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McCabe NH, Stevenson L, Scanlon E, Douglas R, Kennedy S, Keminer O, Windshügel B, Zisterer D, Kennedy RD, Blayney JK, Turkington RC. Identification of Src as a Therapeutic Target in Oesophageal Adenocarcinoma through Functional Genomic and High-Throughput Drug Screening Approaches. Cancers (Basel) 2022; 14:cancers14153726. [PMID: 35954391 PMCID: PMC9367554 DOI: 10.3390/cancers14153726] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 07/15/2022] [Accepted: 07/26/2022] [Indexed: 11/16/2022] Open
Abstract
Drug resistance limits the effectiveness of oesophageal adenocarcinoma (OAC) chemotherapies, leading to a poor prognosis for this disease. Elucidation of the underlying resistance mechanisms is key to enabling the identification of more effective treatments. This study, therefore, aims to identify novel therapeutic and/or chemotherapy sensitising drug targets in OAC. Transcriptional data from a cohort of 273 pre-treatment OAC biopsies, from patients who received neoadjuvant chemotherapy followed by surgical resection, were analysed using gene set enrichment analysis (GSEA) to determine differential gene expression between responding and non-responding OAC tumours. From this, 80 genes were selected for high-throughput siRNA screening in OAC cell lines with or without standard chemotherapy treatment. In parallel, cell viability assays were performed using a panel of FDA-approved drugs and combination index (CI) values were calculated to evaluate drug synergy with standard chemotherapy. Mechanisms of synergy were investigated using western blot, propidium iodide flow cytometry, and proliferation assays. Taken together, the screens identified that targeting Src, using either siRNA or the small molecule inhibitor dasatinib, enhanced the efficacy of chemotherapy in OAC cells. Further in vitro functional analysis confirmed Src inhibition to be synergistic with standard OAC chemotherapies, 5-fluorouracil (5-FU), and cisplatin (CDDP). In conclusion, a compound screen together with a functional genomic approach identified Src as a potential chemosensitising target in OAC, which could be assessed in a clinical study for poor prognosis OAC patients.
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Affiliation(s)
- Niamh H. McCabe
- Patrick G Johnston Centre for Cancer Research, Queen’s University Belfast, Belfast BT9 7AE, UK; (N.H.M.); (L.S.); (E.S.); (R.D.); (S.K.); (J.K.B.)
| | - Leanne Stevenson
- Patrick G Johnston Centre for Cancer Research, Queen’s University Belfast, Belfast BT9 7AE, UK; (N.H.M.); (L.S.); (E.S.); (R.D.); (S.K.); (J.K.B.)
| | - Enya Scanlon
- Patrick G Johnston Centre for Cancer Research, Queen’s University Belfast, Belfast BT9 7AE, UK; (N.H.M.); (L.S.); (E.S.); (R.D.); (S.K.); (J.K.B.)
| | - Rosalie Douglas
- Patrick G Johnston Centre for Cancer Research, Queen’s University Belfast, Belfast BT9 7AE, UK; (N.H.M.); (L.S.); (E.S.); (R.D.); (S.K.); (J.K.B.)
| | - Susanna Kennedy
- Patrick G Johnston Centre for Cancer Research, Queen’s University Belfast, Belfast BT9 7AE, UK; (N.H.M.); (L.S.); (E.S.); (R.D.); (S.K.); (J.K.B.)
| | - Oliver Keminer
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Discovery Research ScreeningPort, 22525 Hamburg, Germany; (O.K.); (B.W.)
- Department of Life Sciences and Chemistry, Jacobs University Bremen, 28759 Bremen, Germany
| | - Björn Windshügel
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Discovery Research ScreeningPort, 22525 Hamburg, Germany; (O.K.); (B.W.)
- Department of Life Sciences and Chemistry, Jacobs University Bremen, 28759 Bremen, Germany
| | - Daniela Zisterer
- Trinity Biomedical Sciences Institute, School of Biochemistry and Immunology, Trinity College Dublin, D08 XW7X Dublin, Ireland;
| | | | - Jaine K. Blayney
- Patrick G Johnston Centre for Cancer Research, Queen’s University Belfast, Belfast BT9 7AE, UK; (N.H.M.); (L.S.); (E.S.); (R.D.); (S.K.); (J.K.B.)
| | - Richard C. Turkington
- Patrick G Johnston Centre for Cancer Research, Queen’s University Belfast, Belfast BT9 7AE, UK; (N.H.M.); (L.S.); (E.S.); (R.D.); (S.K.); (J.K.B.)
