancer remain unsatisfactory. This highlights the need to improve current therapeutic approaches and develop novel therapeutic strategies for treating OAC patients. The advent of immunotherapy has revolutionised treatment across a range of malignancies, however outcomes in OAC show modest results. The inherent resistance of OAC to treatment reflects the complex genomic landscape of this cancer, which displays a lack of ubiquitous driver mutations and large-scale genomic alterations along with high tumour and immune heterogeneity. Research into the immune landscape of OAC is limited, and elucidation of the mechanisms surrounding the immune responses to this complex cancer will result in improved therapeutic approaches. This review explores what is known about the immuno-biology of OAC and explores promising therapeutic avenues that may improve responses to immunotherapeutic regimens.
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Affiliation(s)
- James M Lonie
- The University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, Queensland, Australia.
| | - Andrew P Barbour
- The University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, Queensland, Australia; Princess Alexandra Hospital, Brisbane, Queensland, Australia
| | - Riccardo Dolcetti
- The University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, Queensland, Australia; Sir Peter MacCallum Cancer Centre, The University of Melbourne, Melbourne, Victoria, Australia
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90
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Verma R, Sattar RSA, Nimisha, Apurva, Kumar A, Sharma AK, Sumi MP, Ahmad E, Ali A, Mahajan B, Saluja SS. Cross-talk between next generation sequencing methodologies to identify genomic signatures of esophageal cancer. Crit Rev Oncol Hematol 2021; 162:103348. [PMID: 33961993 DOI: 10.1016/j.critrevonc.2021.103348] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 04/22/2021] [Accepted: 05/01/2021] [Indexed: 02/07/2023] Open
Abstract
The asymptomatic behaviour of esophageal cancerous cells at early stages develops advanced clinical presentation of the disease, resulting in poor prognosis and curbed intervention of therapeutic modalities. The endeavours to detect diagnostic and prognostic markers have been proven futile at the clinical platform. While several biomarkers have been investigated, including CYFRA 21-1, carcinoembryonic antigen and squamous cell carcinoma antigen, their sensitivity has not proved consistently satisfactory across the various stages of esophageal cancer. Hence, there is an impending requirement of biomarkers for early diagnosis and better prognosis. In the recent past, next generation sequencing (NGS) tool has emerged as an important tool to highlight the hallmarks of esophageal cancer (EC). This review summarizes the changes/mutations occurred in tumor cells during carcinogenesis and addresses the contribution of NGS techniques, viz. whole genome sequencing (WGS), RNA-Sequencing and Exome sequencing (ES), in EC. Additionally, this review highlights the connection between the findings from these techniques. An effort has been made to emphasize the genes affected and involved signaling pathway in EC. Further, investigations of these mutated genes would not only shed light on the relevant genes to be studied but also help in the better management and cure through personalized therapy.
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Affiliation(s)
- Renu Verma
- Central Molecular Laboratory, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India
| | - Real Sumayya Abdul Sattar
- Central Molecular Laboratory, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India
| | - Nimisha
- Central Molecular Laboratory, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India
| | - Apurva
- Central Molecular Laboratory, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India
| | - Arun Kumar
- Central Molecular Laboratory, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India
| | - Abhay Kumar Sharma
- Central Molecular Laboratory, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India
| | - Mamta Parveen Sumi
- Central Molecular Laboratory, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India
| | - Ejaj Ahmad
- Central Molecular Laboratory, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India
| | - Asgar Ali
- Department of Biochemistry, All India Institute of Medical Science (AIIMS), Patna, Bihar, India
| | - Bhawna Mahajan
- Central Molecular Laboratory, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India; Department of Biochemistry, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India
| | - Sundeep Singh Saluja
- Central Molecular Laboratory, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India; Department of GI Surgery, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India.
