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Fortunato A, Mallo D, Cisneros L, King LM, Khan A, Curtis C, Ryser MD, Lo JY, Hall A, Marks JR, Hwang ES, Maley CC. Evolutionary Measures Show that Recurrence of DCIS is Distinct from Progression to Breast Cancer. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.08.15.24311949. [PMID: 39185534 PMCID: PMC11343254 DOI: 10.1101/2024.08.15.24311949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/27/2024]
Abstract
Progression from pre-cancers like ductal carcinoma in situ (DCIS) to invasive disease (cancer) is driven by somatic evolution and is altered by clinical interventions. We hypothesized that genetic and/or phenotypic intra-tumor heterogeneity would predict clinical outcomes for DCIS since it serves as the substrate for natural selection among cells. We profiled two samples from two geographically distinct foci from each DCIS in both cross-sectional (N = 119) and longitudinal cohorts (N = 224), with whole exome sequencing, low-pass whole genome sequencing, and a panel of immunohistochemical markers. In the longitudinal cohorts, the only statistically significant predictors of time to non-invasive DCIS recurrence were the combination of treatment (lumpectomy only vs mastectomy or lumpectomy with radiation, HR = 12.13, p = 0.003, Wald test with FDR correction), ER status (HR = 0.16 for ER+ compared to ER-, p = 0.0045), and divergence in SNVs between the two samples (HR = 1.33 per 10% divergence, p = 0.018). SNV divergence also distinguished between pure DCIS and DCIS synchronous with invasive disease in the cross-sectional cohort. In contrast, the only statistically significant predictors of time to progression to invasive disease were the combination of the width of the surgical margin (HR = 0.67 per mm, p = 0.043) and the number of mutations that were detectable at high allele frequencies (HR = 1.30 per 10 SNVs, p = 0.02). These results imply that recurrence with DCIS is a clinical and biological process different from invasive progression. Significance Evolutionary measures of breast pre-cancers associate with local recurrence after surgery, as well as progression to cancer. Recurrence and progression are different biological processes impacted differently by clinical interventions.
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Brosda S, Aoude LG, Bonazzi VF, Patel K, Lonie JM, Belle CJ, Newell F, Koufariotis LT, Addala V, Naeini MM, Pearson JV, Krause L, Waddell N, Barbour AP. Spatial intra-tumour heterogeneity and treatment-induced genomic evolution in oesophageal adenocarcinoma: implications for prognosis and therapy. Genome Med 2024; 16:90. [PMID: 39020404 PMCID: PMC11253399 DOI: 10.1186/s13073-024-01362-z] [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: 12/12/2023] [Accepted: 07/09/2024] [Indexed: 07/19/2024] Open
Abstract
BACKGROUND Oesophageal adenocarcinoma (OAC) is a highly heterogeneous cancer with poor survival. Standard curative treatment is chemotherapy with or without radiotherapy followed by oesophagectomy. Genomic heterogeneity is a feature of OAC and has been linked to treatment resistance. METHODS Whole-genome sequencing data from 59 treatment-naïve and 18 post-treatment samples from 29 OAC patients was analysed. Twenty-seven of these were enrolled in the DOCTOR trial, sponsored by the Australasian Gastro-Intestinal Trials Group. Two biopsies from each treatment-naïve tumour were assessed to define 'shared' (between both samples) and 'private' (present in one sample) mutations. RESULTS Mutational signatures SBS2/13 (APOBEC) and SBS3 (BRCA) were almost exclusively detected in private mutation populations of treatment-naïve tumours. Patients presenting these signatures had significantly worse disease specific survival. Furthermore, mutational signatures associated with platinum-based chemotherapy treatment as well as high platinum enrichment scores were only detected in post-treatment samples. Additionally, clones with high putative neoantigen binding scores were detected in some treatment-naïve samples suggesting immunoediting of clones. CONCLUSIONS This study demonstrates the high intra-tumour heterogeneity in OAC, as well as indicators for treatment-induced changes during tumour evolution. Intra-tumour heterogeneity remains a problem for successful treatment strategies in OAC.
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Affiliation(s)
- Sandra Brosda
- Frazer Institute, The University of Queensland, 37 Kent Street, Woolloongabba, QLD, 4102, Australia.
| | - Lauren G Aoude
- Frazer Institute, The University of Queensland, 37 Kent Street, Woolloongabba, QLD, 4102, Australia
| | - Vanessa F Bonazzi
- Frazer Institute, The University of Queensland, 37 Kent Street, Woolloongabba, QLD, 4102, Australia
| | - Kalpana Patel
- Frazer Institute, The University of Queensland, 37 Kent Street, Woolloongabba, QLD, 4102, Australia
| | - James M Lonie
- Frazer Institute, The University of Queensland, 37 Kent Street, Woolloongabba, QLD, 4102, Australia
| | - Clemence J Belle
- Frazer Institute, The University of Queensland, 37 Kent Street, Woolloongabba, QLD, 4102, Australia
| | - Felicity Newell
- QIMR Berghofer Medical Research Institute, Herston, QLD, 4006, Australia
| | | | - Venkateswar Addala
- QIMR Berghofer Medical Research Institute, Herston, QLD, 4006, Australia
| | - Marjan M Naeini
- QIMR Berghofer Medical Research Institute, Herston, QLD, 4006, Australia
- Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia
- Faculty of Medicine, St Vincent's Clinical School, University of New South Wales, Sydney, NSW, 2052, Australia
| | - John V Pearson
- QIMR Berghofer Medical Research Institute, Herston, QLD, 4006, Australia
| | - Lutz Krause
- Frazer Institute, The University of Queensland, 37 Kent Street, Woolloongabba, QLD, 4102, Australia
- Microba Life Sciences, Brisbane, QLD, 4000, Australia
| | - Nicola Waddell
- QIMR Berghofer Medical Research Institute, Herston, QLD, 4006, Australia
| | - Andrew P Barbour
- Frazer Institute, The University of Queensland, 37 Kent Street, Woolloongabba, QLD, 4102, Australia
- Princess Alexandra Hospital, Woolloongabba, QLD, 4102, Australia
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3
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Zhang S, Xiao X, Yi Y, Wang X, Zhu L, Shen Y, Lin D, Wu C. Tumor initiation and early tumorigenesis: molecular mechanisms and interventional targets. Signal Transduct Target Ther 2024; 9:149. [PMID: 38890350 PMCID: PMC11189549 DOI: 10.1038/s41392-024-01848-7] [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: 01/01/2024] [Revised: 04/23/2024] [Accepted: 04/27/2024] [Indexed: 06/20/2024] Open
Abstract
Tumorigenesis is a multistep process, with oncogenic mutations in a normal cell conferring clonal advantage as the initial event. However, despite pervasive somatic mutations and clonal expansion in normal tissues, their transformation into cancer remains a rare event, indicating the presence of additional driver events for progression to an irreversible, highly heterogeneous, and invasive lesion. Recently, researchers are emphasizing the mechanisms of environmental tumor risk factors and epigenetic alterations that are profoundly influencing early clonal expansion and malignant evolution, independently of inducing mutations. Additionally, clonal evolution in tumorigenesis reflects a multifaceted interplay between cell-intrinsic identities and various cell-extrinsic factors that exert selective pressures to either restrain uncontrolled proliferation or allow specific clones to progress into tumors. However, the mechanisms by which driver events induce both intrinsic cellular competency and remodel environmental stress to facilitate malignant transformation are not fully understood. In this review, we summarize the genetic, epigenetic, and external driver events, and their effects on the co-evolution of the transformed cells and their ecosystem during tumor initiation and early malignant evolution. A deeper understanding of the earliest molecular events holds promise for translational applications, predicting individuals at high-risk of tumor and developing strategies to intercept malignant transformation.
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Affiliation(s)
- Shaosen Zhang
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
- Key Laboratory of Cancer Genomic Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
| | - Xinyi Xiao
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
- Key Laboratory of Cancer Genomic Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
| | - Yonglin Yi
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
- Key Laboratory of Cancer Genomic Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
| | - Xinyu Wang
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
- Key Laboratory of Cancer Genomic Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
| | - Lingxuan Zhu
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
- Key Laboratory of Cancer Genomic Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
- Changping Laboratory, 100021, Beijing, China
| | - Yanrong Shen
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
- Key Laboratory of Cancer Genomic Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
| | - Dongxin Lin
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China.
- Key Laboratory of Cancer Genomic Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China.
- Changping Laboratory, 100021, Beijing, China.
- Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, 211166, China.
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Guangzhou, 510060, China.
| | - Chen Wu
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China.
- Key Laboratory of Cancer Genomic Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China.
- Changping Laboratory, 100021, Beijing, China.
- Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, 211166, China.
- CAMS Oxford Institute, Chinese Academy of Medical Sciences, 100006, Beijing, China.
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Deboever N, Jones CM, Yamashita K, Ajani JA, Hofstetter WL. Advances in diagnosis and management of cancer of the esophagus. BMJ 2024; 385:e074962. [PMID: 38830686 DOI: 10.1136/bmj-2023-074962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 06/05/2024]
Abstract
Esophageal cancer is the seventh most common malignancy worldwide, with over 470 000 new cases diagnosed each year. Two distinct histological subtypes predominate, and should be considered biologically separate disease entities.1 These subtypes are esophageal adenocarcinoma (EAC) and esophageal squamous cell carcinoma (ESCC). Outcomes remain poor regardless of subtype, with most patients presenting with late stage disease.2 Novel strategies to improve early detection of the respective precursor lesions, squamous dysplasia, and Barrett's esophagus offer the potential to improve outcomes. The introduction of a limited number of biologic agents, as well as immune checkpoint inhibitors, is resulting in improvements in the systemic treatment of locally advanced and metastatic esophageal cancer. These developments, coupled with improvements in minimally invasive surgical and endoscopic treatment approaches, as well as adaptive and precision radiotherapy technologies, offer the potential to improve outcomes still further. This review summarizes the latest advances in the diagnosis and management of esophageal cancer, and the developments in understanding of the biology of this disease.
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Affiliation(s)
- Nathaniel Deboever
- Department of Thoracic and Cardiovascular Surgery, MD Anderson Cancer Center, Houston, TX, USA
| | - Christopher M Jones
- Early Cancer Institute, Department of Oncology, University of Cambridge, Cambridge, UK
- Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Kohei Yamashita
- Department of Gastrointestinal Medical Oncology, MD Anderson Cancer Center, Houston, TX, USA
| | - Jaffer A Ajani
- Department of Gastrointestinal Medical Oncology, MD Anderson Cancer Center, Houston, TX, USA
| | - Wayne L Hofstetter
- Department of Thoracic and Cardiovascular Surgery, MD Anderson Cancer Center, Houston, TX, USA
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Edrisi M, Huang X, Ogilvie HA, Nakhleh L. Accurate integration of single-cell DNA and RNA for analyzing intratumor heterogeneity using MaCroDNA. Nat Commun 2023; 14:8262. [PMID: 38092737 PMCID: PMC10719311 DOI: 10.1038/s41467-023-44014-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 11/27/2023] [Indexed: 12/17/2023] Open
Abstract
Cancers develop and progress as mutations accumulate, and with the advent of single-cell DNA and RNA sequencing, researchers can observe these mutations and their transcriptomic effects and predict proteomic changes with remarkable temporal and spatial precision. However, to connect genomic mutations with their transcriptomic and proteomic consequences, cells with either only DNA data or only RNA data must be mapped to a common domain. For this purpose, we present MaCroDNA, a method that uses maximum weighted bipartite matching of per-gene read counts from single-cell DNA and RNA-seq data. Using ground truth information from colorectal cancer data, we demonstrate the advantage of MaCroDNA over existing methods in accuracy and speed. Exemplifying the utility of single-cell data integration in cancer research, we suggest, based on results derived using MaCroDNA, that genomic mutations of large effect size increasingly contribute to differential expression between cells as Barrett's esophagus progresses to esophageal cancer, reaffirming the findings of the previous studies.
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Affiliation(s)
| | - Xiru Huang
- Department of Computer Science, Rice University, Houston, Texas, USA
| | - Huw A Ogilvie
- Department of Computer Science, Rice University, Houston, Texas, USA.
| | - Luay Nakhleh
- Department of Computer Science, Rice University, Houston, Texas, USA.