- Correspondence: ; Tel.: +44-(0)28-9097-2756
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Sharpe BP, Hayden A, Manousopoulou A, Cowie A, Walker RC, Harrington J, Izadi F, Breininger SP, Gibson J, Pickering O, Jaynes E, Kyle E, Saunders JH, Parsons SL, Ritchie AA, Clarke PA, Collier P, Mongan NP, Bates DO, Yacqub-Usman K, Garbis SD, Walters Z, Rose-Zerilli M, Grabowska AM, Underwood TJ. Phosphodiesterase type 5 inhibitors enhance chemotherapy in preclinical models of esophageal adenocarcinoma by targeting cancer-associated fibroblasts. Cell Rep Med 2022; 3:100541. [PMID: 35732148 PMCID: PMC9244979 DOI: 10.1016/j.xcrm.2022.100541] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 12/14/2021] [Accepted: 01/28/2022] [Indexed: 12/03/2022]
Abstract
The chemotherapy resistance of esophageal adenocarcinomas (EACs) is underpinned by cancer cell extrinsic mechanisms of the tumor microenvironment (TME). We demonstrate that, by targeting the tumor-promoting functions of the predominant TME cell type, cancer-associated fibroblasts (CAFs) with phosphodiesterase type 5 inhibitors (PDE5i), we can enhance the efficacy of standard-of-care chemotherapy. In ex vivo conditions, PDE5i prevent the transdifferentiation of normal fibroblasts to CAF and abolish the tumor-promoting function of established EAC CAFs. Using shotgun proteomics and single-cell RNA-seq, we reveal PDE5i-specific regulation of pathways related to fibroblast activation and tumor promotion. Finally, we confirm the efficacy of PDE5i in combination with chemotherapy in close-to-patient and in vivo PDX-based model systems. These findings demonstrate that CAFs drive chemotherapy resistance in EACs and can be targeted by repurposing PDE5i, a safe and well-tolerated class of drug administered to millions of patients world-wide to treat erectile dysfunction.
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Affiliation(s)
- Benjamin P Sharpe
- School of Cancer Sciences, Faculty of Medicine, Room CS B2, MP824, Somers Cancer Research Building, University Hospital Southampton, Tremona Road, Southampton SO16 6YD, UK
| | - Annette Hayden
- School of Cancer Sciences, Faculty of Medicine, Room CS B2, MP824, Somers Cancer Research Building, University Hospital Southampton, Tremona Road, Southampton SO16 6YD, UK
| | | | - Andrew Cowie
- School of Cancer Sciences, Faculty of Medicine, Room CS B2, MP824, Somers Cancer Research Building, University Hospital Southampton, Tremona Road, Southampton SO16 6YD, UK
| | - Robert C Walker
- School of Cancer Sciences, Faculty of Medicine, Room CS B2, MP824, Somers Cancer Research Building, University Hospital Southampton, Tremona Road, Southampton SO16 6YD, UK
| | - Jack Harrington
- School of Cancer Sciences, Faculty of Medicine, Room CS B2, MP824, Somers Cancer Research Building, University Hospital Southampton, Tremona Road, Southampton SO16 6YD, UK
| | - Fereshteh Izadi
- School of Cancer Sciences, Faculty of Medicine, Room CS B2, MP824, Somers Cancer Research Building, University Hospital Southampton, Tremona Road, Southampton SO16 6YD, UK; Centre for NanoHealth, Swansea University Medical School, Singleton Campus, Swansea SA2 8PP, UK
| | - Stella P Breininger
- School of Cancer Sciences, Faculty of Medicine, Room CS B2, MP824, Somers Cancer Research Building, University Hospital Southampton, Tremona Road, Southampton SO16 6YD, UK
| | - Jane Gibson
- School of Cancer Sciences, Faculty of Medicine, Room CS B2, MP824, Somers Cancer Research Building, University Hospital Southampton, Tremona Road, Southampton SO16 6YD, UK
| | - Oliver Pickering
- School of Cancer Sciences, Faculty of Medicine, Room CS B2, MP824, Somers Cancer Research Building, University Hospital Southampton, Tremona Road, Southampton SO16 6YD, UK
| | - Eleanor Jaynes
- University Hospital Southampton NHS Foundation Trust, Southampton SO16 6YD, UK
| | - Ewan Kyle
- School of Cancer Sciences, Faculty of Medicine, Room CS B2, MP824, Somers Cancer Research Building, University Hospital Southampton, Tremona Road, Southampton SO16 6YD, UK
| | - John H Saunders
- Ex Vivo Cancer Pharmacology Centre of Excellence, School of Medicine, Biodiscovery Institute, University of Nottingham, Nottingham NG7 2RD, UK; Salford Royal NHS Foundation Trust, Salford M6 8HD, UK
| | - Simon L Parsons
- Ex Vivo Cancer Pharmacology Centre of Excellence, School of Medicine, Biodiscovery Institute, University of Nottingham, Nottingham NG7 2RD, UK; Nottingham University Hospitals NHS Trust, Hucknall Road, Nottingham NG5 1PB, UK
| | - Alison A Ritchie
- Ex Vivo Cancer Pharmacology Centre of Excellence, School of Medicine, Biodiscovery Institute, University of Nottingham, Nottingham NG7 2RD, UK
| | - Philip A Clarke
- Ex Vivo Cancer Pharmacology Centre of Excellence, School of Medicine, Biodiscovery Institute, University of Nottingham, Nottingham NG7 2RD, UK
| | - Pamela Collier
- Ex Vivo Cancer Pharmacology Centre of Excellence, School of Medicine, Biodiscovery Institute, University of Nottingham, Nottingham NG7 2RD, UK
| | - Nigel P Mongan
- Department of Pharmacology, Weill Cornell Medicine, New York, NY 10065, USA; Biodiscovery Institute, School of Veterinary Medicine and Science, University of Nottingham, Nottingham NG5 1PB, UK
| | - David O Bates
- Ex Vivo Cancer Pharmacology Centre of Excellence, School of Medicine, Biodiscovery Institute, University of Nottingham, Nottingham NG7 2RD, UK
| | - Kiren Yacqub-Usman
- Ex Vivo Cancer Pharmacology Centre of Excellence, School of Medicine, Biodiscovery Institute, University of Nottingham, Nottingham NG7 2RD, UK
| | | | - Zoë Walters
- School of Cancer Sciences, Faculty of Medicine, Room CS B2, MP824, Somers Cancer Research Building, University Hospital Southampton, Tremona Road, Southampton SO16 6YD, UK
| | - Matthew Rose-Zerilli
- School of Cancer Sciences, Faculty of Medicine, Room CS B2, MP824, Somers Cancer Research Building, University Hospital Southampton, Tremona Road, Southampton SO16 6YD, UK
| | - Anna M Grabowska
- Ex Vivo Cancer Pharmacology Centre of Excellence, School of Medicine, Biodiscovery Institute, University of Nottingham, Nottingham NG7 2RD, UK
| | - Timothy J Underwood
- School of Cancer Sciences, Faculty of Medicine, Room CS B2, MP824, Somers Cancer Research Building, University Hospital Southampton, Tremona Road, Southampton SO16 6YD, UK.