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91
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Douville C, Moinova HR, Thota PN, Shaheen NJ, Iyer PG, Canto MI, Wang JS, Dumot JA, Faulx A, Kinzler KW, Papadopoulos N, Vogelstein B, Markowitz SD, Bettegowda C, Willis JE, Chak A. Massively Parallel Sequencing of Esophageal Brushings Enables an Aneuploidy-Based Classification of Patients With Barrett's Esophagus. Gastroenterology 2021; 160:2043-2054.e2. [PMID: 33493502 PMCID: PMC8141353 DOI: 10.1053/j.gastro.2021.01.209] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 01/04/2021] [Accepted: 01/13/2021] [Indexed: 12/15/2022]
Abstract
BACKGROUND & AIMS Aneuploidy has been proposed as a tool to assess progression in patients with Barrett's esophagus (BE), but has heretofore required multiple biopsies. We assessed whether a single esophageal brushing that widely sampled the esophagus could be combined with massively parallel sequencing to characterize aneuploidy and identify patients with disease progression to dysplasia or cancer. METHODS Esophageal brushings were obtained from patients without BE, with non-dysplastic BE (NDBE), low-grade dysplasia (LGD), high-grade dysplasia (HGD), or adenocarcinoma (EAC). To assess aneuploidy, we used RealSeqS, a technique that uses a single primer pair to interrogate ∼350,000 genome-spanning regions and identify specific chromosome arm alterations. A classifier to distinguish NDBE from EAC was trained on results from 79 patients. An independent validation cohort of 268 subjects was used to test the classifier at distinguishing patients at successive phases of BE progression. RESULTS Aneuploidy progression was associated with gains of 1q, 12p, and 20q and losses on 9p and 17p. The entire chromosome 8q was often gained in NDBE, whereas focal gain of 8q24 was identified only when there was dysplasia. Among validation subjects, a classifier incorporating these features with a global measure of aneuploidy scored positive in 96% of EAC, 68% of HGD, but only 7% of NDBE. CONCLUSIONS RealSeqS analysis of esophageal brushings provides a practical and sensitive method to determine aneuploidy in BE patients. It identifies specific chromosome changes that occur early in NDBE and others that occur late and mark progression to dysplasia. The clinical implications of this approach can now be tested in prospective trials.
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Affiliation(s)
- Christopher Douville
- Department of Oncology, the Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland; The Ludwig Center, Johns Hopkins University School of Medicine, Baltimore, Maryland; The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, Maryland; Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Helen R Moinova
- Department of Medicine, Case Western Reserve University, Cleveland, Ohio
| | - Prashanthi N Thota
- Department of Gastroenterology and Hepatology, Cleveland Clinic Foundation, Cleveland, Ohio
| | - Nicholas J Shaheen
- Center for Esophageal Diseases and Swallowing, Department of Medicine, University of North Carolina, Chapel Hill, North Carolina
| | - Prasad G Iyer
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Marcia Irene Canto
- Department of Oncology, the Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Medicine, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Jean S Wang
- Department of Medicine, Washington University in St. Louis, St. Louis, Missouri
| | - John A Dumot
- Department of Medicine, Case Western Reserve University, Cleveland, Ohio
| | - Ashley Faulx
- Department of Medicine, Case Western Reserve University, Cleveland, Ohio
| | - Kenneth W Kinzler
- Department of Oncology, the Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland; The Ludwig Center, Johns Hopkins University School of Medicine, Baltimore, Maryland; The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, Maryland; Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Nickolas Papadopoulos
- Department of Oncology, the Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland; The Ludwig Center, Johns Hopkins University School of Medicine, Baltimore, Maryland; The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, Maryland; Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Bert Vogelstein
- Department of Oncology, the Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland; The Ludwig Center, Johns Hopkins University School of Medicine, Baltimore, Maryland; The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, Maryland; Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland; The Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Sanford D Markowitz
- Department of Medicine, Case Western Reserve University, Cleveland, Ohio; Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, Ohio; Seidman Cancer Center, University Hospitals Cleveland Medical Center, Cleveland, Ohio.
| | - Chetan Bettegowda
- Department of Oncology, the Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland; The Ludwig Center, Johns Hopkins University School of Medicine, Baltimore, Maryland; The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, Maryland; Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Joseph E Willis
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, Ohio; Seidman Cancer Center, University Hospitals Cleveland Medical Center, Cleveland, Ohio; Department of Pathology, Case Western Reserve University, Cleveland, Ohio
| | - Amitabh Chak
- Department of Medicine, Case Western Reserve University, Cleveland, Ohio; Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, Ohio; Seidman Cancer Center, University Hospitals Cleveland Medical Center, Cleveland, Ohio.