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6
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Li S, Hoefnagel SJM, Krishnadath KK. Molecular Biology and Clinical Management of Esophageal Adenocarcinoma. Cancers (Basel) 2023; 15:5410. [PMID: 38001670 PMCID: PMC10670638 DOI: 10.3390/cancers15225410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 11/10/2023] [Accepted: 11/12/2023] [Indexed: 11/26/2023] Open
Abstract
Esophageal adenocarcinoma (EAC) is a highly lethal malignancy. Due to its rising incidence, EAC has become a severe health challenge in Western countries. Current treatment strategies are mainly chosen based on disease stage and clinical features, whereas the biological background is hardly considered. In this study, we performed a comprehensive review of existing studies and discussed how etiology, genetics and epigenetic characteristics, together with the tumor microenvironment, contribute to the malignant behavior and dismal prognosis of EAC. During the development of EAC, several intestinal-type proteins and signaling cascades are induced. The anti-inflammatory and immunosuppressive microenvironment is associated with poor survival. The accumulation of somatic mutations at the early phase and chromosomal structural rearrangements at relatively later time points contribute to the dynamic and heterogeneous genetic landscape of EAC. EAC is also characterized by frequent DNA methylation and dysregulation of microRNAs. We summarize the findings of dysregulations of specific cytokines, chemokines and immune cells in the tumor microenvironment and conclude that DNA methylation and microRNAs vary with each different phase of BE, LGD, HGD, early EAC and invasive EAC. Furthermore, we discuss the suitability of the currently employed therapies in the clinic and possible new therapies in the future. The development of targeted and immune therapies has been hampered by the heterogeneous genetic characteristics of EAC. In view of this, the up-to-date knowledge revealed by this work is absolutely important for future EAC studies and the discovery of new therapeutics.
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Affiliation(s)
- Shulin Li
- Center for Experimental and Molecular Medicine, Amsterdam University Medical Centers, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands;
- Cancer Center Amsterdam, 1081 HV Amsterdam, The Netherlands
| | | | - Kausilia Krishnawatie Krishnadath
- Department of Gastroenterology and Hepatology, Antwerp University Hospital, 2650 Edegem, Belgium
- Laboratory of Experimental Medicine and Pediatrics, University of Antwerp, 2000 Antwerpen, Belgium
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7
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Wani S, Holmberg D, Santoni G, Kauppila JH, Farkkila M, von Euler-Chelpin M, Shaheen NJ, Lagergren J. Magnitude and Time-Trends of Post-Endoscopy Esophageal Adenocarcinoma and Post-Endoscopy Esophageal Neoplasia in a Population-Based Cohort Study: The Nordic Barrett's Esophagus Study. Gastroenterology 2023; 165:909-919.e13. [PMID: 37279832 DOI: 10.1053/j.gastro.2023.05.044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 04/12/2023] [Accepted: 05/14/2023] [Indexed: 06/08/2023]
Abstract
BACKGROUND & AIMS Post-endoscopy esophageal adenocarcinoma (PEEC) and post-endoscopy esophageal neoplasia (PEEN) undermine early cancer detection in Barrett's esophagus (BE). We aimed to assess the magnitude and conduct time-trend analysis of PEEC and PEEN among patients with newly diagnosed BE. METHODS This population-based cohort study was conducted in Denmark, Finland, and Sweden between 2006 and 2020 and included 20,588 patients with newly diagnosed BE. PEEC and PEEN were defined as esophageal adenocarcinoma (EAC) or high-grade dysplasia (HGD)/EAC, respectively, diagnosed 30-365 days from BE diagnosis (index endoscopy). HGD/EAC diagnosed from 0-29 days and HGD/EAC diagnosed >365 days from BE diagnosis (incident HGD/EAC) were assessed. Patients were followed up until HGD/EAC, death, or end of study period. Incidence rates (IR) per 100,000 person-years with 95% confidence interval (95% CI) were calculated using Poisson regression. RESULTS Among 293 patients diagnosed with EAC, 69 (23.5%) were categorized as PEEC, 43 (14.7%) as index EAC, and 181 (61.8%) as incident EAC. The IRs/100,000 person-years for PEEC and incident EAC were 392 (95% CI, 309-496), and 208 (95% CI, 180-241), respectively. Among 279 patients diagnosed with HGD/EAC (Sweden only), 17.2% were categorized as PEEN, 14.6% as index HGD/EAC, and 68.1% as incident HGD/EAC. IRs/100,000 person-years for PEEN, and incident HGD/EAC were 421 (95% CI, 317-558), and 285 (95% CI, 247-328), respectively. Sensitivity analyses that varied time interval for occurrence of PEEC/PEEN demonstrated similar results. A time-trend analysis for IRs demonstrated rising incidence rates of PEEC/PEEN. CONCLUSIONS Almost a quarter of all EACs are detected within a year after an ostensibly negative upper endoscopy in patients with newly diagnosed BE. Interventions to improve detection may reduce PEEC/PEEN rates.
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Affiliation(s)
- Sachin Wani
- Division of Gastroenterology and Hepatology, University of Colorado Anschutz Medical Campus, Aurora, Colorado.
| | - Dag Holmberg
- Department of Molecular Medicine and Surgery, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Giola Santoni
- Department of Molecular Medicine and Surgery, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Joonas H Kauppila
- Department of Molecular Medicine and Surgery, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden; Department of Surgery, Oulu University Hospital and University of Oulu, Oulu, Finland
| | - Martti Farkkila
- Clinic of Gastroenterology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | | | - Nicholas J Shaheen
- Division of Gastroenterology and Hepatology, University of North Carolina, Chapel Hill, North Carolina
| | - Jesper Lagergren
- Department of Molecular Medicine and Surgery, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden; School of Cancer and Pharmaceutical Sciences, King's College London, London, United Kingdom
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Johnson B, Shuai Y, Schweinsberg J, Curtius K. cloneRate: fast estimation of single-cell clonal dynamics using coalescent theory. Bioinformatics 2023; 39:btad561. [PMID: 37699006 PMCID: PMC10534056 DOI: 10.1093/bioinformatics/btad561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 08/25/2023] [Indexed: 09/14/2023] Open
Abstract
MOTIVATION While evolutionary approaches to medicine show promise, measuring evolution itself is difficult due to experimental constraints and the dynamic nature of body systems. In cancer evolution, continuous observation of clonal architecture is impossible, and longitudinal samples from multiple timepoints are rare. Increasingly available DNA sequencing datasets at single-cell resolution enable the reconstruction of past evolution using mutational history, allowing for a better understanding of dynamics prior to detectable disease. There is an unmet need for an accurate, fast, and easy-to-use method to quantify clone growth dynamics from these datasets. RESULTS We derived methods based on coalescent theory for estimating the net growth rate of clones using either reconstructed phylogenies or the number of shared mutations. We applied and validated our analytical methods for estimating the net growth rate of clones, eliminating the need for complex simulations used in previous methods. When applied to hematopoietic data, we show that our estimates may have broad applications to improve mechanistic understanding and prognostic ability. Compared to clones with a single or unknown driver mutation, clones with multiple drivers have significantly increased growth rates (median 0.94 versus 0.25 per year; P = 1.6×10-6). Further, stratifying patients with a myeloproliferative neoplasm (MPN) by the growth rate of their fittest clone shows that higher growth rates are associated with shorter time to MPN diagnosis (median 13.9 versus 26.4 months; P = 0.0026). AVAILABILITY AND IMPLEMENTATION We developed a publicly available R package, cloneRate, to implement our methods (Package website: https://bdj34.github.io/cloneRate/). Source code: https://github.com/bdj34/cloneRate/.
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Affiliation(s)
- Brian Johnson
- Division of Biomedical Informatics, Department of Medicine, University of California San Diego, La Jolla, CA 92093, United States
| | - Yubo Shuai
- Department of Mathematics, University of California San Diego, La Jolla, CA 92093, United States
| | - Jason Schweinsberg
- Department of Mathematics, University of California San Diego, La Jolla, CA 92093, United States
| | - Kit Curtius
- Division of Biomedical Informatics, Department of Medicine, University of California San Diego, La Jolla, CA 92093, United States
- Moores Cancer Center, University of California San Diego, La Jolla, CA 92093, United States
- VA San Diego Healthcare System, San Diego, CA 92161, United States
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9
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Derbal Y. Cell Adaptive Fitness and Cancer Evolutionary Dynamics. Cancer Inform 2023; 22:11769351231154679. [PMID: 36860424 PMCID: PMC9969436 DOI: 10.1177/11769351231154679] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 01/17/2023] [Indexed: 02/26/2023] Open
Abstract
Genome instability of cancer cells translates into increased entropy and lower information processing capacity, leading to metabolic reprograming toward higher energy states, presumed to be aligned with a cancer growth imperative. Dubbed as the cell adaptive fitness, the proposition postulates that the coupling between cell signaling and metabolism constrains cancer evolutionary dynamics along trajectories privileged by the maintenance of metabolic sufficiency for survival. In particular, the conjecture postulates that clonal expansion becomes restricted when genetic alterations induce a sufficiently high level of disorder, that is, high entropy, in the regulatory signaling network, abrogating as a result the ability of cancer cells to successfully replicate, leading to a stage of clonal stagnation. The proposition is analyzed in the context of an in-silico model of tumor evolutionary dynamics to illustrate how cell-inherent adaptive fitness may predictably constrain clonal evolution of tumors, which would have significant implications for the design of adaptive cancer therapies.
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Affiliation(s)
- Youcef Derbal
- Youcef Derbal, Ted Rogers School of
Information Technology Management, Toronto Metropolitan University, 350 Victoria
Street, Toronto, ON M5B 2K3, Canada.
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10
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Barroux M, Horstmann J, Fricke L, Schömig L, Werner M, Kraynova E, Kamarádová K, Fléjou JF, Maerkel B, Kumarasinghe MP, Vieth M, Westerhoff M, Patil DT, Steiger K, Becker KF, Weichert W, Schmid RM, Quante M, Slotta-Huspenina J. Histological evaluation of PAXgene tissue fixation in Barrett’s esophagus and esophageal adenocarcinoma diagnostics. Virchows Arch 2022; 482:887-898. [PMID: 36527466 PMCID: PMC10156762 DOI: 10.1007/s00428-022-03471-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 11/01/2022] [Accepted: 11/30/2022] [Indexed: 12/23/2022]
Abstract
Abstract
The dysplasia grading of Barrett’s esophagus (BE), based on the histomorphological assessment of formalin-fixed, paraffin-embedded (FFPE) tissue, suffers from high interobserver variability leading to an unsatisfactory prediction of cancer risk. Thus, pre-analytic preservation of biological molecules, which could improve risk prediction in BE enabling molecular and genetic analysis, is needed. We aimed to evaluate such a molecular pre-analytic fixation tool, PAXgene-fixed paraffin-embedded (PFPE) biopsies, and their suitability for histomorphological BE diagnostics in comparison to FFPE. In a ring trial, 9 GI pathologists evaluated 116 digital BE slides of non-dysplastic BE (NDBE), low-grade dysplasia (LGD), high-grade dysplasia (HGD), and esophageal adenocarcinomas (EAC) using virtual microscopy. Overall quality, cytological and histomorphological parameters, dysplasia criteria, and diagnosis were analyzed. PFPE showed better preservation of nuclear details as chromatin and nucleoli, whereas overall quality and histomorphologic parameters as visibility of basal lamina, goblet cells, and presence of artifacts were scored as equal to FFPE. The interobserver reproducibility with regard to the diagnosis was best for NDBE and EAC (κF = 0.72–0.75) and poor for LGD and HGD (κF = 0.13–0.3) in both. In conclusion, our data suggest that PFPE allows equally confident histomorphological diagnosis of BE and EAC, introducing a novel tool for molecular analysis and parallel histomorphological evaluation.