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Dhir H, Choudhury M, Patil K, Cheung C, Bodlak A, Pardo D, Adams A, Travaglino S, Rojas JA, Pai SB. Interception of Signaling Circuits of Esophageal Adenocarcinoma Cells by Resveratrol Reveals Molecular and Immunomodulatory Signatures. Cancers (Basel) 2021; 13:cancers13225811. [PMID: 34830970 PMCID: PMC8616317 DOI: 10.3390/cancers13225811] [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: 10/09/2021] [Revised: 11/12/2021] [Accepted: 11/17/2021] [Indexed: 12/20/2022] Open
Abstract
Simple Summary Adenocarcinoma of the esophagus has been on the rise lately. Increase in mortality due to a paucity of efficacious drugs for this cancer prompted us to discover molecular signatures to combat this malady. To this end, we chose resveratrol—a polyphenol and studied its impact on three esophageal adenocarcinoma cell lines (OE33, OE19 and FLO-1) by multilevel profiling. Here, we show the impact of resveratrol on the viability of the three cell systems studied, at the cellular, molecular level and by proteomic analysis. Impact on programmed cell death pathway resulting in an increase in apoptotic and caspase-positive cells were observed. Decrease in Bcl2. levels and impact on reactive oxygen species (ROS) was also observed. Moreover, proteomic profiling highlighted pivotal differentially regulated signaling molecules. Notably, the downregulation of Ku80 by resveratrol could be harnessed for chemo-radiation therapy to prevent DNA break repair after radiation therapy. Additionally, protein profiling has shed light on molecular and immune-modulatory signatures with implications for discovering novel treatments such as chemo-immunotherapy. Abstract Deregulation of signaling pathways due to mutations sets the cell on a path to neoplasia. Therefore, recent reports of increased mutations observed in esophageal tissue reflects the enhanced risk of tumor formation. In fact, adenocarcinoma of the esophagus has been on the rise lately. Increase in mortality due to a paucity of efficacious drugs for this cancer prompted us to discover molecular signatures to combat this malady. To this end, we chose resveratrol—a polyphenol with anticancer property—and studied its impact on three esophageal adenocarcinoma cell lines (OE33, OE19 and FLO-1) by multilevel profiling. Here, we show the impact of resveratrol on the viability of the three adenocarcinoma esophageal cell systems studied, at the cellular level. Furthermore, an analysis at the molecular level revealed that the action was through the programmed cell death pathway, resulting in an increase in apoptotic and caspase-positive cells. The impact on reactive oxygen species (ROS) and a decrease in Bcl2 levels were also observed. Moreover, proteomic profiling highlighted pivotal differentially regulated signaling molecules. The phenotypic effect observed in resveratrol-treated esophageal cells could be due to the stoichiometry per se of the fold changes observed in entities of key signaling pathways. Notably, the downregulation of Ku80 and other pivotal entities by resveratrol could be harnessed for chemo-radiation therapy to prevent DNA break repair after radiation therapy. Additionally, multilevel profiling has shed light on molecular and immune-modulatory signatures with implications for discovering novel treatments, including chemo-immunotherapy, for esophageal adenocarcinomas which are known to be aggressive cancers.