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92
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Nakanishi R, Shimizu T, Kumagai K, Takai A, Marusawa H. Genetic Pathogenesis of Inflammation-Associated Cancers in Digestive Organs. Pathogens 2021; 10:453. [PMID: 33918902 PMCID: PMC8069378 DOI: 10.3390/pathogens10040453] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 03/12/2021] [Accepted: 04/08/2021] [Indexed: 12/20/2022] Open
Abstract
Epidemiological, clinical, and biological studies convincingly demonstrate that chronic inflammation predisposes to the development of human cancers. In digestive organs, inflammation-associated cancers include colitis-associated colorectal cancers, Helicobacter pylori-associated gastric cancer, as well as Barrett's esophagus and esophageal adenocarcinoma associated with chronic duodenogastric-esophageal reflux. Cancer is a genomic disease, and stepwise accumulation of genetic and epigenetic alterations of tumor-related genes leads to the development of tumor cells. Recent genome analyses show that genetic alterations, which are evoked by inflammation, are latently accumulated in inflamed epithelial cells of digestive organs. Production of reactive oxygen and aberrant expression of activation-induced cytidine deaminase, a nucleotide-editing enzyme, could be induced in inflamed gastrointestinal epithelial cells and play a role as a genomic modulator of inflammation-associated carcinogenesis. Understanding the molecular linkage between inflammation and genetic alterations will open up a new field of tumor biology and provide a novel strategy for the prevention of inflammation-associated tumorigenesis.
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Affiliation(s)
- Risa Nakanishi
- Department of Gastroenterology, Red Cross Osaka Hospital, Osaka 543-8555, Japan;
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan; (T.S.); (K.K.); (A.T.)
| | - Takahiro Shimizu
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan; (T.S.); (K.K.); (A.T.)
| | - Ken Kumagai
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan; (T.S.); (K.K.); (A.T.)
| | - Atsushi Takai
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan; (T.S.); (K.K.); (A.T.)
| | - Hiroyuki Marusawa
- Department of Gastroenterology, Red Cross Osaka Hospital, Osaka 543-8555, Japan;
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93
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Abstract
Cancer is a clonal disorder derived from a single ancestor cell and its progenies that are positively selected by acquisition of 'driver mutations'. However, the evolution of positively selected clones does not necessarily imply the presence of cancer. On the contrary, it has become clear that expansion of these clones in phenotypically normal or non-cancer tissues is commonly seen in association with ageing and/or in response to environmental insults and chronic inflammation. Recent studies have reported expansion of clones harbouring mutations in cancer driver genes in the blood, skin, oesophagus, bronchus, liver, endometrium and bladder, where the expansion could be so extensive that tissues undergo remodelling of an almost entire tissue. The presence of common cancer driver mutations in normal tissues suggests a strong link to cancer development, providing an opportunity to understand early carcinogenic processes. Nevertheless, some driver mutations are unique to normal tissues or have a mutation frequency that is much higher in normal tissue than in cancer, indicating that the respective clones may not necessarily be destined for evolution to cancer but even negatively selected for carcinogenesis depending on the mutated gene. Moreover, tissues that are remodelled by genetically altered clones might define functionalities of aged tissues or modified inflammatory processes. In this Review, we provide an overview of major findings on clonal expansion in phenotypically normal or non-cancer tissues and discuss their biological significance not only in cancer development but also in ageing and inflammatory diseases.
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Affiliation(s)
- Nobuyuki Kakiuchi
- Department of Pathology and Tumour Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Seishi Ogawa
- Department of Pathology and Tumour Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto, Japan.
- Department of Medicine, Centre for Haematology and Regenerative Medicine, Karolinska Institute, Stockholm, Sweden.
