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Pilot Study Showing Feasibility of Phosphoproteomic Profiling of Pathway-Level Molecular Alterations in Barrett’s Esophagus. Genes (Basel) 2022; 13:genes13071215. [PMID: 35885999 PMCID: PMC9325186 DOI: 10.3390/genes13071215] [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: 05/13/2022] [Revised: 06/25/2022] [Accepted: 07/05/2022] [Indexed: 11/17/2022] Open
Abstract
(1) Background: Barrett’s esophagus is a major risk factor for esophageal adenocarcinoma. In this pilot study, we employed precision mass spectrometry to map global (phospho)protein perturbations in Barrett’s esophagus lesions and adjacent normal tissue to glean insights into disease progression. (2) Methods: Biopsies were collected from two small but independent cohorts. Comparative analyses were performed between Barrett’s esophagus samples and adjacent matched (normal) tissues from patients with known pathology, while specimens from healthy patients served as additional controls. (3) Results: We identified and quantified 6810 proteins and 6395 phosphosites in the discovery cohort, revealing hundreds of statistically significant differences in protein abundances and phosphorylation states. We identified a robust proteomic signature that accurately classified the disease status of samples from the independent patient cohorts. Pathway-level analysis of the phosphoproteomic profiles revealed the dysregulation of specific cellular processes, including DNA repair, in Barrett’s esophagus relative to paired controls. Comparative analysis with previously published transcriptomic profiles provided independent evidence in support of these preliminary findings. (4) Conclusions: This pilot study establishes the feasibility of using unbiased quantitative phosphoproteomics to identify molecular perturbations associated with disease progression in Barrett’s esophagus to define potentially clinically actionable targets warranting further assessment.
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Evans JA, Carlotti E, Lin ML, Hackett RJ, Haughey MJ, Passman AM, Dunn L, Elia G, Porter RJ, McLean MH, Hughes F, ChinAleong J, Woodland P, Preston SL, Griffin SM, Lovat L, Rodriguez-Justo M, Huang W, Wright NA, Jansen M, McDonald SAC. Clonal Transitions and Phenotypic Evolution in Barrett's Esophagus. Gastroenterology 2022; 162:1197-1209.e13. [PMID: 34973296 PMCID: PMC8972067 DOI: 10.1053/j.gastro.2021.12.271] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 12/21/2021] [Accepted: 12/22/2021] [Indexed: 01/10/2023]
Abstract
BACKGROUND & AIMS Barrett's esophagus (BE) is a risk factor for esophageal adenocarcinoma but our understanding of how it evolves is poorly understood. We investigated BE gland phenotype distribution, the clonal nature of phenotypic change, and how phenotypic diversity plays a role in progression. METHODS Using immunohistochemistry and histology, we analyzed the distribution and the diversity of gland phenotype between and within biopsy specimens from patients with nondysplastic BE and those who had progressed to dysplasia or had developed postesophagectomy BE. Clonal relationships were determined by the presence of shared mutations between distinct gland types using laser capture microdissection sequencing of the mitochondrial genome. RESULTS We identified 5 different gland phenotypes in a cohort of 51 nondysplastic patients where biopsy specimens were taken at the same anatomic site (1.0-2.0 cm superior to the gastroesophageal junction. Here, we observed the same number of glands with 1 and 2 phenotypes, but 3 phenotypes were rare. We showed a common ancestor between parietal cell-containing, mature gastric (oxyntocardiac) and goblet cell-containing, intestinal (specialized) gland phenotypes. Similarly, we have shown a clonal relationship between cardiac-type glands and specialized and mature intestinal glands. Using the Shannon diversity index as a marker of gland diversity, we observed significantly increased phenotypic diversity in patients with BE adjacent to dysplasia and predysplasia compared to nondysplastic BE and postesophagectomy BE, suggesting that diversity develops over time. CONCLUSIONS We showed that the range of BE phenotypes represents an evolutionary process and that changes in gland diversity may play a role in progression. Furthermore, we showed a common ancestry between gastric and intestinal-type glands in BE.
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Affiliation(s)
- James A Evans
- Clonal Dynamics in Epithelia Laboratory, Queen Mary University of London, London, United Kingdom
| | - Emanuela Carlotti
- Clonal Dynamics in Epithelia Laboratory, Queen Mary University of London, London, United Kingdom
| | - Meng-Lay Lin
- Clonal Dynamics in Epithelia Laboratory, Queen Mary University of London, London, United Kingdom
| | - Richard J Hackett
- Clonal Dynamics in Epithelia Laboratory, Queen Mary University of London, London, United Kingdom
| | - Magnus J Haughey
- School of Mathematical Sciences, Queen Mary University of London, London, United Kingdom
| | - Adam M Passman
- Clonal Dynamics in Epithelia Laboratory, Queen Mary University of London, London, United Kingdom
| | - Lorna Dunn
- Northern Institute for Cancer Research, Newcastle University, Newcastle, United Kingdom
| | - George Elia
- Clonal Dynamics in Epithelia Laboratory, Queen Mary University of London, London, United Kingdom
| | - Ross J Porter
- Department of Gastroenterology, University of Aberdeen, Aberdeen, United Kingdom
| | - Mairi H McLean
- Department of Gastroenterology, University of Aberdeen, Aberdeen, United Kingdom
| | - Frances Hughes
- Department of Surgery, Barts Health NHS Trust, Royal London Hospital, London, United Kingdom
| | - Joanne ChinAleong
- Department of Histopathology, Barts Health NHS Trust, Royal London Hospital, London, United Kingdom
| | - Philip Woodland
- Endoscopy Unit, Barts Health NHS Trust, Royal London Hospital, London, United Kingdom
| | - Sean L Preston
- Endoscopy Unit, Barts Health NHS Trust, Royal London Hospital, London, United Kingdom
| | - S Michael Griffin
- School of Mathematical Sciences, Queen Mary University of London, London, United Kingdom; Royal College of Surgeons of Edinburgh, Edinburgh, United Kingdom
| | - Laurence Lovat
- Oeosophagogastric Disorders Centre, Department of Gastroenterology, University College London Hospitals, London, United Kingdom; Research Department of Tissue and Energy, University College London Division of Surgical and Interventional Science, University College London, London, United Kingdom
| | - Manuel Rodriguez-Justo
- Department of Cellular Pathology, University College London Hospitals, London, United Kingdom
| | - Weini Huang
- School of Mathematical Sciences, Queen Mary University of London, London, United Kingdom
| | - Nicholas A Wright
- Epithelial Stem Cell Laboratory, Centre for Cancer Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Marnix Jansen
- Department of Cellular Pathology, University College London Hospitals, London, United Kingdom; UCL Cancer Institute, University College London, London, United Kingdom
| | - Stuart A C McDonald
- Clonal Dynamics in Epithelia Laboratory, Queen Mary University of London, London, United Kingdom.