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Faktor J, Grasso G, Zavadil Kokas F, Kurkowiak M, Mayordomo MY, Kote S, Singh A, Ruidong L, O'Neill JR, Muller P, Goodlett D, Vojtesek B, Hupp T. The effects of p53 gene inactivation on mutant proteome expression in a human melanoma cell model. Biochim Biophys Acta Gen Subj 2020; 1864:129722. [DOI: 10.1016/j.bbagen.2020.129722] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 08/02/2020] [Accepted: 08/24/2020] [Indexed: 12/14/2022]
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Zhang W, Williams TA, Bhagwath AS, Hiermann JS, Peacock CD, Watkins DN, Ding P, Park JY, Montgomery EA, Forastiere AA, Jie C, Cantarel BL, Pham TH, Wang DH. GEAMP, a novel gastroesophageal junction carcinoma cell line derived from a malignant pleural effusion. J Transl Med 2020; 100:16-26. [PMID: 31292541 PMCID: PMC6920545 DOI: 10.1038/s41374-019-0278-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 05/06/2019] [Accepted: 05/06/2019] [Indexed: 02/06/2023] Open
Abstract
Gastroesophageal junction (GEJ) cancer remains a clinically significant disease in Western countries due to its increasing incidence, which mirrors that of esophageal cancer, and poor prognosis. To develop novel and effective approaches for prevention, early detection, and treatment of patients with GEJ cancer, a better understanding of the mechanisms driving pathogenesis and malignant progression of this disease is required. These efforts have been limited by the small number of available cell lines and appropriate preclinical animal models for in vitro and in vivo studies. We have established and characterized a novel GEJ cancer cell line, GEAMP, derived from the malignant pleural effusion of a previously treated GEJ cancer patient. Comprehensive genetic analyses confirmed a clonal relationship between GEAMP cells and the primary tumor. Targeted next-generation sequencing identified 56 nonsynonymous alterations in 51 genes including TP53 and APC, which are commonly altered in GEJ cancer. In addition, multiple copy-number alterations were found including EGFR and K-RAS gene amplifications and loss of CDKN2A and CDKN2B. Histological examination of subcutaneous flank xenografts in nude and NOD-SCID mice showed a carcinoma with mixed squamous and glandular differentiation, suggesting GEAMP cells contain a subpopulation with multipotent potential. Finally, pharmacologic inhibition of the EGFR signaling pathway led to downregulation of key downstream kinases and inhibition of cell proliferation in vitro. Thus, GEAMP represents a valuable addition to the limited number of bona fide GEJ cancer cell lines.
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Affiliation(s)
- Wei Zhang
- Esophageal Diseases Center and Division of Hematology-Oncology, Department of Internal Medicine and the Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Taylor A. Williams
- Esophageal Diseases Center and Division of Hematology-Oncology, Department of Internal Medicine and the Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Ankur S. Bhagwath
- Esophageal Diseases Center and Division of Hematology-Oncology, Department of Internal Medicine and the Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jared S. Hiermann
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Craig D. Peacock
- Translational Hematology and Oncology Research, Cleveland Clinic, Cleveland, OH, USA
| | - D. Neil Watkins
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Peiguo Ding
- Esophageal Diseases Center and Division of Hematology-Oncology, Department of Internal Medicine and the Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jason Y. Park
- Department of Pathology and the Eugene McDermott Center for Human Growth and Development, UT Southwestern Medical Center, Dallas, TX, USA
| | - Elizabeth A. Montgomery
- Division of Gastrointestinal and Liver Pathology, Department of Pathology, Johns Hopkins Hospital, Baltimore, MD, USA
| | - Arlene A. Forastiere
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Chunfa Jie
- Department of Biochemistry and Nutrition, Des Moines University, Des Moines, IA, USA
| | - Brandi L. Cantarel
- Bioinformatics Core Facility, Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Thai H. Pham
- Esophageal Diseases Center and Department of Surgery, University of Texas Southwestern Medical Center, Dallas, TX, USA,VA North Texas Health Care System, Dallas, TX, USA
| | - David H. Wang
- Esophageal Diseases Center and Division of Hematology-Oncology, Department of Internal Medicine and the Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA,VA North Texas Health Care System, Dallas, TX, USA
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6
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Sun Y, Miao N, Sun T. Detect accessible chromatin using ATAC-sequencing, from principle to applications. Hereditas 2019; 156:29. [PMID: 31427911 PMCID: PMC6696680 DOI: 10.1186/s41065-019-0105-9] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 08/12/2019] [Indexed: 02/07/2023] Open
Abstract
Background Chromatin accessibility is crucial for gene expression regulation in specific cells and in multiple biological processes. Assay for Transposase Accessible Chromatin with high-throughput sequencing (ATAC-seq) is an effective way to reveal chromatin accessibility at a genome-wide level. Through ATAC-seq, produced reads from a small number of cells reflect accessible regions that correspond to nucleosome positioning and transcription factor binding sites, due to probing hyperactive Tn5 transposase to DNA sequence. Conclusion In this review, we summarize both principle and features of ATAC-seq, highlight its applications in basic and clinical research. ATAC-seq has generated comprehensive chromatin accessible maps, and is becoming a powerful tool to understand dynamic gene expression regulation in stem cells, early embryos and tumors.