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Affiliation(s)
- Melissa Barroux
- Klinikum Rechts Der Isar, Medical Clinic and Polyclinic II, Technical University of Munich, Munich, Germany.
| | - Julia Horstmann
- Klinikum Rechts Der Isar, Medical Clinic and Polyclinic II, Technical University of Munich, Munich, Germany
| | - Lisa Fricke
- Klinikum Rechts Der Isar, Medical Clinic and Polyclinic II, Technical University of Munich, Munich, Germany
| | - Linus Schömig
- Department of Medicine II, Universitaetsklinikum Freiburg, Freiburg, Germany
| | - Martin Werner
- Institute for Surgical Pathology, Medical Center-University of Freiburg and Faculty of Medicine, University of Freiburg, 79106, Freiburg, Germany
| | - Ekaterina Kraynova
- Department of Pathology, Yaroslavl Regional Cancer Hospital, Yaroslavl, Russian Federation
| | - Katerina Kamarádová
- The Fingerland Department of Pathology, Faculty of Medicine and University Hospital, Charles University, Hradec Králové, Czech Republic
| | - Jean-François Fléjou
- Service d'Anatomie Pathologique, AP-HP, Faculté de Médecine Sorbonne, Hôpital Saint-Antoine, Université, 75012, Paris, France
| | - Bruno Maerkel
- Institute of Pathology and Molecular Diagnostics, University Medical Center Augsburg, Augsburg, Germany
| | - M Priyanthi Kumarasinghe
- Department of Pathology, PathWest Laboratory-University of Western Australia, WA, Perth, Australia
| | - Michael Vieth
- Institute for Pathology, Friedrich-Alexander-University Erlangen-Nuremberg, Klinikum Bayreuth, Bayreuth, Germany
| | | | - Deepa T Patil
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, USA
| | - Katja Steiger
- Institute of Pathology, Technical University of Munich, Munich, Germany
| | | | - Wilko Weichert
- Institute of Pathology, Technical University of Munich, Munich, Germany
| | - Roland M Schmid
- Klinikum Rechts Der Isar, Medical Clinic and Polyclinic II, Technical University of Munich, Munich, Germany
| | - Michael Quante
- Klinikum Rechts Der Isar, Medical Clinic and Polyclinic II, Technical University of Munich, Munich, Germany
- Department of Medicine II, Universitaetsklinikum Freiburg, Freiburg, Germany
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11
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Hoefnagel SJ, Li S, Timmer EM, Meijer SL, Krishnadath KK. Increased PXR and Suppressed T-Cell Signaling Are Associated With Malignant Degeneration of Barrett's Esophagus. GASTRO HEP ADVANCES 2022; 2:63-71. [PMID: 39130159 PMCID: PMC11308616 DOI: 10.1016/j.gastha.2022.08.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 08/18/2022] [Indexed: 08/13/2024]
Abstract
Background and Aims Barrett's esophagus (BE) is the precursor lesion for esophageal adenocarcinoma (EAC). To detect EAC in early stage, patients with BE undergo endoscopic surveillance. Surveillance cohorts largely consist of nondysplastic BE (NDBE) patients with a low annual progression risk (<0.5%). Predictive biomarkers for malignant progression of NDBE could improve efficacy of surveillance. Biomarker research has mostly focused on aberrant protein expression on BE epithelial cells. Moreover, insight in cell signaling driving malignant transformation is unknown. This study uses a data-driven approach to analyze tumor-stroma interaction in NDBE which progressed to high-grade dysplasia or EAC. Methods In this case-control study, we performed RNA sequencing analysis on index NDBE biopsies from 6 patients who, during long-term follow-up, progressed and 7 who did not progress to high-grade dysplasia/EAC. For control samples, squamous and duodenum tissues from BE patients were analyzed. For validation, we used quantitative PCR. Results Significant differences in BE transcriptomic profiles between progressors and nonprogressors were found by principal component and differential expression analyses. Ingenuity pathway analysis indicated that 8 cell signaling pathways were significantly upregulated in the progressors, and 14 pathways were significantly downregulated. The most interesting finding was the upregulation of the xenobiotic metabolism pregnane X receptor signaling pathway in the progressor cohort, while of the downregulated pathways in progressors, several were related to the immune system. Conclusion These novel transcriptomic insights are fundamental for developing (chemo-)preventive therapies. These could be therapies, which protect against toxins, including biles, responsible for pregnane X receptor activation or which enhance protective immune mechanisms. The identified RNA markers are promising biomarkers for improving risk stratification in surveillance programs.
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Affiliation(s)
- Sanne J.M. Hoefnagel
- Center for Experimental and Molecular Medicine, Amsterdam UMC, Location Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
- Department of Gastroenterology and Hepatology, Amsterdam UMC, Location Academic Medical Center, Amsterdam, the Netherlands
- Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - Shulin Li
- Center for Experimental and Molecular Medicine, Amsterdam UMC, Location Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
- Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - Eva M. Timmer
- Center for Experimental and Molecular Medicine, Amsterdam UMC, Location Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
- Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - Sybren L. Meijer
- Cancer Center Amsterdam, Amsterdam, The Netherlands
- Department of Pathology, Amsterdam UMC, Location Academic Medical Center, Amsterdam, the Netherlands
| | - Kausilia K. Krishnadath
- Center for Experimental and Molecular Medicine, Amsterdam UMC, Location Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
- Department of Gastroenterology and Hepatology, Amsterdam UMC, Location Academic Medical Center, Amsterdam, the Netherlands
- Cancer Center Amsterdam, Amsterdam, The Netherlands
- Laboratory of Experimental Medicine and Paediatrics, Department of Gastroenterology and Hepatology, University Hospital Antwerp, University of Antwerp, Edegem, Belgium
- Department of Gastroenterology and Hepatology, Erasmus University MC, Rotterdam, The Netherlands
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12
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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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13
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ctDNA as a biomarker of progression in oesophageal adenocarcinoma. ESMO Open 2022; 7:100452. [PMID: 35798469 PMCID: PMC9271467 DOI: 10.1016/j.esmoop.2022.100452] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 02/09/2022] [Accepted: 02/20/2022] [Indexed: 12/24/2022] Open
Abstract
Background The incidence of oesophageal adenocarcinoma (OAC) is rapidly increasing and despite improvements in treatment, the 5-year survival rate remains poor. Prognostic biomarkers that address the genomic heterogeneity in this highly complex disease will aid the development of precision therapeutics and improve patient survival. The aim of this study was to determine whether circulating tumour DNA (ctDNA) has prognostic significance as a biomarker in OAC patients. Patients and methods We profiled 209 blood and tumour samples from 57 OAC patients. Using a panel of 77 cancer genes, we sequenced ctDNA in plasma samples (n = 127) which were taken at multiple time points before and after therapy. In parallel, we sequenced matched tumour samples from 39 patients using the same gene panel. To assess whether the ctDNA profile reflected the tumour heterogeneity, we sequenced additional multi-region primary tumour samples in 17 patients. In addition, we analysed whole-genome and whole-exome sequencing data from primary tumours for a subset of 18 patients. Results Using a tumour-agnostic approach, we found that detectable ctDNA variants in post-treatment plasma samples were associated with worse disease-specific survival. To evaluate whether the ctDNA originated from the primary tumour, we carried out a tumour-informed analysis which confirmed post-treatment ctDNA variants were associated with worse survival. To determine whether ctDNA could be used as a clinical follow-up test, we assessed blood samples from multiple time points before and after treatment, in a subset of patients. Results showed that the variant allele frequency of ctDNA variants increased with disease recurrence. Conclusion This study demonstrates that ctDNA variants can be detected in patients with OAC and this has potential clinical utility as a prognostic biomarker for survival. Detection of ctDNA variants was associated with worse disease-specific survival in OAC. In a tumour-informed approach, ctDNA variants were confirmed using multiple biopsies from the primary tumour. ctDNA variants reflected the intratumour heterogeneity associated with OAC. ctDNA can be used as a personalised prognostic biomarker for patients with OAC.
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14
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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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15
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Abstract
Integration of ecological and evolutionary features has begun to understand the interplay of tumor heterogeneity, microenvironment, and metastatic potential. Developing a theoretical framework is intrinsic to deciphering tumors' tremendous spatial and longitudinal genetic variation patterns in patients. Here, we propose that tumors can be considered evolutionary island-like ecosystems, that is, isolated systems that undergo evolutionary and spatiotemporal dynamic processes that shape tumor microenvironments and drive the migration of cancer cells. We examine attributes of insular systems and causes of insularity, such as physical distance and connectivity. These properties modulate migration rates of cancer cells through processes causing spatial and temporal isolation of the organs and tissues functioning as a supply of cancer cells for new colonizations. We discuss hypotheses, predictions, and limitations of tumors as islands analogy. We present emerging evidence of tumor insularity in different cancer types and discuss their relevance to the islands model. We suggest that the engagement of tumor insularity into conceptual and mathematical models holds promise to illuminate cancer evolution, tumor heterogeneity, and metastatic potential of cells.
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Affiliation(s)
- Antonia Chroni
- Institute for Genomics and Evolutionary Medicine, Temple University, USA
- Department of Biology, Temple University, USA
| | - Sudhir Kumar
- Institute for Genomics and Evolutionary Medicine, Temple University, USA
- Department of Biology, Temple University, USA
- Center for Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia
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16
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Norita K, Koike T, Saito M, Shinkai H, Ami R, Abe Y, Dairaku N, Inomata Y, Kayaba S, Ishiyama F, Oikawa T, Ohyauchi M, Ito H, Asonuma S, Hoshi T, Kato K, Ohara S, Shimodaira Y, Watanabe K, Shimosegawa T, Masamune A, Iijima K. Long-term endoscopic surveillance for Barrett's esophagus in Japan: Multicenter prospective cohort study. Dig Endosc 2021; 33:1085-1092. [PMID: 33277694 DOI: 10.1111/den.13910] [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: 09/23/2020] [Revised: 12/01/2020] [Accepted: 12/01/2020] [Indexed: 01/07/2023]
Abstract
OBJECTS Although a recent study showed the cancer incidence of Barrett's esophagus (BE) to be 1.2%/year in 251 patient-years in Japan, the long-term outcomes remain unclear. The present study estimated the cancer risk of BE in Japan using our original prospective multicenter cohort. METHODS A total of 98 patients with BE of maximum length of ≥2 cm were enrolled during the period of 2010-2012 and received at least one follow-up endoscopy over 5 years thereafter. Cancer incidence rates with 95% confidence interval for occurrence of esophageal adenocarcinoma (EAC) were calculated as the number of events divided by patient-years of follow-up and were expressed as %/year. RESULTS Overall, the median endoscopic follow-up period was 59.9 (first and third quartiles, 48.5-60.8) months, constituting a total of 427 patient-years of observation. Since two EAC cases developed, the cancer incidence was 0.47% (0.01%-1.81%)/year. The cancer incidence was 0.39% (-0.16% to 2.44%) in 232 patient-years and 0.31% (-0.13% to 1.95%)/year in 318 patient-years for 55 cases with specialized intestinal metaplasia and 70 with BE ≥3 cm (maximum), respectively. At the end of follow-up, 12 of 92 patients (13.0%) died, but none died from EAC. CONCLUSION This is the largest prospective follow-up study with endoscopy to investigate the incidence of EAC in unequivocal BE with the maximum length of ≥2 cm in Japan. Although a further large-scale study will be required to validate our results, the cancer risk of BE in Japan would be lower than previously reported (0.47% vs 1.2%/year).
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Affiliation(s)
- Kazuaki Norita
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Miyagi, Japan
| | - Tomoyuki Koike
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Miyagi, Japan
| | - Masahiro Saito
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Miyagi, Japan
| | - Hirohiko Shinkai
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Miyagi, Japan
| | - Reiko Ami
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Miyagi, Japan
| | - Yasuhiko Abe
- Department of Gastroenterology, Yamagata University Faculty of Medicine, Yamagata, Japan
| | - Naohiro Dairaku
- Department of Gastroenterology, Iwaki Kyoritsu General Hospital, Fukushima, Japan
| | | | - Shoichi Kayaba
- Department of Gastroenterology, Iwate Prefectural Isawa Hospital, Iwate, Japan
| | - Fumitake Ishiyama
- Department of Gastroenterology, Iwate Prefectural Isawa Hospital, Iwate, Japan
| | - Tomoyuki Oikawa
- Department of Gastroenterology, Hachinohe City Hospital, Aomori, Japan
| | - Motoki Ohyauchi
- Department of Gastroenterology, Osaki Citizen Hospital, Miyagi, Japan
| | - Hirotaka Ito
- Department of Gastroenterology, Osaki Citizen Hospital, Miyagi, Japan
| | - Sho Asonuma
- Department of Gastroenterology, South Miyagi Medical Center, Miyagi, Japan
| | - Tatsuya Hoshi
- Department of Gastroenterology, Kesennuma City Hospital, Miyagi, Japan
| | - Katsuaki Kato
- Cancer Detection Center, Miyagi Cancer Society, Miyagi, Japan
| | - Shuichi Ohara
- Department of Gastroenterology, Tohoku Rosai Hospital, Miyagi, Japan
| | - Yosuke Shimodaira
- Department of Gastroenterology, Akita University School of Medicine, Akita, Japan
| | - Kenta Watanabe
- Department of Gastroenterology, Akita University School of Medicine, Akita, Japan
| | - Tooru Shimosegawa
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Miyagi, Japan.,Department of Gastroenterology, South Miyagi Medical Center, Miyagi, Japan
| | - Atsushi Masamune
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Miyagi, Japan
| | - Katsunori Iijima
- Department of Gastroenterology, Akita University School of Medicine, Akita, Japan
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17
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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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18
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Boutry J, Tissot S, Ujvari B, Capp JP, Giraudeau M, Nedelcu AM, Thomas F. The evolution and ecology of benign tumors. Biochim Biophys Acta Rev Cancer 2021; 1877:188643. [PMID: 34715267 DOI: 10.1016/j.bbcan.2021.188643] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 10/22/2021] [Accepted: 10/23/2021] [Indexed: 12/12/2022]
Abstract
Tumors are usually classified into two main categories - benign or malignant, with much more attention being devoted to the second category given that they are usually associated with more severe health issues (i.e., metastatic cancers). Here, we argue that the mechanistic distinction between benign and malignant tumors has narrowed our understanding of neoplastic processes. This review provides the first comprehensive discussion of benign tumors in the context of their evolution and ecology as well as interactions with their hosts. We compare the genetic and epigenetic profiles, cellular activities, and the involvement of viruses in benign and malignant tumors. We also address the impact of intra-tumoral cell composition and its relationship with the tumoral microenvironment. Lastly, we explore the differences in the distribution of benign and malignant neoplasia across the tree of life and provide examples on how benign tumors can also affect individual fitness and consequently the evolutionary trajectories of populations and species. Overall, our goal is to bring attention to the non-cancerous manifestations of tumors, at different scales, and to stimulate research on the evolutionary ecology of host-tumor interactions on a broader scale. Ultimately, we suggest that a better appreciation of the differences and similarities between benign and malignant tumors is fundamental to our understanding of malignancy both at mechanistic and evolutionary levels.
