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Roy A, Chauhan S, Bhattacharya S, Jakhmola V, Tyagi K, Sachdeva A, Wasai A, Mandal S. Runt-related transcription factors in human carcinogenesis: a friend or foe? J Cancer Res Clin Oncol 2023:10.1007/s00432-023-04769-0. [PMID: 37081242 DOI: 10.1007/s00432-023-04769-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 04/08/2023] [Indexed: 04/22/2023]
Abstract
PURPOSE Cancer is one of the deadliest pathologies with more than 19 million new cases and 10 million cancer-related deaths across the globe. Despite development of advanced therapeutic interventions, cancer remains as a fatal pathology due to lack of early prognostic biomarkers, therapy resistance and requires identification of novel drug targets. METHODS Runt-related transcription factors (Runx) family controls several cellular and physiological functions including osteogenesis. Recent literatures from PubMed was mined and the review was written in comprehensive manner RESULTS: Recent literature suggests that aberrant expression of Runx contributes to tumorigenesis of many organs. Conversely, cell- and tissue-specific tumor suppressor roles of Runx are also reported. In this review, we have provided the structural/functional properties of Runx isoforms and its regulation in context of human cancer. Moreover, in an urgent need to discover novel therapeutic interventions against cancer, we comprehensively discussed the reported oncogenic and tumor suppressive roles of Runx isoforms in several tumor types and discussed the discrepancies that may have risen on Runx as a driver of malignant transformation. CONCLUSION Runx may be a novel therapeutic target against a battery of deadly human cancers.
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Affiliation(s)
- Adhiraj Roy
- Amity Institute of Molecular Medicine & Stem Cell Research, Amity University, Sector 125, Noida, Uttar Pradesh, 201303, India.
| | - Shivi Chauhan
- Amity Institute of Molecular Medicine & Stem Cell Research, Amity University, Sector 125, Noida, Uttar Pradesh, 201303, India
| | - Sujata Bhattacharya
- Amity Institute of Molecular Medicine & Stem Cell Research, Amity University, Sector 125, Noida, Uttar Pradesh, 201303, India
| | - Vibhuti Jakhmola
- Amity Institute of Molecular Medicine & Stem Cell Research, Amity University, Sector 125, Noida, Uttar Pradesh, 201303, India
| | - Komal Tyagi
- Amity Institute of Molecular Medicine & Stem Cell Research, Amity University, Sector 125, Noida, Uttar Pradesh, 201303, India
| | - Abha Sachdeva
- Amity Institute of Molecular Medicine & Stem Cell Research, Amity University, Sector 125, Noida, Uttar Pradesh, 201303, India
| | - Abdul Wasai
- Amity Institute of Molecular Medicine & Stem Cell Research, Amity University, Sector 125, Noida, Uttar Pradesh, 201303, India
| | - Supratim Mandal
- Department of Microbiology, University of Kalyani, Kalyani, Nadia, West Bengal, 741235, India
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2
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Ng AWT, Contino G, Killcoyne S, Devonshire G, Hsu R, Abbas S, Su J, Redmond AM, Weaver JMJ, Eldridge MD, Tavaré S, Edwards PAW, Fitzgerald RC. Rearrangement processes and structural variations show evidence of selection in oesophageal adenocarcinomas. Commun Biol 2022; 5:335. [PMID: 35396535 PMCID: PMC8993906 DOI: 10.1038/s42003-022-03238-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 02/25/2022] [Indexed: 11/26/2022] Open
Abstract
Oesophageal adenocarcinoma (OAC) provides an ideal case study to characterize large-scale rearrangements. Using whole genome short-read sequencing of 383 cases, for which 214 had matched whole transcriptomes, we observed structural variations (SV) with a predominance of deletions, tandem duplications and inter-chromosome junctions that could be identified as LINE-1 mobile element (ME) insertions. Complex clusters of rearrangements resembling breakage-fusion-bridge cycles or extrachromosomal circular DNA accounted for 22% of complex SVs affecting known oncogenes. Counting SV events affecting known driver genes substantially increased the recurrence rates of these drivers. After excluding fragile sites, we identified 51 candidate new drivers in genomic regions disrupted by SVs, including ETV5, KAT6B and CLTC. RUNX1 was the most recurrently altered gene (24%), with many deletions inactivating the RUNT domain but preserved the reading frame, suggesting an altered protein product. These findings underscore the importance of identification of SV events in OAC with implications for targeted therapies.