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Affiliation(s)
- Yuanyuan Sun
- Center for Precision Medicine, School of Medicine and School of Biomedical Sciences, Huaqiao University, 668 Jimei Road, Xiamen, 361021 Fujian China
| | - Nan Miao
- Center for Precision Medicine, School of Medicine and School of Biomedical Sciences, Huaqiao University, 668 Jimei Road, Xiamen, 361021 Fujian China
| | - Tao Sun
- Center for Precision Medicine, School of Medicine and School of Biomedical Sciences, Huaqiao University, 668 Jimei Road, Xiamen, 361021 Fujian China
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Mourikis TP, Benedetti L, Foxall E, Temelkovski D, Nulsen J, Perner J, Cereda M, Lagergren J, Howell M, Yau C, Fitzgerald RC, Scaffidi P, Ciccarelli FD. Patient-specific cancer genes contribute to recurrently perturbed pathways and establish therapeutic vulnerabilities in esophageal adenocarcinoma. Nat Commun 2019; 10:3101. [PMID: 31308377 PMCID: PMC6629660 DOI: 10.1038/s41467-019-10898-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 06/04/2019] [Indexed: 12/25/2022] Open
Abstract
The identification of cancer-promoting genetic alterations is challenging particularly in highly unstable and heterogeneous cancers, such as esophageal adenocarcinoma (EAC). Here we describe a machine learning algorithm to identify cancer genes in individual patients considering all types of damaging alterations simultaneously. Analysing 261 EACs from the OCCAMS Consortium, we discover helper genes that, alongside well-known drivers, promote cancer. We confirm the robustness of our approach in 107 additional EACs. Unlike recurrent alterations of known drivers, these cancer helper genes are rare or patient-specific. However, they converge towards perturbations of well-known cancer processes. Recurrence of the same process perturbations, rather than individual genes, divides EACs into six clusters differing in their molecular and clinical features. Experimentally mimicking the alterations of predicted helper genes in cancer and pre-cancer cells validates their contribution to disease progression, while reverting their alterations reveals EAC acquired dependencies that can be exploited in therapy.
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Affiliation(s)
- Thanos P Mourikis
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
- School of Cancer and Pharmaceutical Sciences, King's College London, London, SE11UL, UK
| | - Lorena Benedetti
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
- School of Cancer and Pharmaceutical Sciences, King's College London, London, SE11UL, UK
| | - Elizabeth Foxall
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
- School of Cancer and Pharmaceutical Sciences, King's College London, London, SE11UL, UK
| | - Damjan Temelkovski
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
- School of Cancer and Pharmaceutical Sciences, King's College London, London, SE11UL, UK
| | - Joel Nulsen
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
- School of Cancer and Pharmaceutical Sciences, King's College London, London, SE11UL, UK
| | - Juliane Perner
- MRC Cancer Unit, Hutchison/MRC Research Centre, University of Cambridge, Cambridge, CB2 OXZ, UK
| | - Matteo Cereda
- Italian Institute for Genomic Medicine (IIGM), Turin, 10126, Italy
| | - Jesper Lagergren
- School of Cancer and Pharmaceutical Sciences, King's College London, London, SE11UL, UK
| | - Michael Howell
- High Throughput Screening Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | | | - Rebecca C Fitzgerald
- MRC Cancer Unit, Hutchison/MRC Research Centre, University of Cambridge, Cambridge, CB2 OXZ, UK
| | - Paola Scaffidi
- Cancer Epigenetics Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
- UCL Cancer Institute, University College London, London, WC1E 6DD, UK
| | - Francesca D Ciccarelli
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London, NW1 1AT, UK.
- School of Cancer and Pharmaceutical Sciences, King's College London, London, SE11UL, UK.
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8
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Rogerson C, Britton E, Withey S, Hanley N, Ang YS, Sharrocks AD. Identification of a primitive intestinal transcription factor network shared between esophageal adenocarcinoma and its precancerous precursor state. Genome Res 2019; 29:723-736. [PMID: 30962179 PMCID: PMC6499311 DOI: 10.1101/gr.243345.118] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 04/03/2019] [Indexed: 02/07/2023]
Abstract
Esophageal adenocarcinoma (EAC) is one of the most frequent causes of cancer death, and yet compared to other common cancers, we know relatively little about the molecular composition of this tumor type. To further our understanding of this cancer, we have used open chromatin profiling to decipher the transcriptional regulatory networks that are operational in EAC. We have uncovered a transcription factor network that is usually found in primitive intestinal cells during embryonic development, centered on HNF4A and GATA6. These transcription factors work together to control the EAC transcriptome. We show that this network is activated in Barrett's esophagus, the putative precursor state to EAC, thereby providing novel molecular evidence in support of stepwise malignant transition. Furthermore, we show that HNF4A alone is sufficient to drive chromatin opening and activation of a Barrett's-like chromatin signature when expressed in normal human epithelial cells. Collectively, these data provide a new way to categorize EAC at a genome scale and implicate HNF4A activation as a potential pivotal event in its malignant transition from healthy cells.