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Affiliation(s)
- Justine Boutry
- CREEC/CANECEV, MIVEGEC (CREES), University of Montpellier, CNRS, IRD, Montpellier, France
| | - Sophie Tissot
- CREEC/CANECEV, MIVEGEC (CREES), University of Montpellier, CNRS, IRD, Montpellier, France
| | - Beata Ujvari
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin, University, Vic., Australia
| | - Jean-Pascal Capp
- Toulouse Biotechnology Institute, University of Toulouse, INSA, CNRS, INRAE, Toulouse, France
| | - Mathieu Giraudeau
- CREEC/CANECEV, MIVEGEC (CREES), University of Montpellier, CNRS, IRD, Montpellier, France; LIENSs, UMR 7266 CNRS-La Rochelle Université, 2 Rue Olympe de Gouges, 17000 La Rochelle, France
| | - Aurora M Nedelcu
- Department of Biology, University of New Brunswick, Fredericton, New Brunswick, E3B 5A3, Canada
| | - Frédéric Thomas
- CREEC/CANECEV, MIVEGEC (CREES), University of Montpellier, CNRS, IRD, Montpellier, France.
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19
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Sharma S, George P, Waddell N. Precision diagnostics: Integration of tissue pathology and genomics in cancer. Pathology 2021; 53:809-817. [PMID: 34635323 DOI: 10.1016/j.pathol.2021.08.003] [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: 04/14/2021] [Revised: 08/17/2021] [Accepted: 08/24/2021] [Indexed: 12/09/2022]
Abstract
Traditionally, cancer diagnosis and management has been reactionary in that symptoms lead to investigations, then a diagnosis is followed by clinical management. This process is heavily dependent on tissue diagnosis mainly by histopathology and to a lesser extent, cytopathology. However, in recent times there has been a shift towards precision medicine to enable prevention, prediction and personalisation in healthcare. The core of precision medicine is optimising therapeutic benefit for patients, by using genomic and molecular profiling, analogously termed precision pathology. This review explores (1) the evolution of pathology from a para-clinical discipline to a mainstream medical field integral to oncology tumour boards; (2) its critical role in preventative, diagnostic, therapeutic and follow-up cancer care; (3) the future of tissue pathology in the era of precision oncology; and (4) how pathologists may evolve to future-proof their profession.
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Affiliation(s)
- Sowmya Sharma
- Medlab Pathology, Auburn, NSW, Australia; QIMR Berghofer Medical Research Institute, Department of Genetics and Computational Biology, Brisbane, Qld, Australia; Faculty of Medicine, University of Queensland, Brisbane, Qld, Australia.
| | - Peter George
- Medlab Pathology, Auburn, NSW, Australia; genomiQa, Brisbane, Qld, Australia
| | - Nicola Waddell
- QIMR Berghofer Medical Research Institute, Department of Genetics and Computational Biology, Brisbane, Qld, Australia; Faculty of Medicine, University of Queensland, Brisbane, Qld, Australia; genomiQa, Brisbane, Qld, Australia
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20
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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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21
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Fortunato A, Mallo D, Rupp SM, King LM, Hardman T, Lo JY, Hall A, Marks JR, Hwang ES, Maley CC. A new method to accurately identify single nucleotide variants using small FFPE breast samples. Brief Bioinform 2021; 22:6296507. [PMID: 34117742 PMCID: PMC8574974 DOI: 10.1093/bib/bbab221] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 05/14/2021] [Accepted: 05/20/2021] [Indexed: 11/14/2022] Open
Abstract
Most tissue collections of neoplasms are composed of formalin-fixed and paraffin-embedded (FFPE) excised tumor samples used for routine diagnostics. DNA sequencing is becoming increasingly important in cancer research and clinical management; however it is difficult to accurately sequence DNA from FFPE samples. We developed and validated a new bioinformatic pipeline to use existing variant-calling strategies to robustly identify somatic single nucleotide variants (SNVs) from whole exome sequencing using small amounts of DNA extracted from archival FFPE samples of breast cancers. We optimized this strategy using 28 pairs of technical replicates. After optimization, the mean similarity between replicates increased 5-fold, reaching 88% (range 0-100%), with a mean of 21.4 SNVs (range 1-68) per sample, representing a markedly superior performance to existing tools. We found that the SNV-identification accuracy declined when there was less than 40 ng of DNA available and that insertion-deletion variant calls are less reliable than single base substitutions. As the first application of the new algorithm, we compared samples of ductal carcinoma in situ of the breast to their adjacent invasive ductal carcinoma samples. We observed an increased number of mutations (paired-samples sign test, P < 0.05), and a higher genetic divergence in the invasive samples (paired-samples sign test, P < 0.01). Our method provides a significant improvement in detecting SNVs in FFPE samples over previous approaches.
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Affiliation(s)
- Angelo Fortunato
- Arizona Cancer Evolution Center, Arizona State University, 1001 S. McAllister Ave., Tempe, AZ, 85287, USA.,Biodesign Center for Biocomputing, Security and Society, Arizona State University, 727 E. Tyler St., Tempe, AZ 85281 USA.,School of Life Sciences, Arizona State University, 427 East Tyler Mall, Tempe, AZ 85287, USA
| | - Diego Mallo
- Arizona Cancer Evolution Center, Arizona State University, 1001 S. McAllister Ave., Tempe, AZ, 85287, USA.,Biodesign Center for Biocomputing, Security and Society, Arizona State University, 727 E. Tyler St., Tempe, AZ 85281 USA.,School of Life Sciences, Arizona State University, 427 East Tyler Mall, Tempe, AZ 85287, USA
| | - Shawn M Rupp
- Arizona Cancer Evolution Center, Arizona State University, 1001 S. McAllister Ave., Tempe, AZ, 85287, USA.,Biodesign Center for Biocomputing, Security and Society, Arizona State University, 727 E. Tyler St., Tempe, AZ 85281 USA
| | | | | | - Joseph Y Lo
- Department of Radiology, Duke University, Durham, NC, USA
| | - Allison Hall
- Department of Pathology, Duke University, Durham, NC, USA
| | | | | | - Carlo C Maley
- Arizona Cancer Evolution Center, Arizona State University, 1001 S. McAllister Ave., Tempe, AZ, 85287, USA.,Biodesign Center for Biocomputing, Security and Society, Arizona State University, 727 E. Tyler St., Tempe, AZ 85281 USA.,School of Life Sciences, Arizona State University, 427 East Tyler Mall, Tempe, AZ 85287, USA
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22
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Yalchin M, Baker AM, Graham TA, Hart A. Predicting Colorectal Cancer Occurrence in IBD. Cancers (Basel) 2021; 13:2908. [PMID: 34200768 PMCID: PMC8230430 DOI: 10.3390/cancers13122908] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 05/27/2021] [Accepted: 06/01/2021] [Indexed: 12/13/2022] Open
Abstract
Patients with colonic inflammatory bowel disease (IBD) are at an increased risk of developing colorectal cancer (CRC), and are therefore enrolled into a surveillance programme aimed at detecting dysplasia or early cancer. Current surveillance programmes are guided by clinical, endoscopic or histological predictors of colitis-associated CRC (CA-CRC). We have seen great progress in our understanding of these predictors of disease progression, and advances in endoscopic technique and management, along with improved medical care, has been mirrored by the falling incidence of CA-CRC over the last 50 years. However, more could be done to improve our molecular understanding of CA-CRC progression and enable better risk stratification for patients with IBD. This review summarises the known risk factors associated with CA-CRC and explores the molecular landscape that has the potential to complement and optimise the existing IBD surveillance programme.
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Affiliation(s)
- Mehmet Yalchin
- Inflammatory Bowel Disease Department, St. Mark’s Hospital, Watford R.d., Harrow HA1 3UJ, UK
- Centre for Genomics and Computational Biology, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse S.q., London EC1M 6BQ, UK; (A.-M.B.); (T.A.G.)
| | - Ann-Marie Baker
- Centre for Genomics and Computational Biology, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse S.q., London EC1M 6BQ, UK; (A.-M.B.); (T.A.G.)
| | - Trevor A. Graham
- Centre for Genomics and Computational Biology, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse S.q., London EC1M 6BQ, UK; (A.-M.B.); (T.A.G.)
| | - Ailsa Hart
- Inflammatory Bowel Disease Department, St. Mark’s Hospital, Watford R.d., Harrow HA1 3UJ, UK
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23
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Bajpai M, Panda A, Birudaraju K, Van Gurp J, Chak A, Das KM, Javidian P, Aviv H. Recurring Translocations in Barrett's Esophageal Adenocarcinoma. Front Genet 2021; 12:674741. [PMID: 34178034 PMCID: PMC8220202 DOI: 10.3389/fgene.2021.674741] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 04/26/2021] [Indexed: 12/18/2022] Open
Abstract
Barrett's esophagus (BE) is a premalignant metaplasia in patients with chronic gastroesophageal reflux disease (GERD). BE can progress to esophageal adenocarcinoma (EA) with less than 15% 5-year survival. Chromosomal aneuploidy, deletions, and duplication are early events in BE progression to EA, but reliable diagnostic assays to detect chromosomal markers in premalignant stages of EA arising from BE are lacking. Previously, we investigated chromosomal changes in an in vitro model of acid and bile exposure-induced Barrett's epithelial carcinogenesis (BEC). In addition to detecting changes already known to occur in BE and EA, we also reported a novel recurring chromosomal translocation t(10:16) in the BE cells at an earlier time point before they undergo malignant transformation. In this study, we refine the chromosomal event with the help of fluorescence microscopy techniques as a three-way translocation between chromosomes 2, 10, and 16, t(2:10;16) (p22;q22;q22). We also designed an exclusive fluorescent in situ hybridization for esophageal adenocarcinoma (FISH-EA) assay that detects these chromosomal breakpoints and fusions. We validate the feasibility of the FISH-EA assay to objectively detect these chromosome events in primary tissues by confirming the presence of one of the fusions in paraffin-embedded formalin-fixed human EA tumors. Clinical validation in a larger cohort of BE progressors and non-progressors will confirm the specificity and sensitivity of the FISH-EA assay in identifying malignant potential in the early stages of EA.
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Affiliation(s)
- Manisha Bajpai
- Department of Medicine-Gastroenterology and Hepatology, Rutgers-Robert Wood Johnson Medical School, Rutgers The State University of New Jersey, New Brunswick, NJ, United States.,Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, United States
| | - Anshuman Panda
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, United States
| | - Kristen Birudaraju
- Cytogenetics Laboratory, Department of Pathology, Rutgers-Robert Wood Johnson Medical School, Rutgers The State University of New Jersey, New Brunswick, NJ, United States
| | - James Van Gurp
- Department of Pathology, Rutgers-Robert Wood Johnson Medical School, Rutgers The State University of New Jersey, New Brunswick, NJ, United States
| | - Amitabh Chak
- Division of Gastroenterology and Hepatology, University Hospitals Cleveland Medical Center, Case Western Reserve University School of Medicine, Cleveland, OH, United States
| | - Kiron M Das
- Department of Medicine-Gastroenterology and Hepatology, Rutgers-Robert Wood Johnson Medical School, Rutgers The State University of New Jersey, New Brunswick, NJ, United States.,Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, United States
| | - Parisa Javidian
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, United States.,Department of Pathology, Rutgers-Robert Wood Johnson Medical School, Rutgers The State University of New Jersey, New Brunswick, NJ, United States
| | - Hana Aviv
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, United States.,Cytogenetics Laboratory, Department of Pathology, Rutgers-Robert Wood Johnson Medical School, Rutgers The State University of New Jersey, New Brunswick, NJ, United States
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24
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Abstract
The observation and analysis of intra-tumour heterogeneity (ITH), particularly in genomic studies, has advanced our understanding of the evolutionary forces that shape cancer growth and development. However, only a subset of the variation observed in a single tumour will have an impact on cancer evolution, highlighting the need to distinguish between functional and non-functional ITH. Emerging studies highlight a role for the cancer epigenome, transcriptome and immune microenvironment in functional ITH. Here, we consider the importance of both genetic and non-genetic ITH and their role in tumour evolution, and present the rationale for a broad research focus beyond the cancer genome. Systems-biology analytical approaches will be necessary to outline the scale and importance of functional ITH. By allowing a deeper understanding of tumour evolution this will, in time, encourage development of novel therapies and improve outcomes for patients.