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Affiliation(s)
- Alvin Wei Tian Ng
- Medical Research Council Cancer Unit, Hutchison/Medical Research Council Research Centre, University of Cambridge, Cambridge, UK
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Gianmarco Contino
- Institute of Cancer and Genomic Sciences, College of Medical & Dental Sciences, University of Birmingham, Birmingham, UK
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, B15 2GW, UK
| | - 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
| | - Ginny Devonshire
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Ray Hsu
- Department of Surgery, University of Cambridge, Cambridge, UK
| | - Sujath Abbas
- Medical Research Council Cancer Unit, Hutchison/Medical Research Council Research Centre, University of Cambridge, Cambridge, UK
| | - Jing Su
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Aisling M Redmond
- Medical Research Council Cancer Unit, Hutchison/Medical Research Council Research Centre, University of Cambridge, Cambridge, UK
| | - Jamie M J Weaver
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- Department of Medical Oncology, The Christie NHS Foundation Trust, Manchester, UK
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Matthew D Eldridge
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Simon Tavaré
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- Irving Institute for Cancer Dynamics, Columbia University, New York, USA
- Department of Statistics, Columbia University, New York, USA
- Department of Biological Sciences, Columbia University, New York, USA
| | - Paul A W Edwards
- Medical Research Council Cancer Unit, Hutchison/Medical Research Council Research Centre, University of Cambridge, Cambridge, UK
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Rebecca C Fitzgerald
- Medical Research Council Cancer Unit, Hutchison/Medical Research Council Research Centre, University of Cambridge, Cambridge, UK.
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3
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Dynamic switch of immunity and antitumor effects of metformin in rat spontaneous esophageal carcinogenesis. Cancer Immunol Immunother 2021; 71:777-789. [PMID: 34398301 PMCID: PMC8921146 DOI: 10.1007/s00262-021-03027-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Accepted: 07/29/2021] [Indexed: 11/17/2022]
Abstract
Chronic inflammation contributes to tumor development by creating a local microenvironment that facilitates neoplastic transformation and potentiates the progression of cancer. Esophageal cancer (EC) is an inflammation-associated malignancy with a poor prognosis. The nature of the switch between chronic inflammation of the esophagus and EC-related immunological changes remains unclear. Here, we examined the dynamic alterations of immune cells at different stages of chronic esophagitis, Barrett’s esophagus (BE) and EC using an esophageal spontaneous carcinogenesis rat model. We also investigated the anticancer effects of metformin. To stimulate EC carcinogenesis, chronic gastroduodenal reflux esophagitis via esophagojejunostomy was induced in 120 rats in metformin-treated and non-treated (control) groups. After 40 weeks, BE and EC developed in 96.7% and 63.3% of the control group, and in 66.7% and 23.3% of the metformin-treated group, respectively. Flow cytometric analysis demonstrated that the balance of M1/M2-polarized or phospho-Stat3-positive macrophages, regulatory T, cytotoxic T, natural killer (NK), NK T cells, and Th17 T cells was dynamically changed at each stage of the disease and were resolved by metformin treatment. These findings clarify the immunity in esophageal carcinogenesis and suggest that metformin could suppress this disease by improving the immunosuppressive tumor microenvironment and immune evasion.
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4
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Somatic DNA Copy-Number Alterations Detection for Esophageal Adenocarcinoma Using Digital Polymerase Chain Reaction. Methods Mol Biol 2018. [PMID: 29600372 DOI: 10.1007/978-1-4939-7734-5_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/30/2023]
Abstract
Somatic copy-number alterations are commonly found in cancer and play key roles in activating oncogenes and deactivating tumor suppressor genes. Digital polymerase chain reaction is an effective way to detect the changes in copy number. In esophageal adenocarcinoma, detection of somatic copy-number alterations could predict the prognosis of patients as well as the response to therapy. This chapter will review the methods involved in digital polymerase chain reaction for the research or potential clinical applications in esophageal adenocarcinoma.