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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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Independent Validation of a Tissue Systems Pathology Assay to Predict Future Progression in Nondysplastic Barrett's Esophagus: A Spatial-Temporal Analysis. Clin Transl Gastroenterol 2021; 11:e00244. [PMID: 33108124 PMCID: PMC7544172 DOI: 10.14309/ctg.0000000000000244] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
An automated risk prediction assay has previously been shown to objectively identify patients with nondysplastic Barrett's esophagus (NDBE) who are at increased risk of malignant progression. To evaluate the predictive performance of the assay in 76 patients with NDBE of which 38 progressed to high-grade dysplasia/esophageal adenocarcinoma (progressors) and 38 did not (nonprogressors) and to determine whether assessment of additional (spatial) levels per endoscopy and/or multiple (temporal) time points improves assay performance.
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Garman KS. Drivers of Esophageal Adenocarcinoma and Opportunities for Cancer Interception. Cell Mol Gastroenterol Hepatol 2021; 12:787-788. [PMID: 34029533 PMCID: PMC8348867 DOI: 10.1016/j.jcmgh.2021.04.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 04/27/2021] [Accepted: 04/28/2021] [Indexed: 12/10/2022]
Affiliation(s)
- Katherine S. Garman
- Correspondence Address correspondence to: Katherine S. Garman, MD, Duke University, Division of Gastroenterology, Department of Medicine, Box 3913 DUMC, Durham, North Carolina 27710.
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Frei NF, Konté K, Duits LC, Klaver E, Ten Kate FJ, Offerhaus GJ, Meijer SL, Visser M, Seldenrijk CA, Schoon EJ, Weusten BLAM, Schenk BE, Mallant-Hent RC, Bergman JJ, Pouw RE. The SpaTemp cohort: 168 nondysplastic Barrett's esophagus surveillance patients with and without progression to early neoplasia to evaluate the distribution of biomarkers over space and time. Dis Esophagus 2020; 34:5907935. [PMID: 32944737 PMCID: PMC9155949 DOI: 10.1093/dote/doaa095] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 08/11/2020] [Indexed: 12/11/2022]
Abstract
The ReBus cohort is a matched nested case-control cohort of patients with nondysplastic (ND) Barrett's esophagus (BE) at baseline who progressed (progressors) or did not progress (nonprogressors) to high-grade dysplasia (HGD) or cancer. This cohort is constructed using the most stringent inclusion criteria to optimize explorative studies on biomarkers predicting malignant progression in NDBE. These explorative studies may benefit from expanding the number of cases and by incorporating samples that allow assessment of the biomarker over space (spatial variability) and over time (temporal variability). To (i) update the ReBus cohort by identifying new progressors and (ii) identify progressors and nonprogressors within the updated ReBus cohort containing spatial and temporal information. The ReBus cohort was updated by identifying Barrett's patients referred for endoscopic work-up of neoplasia at 4 tertiary referral centers. Progressors and nonprogressors with a multilevel (spatial) endoscopy and additional prior (temporal) endoscopies were identified to evaluate biomarkers over space and over time. The original ReBus cohort consisted of 165 progressors and 723 nonprogressors. We identified 65 new progressors meeting the same strict selection criteria, resulting in a total number of 230 progressors and 723 matched nonprogressors in the updated ReBus cohort. Within the updated cohort, 61 progressors and 107 nonprogressors (mean age 61 ± 10 years) with a spatial endoscopy (median level 3 [2-4]) were identified. 33/61 progressors and 50/107 nonprogressors had a median of 3 (2-4) additional temporal endoscopies. Our updated ReBus cohort consists of 230 progressors and 723 matched nonprogressors using the most strict selection criteria. In a subgroup of 168 Barrett's patients (the SpaTemp cohort), multiple levels have been sampled at baseline and during follow-up providing a unique platform to study spatial and temporal distribution of biomarkers in BE.
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Affiliation(s)
- N F Frei
- Department of Gastroenterology and Hepatology, Amsterdam UMC, location Vrije Universiteit, Amsterdam, The Netherlands
| | - K Konté
- Department of Gastroenterology and Hepatology, Amsterdam UMC, location Vrije Universiteit, Amsterdam, The Netherlands
| | - L C Duits
- Department of Gastroenterology and Hepatology, Amsterdam UMC, location Vrije Universiteit, Amsterdam, The Netherlands
| | - E Klaver
- Department of Gastroenterology and Hepatology, Amsterdam UMC, location Vrije Universiteit, Amsterdam, The Netherlands
| | - F J Ten Kate
- Department of Pathology, University Medical Center, Utrecht, The Netherlands
| | - G J Offerhaus
- Department of Pathology, University Medical Center, Utrecht, The Netherlands
| | - S L Meijer
- Department of Pathology, Amsterdam UMC, location Academic Medical Center, Amsterdam, The Netherlands
| | - M Visser
- Department of Pathology, Symbiant BV, Zaans Medical Center, Zaandam, The Netherlands
| | - C A Seldenrijk
- Department of Pathology, Pathology-DNA BV, St. Antonius Hospital, Nieuwegein, The Netherlands
| | - E J Schoon
- Department of Gastroenterology and Hepatology, Catharina Hospital, Eindhoven, The Netherlands
| | - B L A M Weusten
- Department of Gastroenterology and Hepatology, St. Antonius Hospital, Nieuwegein, The Netherlands
| | - B E Schenk
- Department of Gastroenterology and Hepatology, Isala Klinieken, Zwolle, The Netherlands
| | - R C Mallant-Hent
- Department of Gastroenterology, Flevo Hospital, Almere, the Netherlands
| | - J J Bergman
- Department of Gastroenterology and Hepatology, Amsterdam UMC, location Vrije Universiteit, Amsterdam, The Netherlands
| | - R E Pouw
- Address correspondence to: R. E. Pouw, MD, PhD, Department of Gastroenterology and Hepatology, Amsterdam UMC, location Vrije Universiteit, Amsterdam, The Netherlands.