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Affiliation(s)
- Connor Rogerson
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, United Kingdom
| | - Edward Britton
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, United Kingdom
| | - Sarah Withey
- School of Medical Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Sciences Centre, University of Manchester, Manchester M13 9PT, United Kingdom
| | - Neil Hanley
- School of Medical Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Sciences Centre, University of Manchester, Manchester M13 9PT, United Kingdom.,Endocrinology Department, Central Manchester University Hospitals NHS Foundation Trust, Manchester M13 9WU, United Kingdom
| | - Yeng S Ang
- School of Medical Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Sciences Centre, University of Manchester, Manchester M13 9PT, United Kingdom.,GI Science Centre, Salford Royal NHS FT, University of Manchester, Salford M6 8HD, United Kingdom
| | - Andrew D Sharrocks
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, United Kingdom
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Shrestha RK, Ding P, Jones JDG, MacLean D. A workflow for simplified analysis of ATAC-cap-seq data in R. Gigascience 2018; 7:5046606. [PMID: 29961827 PMCID: PMC6047409 DOI: 10.1093/gigascience/giy080] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 06/25/2018] [Indexed: 01/15/2023] Open
Abstract
Background Assay for Transposase-Accessible Chromatin (ATAC)-cap-seq is a high-throughput sequencing method that combines ATAC-seq with targeted nucleic acid enrichment of precipitated DNA fragments. There are increased analytical difficulties arising from working with a set of regions of interest that may be small in number and biologically dependent. Common statistical pipelines for RNA sequencing might be assumed to apply but can give misleading results on ATAC-cap-seq data. A tool is needed to allow a nonspecialist user to quickly and easily summarize data and apply sensible and effective normalization and analysis. Results We developed atacR to allow a user to easily analyze their ATAC enrichment experiment. It provides comprehensive summary functions and diagnostic plots for studying enriched tag abundance. Application of between-sample normalization is made straightforward. Functions for normalizing based on user-defined control regions, whole library size, and regions selected from the least variable regions in a dataset are provided. Three methods for detecting differential abundance of tags from enriched methods are provided, including bootstrap t, Bayes factor, and a wrapped version of the standard exact test in the edgeR package. We compared the precision, recall, and F-score of each detection method on resampled datasets at varying replicate, significance threshold, and genes changed and found that the Bayes factor method had the greatest overall detection power, though edgeR was slightly stronger in simulations with lower numbers of genes changed. Conclusions Our package allows a nonspecialist user to easily and effectively apply methods appropriate to the analysis of ATAC-cap-seq in a reproducible manner. The package is implemented in pure R and is fully interoperable with common workflows in Bioconductor.
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Affiliation(s)
| | - Pingtao Ding
- Sainsbury Laboratory, Norwich Research Park, Norwich, UK, NR4 7UH
| | | | - Dan MacLean
- Sainsbury Laboratory, Norwich Research Park, Norwich, UK, NR4 7UH
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10
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Walker RC, Underwood TJ. Molecular pathways in the development and treatment of oesophageal cancer. Best Pract Res Clin Gastroenterol 2018; 36-37:9-15. [PMID: 30551862 DOI: 10.1016/j.bpg.2018.11.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 11/20/2018] [Indexed: 02/07/2023]
Abstract
The molecular pathways involved in the development and treatment of oesophageal cancer are complex. Recent large-scale genome sequencing studies have delivered novel insights into aetiology and possible targeted treatments. Oesophageal squamous cell carcinoma (OSCC) and adenocarcinoma (OAC) are distinct entities. At the molecular level OSCC is more similar to squamous cell cancers in other organs than OAC. Whilst considerable heterogeneity exists in both tumour types new data suggests that driver gene events and mutational signatures may be able to categorise tumours into potentially actionable subtypes. Taken together these findings not only suggest new avenues for treatments in a cancer type with appalling outcomes, but also a new era of molecular rather than purely anatomical classification and staging of oesophageal cancer.
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Affiliation(s)
- Robert Charles Walker
- Cancer Research UK and Royal College of Surgeons of England Clinical Research Training Fellow, University of Southampton, UK
| | - Timothy James Underwood
- Cancer Research UK and Royal College of Surgeons of England Advanced Clinician Scientist Fellow, University of Southampton, UK.
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11
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Vrana D, Hlavac V, Brynychova V, Vaclavikova R, Neoral C, Vrba J, Aujesky R, Matzenauer M, Melichar B, Soucek P. ABC Transporters and Their Role in the Neoadjuvant Treatment of Esophageal Cancer. Int J Mol Sci 2018; 19:E868. [PMID: 29543757 PMCID: PMC5877729 DOI: 10.3390/ijms19030868] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 03/07/2018] [Accepted: 03/13/2018] [Indexed: 12/12/2022] Open
Abstract
The prognosis of esophageal cancer (EC) is poor, despite considerable effort of both experimental scientists and clinicians. The tri-modality treatment consisting of neoadjuvant chemoradiation followed by surgery has remained the gold standard over decades, unfortunately, without significant progress in recent years. Suitable prognostic factors indicating which patients will benefit from this tri-modality treatment are missing. Some patients rapidly progress on the neoadjuvant chemoradiotherapy, which is thus useless and sometimes even harmful. At the same time, other patients achieve complete remission on neoadjuvant chemoradiotherapy and subsequent surgery may increase their risk of morbidity and mortality. The prognosis of patients ranges from excellent to extremely poor. Considering these differences, the role of drug metabolizing enzymes and transporters, among other factors, in the EC response to chemotherapy may be more important compared, for example, with pancreatic cancer where all patients progress on chemotherapy regardless of the treatment or disease stage. This review surveys published literature describing the potential role of ATP-binding cassette transporters, the genetic polymorphisms, epigenetic regulations, and phenotypic changes in the prognosis and therapy of EC. The review provides knowledge base for further research of potential predictive biomarkers that will allow the stratification of patients into defined groups for optimal therapeutic outcome.