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Affiliation(s)
- James R M Black
- Cancer Genome Evolution Research Group, University College London Cancer Institute, London, UK
- Cancer Research UK Lung Cancer Center of Excellence, University College London Cancer Institute, London, UK
| | - Nicholas McGranahan
- Cancer Genome Evolution Research Group, University College London Cancer Institute, London, UK.
- Cancer Research UK Lung Cancer Center of Excellence, University College London Cancer Institute, London, UK.
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25
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Kunzmann AT, Coleman HG, Johnston BT, Turkington RC, McManus D, Anderson LA, Thrift AP. Does Risk of Progression from Barrett's Esophagus to Esophageal Adenocarcinoma Change Based on the Number of Non-dysplastic Endoscopies? Dig Dis Sci 2021; 66:1965-1973. [PMID: 32734400 PMCID: PMC7855450 DOI: 10.1007/s10620-020-06483-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 07/04/2020] [Indexed: 12/11/2022]
Abstract
BACKGROUND There is a large Barrett's esophagus patient population undergoing endoscopic surveillance. Methods to stratify patients into higher and lower risk groups may enable more varied surveillance intervals for patients with non-dysplastic Barrett's esophagus that could optimize use of endoscopy resources. OBJECTIVE We aimed to assess whether risk of progression to esophageal adenocarcinoma differed in patients with multiple endoscopic biopsies negative for dysplasia. METHODS We conducted a retrospective cohort study among individuals from the population-based Northern Ireland Barrett's register with a histologically confirmed diagnosis of non-dysplastic Barrett's esophagus (with intestinal metaplasia) between 1993 and 2010, who had at least one endoscopic biopsy conducted at least 12 months after diagnosis. We used Poisson regression to estimate incidence rate ratios (IRR) and 95% confidence intervals (CI) for the association between number of successive endoscopies showing non-dysplastic Barrett's esophagus and risk of esophageal adenocarcinoma alone, and combined with high-grade dysplasia, at the next endoscopy. RESULTS We identified 1761 individuals who met our eligibility criteria. Subsequent risk of progression to esophageal adenocarcinoma was lower at the next endoscopy following two endoscopies showing non-dysplastic Barrett's esophagus (IRR 0.26, 95% CI 0.10-0.66) than following one endoscopy showing non-dysplastic Barrett's esophagus. Similar findings were apparent for risk of progression to esophageal adenocarcinoma or high-grade dysplasia (IRR 0.41, 95% CI 0.22-0.79). CONCLUSION The lower risk of malignant progression in individuals with persistent non-dysplastic Barrett's esophagus over two consecutive endoscopic biopsies but not for longer term persistence does not support hypotheses of persistence being an indicator of less biologically aggressive lesions. Instead, the initial difference may be attributable to post-endoscopy cancers and support the necessity of adhering to robust quality standards for endoscopic procedures.
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Affiliation(s)
- Andrew T Kunzmann
- Institute of Clinical Sciences Block B, Cancer Epidemiology and Health Services Research Group, Centre for Public Health, Royal Victoria Hospital, Queen's University Belfast, Belfast, Northern Ireland, BT12 6BA, UK.
| | - Helen G Coleman
- Institute of Clinical Sciences Block B, Cancer Epidemiology and Health Services Research Group, Centre for Public Health, Royal Victoria Hospital, Queen's University Belfast, Belfast, Northern Ireland, BT12 6BA, UK
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK
| | - Brian T Johnston
- Royal Victoria Hospital, Belfast Health & Social Care Trust, Belfast, UK
| | - Richard C Turkington
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK
- Belfast City Hospital, Belfast Health & Social Care Trust, Belfast, UK
| | - Damian McManus
- Department of Pathology, Belfast Health & Social Care Trust, Belfast, UK
| | - Lesley A Anderson
- Institute of Clinical Sciences Block B, Cancer Epidemiology and Health Services Research Group, Centre for Public Health, Royal Victoria Hospital, Queen's University Belfast, Belfast, Northern Ireland, BT12 6BA, UK
- Northern Ireland Cancer Registry, Queen's University Belfast, Belfast, UK
| | - Aaron P Thrift
- Section of Epidemiology and Population Sciences, Department of Medicine, Baylor College of Medicine, Houston, TX, USA
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
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26
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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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27
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Souza RF, Spechler SJ. Advances in Biomarkers for Risk Stratification in Barrett's Esophagus. Gastrointest Endosc Clin N Am 2021; 31:105-115. [PMID: 33213790 DOI: 10.1016/j.giec.2020.08.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Dysplasia currently is the primary biomarker used to risk stratify patients with Barrett's esophagus, but dysplasia has a number of considerable limitations in this regard. Thus, investigators over the years have explored innumerable alternative molecular biomarkers for risk stratification in Barrett's esophagus. This report focuses only on those biomarkers that appear most promising based on the availability of multiple published studies corroborating good results, and on the commercial availability of the test. These promising biomarkers include p53 immunostaining, TissueCypher, BarreGEN, and wide-area transepithelial sampling with computer-assisted 3-dimensional analysis (WATS3D).
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Affiliation(s)
- Rhonda F Souza
- Division of Gastroenterology, Center for Esophageal Diseases, Baylor University Medical Center at Dallas, Center for Esophageal Research, Baylor Scott & White Research Institute, 3500 Gaston Avenue, 2 Hoblitzelle, Suite 250, Dallas, TX 75246, USA.
| | - Stuart Jon Spechler
- Division of Gastroenterology, Center for Esophageal Diseases, Baylor University Medical Center at Dallas, Center for Esophageal Research, Baylor Scott & White Research Institute, 3500 Gaston Avenue, 2 Hoblitzelle, Suite 250, Dallas, TX 75246, USA
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28
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29
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Genomic copy number predicts esophageal cancer years before transformation. Nat Med 2020; 26:1726-1732. [PMID: 32895572 DOI: 10.1038/s41591-020-1033-y] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 07/23/2020] [Indexed: 12/14/2022]
Abstract
Recent studies show that aneuploidy and driver gene mutations precede cancer diagnosis by many years1-4. We assess whether these genomic signals can be used for early detection and pre-emptive cancer treatment using the neoplastic precursor lesion Barrett's esophagus as an exemplar5. Shallow whole-genome sequencing of 777 biopsies, sampled from 88 patients in Barrett's esophagus surveillance over a period of up to 15 years, shows that genomic signals can distinguish progressive from stable disease even 10 years before histopathological transformation. These findings are validated on two independent cohorts of 76 and 248 patients. These methods are low-cost and applicable to standard clinical biopsy samples. Compared with current management guidelines based on histopathology and clinical presentation, genomic classification enables earlier treatment for high-risk patients as well as reduction of unnecessary treatment and monitoring for patients who are unlikely to develop cancer.
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30
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Noble R, Burley JT, Le Sueur C, Hochberg ME. When, why and how tumour clonal diversity predicts survival. Evol Appl 2020; 13:1558-1568. [PMID: 32821272 PMCID: PMC7428820 DOI: 10.1111/eva.13057] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 06/24/2020] [Accepted: 06/25/2020] [Indexed: 12/23/2022] Open
Abstract
The utility of intratumour heterogeneity as a prognostic biomarker is the subject of ongoing clinical investigation. However, the relationship between this marker and its clinical impact is mediated by an evolutionary process that is not well understood. Here, we employ a spatial computational model of tumour evolution to assess when, why and how intratumour heterogeneity can be used to forecast tumour growth rate and progression-free survival. We identify three conditions that can lead to a positive correlation between clonal diversity and subsequent growth rate: diversity is measured early in tumour development; selective sweeps are rare; and/or tumours vary in the rate at which they acquire driver mutations. Opposite conditions typically lead to negative correlation. In cohorts of tumours with diverse evolutionary parameters, we find that clonal diversity is a reliable predictor of both growth rate and progression-free survival. We thus offer explanations-grounded in evolutionary theory-for empirical findings in various cancers, including survival analyses reported in the recent TRACERx Renal study of clear-cell renal cell carcinoma. Our work informs the search for new prognostic biomarkers and contributes to the development of predictive oncology.
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Affiliation(s)
- Robert Noble
- Department of Biosystems Science and EngineeringETH ZurichBaselSwitzerland
- SIB Swiss Institute of BioinformaticsBaselSwitzerland
- Department of Evolutionary Biology and Environmental StudiesUniversity of ZurichZurichSwitzerland
- Present address:
Department of MathematicsCity, University of LondonLondonUK
| | - John T. Burley
- Department of Ecology and Evolutionary BiologyBrown UniversityProvidenceRIUSA
- Institute at Brown for Environment and SocietyBrown UniversityProvidenceRIUSA
| | - Cécile Le Sueur
- Department of Biosystems Science and EngineeringETH ZurichBaselSwitzerland
| | - Michael E. Hochberg
- Institut des Sciences de l’EvolutionUniversity of MontpellierMontpellierFrance
- Santa Fe InstituteNMUSA
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31
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Bozic I, Wu CJ. Delineating the evolutionary dynamics of cancer from theory to reality. ACTA ACUST UNITED AC 2020; 1:580-588. [DOI: 10.1038/s43018-020-0079-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 05/18/2020] [Indexed: 01/08/2023]
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32
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Yang L, Zhang J, Yang G, Xu H, Lin J, Shao L, Li J, Guo C, Du Y, Guo L, Li X, Han-Zhang H, Wang C, Chuai S, Ye J, Kang Q, Liu H, Ying J, Wang Y. The prognostic value of a Methylome-based Malignancy Density Scoring System to predict recurrence risk in early-stage Lung Adenocarcinoma. Theranostics 2020; 10:7635-7644. [PMID: 32685009 PMCID: PMC7359091 DOI: 10.7150/thno.44229] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 06/01/2020] [Indexed: 12/11/2022] Open
Abstract
Current NCCN guidelines do not recommend the use of adjuvant chemotherapy for stage IA lung adenocarcinoma patients with R0 surgery. However, 25% to 40% of patients with stage IA disease experience recurrence. Stratifying patients according to the recurrence risk may tailor adjuvant therapy and surveillance imaging for those with a higher risk. However, prognostic markers are often identified by comparing high-risk and low-risk cases which might introduce bias due to the widespread interpatient heterogeneity. Here, we developed a scoring system quantifying the degree of field cancerization in adjacent normal tissues and revealed its association with disease-free survival (DFS). Methods: We recruited a cohort of 44 patients with resected stage IA lung adenocarcinoma who did not receive adjuvant therapy. Both tumor and adjacent normal tissues were obtained from each patient and subjected to capture-based targeted genomic and epigenomic profiling. A novel methylome-based scoring system namely malignancy density ratio (MD ratio) was developed based on 39 patients by comparing tumor and corresponding adjacent normal tissues of each patient. A MD score was then obtained by Wald statistics. The correlations of MD ratio, MD score, and genomic features with clinical outcome were investigated. Results: Patients with a high-risk MD ratio showed a significantly shorter postsurgical DFS compared with those with a low-risk MD ratio (HR=4.47, P=0.01). The MD ratio was not associated with T stage (P=1), tumor cell fraction (P=0.748) nor inflammatory status (p=0.548). Patients with a high-risk MD score also demonstrated an inferior DFS (HR=4.69, P=0.039). In addition, multivariate analysis revealed EGFR 19 del (HR=5.39, P=0.012) and MD score (HR= 7.90, P=0.01) were independent prognostic markers. Conclusion: The novel methylome-based scoring system, developed by comparing the signatures between tumor and corresponding adjacent normal tissues of individual patients, largely minimizes the bias of interpatient heterogeneity and reveals a robust prognostic value in patients with resected lung adenocarcinoma.