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Westra WM, Rygiel AM, Mostafavi N, de Wit GMJ, Roes AL, Moons LMG, Peppelenbosch MP, Ouburg S, Morré SA, Jacobs M, Siersema PD, Repping S, Wang KK, Krishnadath KK. The Y-chromosome F haplogroup contributes to the development of Barrett's esophagus-associated esophageal adenocarcinoma in a white male population. Dis Esophagus 2020; 33:5780184. [PMID: 32129453 PMCID: PMC7471775 DOI: 10.1093/dote/doaa011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 02/03/2020] [Accepted: 02/06/2020] [Indexed: 12/11/2022]
Abstract
Barrett's esophagus (BE) is a metaplastic condition of the distal esophagus, resulting from longstanding gastroesophageal reflux disease (GERD). BE predisposes for the highly malignant esophageal adenocarcinoma (EAC). Both BE and EAC have the highest frequencies in white males. Only a subset of patients with GERD develop BE, while <0.5% of BE will progress to EAC. Therefore, it is most likely that the development of BE and EAC is associated with underlying genetic factors. We hypothesized that in white males, Y-chromosomal haplogroups are associated with BE and EAC. To investigate this we conducted a multicenter study studying the frequencies of the Y-chromosomal haplogroups in GERD, BE, and EAC patients. We used genomic analysis by polymerase chain reaction and restriction fragment length polymorphism to determine the frequency of six Y-chromosomal haplogroups (DE, F(xJ,xK), K(xP), J, P(xR1a), and R1a) between GERD, BE, and EAC in a cohort of 1,365 white males, including 612 GERD, 753 BE patients, while 178 of the BE patients also had BE-associated EAC. Univariate logistic regression analysis was used to compare the outcomes. In this study, we found the R1a (6% vs. 9%, P = 0.04) and K (3% vs. 6%, P = 0.035) to be significantly underrepresented in BE patients as compared to GERD patients with an odds ratio (OR) of 0.63 (95% CI 0.42-0.95, P = 0.03) and of 0.56 (95% CI 0.33-0.96, P = 0.03), respectively, while the K haplogroup was protective against EAC (OR 0.30; 95% CI 0.07-0.86, P = 0.05). A significant overrepresentation of the F haplogroup was found in EAC compared to BE and GERD patients (34% vs. 27% and 23%, respectively). The F haplogroup was found to be a risk factor for EAC with an OR of 1.5 (95% CI 1.03-2.19, P = 0.03). We identified the R1a and K haplogroups as protective factors against development of BE. These haplogroups have low frequencies in white male populations. Of importance is that we could link the presence of the predominantly occurring F haplogroup in white males to EAC. It is possible that this F haplogroup is associated to genetic variants that predispose for the EAC development. In future, the haplogroups could be applied to improve stratification of BE and GERD patients with increased risk to develop BE and/or EAC.
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Affiliation(s)
- W M Westra
- CEMM, Amsterdam UMC-AMC, Amsterdam, The Netherlands,Department of Gastroenterology and Hepatology, Mayo Foundation, Rochester, MN, USA,Department of Gastroenterology and Hepatology, Amsterdam UMC-AMC, Amsterdam, The Netherlands
| | - A M Rygiel
- CEMM, Amsterdam UMC-AMC, Amsterdam, The Netherlands,Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland
| | - N Mostafavi
- Biostatistical Unit, Department of Gastroenterology, Amsterdam UMC, Amsterdam, The Netherlands
| | - G M J de Wit
- CEMM, Amsterdam UMC-AMC, Amsterdam, The Netherlands
| | - A L Roes
- CEMM, Amsterdam UMC-AMC, Amsterdam, The Netherlands
| | - L M G Moons
- Department of Gastroenterology and Hepatology, UMC Utrecht, The Netherlands
| | - M P Peppelenbosch
- Department of Gastroenterology and Hepatology, Erasmus MC, Rotterdam, The Netherlands
| | - S Ouburg
- Department of Medical Microbiology and Infection Control, Amsterdam UMC-VUMC, Amsterdam, The Netherlands
| | - S A Morré
- Department of Medical Microbiology and Infection Control, Amsterdam UMC-VUMC, Amsterdam, The Netherlands,Department of Genetics and Cell Biology, Maastricht University, Maastricht, The Netherlands
| | - M Jacobs
- Department of Gastroenterology and Hepatology, Amsterdam UMC-VUMC, Amsterdam, The Netherlands
| | - P D Siersema
- Department of Gastroenterology and Hepatology, Radboud UMC, Nijmegen, The Netherlands
| | - S Repping
- Department of Reproductive Medicine, Amsterdam UMC-AMC, Amsterdam, The Netherlands
| | - K K Wang
- Department of Gastroenterology and Hepatology, Mayo Foundation, Rochester, MN, USA
| | - K K Krishnadath
- Department of Gastroenterology and Hepatology, Amsterdam UMC-AMC, Amsterdam, The Netherlands,Address correspondence to: Professor Kausilia K. Krishnadath, MD, PhD, Gastroenterology and Hepatology, Amsterdam UMC-AMC, Amsterdam, C2-321, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands.