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94
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Gotovac JR, Kader T, Milne JV, Fujihara KM, Lara-Gonzalez LE, Gorringe KL, Kalimuthu SN, Jayawardana MW, Duong CP, Phillips WA, Clemons NJ. Loss of SMAD4 Is Sufficient to Promote Tumorigenesis in a Model of Dysplastic Barrett's Esophagus. Cell Mol Gastroenterol Hepatol 2021; 12:689-713. [PMID: 33774196 PMCID: PMC8267443 DOI: 10.1016/j.jcmgh.2021.03.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 03/14/2021] [Accepted: 03/16/2021] [Indexed: 12/13/2022]
Abstract
BACKGROUND & AIMS Esophageal adenocarcinoma (EAC) develops from its precursor Barrett's esophagus through intermediate stages of low- and high-grade dysplasia. However, knowledge of genetic drivers and molecular mechanisms implicated in disease progression is limited. Herein, we investigated the effect of Mothers against decapentaplegic homolog 4 (SMAD4) loss on transforming growth factor β (TGF-β) signaling functionality and in vivo tumorigenicity in high-grade dysplastic Barrett's cells. METHODS An in vivo xenograft model was used to test tumorigenicity of SMAD4 knockdown or knockout in CP-B high-grade dysplastic Barrett's cells. RT2 polymerase chain reaction arrays were used to analyze TGF-β signaling functionality, and low-coverage whole-genome sequencing was performed to detect copy number alterations upon SMAD4 loss. RESULTS We found that SMAD4 knockout significantly alters the TGF-β pathway target gene expression profile. SMAD4 knockout positively regulates potential oncogenes such as CRYAB, ACTA2, and CDC6, whereas the CDKN2A/B tumor-suppressor locus was regulated negatively. We verified that SMAD4 in combination with CDC6-CDKN2A/B or CRYAB genetic alterations in patient tumors have significant predictive value for poor prognosis. Importantly, we investigated the effect of SMAD4 inactivation in Barrett's tumorigenesis. We found that genetic knockdown or knockout of SMAD4 was sufficient to promote tumorigenesis in dysplastic Barrett's esophagus cells in vivo. Progression to invasive EAC was accompanied by distinctive and consistent copy number alterations in SMAD4 knockdown or knockout xenografts. CONCLUSIONS Altogether, up-regulation of oncogenes, down-regulation of tumor-suppressor genes, and chromosomal instability within the tumors after SMAD4 loss implicates SMAD4 as a protector of genome integrity in EAC development and progression. Foremost, SMAD4 loss promotes tumorigenesis from dysplastic Barrett's toward EAC.
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Affiliation(s)
- Jovana R Gotovac
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia; Sir Peter MacCallum Department of Oncology, Parkville, Victoria, Australia
| | - Tanjina Kader
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia; Sir Peter MacCallum Department of Oncology, Parkville, Victoria, Australia
| | - Julia V Milne
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia; Sir Peter MacCallum Department of Oncology, Parkville, Victoria, Australia
| | - Kenji M Fujihara
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia; Sir Peter MacCallum Department of Oncology, Parkville, Victoria, Australia
| | - Luis E Lara-Gonzalez
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia; Sir Peter MacCallum Department of Oncology, Parkville, Victoria, Australia
| | - Kylie L Gorringe
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia; Sir Peter MacCallum Department of Oncology, Parkville, Victoria, Australia
| | - Sangeetha N Kalimuthu
- Anatomical Pathology, Laboratory Medicine Program, University Health Network, Toronto, Ontario, Canada; Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Madawa W Jayawardana
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia; Sir Peter MacCallum Department of Oncology, Parkville, Victoria, Australia
| | - Cuong P Duong
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia; Sir Peter MacCallum Department of Oncology, Parkville, Victoria, Australia
| | - Wayne A Phillips
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia; Sir Peter MacCallum Department of Oncology, Parkville, Victoria, Australia; Department of Surgery, St Vincent's Hospital, The University of Melbourne, Parkville, Victoria, Australia
| | - Nicholas J Clemons
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia; Sir Peter MacCallum Department of Oncology, Parkville, Victoria, Australia.
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95
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de Bitter TJJ, Kroeze LI, de Reuver PR, van Vliet S, Vink-Börger E, von Rhein D, Jansen EAM, Nagtegaal ID, Ligtenberg MJL, van der Post RS. Unraveling Neuroendocrine Gallbladder Cancer: Comprehensive Clinicopathologic and Molecular Characterization. JCO Precis Oncol 2021; 5:PO.20.00487. [PMID: 34036234 PMCID: PMC8140808 DOI: 10.1200/po.20.00487] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 01/19/2021] [Accepted: 02/01/2021] [Indexed: 12/23/2022] Open
Abstract
PURPOSE Neuroendocrine carcinomas and mixed neuroendocrine non-neuroendocrine neoplasms of the gallbladder (NE GBC) are rare and highly aggressive entities. The cell of origin of NE GBC has been a matter of controversy. Here, we performed a comparative histopathologic and molecular analysis of NE GBC cases and, if present, associated precancerous lesions. PATIENTS AND METHODS We selected cases diagnosed between 2000 and 2019 in the Netherlands. Precursors and carcinomas were immunohistochemically compared and analyzed for mutations, gene amplifications, microsatellite instability, and tumor mutational burden using an next-generation sequencing panel containing 523 cancer-related genes. In addition, presence of fusion genes was analyzed using a panel of 55 genes. RESULTS Sixty percent of neuroendocrine cases (6/10) presented with a precursor lesion, either intracholecystic papillary neoplasm (n = 3) or biliary intraepithelial neoplasia (n = 3). Immunohistochemically, neuroendocrine components were different from the epithelial precursor lesions. Molecular profiling, however, revealed TP53 mutations shared between different components in five of six cases, indicating a clonal relation. Furthermore, 40% of cases (4/10) harbored at least one potentially actionable alteration. This included (likely) pathogenic mutations in RAD54L, ATM, and BRCA2; amplifications of ERBB2 and MDM2; and a gene fusion involving FGFR3-TACC3. All cases were microsatellite-stable and had a tumor mutational burden of < 10 mutations/Mb. CONCLUSION Our data provide insight into the development of NE GBC and suggest a common origin of precancerous epithelial lesions and invasive neuroendocrine components, favoring the hypothesis of lineage transformation. Moreover, nearly half of the NE GBCs carried at least one potentially actionable molecular alteration, highlighting the importance of molecular testing in this highly lethal cancer.