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Affiliation(s)
- David Vrana
- Department of Oncology, Faculty of Medicine and Dentistry, Palacky University, Hnevotinska 976/3, 77515 Olomouc, Czech Republic.
| | - Viktor Hlavac
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 76, 32300 Pilsen, Czech Republic.
| | - Veronika Brynychova
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 76, 32300 Pilsen, Czech Republic.
| | - Radka Vaclavikova
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 76, 32300 Pilsen, Czech Republic.
| | - Cestmir Neoral
- Department of Surgery, Faculty of Medicine and Dentistry, Palacky University, Hnevotinska 976/3, 77515 Olomouc, Czech Republic.
| | - Jiri Vrba
- Department of Surgery, Faculty of Medicine and Dentistry, Palacky University, Hnevotinska 976/3, 77515 Olomouc, Czech Republic.
| | - Rene Aujesky
- Department of Surgery, Faculty of Medicine and Dentistry, Palacky University, Hnevotinska 976/3, 77515 Olomouc, Czech Republic.
| | - Marcel Matzenauer
- Department of Oncology, Faculty of Medicine and Dentistry, Palacky University, Hnevotinska 976/3, 77515 Olomouc, Czech Republic.
| | - Bohuslav Melichar
- Department of Oncology, Faculty of Medicine and Dentistry, Palacky University, Hnevotinska 976/3, 77515 Olomouc, Czech Republic.
| | - Pavel Soucek
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 76, 32300 Pilsen, Czech Republic.
- Department of Surgery, Faculty Hospital Pilsen, Alej Svobody 80, 30460 Pilsen, Czech Republic.
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12
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Whelan KA, Muir AB, Nakagawa H. Esophageal 3D Culture Systems as Modeling Tools in Esophageal Epithelial Pathobiology and Personalized Medicine. Cell Mol Gastroenterol Hepatol 2018; 5:461-478. [PMID: 29713660 PMCID: PMC5924738 DOI: 10.1016/j.jcmgh.2018.01.011] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 01/11/2018] [Indexed: 12/13/2022]
Abstract
The stratified squamous epithelium of the esophagus shows a proliferative basal layer of keratinocytes that undergo terminal differentiation in overlying suprabasal layers. Esophageal pathologies, including eosinophilic esophagitis, gastroesophageal reflux disease, Barrett's esophagus, squamous cell carcinoma, and adenocarcinoma, cause perturbations in the esophageal epithelial proliferation-differentiation gradient. Three-dimensional (3D) culture platforms mimicking in vivo esophageal epithelial tissue architecture ex vivo have emerged as powerful experimental tools for the investigation of esophageal biology in the context of homeostasis and pathology. Herein, we describe types of 3D culture that are used to model the esophagus, including organotypic, organoid, and spheroid culture systems. We discuss the development and optimization of various esophageal 3D culture models; highlight the applications, strengths, and limitations of each method; and summarize how these models have been used to evaluate the esophagus under homeostatic conditions as well as under the duress of inflammation and precancerous/cancerous conditions. Finally, we present future perspectives regarding the use of esophageal 3D models in basic science research as well as translational studies with the potential for personalized medicine.
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Key Words
- 3D, 3-dimensional
- BE, Barrett’s esophagus
- COX, cyclooxygenase
- CSC, cancer stem cell
- EADC, esophageal adenocarcinoma
- EGF, epidermal growth factor
- EGFR, epidermal growth factor receptor
- EMT, epithelial-mesenchymal transition
- ESCC, esophageal squamous cell carcinoma
- EoE, eosinophilic esophagitis
- Esophageal Disease
- FEF3, primary human fetal esophageal fibroblast
- GERD, gastroesophageal reflux disease
- OTC, organotypic 3-dimensional culture
- Organoid
- Organotypic Culture
- STAT3, signal transducer and activator of transcription-3
- Spheroid Culture
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Affiliation(s)
- Kelly A. Whelan
- Pathology and Laboratory Medicine, Fels Institute for Cancer Research and Molecular Biology, Lewis Katz School of Medicine at Temple University, Philadelphia, Pennsylvania
| | - Amanda B. Muir
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
- Correspondence Address correspondence to: Amanda B. Muir, MD, Children's Hospital of Philadelphia, 3615 Civic Center Boulevard, Abramson Research Center 902E, Philadelphia, Pennsylvania 19103. fax: (267) 426–7814.
| | - Hiroshi Nakagawa
- Division of Gastroenterology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, Pennsylvania
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13
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Lee KTW, Smith RA, Gopalan V, Lam AK. Targeted Single Gene Mutation in Esophageal Adenocarcinoma. Methods Mol Biol 2018; 1756:213-229. [PMID: 29600373 DOI: 10.1007/978-1-4939-7734-5_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023]
Abstract
Esophageal adenocarcinoma is heterogeneous and studies have reviewed many important mutations that contribute to the pathogenesis of the cancer. These discoveries have helped paved the way into identifying new gene markers or gene targets to develop novel molecular directed therapy for better patient outcomes in esophageal adenocarcinoma. Despite the recent bloom in next-generation sequencing, Sanger sequencing still represents the gold standard method for the study of the driver genes in esophageal adenocarcinoma. This chapter focuses on the sequencing techniques in identification of single gene mutations.