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Kennedy SR, Zhang Y, Risques RA. Cancer-Associated Mutations but No Cancer: Insights into the Early Steps of Carcinogenesis and Implications for Early Cancer Detection. Trends Cancer 2019; 5:531-540. [PMID: 31474358 PMCID: PMC8765002 DOI: 10.1016/j.trecan.2019.07.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 07/16/2019] [Accepted: 07/18/2019] [Indexed: 01/02/2023]
Abstract
Cancer is a disease of aging fueled by the accumulation of somatic mutations. While mutations in tumors are well characterized, little is known about the early mutational processes that initiate tumorigenesis. Recent advances in next-generation sequencing (NGS) have enabled the detection of mutations in normal tissue, revealing an unanticipated high level of age-related somatic mutations affecting most individuals and tissues. Surprisingly, many of these mutations are similar to mutations commonly found in tumors, suggesting an ongoing process of positive selection and clonal expansion akin to what occurs in cancer, but within normal tissue. Here we discuss some of the most important biological and clinical implications of these novel findings, with a special focus on their impact for cancer detection and prediction.
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Affiliation(s)
- Scott R Kennedy
- Department of Pathology, University of Washington, Seattle, WA, USA
| | - Yuezheng Zhang
- Department of Pathology, University of Washington, Seattle, WA, USA
| | - Rosa Ana Risques
- Department of Pathology, University of Washington, Seattle, WA, USA.
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UGT2B17 and miR-224 contribute to hormone dependency trends in adenocarcinoma and squamous cell carcinoma of esophagus. Biosci Rep 2019; 39:BSR20190472. [PMID: 31164411 PMCID: PMC6609598 DOI: 10.1042/bsr20190472] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 05/09/2019] [Accepted: 05/22/2019] [Indexed: 12/13/2022] Open
Abstract
Esophageal squamous cell carcinoma (ESCC) and esophageal adenocarcinoma (EA) are the two main subtypes of esophageal cancer. Genetics underpinnings of EA are substantially less understood than that of ESCC. A large-scale relation data analysis was conducted to explore the genes implicated with either EA or ESCC, or both. Each gene linked to ESCC but not EA was further explored in mega-analysis of six independently collected EA RNA expression datasets. A multiple linear regression (MLR) model was built to study the possible influence of sample size, population region, and study date on the gene expression data in EA. Finally, a functional pathway analysis was conducted to identify the possible linkage between EA and the genes identified as novel significant contributors. We have identified 276 genes associated with EA, 1088 with ESCC, with a significant (P<5.14e-143) overlap between these two gene groups (n=157). Mega-analysis showed that two ESCC-related genes, UGT2B17 and MIR224, were significantly associated with EA (P-value <1e-10), with multiple connecting pathways revealed by functional analysis. ESCC and EA share some common pathophysiological pathways. Further study of UGT2B17 and MIR224, which are differentially dysregulated in ESCC and EA tumors, is warranted. Enhanced expression of UGT2B17 and the lack of miR-224 signaling may contribute to the responsiveness of EA to the male sex steroids.
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Hegyi P, Maléth J, Walters JR, Hofmann AF, Keely SJ. Guts and Gall: Bile Acids in Regulation of Intestinal Epithelial Function in Health and Disease. Physiol Rev 2019; 98:1983-2023. [PMID: 30067158 DOI: 10.1152/physrev.00054.2017] [Citation(s) in RCA: 148] [Impact Index Per Article: 29.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Epithelial cells line the entire surface of the gastrointestinal tract and its accessory organs where they primarily function in transporting digestive enzymes, nutrients, electrolytes, and fluid to and from the luminal contents. At the same time, epithelial cells are responsible for forming a physical and biochemical barrier that prevents the entry into the body of harmful agents, such as bacteria and their toxins. Dysregulation of epithelial transport and barrier function is associated with the pathogenesis of a number of conditions throughout the intestine, such as inflammatory bowel disease, chronic diarrhea, pancreatitis, reflux esophagitis, and cancer. Driven by discovery of specific receptors on intestinal epithelial cells, new insights into mechanisms that control their synthesis and enterohepatic circulation, and a growing appreciation of their roles as bioactive bacterial metabolites, bile acids are currently receiving a great deal of interest as critical regulators of epithelial function in health and disease. This review aims to summarize recent advances in this field and to highlight how bile acids are now emerging as exciting new targets for disease intervention.
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Affiliation(s)
- Peter Hegyi
- Momentum Translational Gastroenterology Research Group, Hungarian Academy of Sciences-University of Szeged , Szeged , Hungary ; Institute for Translational Medicine, Medical School, University of Pécs , Pécs , Hungary ; Momentum Epithelial Cell Signalling and Secretion Research Group and First Department of Medicine, University of Szeged , Szeged , Hungary ; Division of Digestive Diseases, Department of Gastroenterology, Hammersmith Hospital, Imperial College London , London , United Kingdom ; Division of Gastroenterology, Department of Medicine, University of California, San Diego, La Jolla, California ; and Department of Molecular Medicine, Royal College of Surgeons in Ireland, Education and Research Centre, Beaumont Hospital , Dublin , Ireland
| | - Joszef Maléth
- Momentum Translational Gastroenterology Research Group, Hungarian Academy of Sciences-University of Szeged , Szeged , Hungary ; Institute for Translational Medicine, Medical School, University of Pécs , Pécs , Hungary ; Momentum Epithelial Cell Signalling and Secretion Research Group and First Department of Medicine, University of Szeged , Szeged , Hungary ; Division of Digestive Diseases, Department of Gastroenterology, Hammersmith Hospital, Imperial College London , London , United Kingdom ; Division of Gastroenterology, Department of Medicine, University of California, San Diego, La Jolla, California ; and Department of Molecular Medicine, Royal College of Surgeons in Ireland, Education and Research Centre, Beaumont Hospital , Dublin , Ireland
| | - Julian R Walters