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5
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Mito JK, Agoston AT, Dal Cin P, Srivastava A. Prevalence and significance of HMGA2 expression in oesophageal adenocarcinoma. Histopathology 2017; 71:909-917. [PMID: 28710822 DOI: 10.1111/his.13310] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Accepted: 07/12/2017] [Indexed: 12/20/2022]
Abstract
AIMS Oesophageal adenocarcinoma (EAC) tumorigenesis has been linked primarily to loss-of-function mutations in tumour suppressor genes. Knowledge of specific oncogenes that drive tumour progression, and their relationship to outcomes, is limited. High mobility group AT-hook 2 (HMGA2) has been reported to be amplified in a subset of EACs, but the clinicopathological and prognostic implications of HMGA2 expression in EAC are unknown. METHODS AND RESULTS We performed HMGA2 immunohistochemistry and fluorescence in-situ hybridization (FISH) in EAC to determine its clinicopathological and prognostic significance. Ninety-one primary EAC resections without neoadjuvant treatment were identified and immunohistochemistry for HMGA2 was performed. The presence or absence of nuclear staining was evaluated and correlated with predetermined clinicopathological parameters and patient outcomes. A selected subset of tumours was subjected to FISH to identify alterations at the HMGA2 locus. HMGA2 expression was present in 25 of 91 (27.4%) tumours. HMGA2-expressing cells were present in solid, poorly differentiated areas of the tumours at the invasive front, or as single infiltrating cells. FISH showed that three to four copies of HMGA2 are frequently present in EAC irrespective of HMGA2 protein expression and that high level HMGA2 amplification is a rare event. HMGA2 expression was associated with numerous adverse clinicopathological parameters, including higher T- and N-stage, the presence of lymphovascular invasion and with a worse recurrence-free and overall survival. CONCLUSION Our data suggest that HMGA2 is regulated in EAC primarily through non-chromosomal-level alterations that lead to increased HMGA2 expression. HMGA2-positive EAC correlates with adverse pathological features and worse patient outcomes.
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Affiliation(s)
- Jeffrey K Mito
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Agoston T Agoston
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Paola Dal Cin
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Amitabh Srivastava
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
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6
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Activin a signaling regulates cell invasion and proliferation in esophageal adenocarcinoma. Oncotarget 2016; 6:34228-44. [PMID: 26447543 PMCID: PMC4741448 DOI: 10.18632/oncotarget.5349] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 09/24/2015] [Indexed: 12/29/2022] Open
Abstract
TGFβ signaling has been implicated in the metaplasia from squamous epithelia to Barrett's esophagus and, ultimately, esophageal adenocarcinoma. The role of the family member Activin A in Barrett's tumorigenesis is less well established. As tumorigenesis is influenced by factors in the tumor microenvironment, such as fibroblasts and the extracellular matrix, we aimed to determine if epithelial cell-derived Activin affects initiation and progression differently than Activin signaling stimulation from a mimicked stromal source. Using Barrett's esophagus cells, CPB, and the esophageal adenocarcinoma cell lines OE33 and FLO-1, we showed that Activin reduces colony formation only in CPB cells. Epithelial cell overexpression of Activin increased cell migration and invasion in Boyden chamber assays in CPB and FLO-1 cells, which exhibited mesenchymal features such as the expression of the CD44 standard form, vimentin, and MT1-MMP. When grown in organotypic reconstructs, OE33 cells expressed E-cadherin and Keratin 8. As mesenchymal characteristics have been associated with the acquisition of stem cell-like features, we analyzed the expression and localization of SOX9, showing nuclear localization of SOX9 in esophageal CPB and FLO-1 cells.In conclusion, we show a role for autocrine Activin signaling in the regulation of colony formation, cell migration and invasion in Barrett's tumorigenesis.