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Affiliation(s)
- Katherine T W Lee
- Cancer Molecular Pathology of School of Medicine, Griffith University, Gold Coast, Australia
| | - Robert A Smith
- Genomics Research Centre, School of Biomedical Science, Institute of Health and Biomedical Innovation, Queensland University of Technology, Kelvin Grove, QLD, Australia
| | - Vinod Gopalan
- Cancer Molecular Pathology of School of Medicine, Griffith University, Gold Coast, Australia
| | - Alfred K Lam
- Cancer Molecular Pathology of School of Medicine, Griffith University, Gold Coast, Australia.
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14
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Britton E, Rogerson C, Mehta S, Li Y, Li X, the OCCAMS consortium, Fitzgerald RC, Ang YS, Sharrocks AD. Open chromatin profiling identifies AP1 as a transcriptional regulator in oesophageal adenocarcinoma. PLoS Genet 2017; 13:e1006879. [PMID: 28859074 PMCID: PMC5578490 DOI: 10.1371/journal.pgen.1006879] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 06/20/2017] [Indexed: 01/04/2023] Open
Abstract
Oesophageal adenocarcinoma (OAC) is one of the ten most prevalent forms of cancer and is showing a rapid increase in incidence and yet exhibits poor survival rates. Compared to many other common cancers, the molecular changes that occur in this disease are relatively poorly understood. However, genes encoding chromatin remodeling enzymes are frequently mutated in OAC. This is consistent with the emerging concept that cancer cells exhibit reprogramming of their chromatin environment which leads to subsequent changes in their transcriptional profile. Here, we have used ATAC-seq to interrogate the chromatin changes that occur in OAC using both cell lines and patient-derived material. We demonstrate that there are substantial changes in the regulatory chromatin environment in the cancer cells and using this data we have uncovered an important role for ETS and AP1 transcription factors in driving the changes in gene expression found in OAC cells.
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Affiliation(s)
- Edward Britton
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Connor Rogerson
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Shaveta Mehta
- School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
- Christie Hospital, Manchester, United Kingdom
| | - Yaoyong Li
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Xiaodun Li
- MRC Cancer Unit, Hutchison/MRC Research Centre, University of Cambridge, Cambridge, United Kingdom
| | | | - Rebecca C. Fitzgerald
- MRC Cancer Unit, Hutchison/MRC Research Centre, University of Cambridge, Cambridge, United Kingdom
| | - Yeng S. Ang
- School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
- GI Science Centre, Salford Royal NHS FT, University of Manchester, Stott Lane, Salford, United Kingdom
| | - Andrew D. Sharrocks
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
- MRC Cancer Unit, Hutchison/MRC Research Centre, University of Cambridge, Cambridge, United Kingdom
- GI Science Centre, Salford Royal NHS FT, University of Manchester, Stott Lane, Salford, United Kingdom
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15
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West MA, Roman A, Sayan E, Primrose JN, Wedge SR, Underwood TJ, Mirnezami AH. A minimum core outcome dataset for the reporting of preclinical chemotherapeutic drug studies: Lessons learned from multiple discordant methodologies in the setting of colorectal cancer. Crit Rev Oncol Hematol 2017; 112:80-102. [PMID: 28325268 DOI: 10.1016/j.critrevonc.2017.02.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 01/11/2017] [Accepted: 02/13/2017] [Indexed: 12/27/2022] Open
Abstract
In vivo studies in animal models are critical tools necessary to study the fundamental complexity of carcinogenesis. A constant strive to improve animal models in cancer exists, especially those investigating the use of chemotherapeutic effectiveness. In the present systematic review, colorectal cancer (CRC) is used as an example to highlight and critically evaluate the range of reporting strategies used when investigating chemotherapeutic agents in the preclinical setting. A systematic review examining the methodology and reporting of preclinical chemotherapeutic drug studies using CRC murine models was conducted. A total of 45 studies were included in this systematic review. The literature was found to be highly heterogeneous with various cell lines, animal strains, animal ages and chemotherapeutic compounds/regimens tested, proving difficult to compare outcomes between similar studies or indeed gain any significant insight into which chemotherapeutic regimen caused adverse events. From this analysis we propose a minimum core outcome dataset that could be regarded as a standardised way of reporting results from in vivo experimentation.
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Affiliation(s)
- M A West
- University Surgery, University of Southampton, Southampton General Hospital, Southampton SO16 6YD, UK; Academic Unit of Cancer Sciences, Somers Cancer Research Building, University of Southampton, UK.
| | - A Roman
- University Surgery, University of Southampton, Southampton General Hospital, Southampton SO16 6YD, UK; Academic Unit of Cancer Sciences, Somers Cancer Research Building, University of Southampton, UK
| | - E Sayan
- Academic Unit of Cancer Sciences, Somers Cancer Research Building, University of Southampton, UK
| | - J N Primrose
- University Surgery, University of Southampton, Southampton General Hospital, Southampton SO16 6YD, UK; Academic Unit of Cancer Sciences, Somers Cancer Research Building, University of Southampton, UK
| | - S R Wedge
- Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, UK
| | - T J Underwood
- University Surgery, University of Southampton, Southampton General Hospital, Southampton SO16 6YD, UK; Academic Unit of Cancer Sciences, Somers Cancer Research Building, University of Southampton, UK
| | - A H Mirnezami
- University Surgery, University of Southampton, Southampton General Hospital, Southampton SO16 6YD, UK; Academic Unit of Cancer Sciences, Somers Cancer Research Building, University of Southampton, UK
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