- Momentum Translational Gastroenterology Research Group, Hungarian Academy of Sciences-University of Szeged , Szeged , Hungary ; Institute for Translational Medicine, Medical School, University of Pécs , Pécs , Hungary ; Momentum Epithelial Cell Signalling and Secretion Research Group and First Department of Medicine, University of Szeged , Szeged , Hungary ; Division of Digestive Diseases, Department of Gastroenterology, Hammersmith Hospital, Imperial College London , London , United Kingdom ; Division of Gastroenterology, Department of Medicine, University of California, San Diego, La Jolla, California ; and Department of Molecular Medicine, Royal College of Surgeons in Ireland, Education and Research Centre, Beaumont Hospital , Dublin , Ireland
| | - Alan F Hofmann
- Momentum Translational Gastroenterology Research Group, Hungarian Academy of Sciences-University of Szeged , Szeged , Hungary ; Institute for Translational Medicine, Medical School, University of Pécs , Pécs , Hungary ; Momentum Epithelial Cell Signalling and Secretion Research Group and First Department of Medicine, University of Szeged , Szeged , Hungary ; Division of Digestive Diseases, Department of Gastroenterology, Hammersmith Hospital, Imperial College London , London , United Kingdom ; Division of Gastroenterology, Department of Medicine, University of California, San Diego, La Jolla, California ; and Department of Molecular Medicine, Royal College of Surgeons in Ireland, Education and Research Centre, Beaumont Hospital , Dublin , Ireland
| | - Stephen J Keely
- Momentum Translational Gastroenterology Research Group, Hungarian Academy of Sciences-University of Szeged , Szeged , Hungary ; Institute for Translational Medicine, Medical School, University of Pécs , Pécs , Hungary ; Momentum Epithelial Cell Signalling and Secretion Research Group and First Department of Medicine, University of Szeged , Szeged , Hungary ; Division of Digestive Diseases, Department of Gastroenterology, Hammersmith Hospital, Imperial College London , London , United Kingdom ; Division of Gastroenterology, Department of Medicine, University of California, San Diego, La Jolla, California ; and Department of Molecular Medicine, Royal College of Surgeons in Ireland, Education and Research Centre, Beaumont Hospital , Dublin , Ireland
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11
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Qureshi AP, Stachler MD, Haque O, Odze RD. Biomarkers for Barrett's esophagus - a contemporary review. Expert Rev Mol Diagn 2018; 18:939-946. [PMID: 30345836 DOI: 10.1080/14737159.2018.1538793] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
INTRODUCTION Esophageal adenocarcinoma (EAC) has a poor 5-year survival rate (10%-18%), and incidence has increased dramatically in the past three decades. Barrett's esophagus (BE) is the precursor lesion to EAC and is the replacement of the normally squamous lined esophagus with columnar cells that develop an intestinal phenotype characterized by the presence of goblet cells. Given the known precursor state, EAC is amenable to screening and surveillance strategies (analogous to colon cancer). However, unlike from colon cancer screening, BE poses challenges that make effective screening difficult. Robust and concerted effort is under way to find biomarkers of BE. Areas covered: This review summarizes current known biomarkers for BE. These include dysplasia, genomic markers, and gene expression alterations that occur early in the dysplasia/carcinoma sequence. Expert commentary: Despite the tremendous breadth of work in studying molecular advances, the ideal biomarker for BE has not yet been discerned. This review comments on innovations in the field of BE research that combine state-of-the-art molecular advances with simple technologies.
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Affiliation(s)
- Alia P Qureshi
- a Beth Israel Deaconess Medical Center, Department of Surgery , Harvard Medical School , Boston , MA
| | - Matthew D Stachler
- b Department of Pathology, Harvard Medical School , Brigham and Women's Hospital , Boston , MA
| | - Omar Haque
- a Beth Israel Deaconess Medical Center, Department of Surgery , Harvard Medical School , Boston , MA
| | - Robert D Odze
- b Department of Pathology, Harvard Medical School , Brigham and Women's Hospital , Boston , MA
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12
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Abstract
The currently recommended approach to managing cancer risk for patients with Barrett's esophagus is endoscopic surveillance including a biopsy protocol to sample the esophageal tissue randomly to detect dysplasia. However, there are numerous limitations in this practice that rely on the histopathological grading of dysplasia alone to make clinical decisions. The availability of in silico models demonstrating the potential cost-effectiveness of biomarker-based stratification has increased interest in finding a clinically relevant "Barrett's biomarker." The success of endoscopic eradication therapy in preventing neoplastic progression of dysplastic Barrett's esophagus has promoted the desire to stratify non-dysplastic Barrett's esophagus to those with "high risk" that may benefit from endotherapy. Furthermore, on the other end of the spectrum, there is interest in searching for a "low risk" marker that may identify those that would not likely benefit from endoscopy screening or surveillance. This review highlights recent data from the genomics (r)evolution revealing new genetic biomarkers of susceptibility to the development of Barrett's esophagus and novel pathways for its neoplastic progression, addresses the development of new modes of tissue sampling and imaging to detect early neoplasia in Barrett's esophagus, and discusses current progress in moving biomarkers from the laboratory into clinical practice in the era of precision medicine.
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13
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Screening patients for Barrett esophagus: Why, who, and how. TECHNIQUES IN GASTROINTESTINAL ENDOSCOPY 2018. [DOI: 10.1016/j.tgie.2018.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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14
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Abstract
Where does cancer come from? Although the cell-of-origin is difficult to pinpoint, cancer clones harbor information about their clonal ancestries. In an effort to find cells before they evolve into a life-threatening cancer, physicians currently diagnose premalignant diseases at frequencies that substantially exceed those of clinical cancers. Cancer risk prediction relies on our ability to distinguish between which premalignant features will lead to cancer mortality and which are characteristic of inconsequential disease. Here, we review the evolution of cancer from premalignant disease, and discuss the concept that even phenotypically normal cell progenies inherently gain more malignant potential with age. We describe the hurdles of prognosticating cancer risk in premalignant disease by making reference to the underlying continuous and multivariate natures of genotypes and phenotypes and the particular challenge inherent in defining a cell lineage as "cancerized."