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Pusung M, Zeki S, Fitzgerald R. Genomics of Esophageal Cancer and Biomarkers for Early Detection. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 908:237-63. [PMID: 27573775 DOI: 10.1007/978-3-319-41388-4_12] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In-depth molecular characterization of esophageal oncogenesis has improved over the recent years. Advancement in molecular biology and bioinformatics has led to better understanding of its genomic landscape. More specifically, analysis of its pathogenesis at the genetic level has uncovered the involvement of a number of tumor suppressor genes, cell cycle regulators, and receptor tyrosine kinases. Due to its poor prognosis, the development of clinically applicable biomarkers for diagnosis, progression, and treatment has been the focus of many research studies concentrating on upper gastrointestinal malignancies. As in other cancers, early detection and subsequent intervention of the preneoplastic condition significantly improves patient outcomes. Currently, clinically approved surveillance practices heavily depend on expensive, invasive, and sampling-error-prone endoscopic procedures. There is, therefore, a great demand to establish clearly reliable biomarkers that could identify those patients at higher risk of neoplastic progression and hence would greatly benefit from further monitoring and/or intervention. This chapter will present the most recent advances in the analysis of the esophageal cancer genome serving as basis for biomarker development.
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Affiliation(s)
- Mark Pusung
- MRC Cancer Unit, University of Cambridge, Cambridge, UK
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8
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Dodbiba L, Teichman J, Fleet A, Thai H, Starmans MHW, Navab R, Chen Z, Girgis H, Eng L, Espin-Garcia O, Shen X, Bandarchi B, Schwock J, Tsao MS, El-Zimaity H, Der SD, Xu W, Bristow RG, Darling GE, Boutros PC, Ailles LE, Liu G. Appropriateness of using patient-derived xenograft models for pharmacologic evaluation of novel therapies for esophageal/gastro-esophageal junction cancers. PLoS One 2015; 10:e0121872. [PMID: 25826681 PMCID: PMC4380353 DOI: 10.1371/journal.pone.0121872] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2014] [Accepted: 02/17/2015] [Indexed: 01/01/2023] Open
Abstract
The high morbidity and mortality of patients with esophageal (E) and gastro-esophageal junction (GEJ) cancers, warrants new pre-clinical models for drug testing. The utility of primary tumor xenografts (PTXGs) as pre-clinical models was assessed. Clinicopathological, immunohistochemical markers (p53, p16, Ki-67, Her-2/neu and EGFR), and global mRNA abundance profiles were evaluated to determine selection biases of samples implanted or engrafted, compared with the underlying population. Nine primary E/GEJ adenocarcinoma xenograft lines were further characterized for the spectrum and stability of gene/protein expression over passages. Seven primary esophageal adenocarcinoma xenograft lines were treated with individual or combination chemotherapy. Tumors that were implanted (n=55) in NOD/SCID mice had features suggestive of more aggressive biology than tumors that were never implanted (n=32). Of those implanted, 21/55 engrafted; engraftment was associated with poorly differentiated tumors (p=0.04) and older patients (p=0.01). Expression of immunohistochemical markers were similar between patient sample and corresponding xenograft. mRNA differences observed between patient tumors and first passage xenografts were largely due to loss of human stroma in xenografts. mRNA patterns of early vs late passage xenografts and of small vs large tumors of the same passage were similar. Complete resistance was present in 2/7 xenografts while the remaining tumors showed varying degrees of sensitivity, that remained constant across passages. Because of their ability to recapitulate primary tumor characteristics during engraftment and across serial passaging, PTXGs can be useful clinical systems for assessment of drug sensitivity of human E/GEJ cancers.