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33
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Hoefnagel SJM, Mostafavi N, Timmer MR, Lau CT, Meijer SL, Wang KK, Krishnadath KK. A genomic biomarker-based model for cancer risk stratification of non-dysplastic Barrett's esophagus patients after extended follow up; results from Dutch surveillance cohorts. PLoS One 2020; 15:e0231419. [PMID: 32282835 PMCID: PMC7153893 DOI: 10.1371/journal.pone.0231419] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Accepted: 03/23/2020] [Indexed: 12/19/2022] Open
Abstract
Barrett’s esophagus is the only known mucosal precursor for the highly malignant esophageal adenocarcinoma. Malignant degeneration of non-dysplastic Barrett’s esophagus occurs in < 0.6% per year in Dutch surveillance cohorts. Therefore, it has been proposed to increase the surveillance intervals from 3 to 5 years, potentially increasing development of advanced stage interval cancers. To prevent such cases robust biomarkers for more optimal stratification over longer follow up periods for non-dysplastic Barrett’s patients are required. In this multi-center study, aberrations for chromosomes 7, 17, and structural abnormalities for c-MYC, CDKN2A, TP53, Her-2/neu and 20q assessed by DNA fluorescence in situ hybridization on brush cytology specimens, were used to determine marker scores and to perform clonal diversity measurements, as described previously. In this study, these genetic biomarkers were combined with clinical variables and analyzed to obtain the most efficient cancer prediction model after an extended period of follow-up (median time of 7 years) by applying Cox regression modeling, bootstrapping and leave-one-out analyses. A total of 334 patients with Barrett’s esophagus without dysplasia from 6 community hospitals (n = 220) and one academic center (n = 114) were included. The annual progression rate to high grade dysplasia and/or esophageal adenocarcinoma was 1.3%, and to adenocarcinoma alone 0.85%. A prediction model including age, Barrett circumferential length, and a clonicity score over the genomic set including chromosomes 7, 17, 20q and c-MYC, resulted in an area under the curve of 0.88. The sensitivity and specificity of this model were 0.91 and 0.38. The positive and negative predictive values were 0.13 (95% CI 0.09 to 0.19) and 0.97 (95% CI 0.93 to 0.99). We propose the implementation of the model to identify non-dysplastic Barrett’s patients, who are required to remain in surveillance programs with 3-yearly surveillance intervals from those that can benefit from less frequent or no surveillance.
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Affiliation(s)
- S. J. M. Hoefnagel
- Center for Experimental and Molecular Medicine, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- Department of Gastroenterology and Hepatology, Amsterdam UMC, Amsterdam, The Netherlands
| | - N. Mostafavi
- Department of Gastroenterology and Hepatology, Amsterdam UMC, Amsterdam, The Netherlands
| | - M. R. Timmer
- Center for Experimental and Molecular Medicine, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- Department of Gastroenterology and Hepatology, Amsterdam UMC, Amsterdam, The Netherlands
| | - C. T. Lau
- Center for Experimental and Molecular Medicine, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - S. L. Meijer
- Department of Pathology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - K. K. Wang
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota, United States of America
| | - K. K. Krishnadath
- Center for Experimental and Molecular Medicine, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- Department of Gastroenterology and Hepatology, Amsterdam UMC, Amsterdam, The Netherlands
- * E-mail:
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34
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Assessing Cell Activities rather than Identities to Interpret Intra-Tumor Phenotypic Diversity and Its Dynamics. iScience 2020; 23:101061. [PMID: 32361272 PMCID: PMC7195534 DOI: 10.1016/j.isci.2020.101061] [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: 11/27/2019] [Revised: 03/02/2020] [Accepted: 04/09/2020] [Indexed: 12/26/2022] Open
Abstract
Despite advances in single-cell and molecular techniques, it is still unclear how to best quantify phenotypic heterogeneity in cancer cells that evolved beyond normal, known classifications. We present an approach to phenotypically characterize cells based on their activities rather than static classifications. We validated the detectability of specific activities (epithelial-mesenchymal transition, glycolysis) in single cells, using targeted RT-qPCR analyses and in vitro inductions. We analyzed 50 established activity signatures as a basis for phenotypic description in public data and computed cell-cell distances in 28,513 cells from 85 patients and 8 public datasets. Despite not relying on any classification, our measure correlated with standard diversity indices in populations of known structure. We identified bottlenecks as phenotypic diversity reduced upon colorectal cancer initiation. This suggests that focusing on what cancer cells do rather than what they are can quantify phenotypic diversity in universal fashion, to better understand and predict intra-tumor heterogeneity dynamics. Cells categorized as having the same identity can perform different activities Single-cell expression data can be used to infer the activities cells take part in Activity profiles provide a basis to measure phenotypic cell-cell divergence Cell activity can quantify intra-tumor heterogeneity more fully than identity
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35
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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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36
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The cyclical hit model: how paligenosis might establish the mutational landscape in Barrett's esophagus and esophageal adenocarcinoma. Curr Opin Gastroenterol 2019; 35:363-370. [PMID: 31021922 DOI: 10.1097/mog.0000000000000540] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
PURPOSE OF REVIEW In this review, we explore a paligenosis-based model to explain Barrett's esophagus development and progression: 'the cyclical hit model.' RECENT FINDINGS Genomic analyses have highlighted the high mutational burden of esophageal adenocarcinoma, Barrett's esophagus, and even normal esophageal epithelium. Somatic mutations in key genes including TP53 occur early in the neoplastic progression sequence of Barrett's esophagus, whereas chromosomal amplification resulting in oncogene activation occurs as a critical late event. Paligenosis is a shared injury response mechanism characterized by activation of autophagy, expression of progenitor markers, and increased mTORC signaling-induced cell-cycle reentry. In the setting of chronic injury/inflammation, cycles of paligenosis may allow accumulation of mutations until eventually the mutational burden, in concert perhaps with mutations in key driver oncogenes, finally alters the cell's ability to redifferentiate, leading to the emergence of a potential neoplastic clone. SUMMARY Under conditions of chronic gastroesophageal refluxate exposure, the normal esophageal squamous epithelium might undergo multiple cycles of paligenosis, allowing initially silent mutations to accumulate until key events impart mutant clones with an oncogenic survival advantage.
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Tokutomi N, Moyret‐Lalle C, Puisieux A, Sugano S, Martinez P. Quantifying local malignant adaptation in tissue-specific evolutionary trajectories by harnessing cancer's repeatability at the genetic level. Evol Appl 2019; 12:1062-1075. [PMID: 31080515 PMCID: PMC6503823 DOI: 10.1111/eva.12781] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 12/03/2018] [Accepted: 02/07/2019] [Indexed: 02/06/2023] Open
Abstract
Cancer is a potentially lethal disease, in which patients with nearly identical genetic backgrounds can develop a similar pathology through distinct combinations of genetic alterations. We aimed to reconstruct the evolutionary process underlying tumour initiation, using the combination of convergence and discrepancies observed across 2,742 cancer genomes from nine tumour types. We developed a framework using the repeatability of cancer development to score the local malignant adaptation (LMA) of genetic clones, as their potential to malignantly progress and invade their environment of origin. Using this framework, we found that premalignant skin and colorectal lesions appeared specifically adapted to their local environment, yet insufficiently for full cancerous transformation. We found that metastatic clones were more adapted to the site of origin than to the invaded tissue, suggesting that genetics may be more important for local progression than for the invasion of distant organs. In addition, we used network analyses to investigate evolutionary properties at the system-level, highlighting that different dynamics of malignant progression can be modelled by such a framework in tumour-type-specific fashion. We find that occurrence-based methods can be used to specifically recapitulate the process of cancer initiation and progression, as well as to evaluate the adaptation of genetic clones to given environments. The repeatability observed in the evolution of most tumour types could therefore be harnessed to better predict the trajectories likely to be taken by tumours and preneoplastic lesions in the future.
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Affiliation(s)
- Natsuki Tokutomi
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier SciencesThe University of TokyoTokyoJapan
| | - Caroline Moyret‐Lalle
- Univ Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon BérardCancer Research Center of LyonLyonFrance
| | - Alain Puisieux
- Univ Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon BérardCancer Research Center of LyonLyonFrance
| | - Sumio Sugano
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier SciencesThe University of TokyoTokyoJapan
| | - Pierre Martinez
- Univ Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon BérardCancer Research Center of LyonLyonFrance
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38
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Gruber M, Bozic I, Leshchiner I, Livitz D, Stevenson K, Rassenti L, Rosebrock D, Taylor-Weiner A, Olive O, Goyetche R, Fernandes SM, Sun J, Stewart C, Wong A, Cibulskis C, Zhang W, Reiter JG, Gerold JM, Gribben JG, Rai KR, Keating MJ, Brown JR, Neuberg D, Kipps TJ, Nowak MA, Getz G, Wu CJ. Growth dynamics in naturally progressing chronic lymphocytic leukaemia. Nature 2019; 570:474-479. [PMID: 31142838 PMCID: PMC6630176 DOI: 10.1038/s41586-019-1252-x] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2017] [Accepted: 05/01/2019] [Indexed: 01/01/2023]
Abstract
How the genomic features of a patient's cancer relate to individual disease kinetics remains poorly understood. Here we used the indolent growth dynamics of chronic lymphocytic leukaemia (CLL) to analyse the growth rates and corresponding genomic patterns of leukaemia cells from 107 patients with CLL, spanning decades-long disease courses. We found that CLL commonly demonstrates not only exponential expansion but also logistic growth, which is sigmoidal and reaches a certain steady-state level. Each growth pattern was associated with marked differences in genetic composition, the pace of disease progression and the extent of clonal evolution. In a subset of patients, whose serial samples underwent next-generation sequencing, we found that dynamic changes in the disease course of CLL were shaped by the genetic events that were already present in the early slow-growing stages. Finally, by analysing the growth rates of subclones compared with their parental clones, we quantified the growth advantage conferred by putative CLL drivers in vivo.
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MESH Headings
- Cell Proliferation/drug effects
- Clone Cells/drug effects
- Clone Cells/pathology
- Cohort Studies
- Disease Progression
- Evolution, Molecular
- Female
- High-Throughput Nucleotide Sequencing
- Humans
- Leukemia, Lymphocytic, Chronic, B-Cell/drug therapy
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/pathology
- Male
- Neoplasm Recurrence, Local/genetics
- Neoplasm Recurrence, Local/pathology
- Recurrence
- Reproducibility of Results
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Affiliation(s)
- Michaela Gruber
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Internal Medicine I, Division of Haematology and Haemostaseology, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Ivana Bozic
- Department of Applied Mathematics, University of Washington, Seattle, WA, USA
| | | | | | - Kristen Stevenson
- Department of Biostatistics and Computational Biology, Dana Farber Cancer Institute, Boston, MA, USA
| | - Laura Rassenti
- Department of Medicine, University of California at San Diego Moores Cancer Center, La Jolla, CA, USA
| | | | | | - Oriol Olive
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Reaha Goyetche
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Stacey M Fernandes
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jing Sun
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Chip Stewart
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Alicia Wong
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Wandi Zhang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Johannes G Reiter
- Program for Evolutionary Dynamics, Harvard University, Cambridge, MA, USA
| | - Jeffrey M Gerold
- Program for Evolutionary Dynamics, Harvard University, Cambridge, MA, USA
| | - John G Gribben
- Barts Cancer Institute, Queen Mary, University of London, London, UK
| | - Kanti R Rai
- Hofstra North Shore-LIJ School of Medicine, Lake Success, NY, USA
| | | | - Jennifer R Brown
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Donna Neuberg
- Department of Biostatistics and Computational Biology, Dana Farber Cancer Institute, Boston, MA, USA
| | - Thomas J Kipps
- Department of Medicine, University of California at San Diego Moores Cancer Center, La Jolla, CA, USA
| | - Martin A Nowak
- Program for Evolutionary Dynamics, Harvard University, Cambridge, MA, USA
- Department of Mathematics and Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Gad Getz
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Harvard Medical School, Boston, MA, USA.
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA.
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA.
| | - Catherine J Wu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
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39
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Peters Y, Al-Kaabi A, Shaheen NJ, Chak A, Blum A, Souza RF, Di Pietro M, Iyer PG, Pech O, Fitzgerald RC, Siersema PD. Barrett oesophagus. Nat Rev Dis Primers 2019; 5:35. [PMID: 31123267 DOI: 10.1038/s41572-019-0086-z] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Barrett oesophagus (BE), the only known histological precursor of oesophageal adenocarcinoma (EAC), is a condition in which the squamous epithelium of the oesophagus is replaced by columnar epithelium as an adaptive response to gastro-oesophageal reflux. EAC has one of the fastest rising incidences of cancers in Western countries and has a dismal prognosis. BE is usually detected during endoscopic examination, and diagnosis is confirmed by the histological presence of intestinal metaplasia. Advances in genomics and transcriptomics have improved our understanding of the pathogenesis and malignant progression of intestinal metaplasia. As the majority of EAC cases are diagnosed in individuals without a known history of BE, screening for BE could potentially decrease disease-related mortality. Owing to the pre-malignant nature of BE, endoscopic surveillance of patients with BE is imperative for early detection and treatment of dysplasia to prevent further progression to invasive EAC. Developments in endoscopic therapy have resulted in a major shift in the treatment of patients with BE who have dysplasia or early EAC, from surgical resection to endoscopic resection and ablation. In addition to symptom control by optimization of lifestyle and pharmacological therapy with proton pump inhibitors, chemopreventive strategies based on NSAIDs and statins are currently being investigated for BE management.