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Affiliation(s)
- Kit Curtius
- Centre for Tumor Biology, Barts Cancer Institute, EC1M 6BQ London, United Kingdom
| | - Nicholas A Wright
- Centre for Tumor Biology, Barts Cancer Institute, EC1M 6BQ London, United Kingdom
| | - Trevor A Graham
- Centre for Tumor Biology, Barts Cancer Institute, EC1M 6BQ London, United Kingdom
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15
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Abstract
The “chronology of cancer” is a concept that describes the nature of cancers through the measure of time. The field extends from carcinogenesis to development, progression, and metastasis. Carcinogenesis is a multi-step process, which results from the accumulation of multiple genetic or epigenetic alterations. Various chronologies of gastrointestinal cancers have been reported for carcinogenesis caused by different risk factors. These chronologies are useful for developing cancer prevention strategies. The tumor growth rate is one of the most important factors in this field. Combining the factors of time and tumor growth enables us to estimate the time at which cancer or metastasis occurred, retrospectively, and to predict the survival of cancer patients, prospectively. It is noteworthy that these chronologies differ significantly among individual cases, even of cancers derived from the same organ. Thus, they are useful for individualization. We can apply the knowledge obtained in this field to the basic research and the diagnosis and treatment of cancers. The chronology of cancer is a classical but interesting field, which helps us consider and explore the essence of cancer. We review the topics related to the chronology of gastrointestinal cancer, ranging from carcinogenesis to metastasis.
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16
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Nwachokor J, Tawfik O, Danley M, Mathur S, House J, Sharma P, Christenson LK, Bansal A. Quantitation of spatial and temporal variability of biomarkers for Barrett's Esophagus. Dis Esophagus 2017; 30:1-8. [PMID: 28859356 PMCID: PMC6036660 DOI: 10.1093/dote/dox023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/07/2017] [Accepted: 03/03/2017] [Indexed: 12/11/2022]
Abstract
Chemoprevention and risk-stratification studies in Barrett's esophagus (BE) rely on biomarkers but the variability in their temporal and spatial expression is unknown. If such variability exists, it will impact sampling techniques and sample size calculations. Specimens from three levels of biopsies over two serial endoscopies in nondysplastic BE patients were analyzed for aneuploidy, proliferation markers (Ki67, Mcm2), and cell cycle markers (cyclin A and cyclin D1). A modification of the image cytometry technique, where cytokeratin staining automatically distinguished epithelial and stromal cells, measured aneuploidy on whole tissue sections. Other biomarkers were studied by immunohistochemistry. Coefficient of variability (SD/mean) was calculated; a value <10% indicated low variability. A total of 120 specimens (20 subjects each with three biopsy levels at two time points) from nondysplastic BE patients (71 ± 8.8 years, all Caucasian, 90% males, C5.1M7.5 ± 3.4 cm) were analyzed. The mean interval between endoscopies was 32.8 ± 8.4 months. Aneuploidy had a spatial variability of 6.8% at visit 1 (mean diploid index: 1.1 ± 0.09) and 7.9% at visit 2 (mean diploid index: 1.1 ± 0.06) and a temporal variability of 7.0-8.1% for the three levels. For other biomarkers, the spatial variability ranged from ∼5 to 30% at visit 1 and 11-92% at visit 2 and the temporal variability ranged from 0 to 77%. To conclude, of all the biomarkers, only aneuploidy had both spatial and temporal variability of <10%. Spatial and temporal variability were biomarker dependent and could be as high as 90% even without progression. These data will be useful to design chemoprevention and risk-stratification studies in BE.
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Affiliation(s)
| | - O. Tawfik
- Pathology and Laboratory Medicine, the University of Kansas School of Medicine,The Kansas Cancer Institute, Kansas City, KS
| | - M. Danley
- Pathology and Laboratory Medicine, the University of Kansas School of Medicine
| | - S. Mathur
- Pathology and Laboratory Medicine, the University of Kansas School of Medicine,Department of Pathology and Laboratory Medicine, the Veterans Affairs Medical Center
| | - J. House
- Department of Biostatistics, Saint Lukes Mid-America Heart Institute
| | - P. Sharma
- The Kansas Cancer Institute, Kansas City, KS,Department of Gastroenterology and Hepatology, the Veterans Affairs Medical Center, Kansas City, MO,Departments of Gastroenterology and Hepatology
| | - L. K. Christenson
- Molecular and Integrative Physiology, the University of Kansas Medical Center, Kansas City, KS
| | - A. Bansal
- The Kansas Cancer Institute, Kansas City, KS,Department of Gastroenterology and Hepatology, the Veterans Affairs Medical Center, Kansas City, MO,Departments of Gastroenterology and Hepatology
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17
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Abstract
OBJECTIVES Patients with esophageal atresia/tracheoesophageal fistula (EA-TEF) can develop Barrett esophagus as a long-term consequence of their condition. Intestinal metaplasia (IM), a risk factor for developing adenocarcinoma of the esophagus, has not been well characterized in the pediatric population. METHODS Retrospective review of patients with EA-TEF followed at 3 academic pediatric centers between the years 1997 and 2014. RESULTS Among 542 children and adolescents, 1.3% (7 patients, 5 girls) were diagnosed with IM based on endoscopy and pathology. Six of the patients had EA-TEF type C, whereas the last patient had a "long gap" type A atresia. Patients were diagnosed with gastric metaplasia either before the IM diagnosis in 4 patients or concomitantly in 3. The median (range) age of diagnosis for gastric metaplasia was 7.9 (range 2-17.2) and for IM 10.9 (2-17.2) years. Gastroesophageal reflux (GER) symptoms were nonspecific. Five patients were on proton pump inhibitor therapy for symptomatic GER at the time of diagnosis of IM. 2 of the 7 patients had previously undergone Nissen fundoplication. One patient, who had undergone a Nissen fundoplication, was restarted on proton pump inhibitor once the diagnosis of IM was made. All patients had repeated endoscopy and dysplasia was not observed with a median follow-up of 1.7 (range 1-4.9) years. CONCLUSIONS IM occurs in patients with EA-TEF, some as young as 2 years. Therefore, early endoscopic surveillance should be considered in this GER-prone population.