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Affiliation(s)
- Lorin Dodbiba
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Wayne State University, School of Medicine, Detroit, Michigan, United States of America
| | - Jennifer Teichman
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | | | - Henry Thai
- University Health Network, Princess Margaret Hospital, Toronto, ON, Canada
| | - Maud H. W. Starmans
- Informatics and Biocomputing Program, Ontario Institute for Cancer Research, Toronto, Canada
- Department of Radiation Oncology (Maastro), GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, Netherlands
| | - Roya Navab
- Ontario Cancer Institute, Toronto, ON, Canada
| | - Zhuo Chen
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Hala Girgis
- Department of Anatomical Pathology, Toronto General Hospital, Toronto, ON, Canada
| | - Lawson Eng
- Ontario Cancer Institute, Toronto, ON, Canada
| | - Osvaldo Espin-Garcia
- Informatics and Biocomputing Program, Ontario Institute for Cancer Research, Toronto, Canada
| | - Xiaowei Shen
- Informatics and Biocomputing Program, Ontario Institute for Cancer Research, Toronto, Canada
| | | | - Joerg Schwock
- Department of Anatomical Pathology, Toronto General Hospital, Toronto, ON, Canada
| | - Ming-Sound Tsao
- Ontario Cancer Institute, Toronto, ON, Canada
- University Health Network, Princess Margaret Hospital, Toronto, ON, Canada
- Department of Anatomical Pathology, Toronto General Hospital, Toronto, ON, Canada
| | - Hala El-Zimaity
- University Health Network, Princess Margaret Hospital, Toronto, ON, Canada
- Department of Anatomical Pathology, Toronto General Hospital, Toronto, ON, Canada
| | | | - Wei Xu
- Informatics and Biocomputing Program, Ontario Institute for Cancer Research, Toronto, Canada
- Department of Biostatistics, Princess Margaret Hospital, Toronto, Canada
| | - Robert G. Bristow
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Ontario Cancer Institute, Toronto, ON, Canada
| | - Gail E. Darling
- Division of Thoracic Surgery, Toronto General Hospital, Toronto, ON, Canada
| | - Paul C. Boutros
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Informatics and Biocomputing Program, Ontario Institute for Cancer Research, Toronto, Canada
- Department of Pharmacology & Toxicology, University of Toronto, Toronto, ON, Canada
| | - Laurie E. Ailles
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Ontario Cancer Institute, Toronto, ON, Canada
| | - Geoffrey Liu
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Ontario Cancer Institute, Toronto, ON, Canada
- Division of Epidemiology, Dalla Lana School of Public Health, Toronto, Canada
- * E-mail:
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9
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Read M, Liu D, Duong CP, Cullinane C, Murray WK, Fennell CM, Shortt J, Westerman D, Burton P, Clemons NJ, Phillips WA. Intramuscular Transplantation Improves Engraftment Rates for Esophageal Patient-Derived Tumor Xenografts. Ann Surg Oncol 2015; 23:305-11. [PMID: 25691278 DOI: 10.1245/s10434-015-4425-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Indexed: 12/20/2022]
Abstract
BACKGROUND Recently, there has been an increase in the availability of targeted molecular therapies for cancer treatment. The application of these approaches to esophageal cancer, however, has been hampered by the relative lack of appropriate models for preclinical testing. Patient-derived tumor xenograft (PDTX) models are gaining popularity for studying many cancers. Unfortunately, it has proven difficult to generate xenografts from esophageal cancer using these models. The purpose of this study was to improve the engraftment efficiency of esophageal PDTXs. METHODS Fresh pieces of esophageal tumors obtained from endoscopic biopsies or resected specimens were collected from 23 patients. The tumors were then coated in Matrigel and transplanted in immunocompromised mice subcutaneously (n = 6) and/or using a novel implantation technique whereby the tumor is placed in a dorsal intramuscular pocket (n = 18). They are then monitored for engraftment. RESULTS With the novel intramuscular technique, successful engraftment was achieved for all 18 patient tumors. Among these PDTXs, 13 recapitulated the original patient tumors with respect to degree of differentiation, molecular and genetic profiles, and chemotherapeutic response. Lymphomatous transformation was observed in the other five PDTXs. Successful engraftment was achieved for only one of six patient tumors using the classic subcutaneous approach. DISCUSSION We achieved a much higher engraftment rate of PDTXs using our novel intramuscular transplant technique than has been reported in other published studies. It is hoped that this advancement will help expedite the development and testing of new therapies for esophageal cancer.