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Affiliation(s)
- Tessa J J de Bitter
- Department of Pathology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Leonie I Kroeze
- Department of Pathology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Philip R de Reuver
- Department of Surgery, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Shannon van Vliet
- Department of Pathology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Elisa Vink-Börger
- Department of Pathology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Daniel von Rhein
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Erik A M Jansen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Iris D Nagtegaal
- Department of Pathology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Marjolijn J L Ligtenberg
- Department of Pathology, Radboud University Medical Center, Nijmegen, the Netherlands.,Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Rachel S van der Post
- Department of Pathology, Radboud University Medical Center, Nijmegen, the Netherlands
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Washington MK, Goldberg RM, Chang GJ, Limburg P, Lam AK, Salto-Tellez M, Arends MJ, Nagtegaal ID, Klimstra DS, Rugge M, Schirmacher P, Lazar AJ, Odze RD, Carneiro F, Fukayama M, Cree IA. Diagnosis of digestive system tumours. Int J Cancer 2021; 148:1040-1050. [PMID: 32674220 DOI: 10.1002/ijc.33210] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 06/09/2020] [Accepted: 06/11/2020] [Indexed: 12/12/2022]
Abstract
The WHO Classification of Tumours provides the international standards for the classification and diagnosis of tumours. It enables direct comparisons to be made between different countries. In the new fifth edition, the series has gone digital with the launch of a website as well as a series of books, known widely as the WHO Blue Books. The first volume to be produced is on the classification of Digestive System tumours, replacing the successful 2010 version. It has been rewritten and updated accordingly. This article summarises the major diagnostic innovations that have occurred over the last decade and that have now been incorporated in the classification. As an example, it incorporates the recently proposed classification of neuroendocrine tumours, based on the recognition that neuroendocrine tumours and carcinomas differ substantially in the genetic abnormalities that drive their growth, findings relevant to treatment selection and outcome prediction. Several themes have emerged during the production process. One is the importance of the progression from hyperplasia to dysplasia to carcinoma in the evolution of the malignant process. Advances in imaging techniques and endoscopy have resulted in enhanced access to precancerous lesions in the gastrointestinal and biliary tract, necessitating both changes in classification schema and clinical practice. Diagnosis of tumours is no longer the sole purview of pathologists, and some patients now receive treatment before tissue is obtained, based on clinical, radiological and liquid biopsy results. This makes the classification relevant to many disciplines involved in the care of patients with tumours of the digestive system.