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18
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Steccanella F, Costanzo A, Petrelli F. Editorial on role of p53 in esophageal cancer from a meta-analysis of 16 studies by Fisher et al.. J Thorac Dis 2017; 9:1450-1452. [PMID: 28740655 DOI: 10.21037/jtd.2017.05.72] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Francesca Steccanella
- Surgical Oncology Unit, Surgery Department, Oncology Department, ASST Bergamo Ovest, Treviglio (BG), Italy
| | - Antonio Costanzo
- Surgical Oncology Unit, Surgery Department, Oncology Department, ASST Bergamo Ovest, Treviglio (BG), Italy
| | - Fausto Petrelli
- Medical Oncology Unit, Oncology Department, ASST Bergamo Ovest, Treviglio (BG), Italy
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19
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Bijlsma MF, Sadanandam A, Tan P, Vermeulen L. Molecular subtypes in cancers of the gastrointestinal tract. Nat Rev Gastroenterol Hepatol 2017; 14:333-342. [PMID: 28400627 DOI: 10.1038/nrgastro.2017.33] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Malignancies of the gastrointestinal tract are among the most common human cancers. The distinct tissues of origin give rise to a diverse set of diseases, such as colorectal cancer, pancreatic carcinoma and gastric cancers, with each associating with specific clinical features. Genomic and transcriptomic analyses have further defined the heterogeneity that occurs within these cancers by identifying so-called molecular subtypes. These subtypes are characterized by specific genetic aberrations and expression signatures that suggest important biological differences. Although at first sight this subdivision of organ-specific cancers might increase the complexity of classification, closer analysis suggests that the subtypes detected in the various malignancies are recurring. For example, nearly all gastrointestinal cancers appear to present with subtypes that are either characterized by a mesenchymal gene expression signatures, extensive immune infiltration or metabolic dysregulation. Additionally, in each of the gastrointestinal malignancies, a 'canonical' subtype is recognized that retains characteristic features of the epithelial tissue of origin. These common themes can enhance our collective understanding of these malignancies, and could perhaps be therapeutically exploited. In this Review, the identification of subtypes in the various gastrointestinal cancer types are discussed along with how they could be incorporated into clinical practice.
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Affiliation(s)
- Maarten F Bijlsma
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Academic Medical Center, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Anguraj Sadanandam
- Division of Molecular Pathology, The Institute of Cancer Research, 15 Cotswold Road, London SM2 5NG, UK
| | - Patrick Tan
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
| | - Louis Vermeulen
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Academic Medical Center, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
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20
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Abstract
Gastric adenocarcinoma, esophageal adenocarcinoma, and esophageal squamous cell carcinoma are among the most prevalent and deadly of malignancies worldwide. Screening and prevention programs will be critical to finally improving outcomes in these diseases. For gastric adenocarcinoma, screening in high-risk populations has significantly reduced mortality. More research is needed on screening high-risk individuals in low-risk populations. For esophageal adenocarcinoma, work is needed to develop efficient and effective techniques in mass screening programs. For most Western populations, current screening is not cost effective. Avoiding environmental risk factors is critical to reducing the incidence of this deadly illness.
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Affiliation(s)
- Liam Zakko
- Division of Gastroenterology and Hepatology, Mayo Clinic, 200 2nd St. SW, Rochester, MN 55905, USA
| | - Lori Lutzke
- Barrett's Esophagus Unit, Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First Street Northwest, Rochester, MN, USA
| | - Kenneth K Wang
- Division of Gastroenterology and Hepatology, Mayo Clinic, 200 2nd St. SW, Rochester, MN 55905, USA.
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21
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Abstract
In The Cancer Genome Atlas the goals were to define how to treat advanced cancers with targeted therapy. However, the challenges facing cancer interception for early detection and prevention include length bias in which current screening and surveillance approaches frequently miss rapidly progressing cancers that then present at advanced stages in the clinic with symptoms (underdiagnosis). In contrast, many early detection strategies detect benign conditions that may never progress to cancer during a lifetime, and the patient dies of unrelated causes (overdiagnosis). This challenge to cancer interception is believed to be due to the speed at which the neoplasm evolves, called length bias sampling; rapidly progressing cancers are missed by current early detection strategies. In contrast, slowly or non-progressing cancers or their precursors are selectively detected. This has led to the concept of cancer interception, which can be defined as active interception of a biological process that drives cancer development before the patient presents in the clinic with an advanced, symptomatic cancer. The solutions needed to advance strategies for cancer interception require assessing the rate at which the cancer evolves over time and space. This is an essential challenge that needs to be addressed by robust study designs including normal and non-progressing controls when known to be appropriate.
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Affiliation(s)
- Brian J. Reid
- Correspondence Address correspondence to: Brian J. Reid, MD, PhD, 1100 Fairview Avenue N, C1-157, PO Box 19024, Seattle, Washington 98109-1024. fax: (206) 667-6192.1100 Fairview Avenue N, C1-157, PO Box 19024SeattleWashington 98109-1024
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22
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Brandtner AK, Quante M. Risk prediction in Barrett's esophagus - aspects of a combination of molecular and epidemiologic biomarkers reflecting alterations of the microenvironment. Scand J Clin Lab Invest 2016; 245:S63-S69. [PMID: 27467504 DOI: 10.1080/00365513.2016.1210327] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Barrett's esophagus (BE) is a chronic, metaplastic lesion of the esophagus and the only known precursor of esophageal adenocarcinoma. The identification of risk factors to assess the risk for BE and their correspondence with hallmarks of malignant progression for early stratification purposes is critically needed. Data legitimate the assumption that aside of reflux symptoms and related conditions, also demographic and environmental factors are thought to be associated with the risk for BE and its progression to esophageal adenocarcinoma. Molecular biomarkers and inflammatory mechanisms are subjects of intensive research and dispone of promising features regarding risk assessment especially for progressive BE. The amount of investigated epidemiologic factors, as well as discovered biomarkers gets confusingly large. Despite the recognized potential relevance of environmental and molecular factors, the efforts to date have resulted in moderately applicable risk estimates. More prospective data is needed to allow an imputation of the mostly retrospectively assessed factors to reappraise their meaningfulness in risk prediction approaches.