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Affiliation(s)
- Yonne Peters
- Department of Gastroenterology and Hepatology, Radboud University Medical Center, Nijmegen, Netherlands
| | - Ali Al-Kaabi
- Department of Gastroenterology and Hepatology, Radboud University Medical Center, Nijmegen, Netherlands
| | - Nicholas J Shaheen
- Division of Gastroenterology and Hepatology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Amitabh Chak
- Division of Gastroenterology and Liver Diseases, Case Western Reserve University, Cleveland, OH, USA
| | - Andrew Blum
- Division of Gastroenterology and Liver Diseases, Case Western Reserve University, Cleveland, OH, USA
| | - Rhonda F Souza
- Department of Medicine and the Center for Esophageal Diseases, Baylor University Medical Center at Dallas and the Center for Esophageal Research, Baylor Scott and White Research Institute, Dallas, TX, USA
| | | | - Prasad G Iyer
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
| | - Oliver Pech
- Department of Gastroenterology, St John of God Hospital, Regensburg, Germany
| | | | - Peter D Siersema
- Department of Gastroenterology and Hepatology, Radboud University Medical Center, Nijmegen, Netherlands.
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Williams MJ, Sottoriva A, Graham TA. Measuring Clonal Evolution in Cancer with Genomics. Annu Rev Genomics Hum Genet 2019; 20:309-329. [PMID: 31059289 DOI: 10.1146/annurev-genom-083117-021712] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Cancers originate from somatic cells in the human body that have accumulated genetic alterations. These mutations modify the phenotype of the cells, allowing them to escape the homeostatic regulation that maintains normal cell number. Viewed through the lens of evolutionary biology, the transformation of normal cells into malignant cells is evolution in action. Evolution continues throughout cancer growth, progression, treatment resistance, and disease relapse, driven by adaptation to changes in the cancer's environment, and intratumor heterogeneity is an inevitable consequence of this evolutionary process. Genomics provides a powerful means to characterize tumor evolution, enabling quantitative measurement of evolving clones across space and time. In this review, we discuss concepts and approaches to quantify and measure this evolutionary process in cancer using genomics.
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Affiliation(s)
- Marc J Williams
- Evolution and Cancer Laboratory, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, United Kingdom; ,
| | - Andrea Sottoriva
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London SM2 5NG, United Kingdom
| | - Trevor A Graham
- Evolution and Cancer Laboratory, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, United Kingdom; ,
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41
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Nesteruk K, Spaander MCW, Leeuwenburgh I, Peppelenbosch MP, Fuhler GM. Achalasia and associated esophageal cancer risk: What lessons can we learn from the molecular analysis of Barrett's-associated adenocarcinoma? Biochim Biophys Acta Rev Cancer 2019; 1872:188291. [PMID: 31059738 DOI: 10.1016/j.bbcan.2019.04.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 04/02/2019] [Accepted: 04/29/2019] [Indexed: 02/08/2023]
Abstract
Idiopathic achalasia and Barrett's esophagus (BE) are preneoplastic conditions of the esophagus. BE increases the risk of esophageal adenocarcinoma (EAC), while achalasia is associated with both EAC and esophageal squamous cell carcinoma (ESCC). However, while the molecular mechanisms underlying the transformation of esophageal epithelial cells in BE are relatively well characterized, less is known regarding these processes in achalasia. Nevertheless, both conditions are associated with chronic inflammation and BE can occur in achalasia patients, and it is likely that similar processes underlie cancer risk in both diseases. The present review will discuss possible lessons that we can learn from the molecular analysis of BE for the study of achalasia-associated cancer and contrast findings in BE with those in achalasia. First, we will describe cellular fate during development of BE, EAC, and ESCC, and consider the inflammatory status of the epithelial barrier in BE and achalasia in terms of its contribution to carcinogenesis. Next, we will summarize current data on genetic alterations and molecular pathways involved in these processes. Lastly, the plausible role of the microbiota in achalasia-associated carcinogenesis and its contribution to abnormal lower esophageal sphincter (LES) functioning, the maintenance of chronic inflammatory status and influence on the esophageal mucosa through carcinogenic by-products, will be discussed.
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Affiliation(s)
- K Nesteruk
- Department of Gastroenterology and Hepatology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - M C W Spaander
- Department of Gastroenterology and Hepatology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - I Leeuwenburgh
- Department of Gastroenterology and Hepatology, Franciscus Gasthuis, Rotterdam, the Netherlands
| | - M P Peppelenbosch
- Department of Gastroenterology and Hepatology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - G M Fuhler
- Department of Gastroenterology and Hepatology, Erasmus University Medical Center, Rotterdam, the Netherlands..
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42
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Peters Y, Honing J, Kievit W, Kestens C, Pestman W, Nagtegaal ID, van der Post RS, Siersema PD. Incidence of Progression of Persistent Nondysplastic Barrett's Esophagus to Malignancy. Clin Gastroenterol Hepatol 2019; 17:869-877.e5. [PMID: 30213587 DOI: 10.1016/j.cgh.2018.08.033] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 07/23/2018] [Accepted: 08/09/2018] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS The risk of esophageal adenocarcinoma (EAC) in patients with non-dysplastic Barrett's esophagus (NDBE) is low, so there is debate over the role of ongoing surveillance for patients with NDBE. It is important to identify patients at low risk for progression. We assessed cancer risk based on the subsequent number of endoscopies showing persistence of NDBE in a nationwide study in the Netherlands. METHODS In a population-based study, patients with a first diagnosis of NDBE were selected from the Dutch nationwide registry of histopathology. We calculated incidence rates and incidence rate ratios (IRR) for high-grade dysplasia (HGD) and EAC to determine whether the number of endoscopies negative for dysplasia and the persistence of NDBE over time associate with progression to malignancy. RESULTS We identified 12,728 patients with NDBE during 2003 and 2013. HGD or EAC developed in 436 patients (3.4%) during 64,537 person-years of follow up (median, 4.9 years). The rate of progression to HGD or EAC was 0.68 (95% CI, 0.61-0.74) per 100 person-years. In patients with 2 consecutive endoscopies showing NDBE, the rate of progression to HGD or EAC decreased to 0.55 (95% CI, 0.46-0.64) per 100 person-years (IRR, 0.72; 95% CI, 0.60-0.87). Overall, the incidence of HGD or EAC decreased by 14% for each year of progression-free follow-up (IRR, 0.86; 95% CI, 0.81-0.92). CONCLUSION In a population-based study in the Netherlands, we found patients with stable NDBE to have a low risk of progression to HGD or EAC. These findings indicate that surveillance intervals might be lengthened or even discontinued in subgroups patients with persistent NDBE.
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Affiliation(s)
- Yonne Peters
- Department of Gastroenterology and Hepatology, Radboud University Medical Center, Nijmegen, the Netherlands.
| | - Judith Honing
- Department of Gastroenterology and Hepatology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Wietske Kievit
- Radboud Institute for Health Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Christine Kestens
- Department of Gastroenterology and Hepatology, UMC Utrecht, Utrecht, the Netherlands
| | - Wiebe Pestman
- Department for Health Evidence, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Iris D Nagtegaal
- Department of Pathology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Rachel S van der Post
- Department of Pathology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Peter D Siersema
- Department of Gastroenterology and Hepatology, Radboud University Medical Center, Nijmegen, the Netherlands
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43
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Taylor-King JP, Baratchart E, Dhawan A, Coker EA, Rye IH, Russnes H, Chapman SJ, Basanta D, Marusyk A. Simulated ablation for detection of cells impacting paracrine signalling in histology analysis. MATHEMATICAL MEDICINE AND BIOLOGY-A JOURNAL OF THE IMA 2019; 36:93-112. [PMID: 29452382 DOI: 10.1093/imammb/dqx022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Accepted: 12/21/2017] [Indexed: 02/07/2023]
Abstract
Intra-tumour phenotypic heterogeneity limits accuracy of clinical diagnostics and hampers the efficiency of anti-cancer therapies. Dealing with this cellular heterogeneity requires adequate understanding of its sources, which is extremely difficult, as phenotypes of tumour cells integrate hardwired (epi)mutational differences with the dynamic responses to microenvironmental cues. The later comes in form of both direct physical interactions, as well as inputs from gradients of secreted signalling molecules. Furthermore, tumour cells can not only receive microenvironmental cues, but also produce them. Despite high biological and clinical importance of understanding spatial aspects of paracrine signaling, adequate research tools are largely lacking. Here, a partial differential equation (PDE)-based mathematical model is developed that mimics the process of cell ablation. This model suggests how each cell might contribute to the microenvironment by either absorbing or secreting diffusible factors, and quantifies the extent to which observed intensities can be explained via diffusion-mediated signalling. The model allows for the separation of phenotypic responses to signalling gradients within tumour microenvironments from the combined influence of responses mediated by direct physical contact and hardwired (epi)genetic differences. The method is applied to a multi-channel immunofluorescence in situ hybridisation (iFISH)-stained breast cancer histological specimen, and correlations are investigated between: HER2 gene amplification, HER2 protein expression and cell interaction with the diffusible microenvironment. This approach allows partial deconvolution of the complex inputs that shape phenotypic heterogeneity of tumour cells and identifies cells that significantly impact gradients of signalling molecules.
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Affiliation(s)
- Jake P Taylor-King
- Mathematical Institute, University of Oxford, Oxford, UK.,Department of Integrated Mathematical Oncology, Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA.,Institute of Molecular Systems Biology, Department of Biology, ETHZ, Zurich, Switzerland
| | - Etienne Baratchart
- Department of Integrated Mathematical Oncology, Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Andrew Dhawan
- Department of Oncology, University of Oxford, Oxford, UK
| | - Elizabeth A Coker
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - Inga Hansine Rye
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Oslo, Norway
| | - Hege Russnes
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Oslo, Norway.,Department of Pathology, Oslo University Hospital, Oslo, Norway
| | - S Jon Chapman
- Mathematical Institute, University of Oxford, Oxford, UK
| | - David Basanta
- Department of Integrated Mathematical Oncology, Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Andriy Marusyk
- Department of Cancer Imaging and Metabolism, Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
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44
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Fiedler D, Heselmeyer-Haddad K, Hirsch D, Hernandez LS, Torres I, Wangsa D, Hu Y, Zapata L, Rueschoff J, Belle S, Ried T, Gaiser T. Single-cell genetic analysis of clonal dynamics in colorectal adenomas indicates CDX2 gain as a predictor of recurrence. Int J Cancer 2018; 144:1561-1573. [PMID: 30229897 DOI: 10.1002/ijc.31869] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 07/11/2018] [Accepted: 08/13/2018] [Indexed: 12/19/2022]
Abstract
Colorectal adenomas are common precancerous lesions with the potential for malignant transformation to colorectal adenocarcinoma. Endoscopic polypectomy provides an opportunity for cancer prevention; however, recurrence rates are high. We collected formalin-fixed paraffin-embedded tissue of 15 primary adenomas with recurrence, 15 adenomas without recurrence, and 14 matched pair samples (primary adenoma and the corresponding recurrent adenoma). The samples were analysed by array-comparative genomic hybridisation (aCGH) and single-cell multiplex interphase fluorescence in situ hybridisation (miFISH) to understand clonal evolution, to examine the dynamics of copy number alterations (CNAs) and to identify molecular markers for recurrence prediction. The miFISH probe panel consisted of 14 colorectal carcinogenesis-relevant genes (COX2, PIK3CA, APC, CLIC1, EGFR, MYC, CCND1, CDX2, CDH1, TP53, HER2, SMAD7, SMAD4 and ZNF217), and a centromere probe (CEP10). The aCGH analysis confirmed the genetic landscape typical for colorectal tumorigenesis, that is, CNAs of chromosomes 7, 13q, 18 and 20q. Focal aberrations (≤10 Mbp) were mapped to chromosome bands 6p22.1-p21.33 (33.3%), 7q22.1 (31.4%) and 16q21 (29.4%). MiFISH detected gains of EGFR (23.6%), CDX2 (21.8%) and ZNF217 (18.2%). Most adenomas exhibited a major clone population which was accompanied by multiple smaller clone populations. Gains of CDX2 were exclusively seen in primary adenomas with recurrence (25%) compared to primary adenomas without recurrence (0%). Generation of phylogenetic trees for matched pair samples revealed four distinct patterns of clonal dynamics. In conclusion, adenoma development and recurrence are complex genetic processes driven by multiple CNAs whose evaluations by miFISH, with emphasis on CDX2, might serve as a predictor of recurrence.