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Affiliation(s)
| | - Richard M Goldberg
- West Virginia University Cancer Institute and the Mary Babb Randolph Cancer Center, Morgantown, West Virginia, USA
| | - George J Chang
- Department of Surgical Oncology, University of Texas M.D. Anderson Cancer Center, Houston, Texas, USA
| | - Paul Limburg
- Division of Gastroenterology & Hepatology, Mayo Clinic, Rochester, Minnesota, USA
| | - Alfred K Lam
- Pathology, School of Medicine, Gold Coast campus, Griffith University, Gold Coast, Queensland, Australia
| | - Manuel Salto-Tellez
- Queen's Precision Medicine Centre of Excellence, Queen's University Belfast, Belfast Health & Social Care Trust, Belfast, UK
| | - Mark J Arends
- Cancer Research UK Edinburgh Centre, MRC Institute of Genetics & Molecular Medicine, The University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Iris D Nagtegaal
- Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - David S Klimstra
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | | | | | - Alexander J Lazar
- Departments of Pathology, Genomic Medicine, and Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | | | | | - Masashi Fukayama
- Department of Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Ian A Cree
- WHO Classification of Tumours Group, International Agency for Research on Cancer (IARC), World Health Organization, Lyon, France
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97
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Bornschein J, Quante M, Jansen M. The complexity of cancer origins at the gastro-oesophageal junction. Best Pract Res Clin Gastroenterol 2021; 50-51:101729. [PMID: 33975686 DOI: 10.1016/j.bpg.2021.101729] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 02/08/2021] [Indexed: 01/31/2023]
Abstract
Chronic acid-biliary reflux and Helicobacter pylori infection are instrumental environmental drivers of cancer initiation and progression in the upper gastrointestinal tract. Remarkably, although these environmental carcinogens are quite dissimilar, the tumour progression cascade these carcinogens engender is highly comparable. For this reason, studies of malignant progression occurring at the anatomic borderland between the oesophagus and the stomach have traditionally lumped junctional adenocarcinomas with either oesophageal adenocarcinoma or gastric adenocarcinoma. Whilst studies have revealed remarkable epidemiological and genetic similarities of these cancers and their associated premalignant conditions, these works have also revealed some key differences. This highlights that further scientific effort demands a dedicated focus on the understanding of the cell-cell interaction between the epithelium and the local microenvironment in this anatomic region. We here review available evidence with regards to tumour progression occurring at the gastro-oesophageal junction and contrast it with available data on cancer evolution in the metaplastic oesophagus and distal stomach.
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Affiliation(s)
- Jan Bornschein
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, United Kingdom and NIHR Oxford Biomedical Research Centre, Oxford, United Kingdom.
| | - Michael Quante
- Klinik für Innere Medizin II, Universitätsklinikum Freiburg, Germany
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98
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Lv J, Yan L, Lu Y, Liu D, Niu J, Yin L. Sclonal architectures predict clinical outcome in colon adenocarcinoma. J Cell Mol Med 2021; 25:1796-1800. [PMID: 33369051 PMCID: PMC7875899 DOI: 10.1111/jcmm.16208] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 12/04/2020] [Accepted: 12/07/2020] [Indexed: 01/09/2023] Open
Affiliation(s)
- Ji Lv
- Department of surgeryThe First Hospital of QinhuangdaoQinhuangdaoChina
| | - Lili Yan
- Department of surgeryThe First Hospital of QinhuangdaoQinhuangdaoChina
| | - Yang Lu
- Department of surgeryThe First Hospital of QinhuangdaoQinhuangdaoChina
| | - Dongfeng Liu
- Department of surgeryThe First Hospital of QinhuangdaoQinhuangdaoChina
| | - Jia Niu
- Department of surgeryThe First Hospital of QinhuangdaoQinhuangdaoChina
| | - Liyong Yin
- Department of NeurologyThe First Hospital of QinhuangdaoQinhuangdaoChina
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99
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Smith LP, Yamato JA, Galipeau PC, Paulson TG, Li X, Sanchez CA, Reid BJ, Kuhner MK. Within-patient phylogenetic reconstruction reveals early events in Barrett's Esophagus. Evol Appl 2021; 14:399-415. [PMID: 33664784 PMCID: PMC7896700 DOI: 10.1111/eva.13125] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 08/20/2020] [Accepted: 08/25/2020] [Indexed: 12/22/2022] Open
Abstract
Barrett's Esophagus is a neoplastic condition which progresses to esophageal adenocarcinoma in 5% of cases. Key events affecting the outcome likely occur before diagnosis of Barrett's and cannot be directly observed; we use phylogenetic analysis to infer such past events. We performed whole-genome sequencing on 4-6 samples from 40 cancer outcome and 40 noncancer outcome patients with Barrett's Esophagus, and inferred within-patient phylogenies of deconvoluted clonal lineages. Spatially proximate lineages clustered in the phylogenies, but temporally proximate ones did not. Lineages with inferred loss-of-function mutations in both copies of TP53 and CDKN2A showed enhanced spatial spread, whereas lineages with loss-of-function mutations in other frequently mutated loci did not. We propose a two-phase model with expansions of TP53 and CKDN2A mutant lineages during initial growth of the segment, followed by relative stasis. Subsequent to initial expansion, mutations in these loci as well as ARID1A and SMARCA4 may show a local selective advantage but do not expand far: The spatial structure of the Barrett's segment remains stable during surveillance even in patients who go on to cancer. We conclude that the cancer/noncancer outcome is strongly affected by early steps in formation of the Barrett's segment.