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Affiliation(s)
- Anna K Brandtner
- a II. Medizinische Klinik, Klinikum Rechts der Isar , Technische Universität München , Munich , Germany
- b Inflammation Research Unit, Department of Internal Medicine I , Medical University of Innsbruck , Innsbruck , Austria
| | - Michael Quante
- a II. Medizinische Klinik, Klinikum Rechts der Isar , Technische Universität München , Munich , Germany
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23
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Hui YY, Chen X, Wang BM. Yesterday and today of Barrett's esophagus: Historical evolution and research hotspots. Shijie Huaren Xiaohua Zazhi 2016; 24:3077-3086. [DOI: 10.11569/wcjd.v24.i20.3077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
It has been more than 60 years since the concept of Barrett's esophagus (BE) was put forward, and over these a few decades, we have made great progress in the diagnosis and treatment of BE. BE does not cause clinical symptoms, but it attracts wide attention, because it is an important precursor lesion of esophageal adenocarcinoma. The purpose of this article is to review the process of the recognition of BE and the current research hotspots as well as to discuss the current status of esophageal adenocarcinoma screening in BE patients. We aim to provide clinicians with an overview of the ins and outs of the disease, which will help them improve the diagnosis and treatment of BE in clinical practice and provide patients with beneficial treatment.
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24
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Abstract
The article by Banerjee and colleagues published in this issue of the journal involving a randomized control prevention trial of ursodeoxycholic acid (UDCA) in Barrett esophagus reported a null outcome despite being well designed and executed. Possible reasons for this null outcome are discussed focusing on use of surrogate endpoints in the trial. The trial is especially topical because it comes at a time when there are calls for a Pre-Cancer Genome Atlas (PCGA) for "understanding the earliest molecular and cellular events associated with cancer initiation…" This commentary discusses current concepts in prevention research including branched evolution that leads to therapeutic resistance. Length bias sampling postulates underdiagnosis is due to rapidly progressing disease that is difficult to detect by screening because it progresses to cancer too rapidly and that overdiagnosis is the result of very slowly or nonprogressing disease that is easy to detect by screening because it persists for a lifetime and the patient dies of unrelated causes. Finally, it also explores study designs, including surrogate endpoints in Barrett esophagus trials, and opportunities and pitfalls for a PCGA in the context of high levels of over and underdiagnosis of Barrett esophagus as well as many other cancers and their precursors. Cancer Prev Res; 9(7); 512-7. ©2016 AACRSee related article by Banerjee, et al., p. 528.
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Affiliation(s)
- Brian J Reid
- Divisions of Human Biology and Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington. Departments of Genome Sciences and Medicine, University of Washington, Seattle, Washington.
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25
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Carvajal Carmona LG, Tomlinson I. The Hunting of the Snark: Whither Genome-Wide Association Studies for Colorectal Cancer? Gastroenterology 2016; 150:1528-1530. [PMID: 27133396 DOI: 10.1053/j.gastro.2016.04.021] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Affiliation(s)
- Luis G Carvajal Carmona
- Genome Center and Department of Biochemistry and Molecular Medicine, School of Medicine, University of California, Davis, California.
| | - Ian Tomlinson
- Oxford Centre for Cancer Gene Research, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
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26
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Isomoto H. Optical coherence tomography in Barrett's esophagus and the road to virtual optical pathology. Dig Endosc 2016; 28:425-426. [PMID: 27177796 DOI: 10.1111/den.12656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Revised: 03/13/2016] [Accepted: 03/16/2016] [Indexed: 02/08/2023]
Affiliation(s)
- Hajime Isomoto
- Division of Medicine and Clinical Science, Department of Multidisciplinary Internal Medicine, Tottori University Faculty of Medicine, Yonago, Japan
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27
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Whole-Genome Sequencing Reveals Diverse Models of Structural Variations in Esophageal Squamous Cell Carcinoma. Am J Hum Genet 2016; 98:256-74. [PMID: 26833333 PMCID: PMC4746371 DOI: 10.1016/j.ajhg.2015.12.013] [Citation(s) in RCA: 96] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2015] [Accepted: 12/15/2015] [Indexed: 01/02/2023] Open
Abstract
Comprehensive identification of somatic structural variations (SVs) and understanding their mutational mechanisms in cancer might contribute to understanding biological differences and help to identify new therapeutic targets. Unfortunately, characterization of complex SVs across the whole genome and the mutational mechanisms underlying esophageal squamous cell carcinoma (ESCC) is largely unclear. To define a comprehensive catalog of somatic SVs, affected target genes, and their underlying mechanisms in ESCC, we re-analyzed whole-genome sequencing (WGS) data from 31 ESCCs using Meerkat algorithm to predict somatic SVs and Patchwork to determine copy-number changes. We found deletions and translocations with NHEJ and alt-EJ signature as the dominant SV types, and 16% of deletions were complex deletions. SVs frequently led to disruption of cancer-associated genes (e.g., CDKN2A and NOTCH1) with different mutational mechanisms. Moreover, chromothripsis, kataegis, and breakage-fusion-bridge (BFB) were identified as contributing to locally mis-arranged chromosomes that occurred in 55% of ESCCs. These genomic catastrophes led to amplification of oncogene through chromothripsis-derived double-minute chromosome formation (e.g., FGFR1 and LETM2) or BFB-affected chromosomes (e.g., CCND1, EGFR, ERBB2, MMPs, and MYC), with approximately 30% of ESCCs harboring BFB-derived CCND1 amplification. Furthermore, analyses of copy-number alterations reveal high frequency of whole-genome duplication (WGD) and recurrent focal amplification of CDCA7 that might act as a potential oncogene in ESCC. Our findings reveal molecular defects such as chromothripsis and BFB in malignant transformation of ESCCs and demonstrate diverse models of SVs-derived target genes in ESCCs. These genome-wide SV profiles and their underlying mechanisms provide preventive, diagnostic, and therapeutic implications for ESCCs.
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28
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Affiliation(s)
- John M. Carethers
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan,Correspondence: John M. Carethers, M.D., Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, TEL: 734-615-1717, FAX: 734-615-2645,
| | - Jonathan Braun
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Bruce E. Sands
- Dr. Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, New York
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