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Affiliation(s)
- David Fiedler
- Institute of Pathology, University Medical Center Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Kerstin Heselmeyer-Haddad
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Daniela Hirsch
- Institute of Pathology, University Medical Center Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Leanora S Hernandez
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Irianna Torres
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Darawalee Wangsa
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Yue Hu
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Luis Zapata
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, United Kingdom.,Genomic and Epigenomic Variation in Disease Group, Centre for Genomic Regulation (CGR), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | | | - Sebastian Belle
- Department of Internal Medicine II, University Medical Center Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany.,Central Interdisciplinary Endoscopy Unit, University Medical Center Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Thomas Ried
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Timo Gaiser
- Institute of Pathology, University Medical Center Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
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Al Bakir I, Curtius K, Graham TA. From Colitis to Cancer: An Evolutionary Trajectory That Merges Maths and Biology. Front Immunol 2018; 9:2368. [PMID: 30386335 PMCID: PMC6198656 DOI: 10.3389/fimmu.2018.02368] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 09/24/2018] [Indexed: 12/25/2022] Open
Abstract
Patients with inflammatory bowel disease have an increased risk of developing colorectal cancer, and this risk is related to disease duration, extent, and cumulative inflammation burden. Carcinogenesis follows the principles of Darwinian evolution, whereby somatic cells acquire genomic alterations that provide them with a survival and/or growth advantage. Colitis represents a unique situation whereby routine surveillance endoscopy provides a serendipitous opportunity to observe somatic evolution over space and time in vivo in a human organ. Moreover, somatic evolution in colitis is evolution in the ‘fast lane': the repeated rounds of inflammation and mucosal healing that are characteristic of the disease accelerate the evolutionary process and likely provide a strong selective pressure for inflammation-adapted phenotypic traits. In this review, we discuss the evolutionary dynamics of pre-neoplastic clones in colitis with a focus on how measuring their evolutionary trajectories could deliver a powerful way to predict future cancer occurrence. Measurements of somatic evolution require an interdisciplinary approach that combines quantitative measurement of the genotype, phenotype and the microenvironment of somatic cells–paying particular attention to spatial heterogeneity across the colon–together with mathematical modeling to interpret these data within an evolutionary framework. Here we take a practical approach in discussing how and why the different “evolutionary ingredients” can and should be measured, together with our viewpoint on subsequent translation into clinical practice. We highlight the open questions in the evolution of colitis-associated cancer as a stimulus for future work.
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Affiliation(s)
- Ibrahim Al Bakir
- Evolution and Cancer Laboratory, Centre for Tumour Biology, Barts Cancer Institute, London, United Kingdom.,Inflammatory Bowel Disease Unit, St Mark's Hospital, Harrow, United Kingdom
| | - Kit Curtius
- Evolution and Cancer Laboratory, Centre for Tumour Biology, Barts Cancer Institute, London, United Kingdom
| | - Trevor A Graham
- Evolution and Cancer Laboratory, Centre for Tumour Biology, Barts Cancer Institute, London, United Kingdom
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Wright NA. Is Barrett's-Associated Esophageal Adenocarcinoma a Clonal Disease? Dig Dis Sci 2018; 63:2022-2027. [PMID: 29951796 DOI: 10.1007/s10620-018-5164-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
In this study, we argue that the basic clonal unit that makes up the Barrett's segment is at the level of the gland. There is expansion of this clonal unit, the gland, by fission, and there is evidence that the Barrett's segment is itself a clonal proliferation. Barrett's esophagus arises from both goblet cell-containing metaplasia and non-goblet cell-containing metaplasia and may arise from a stable clone, but the genomic changes occurring are subject to selection, usually with little or no evolution, appearing indolent from the evolutionary perspective. Genomic changes leading to dysplastic phenotypes are selected, but without any single clone predominating within the segment.
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Affiliation(s)
- Nicholas A Wright
- Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London, EC1M 6BQ, UK.
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47
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Abstract
The incidence of esophageal adenocarcinoma (EAC) and its precursor lesion Barrett's esophagus (BE) has been increasing steadily in the western world in recent decades. Understanding the cellular origins of BE and the conditions responsible for their malignant transformation would greatly facilitate risk assessment and identification of patients at risk of progression, but this topic remains a source of debate. Here, we review recent findings that have provided support for the gastroesophageal junction (GEJ) as the main source of stem cells that give rise to BE and EAC. These include both gastric cardia cells and transitional basal cells. Furthermore, we discuss the role of chronic injury and inflammation in a tumor microenvironment as a major factor in promoting stem cell expansion and proliferation as well as transformation of the GEJ-derived stem cells and progression to EAC. We conclude that there exists a large amount of empirical support for the GEJ as the likely source of BE stem cells. While BE seems to resemble a successful adaptation to esophageal damage, carcinogenesis appears as a consequence of natural selection at the level of GEJ stem cells, and later glands, that expand into the esophagus wherein the local ecology creates the selective landscape for cancer progression.
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48
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Inadomi J, Alastal H, Bonavina L, Gross S, Hunt RH, Mashimo H, di Pietro M, Rhee H, Shah M, Tolone S, Wang DH, Xie SH. Recent advances in Barrett's esophagus. Ann N Y Acad Sci 2018; 1434:227-238. [PMID: 29974975 DOI: 10.1111/nyas.13909] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 05/21/2018] [Accepted: 05/29/2018] [Indexed: 12/20/2022]
Abstract
Barrett's esophagus (BE) is the only known precursor of esophageal adenocarcinoma, one of the few cancers with increasing incidence in developed countries. The pathogenesis of BE is unclear with regard to either the cellular origin of this metaplastic epithelium or the manner in which malignant transformation occurs, although recent data indicate a possible junctional origin of stem cells for BE. Treatment of BE may be achieved using endoscopic eradication therapy; however, there is a lack of discriminatory tools to identify individuals at sufficient risk for cancer development in whom intervention is warranted. Reduction in gastroesophageal reflux of gastric contents including acid is mandatory to achieve remission from BE after endoscopic ablation, and can be achieved using medical or nonmedical interventions. Research topics of greatest interest include the mechanism of BE development and transformation to cancer, risk stratification methods to identify individuals who may benefit from ablation of BE, optimization of eradication therapy, and surveillance methods to ensure that remission is maintained after eradication is achieved.
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Affiliation(s)
- John Inadomi
- Division of Gastroenterology, University of Washington School of Medicine, Seattle, Washington
| | - Hani Alastal
- MRC Cancer Unit at the University of Cambridge, Cambridge, UK.,Faculty of Life Sciences and Education, University of South Wales, Newport City, UK
| | - Luigi Bonavina
- Department of Biomedical Sciences for Health, University of Milano School of Medicine, Milan, Italy.,Division of General Surgery, IRCCS Policlinico San Donato, Milan, Italy
| | - Seth Gross
- Division of Gastroenterology, New York University, New York, New York
| | | | - Hiroshi Mashimo
- Division of Gastroenterology, Harvard Medical School, Boston, Massachusetts.,VA Boston Healthcare System, Boston, Massachusetts
| | | | - Horace Rhee
- Division of Gastroenterology and Hepatology, Stanford University, Palo Alto, California
| | - Marmy Shah
- Division of Gastroenterology, Loyola University Chicago Stritch School of Medicine, Chicago, Illinois
| | - Salvatore Tolone
- Division of General, Mini-Invasive and Bariatric Surgery, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - David H Wang
- Division of Hematology and Oncology, UT Southwestern Medical Center and VA North Texas Health Care System, Dallas, Texas
| | - Shao-Hua Xie
- Department of Molecular Medicine and Surgery, Karolinska Institute, Stockholm, Sweden
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49
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Kohoutova D, Haidry R, Banks M, Butt MA, Dunn J, Thorpe S, Lovat L. Long-term outcomes of the randomized controlled trial comparing 5-aminolaevulinic acid and Photofrin photodynamic therapy for Barrett's oesophagus related neoplasia. Scand J Gastroenterol 2018; 53:527-532. [PMID: 29161901 DOI: 10.1080/00365521.2017.1403646] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
OBJECTIVE Photodynamic therapy (PDT) was used as therapy for early neoplasia associated with Barrett's oesophagus (BE). This is 5-year follow-up of patients enrolled into randomised controlled trial of 5-aminolaevulinic acid (ALA) vs. Photofrin PDT. METHODS Biopsies were taken from original Barrett's segment during endoscopic follow up using Seattle protocol. Endoscopic mucosal resection (EMR) ± radiofrequency ablation (RFA) was preferred therapy in patients who failed PDT and/or had recurrent neoplasia. RESULTS Fifty eight of 64 patients enrolled in the original trial were followed up including 31 patients treated with ALA PDT (17 patients with ≤6 cm, 14 patients with >6 cm segment of BE) and 27 treated with Photofrin PDT (14 patients with ≤6 cm, 13 patients with >6 cm BE). Initial success was achieved in 65% (20/31) ALA and 48% (13/27) Photofrin patients (p = .289). Thirty five percent patients (7/20) relapsed in ALA group and 54% (7/13) relapsed in Photofrin group (p = .472). At a median follow-up of 67 months, no significant difference was found in long-term complete reversal of intestinal metaplasia (CR-IM) and complete reversal of dysplasia (CR-D) between ALA and Photofrin groups (78% vs. 63%; p = .18; 90% vs. 76%; p = .26). Original length of BE did not alter long-term outcome. Four patients from each group progressed to invasive oesophageal adenocarcinoma. Initial success of ALA PDT was associated with significantly better likelihood of long-term remission (p = .03). CONCLUSIONS Initial response to PDT plays key role in long term outcome. RFA ± EMR have, however, become preferred minimally invasive ablative therapy for BE-related neoplasia due to poor efficacy of PDT.
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Affiliation(s)
- Darina Kohoutova
- a Division of Surgery & Interventional Science , University College London , London , UK.,b Division of GI Services , University College London Hospital , London , UK
| | - Rehan Haidry
- a Division of Surgery & Interventional Science , University College London , London , UK.,b Division of GI Services , University College London Hospital , London , UK
| | - Matthew Banks
- a Division of Surgery & Interventional Science , University College London , London , UK.,b Division of GI Services , University College London Hospital , London , UK
| | - Mohammed Adil Butt
- a Division of Surgery & Interventional Science , University College London , London , UK.,b Division of GI Services , University College London Hospital , London , UK
| | - Jason Dunn
- c Guy's and St Thomas' NHS Foundation Trust , London , UK
| | - Sally Thorpe
- b Division of GI Services , University College London Hospital , London , UK
| | - Laurence Lovat
- a Division of Surgery & Interventional Science , University College London , London , UK.,b Division of GI Services , University College London Hospital , London , UK
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50
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Barret M, Prat F. Diagnosis and treatment of superficial esophageal cancer. Ann Gastroenterol 2018; 31:256-265. [PMID: 29720850 PMCID: PMC5924847 DOI: 10.20524/aog.2018.0252] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 01/29/2018] [Indexed: 02/07/2023] Open
Abstract
Endoscopy allows for the screening, early diagnosis, treatment and follow up of superficial esophageal cancer. Endoscopic submucosal dissection has become the gold standard for the resection of superficial squamous cell neoplasia. Combinations of endoscopic mucosal resection and radiofrequency ablation are the mainstay of the management of Barrett’s associated neoplasia. However, protruded, non-lifting or large lesions may be better managed by endoscopic submucosal dissection. Novel ablation tools, such as argon plasma coagulation with submucosal lifting and cryoablation balloons, are being developed for the treatment of residual Barrett’s esophagus, since iatrogenic strictures still hamper the development of extensive circumferential resections in the esophagus. Optimal surveillance modalities after endoscopic resection are still to be determined. The assessment of the risk of lymph-node metastases, as well as of the need for additional treatments based on qualitative and quantitative histological criteria, balanced to the patient’s condition, requires a dedicated multidisciplinary team decision process. The need for trained endoscopists, expert pathologists and surgeons, and specialized multidisciplinary meetings underlines the role of expert centers in the management of superficial esophageal cancer.
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Affiliation(s)
- Maximilien Barret
- Department of Gastroenterology and Digestive Oncology, Cochin Hospital, Paris, France
| | - Frédéric Prat
- Department of Gastroenterology and Digestive Oncology, Cochin Hospital, Paris, France
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