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Affiliation(s)
- Lucian P. Smith
- Department of Genome SciencesUniversity of WashingtonSeattleWAUSA
| | - Jon A. Yamato
- Department of Genome SciencesUniversity of WashingtonSeattleWAUSA
| | | | - Thomas G. Paulson
- Division of Human BiologyFred Hutchinson Cancer Research CenterSeattleWAUSA
| | - Xiaohong Li
- Division of Human BiologyFred Hutchinson Cancer Research CenterSeattleWAUSA
| | - Carissa A. Sanchez
- Division of Human BiologyFred Hutchinson Cancer Research CenterSeattleWAUSA
| | - Brian J. Reid
- Department of Genome SciencesUniversity of WashingtonSeattleWAUSA
- Division of Human BiologyFred Hutchinson Cancer Research CenterSeattleWAUSA
- Department of MedicineUniversity of WashingtonSeattleWAUSA
| | - Mary K. Kuhner
- Department of Genome SciencesUniversity of WashingtonSeattleWAUSA
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100
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Chong IY, Starling N, Rust A, Alexander J, Aronson L, Llorca-Cardenosa M, Chauhan R, Chaudry A, Kumar S, Fenwick K, Assiotis I, Matthews N, Begum R, Wotherspoon A, Terlizzo M, Watkins D, Chau I, Lord CJ, Haider S, Rao S, Cunningham D. The Mutational Concordance of Fixed Formalin Paraffin Embedded and Fresh Frozen Gastro-Oesophageal Tumours Using Whole Exome Sequencing. J Clin Med 2021; 10:E215. [PMID: 33435284 PMCID: PMC7826535 DOI: 10.3390/jcm10020215] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 01/01/2021] [Accepted: 01/04/2021] [Indexed: 12/31/2022] Open
Abstract
1. BACKGROUND The application of massively parallel sequencing has led to the identification of aberrant druggable pathways and somatic mutations within therapeutically relevant genes in gastro-oesophageal cancer. Given the widespread use of formalin-fixed paraffin-embedded (FFPE) samples in the study of this disease, it would be beneficial, especially for the purposes of biomarker evaluation, to assess the concordance between comprehensive exome-wide sequencing data from archival FFPE samples originating from a prospective clinical study and those derived from fresh-frozen material. 2. METHODS We analysed whole-exome sequencing data to define the mutational concordance of 16 matched fresh-frozen and FFPE gastro-oesophageal tumours (N = 32) from a prospective clinical study. We assessed DNA integrity prior to sequencing and then identified coding mutations in genes that have previously been implicated in other cancers. In addition, we calculated the mutant-allele heterogeneity (MATH) for these samples. 3. RESULTS Although there was increased degradation of DNA in FFPE samples compared with frozen samples, sequencing data from only two FFPE samples failed to reach an adequate mapping quality threshold. Using a filtering threshold of mutant read counts of at least ten and a minimum of 5% variant allele frequency (VAF) we found that there was a high median mutational concordance of 97% (range 80.1-98.68%) between fresh-frozen and FFPE gastro-oesophageal tumour-derived exomes. However, the majority of FFPE tumours had higher mutant-allele heterogeneity (MATH) scores when compared with corresponding frozen tumours (p < 0.001), suggesting that FFPE-based exome sequencing is likely to over-represent tumour heterogeneity in FFPE samples compared to fresh-frozen samples. Furthermore, we identified coding mutations in 120 cancer-related genes, including those associated with chromatin remodelling and Wnt/β-catenin and Receptor Tyrosine Kinase signalling. 4. CONCLUSIONS These data suggest that comprehensive genomic data can be generated from exome sequencing of selected DNA samples extracted from archival FFPE gastro-oesophageal tumour tissues within the context of prospective clinical trials.
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Affiliation(s)
- Irene Y. Chong
- The Division of Molecular Pathology, The Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK; (L.A.); (M.L.-C.)
- The Royal Marsden Hospital NHS Foundation Trust, 203 Fulham Road, London SW3 6JJ, UK; (N.S.); (A.C.); (S.K.); (R.B.); (A.W.); (M.T.); (D.W.); (I.C.); (S.R.); (D.C.)
| | - Naureen Starling
- The Royal Marsden Hospital NHS Foundation Trust, 203 Fulham Road, London SW3 6JJ, UK; (N.S.); (A.C.); (S.K.); (R.B.); (A.W.); (M.T.); (D.W.); (I.C.); (S.R.); (D.C.)
| | - Alistair Rust
- The Tissue Profiling Unit, The Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK; (A.R.); (R.C.); (K.F.); (I.A.); (N.M.)
| | - John Alexander
- Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London SW3 6JB, UK; (J.A.); (C.J.L.); (S.H.)
| | - Lauren Aronson
- The Division of Molecular Pathology, The Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK; (L.A.); (M.L.-C.)
| | - Marta Llorca-Cardenosa
- The Division of Molecular Pathology, The Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK; (L.A.); (M.L.-C.)
| | - Ritika Chauhan
- The Tissue Profiling Unit, The Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK; (A.R.); (R.C.); (K.F.); (I.A.); (N.M.)
| | - Asif Chaudry
- The Royal Marsden Hospital NHS Foundation Trust, 203 Fulham Road, London SW3 6JJ, UK; (N.S.); (A.C.); (S.K.); (R.B.); (A.W.); (M.T.); (D.W.); (I.C.); (S.R.); (D.C.)
| | - Sacheen Kumar
- The Royal Marsden Hospital NHS Foundation Trust, 203 Fulham Road, London SW3 6JJ, UK; (N.S.); (A.C.); (S.K.); (R.B.); (A.W.); (M.T.); (D.W.); (I.C.); (S.R.); (D.C.)
| | - Kerry Fenwick
- The Tissue Profiling Unit, The Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK; (A.R.); (R.C.); (K.F.); (I.A.); (N.M.)
| | - Ioannis Assiotis
- The Tissue Profiling Unit, The Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK; (A.R.); (R.C.); (K.F.); (I.A.); (N.M.)
| | - Nik Matthews
- The Tissue Profiling Unit, The Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK; (A.R.); (R.C.); (K.F.); (I.A.); (N.M.)
| | - Ruwaida Begum
- The Royal Marsden Hospital NHS Foundation Trust, 203 Fulham Road, London SW3 6JJ, UK; (N.S.); (A.C.); (S.K.); (R.B.); (A.W.); (M.T.); (D.W.); (I.C.); (S.R.); (D.C.)
| | - Andrew Wotherspoon
- The Royal Marsden Hospital NHS Foundation Trust, 203 Fulham Road, London SW3 6JJ, UK; (N.S.); (A.C.); (S.K.); (R.B.); (A.W.); (M.T.); (D.W.); (I.C.); (S.R.); (D.C.)
| | - Monica Terlizzo
- The Royal Marsden Hospital NHS Foundation Trust, 203 Fulham Road, London SW3 6JJ, UK; (N.S.); (A.C.); (S.K.); (R.B.); (A.W.); (M.T.); (D.W.); (I.C.); (S.R.); (D.C.)
| | - David Watkins
- The Royal Marsden Hospital NHS Foundation Trust, 203 Fulham Road, London SW3 6JJ, UK; (N.S.); (A.C.); (S.K.); (R.B.); (A.W.); (M.T.); (D.W.); (I.C.); (S.R.); (D.C.)
| | - Ian Chau
- The Royal Marsden Hospital NHS Foundation Trust, 203 Fulham Road, London SW3 6JJ, UK; (N.S.); (A.C.); (S.K.); (R.B.); (A.W.); (M.T.); (D.W.); (I.C.); (S.R.); (D.C.)
| | - Christopher J. Lord
- Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London SW3 6JB, UK; (J.A.); (C.J.L.); (S.H.)
| | - Syed Haider
- Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London SW3 6JB, UK; (J.A.); (C.J.L.); (S.H.)
| | - Sheela Rao
- The Royal Marsden Hospital NHS Foundation Trust, 203 Fulham Road, London SW3 6JJ, UK; (N.S.); (A.C.); (S.K.); (R.B.); (A.W.); (M.T.); (D.W.); (I.C.); (S.R.); (D.C.)
| | - David Cunningham
- The Royal Marsden Hospital NHS Foundation Trust, 203 Fulham Road, London SW3 6JJ, UK; (N.S.); (A.C.); (S.K.); (R.B.); (A.W.); (M.T.); (D.W.); (I.C.); (S.R.); (D.C.)
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