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Affiliation(s)
- Matthew Read
- Surgical Oncology Research Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - David Liu
- Surgical Oncology Research Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - Cuong P Duong
- Surgical Oncology Research Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.,Division of Cancer Surgery, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Carleen Cullinane
- Surgical Oncology Research Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - William K Murray
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Christina M Fennell
- Surgical Oncology Research Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - Jake Shortt
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia.,School of Clinical Sciences at Monash Health, Melbourne, Australia.,Faculty of Medicine, Nursing & Health Sciences, Monash University, Melbourne, Australia
| | - David Westerman
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Australia.,University of Melbourne, Melbourne, Australia
| | - Paul Burton
- Monash University Centre for Obesity Research and Education, Alfred Hospital, Melbourne, Australia.,Cabrini Hospital, Melbourne, VIC, Australia
| | - Nicholas J Clemons
- Surgical Oncology Research Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia.,Department of Surgery (St. Vincent's Hospital), University of Melbourne, Melbourne, VIC, Australia
| | - Wayne A Phillips
- Surgical Oncology Research Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia. .,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia. .,Division of Cancer Surgery, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia. .,Department of Surgery (St. Vincent's Hospital), University of Melbourne, Melbourne, VIC, Australia.
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10
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Dulak AM, Stojanov P, Peng S, Lawrence MS, Fox C, Stewart C, Bandla S, Imamura Y, Schumacher SE, Shefler E, McKenna A, Cibulskis K, Sivachenko A, Carter SL, Saksena G, Voet D, Ramos AH, Auclair D, Thompson K, Sougnez C, Onofrio RC, Guiducci C, Beroukhim R, Zhou D, Lin L, Lin J, Reddy R, Chang A, Luketich JD, Pennathur A, Ogino S, Golub TR, Gabriel SB, Lander ES, Beer DG, Godfrey TE, Getz G, Bass AJ. Exome and whole-genome sequencing of esophageal adenocarcinoma identifies recurrent driver events and mutational complexity. Nat Genet 2013; 45:478-86. [PMID: 23525077 PMCID: PMC3678719 DOI: 10.1038/ng.2591] [Citation(s) in RCA: 578] [Impact Index Per Article: 52.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2012] [Accepted: 03/01/2013] [Indexed: 12/11/2022]
Abstract
The incidence of esophageal adenocarcinoma (EAC) has risen 600% over the last 30 years. With a 5-year survival rate of ~15%, the identification of new therapeutic targets for EAC is greatly important. We analyze the mutation spectra from whole-exome sequencing of 149 EAC tumor-normal pairs, 15 of which have also been subjected to whole-genome sequencing. We identify a mutational signature defined by a high prevalence of A>C transversions at AA dinucleotides. Statistical analysis of exome data identified 26 significantly mutated genes. Of these genes, five (TP53, CDKN2A, SMAD4, ARID1A and PIK3CA) have previously been implicated in EAC. The new significantly mutated genes include chromatin-modifying factors and candidate contributors SPG20, TLR4, ELMO1 and DOCK2. Functional analyses of EAC-derived mutations in ELMO1 identifies increased cellular invasion. Therefore, we suggest the potential activation of the RAC1 pathway as a contributor to EAC tumorigenesis.
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Affiliation(s)
- Austin M. Dulak
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Cancer Program, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Petar Stojanov
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Cancer Program, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Shouyong Peng
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Cancer Program, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Michael S. Lawrence
- Cancer Program, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Cameron Fox
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Chip Stewart
- Cancer Program, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Santhoshi Bandla
- Department of Surgery, University of Rochester, Rochester, NY 14642, USA
| | - Yu Imamura
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Steven E. Schumacher
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Cancer Program, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Erica Shefler
- Cancer Program, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Aaron McKenna
- Cancer Program, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Kristian Cibulskis
- Cancer Program, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Andrey Sivachenko
- Cancer Program, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Scott L. Carter
- Cancer Program, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Gordon Saksena
- Cancer Program, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Douglas Voet
- Cancer Program, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Alex H. Ramos
- Cancer Program, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Daniel Auclair
- Cancer Program, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Kristin Thompson
- Cancer Program, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Carrie Sougnez
- Cancer Program, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Robert C. Onofrio
- Cancer Program, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Candace Guiducci
- Cancer Program, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Rameen Beroukhim
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Cancer Program, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Brigham and Women’s Hospital, Boston, MA, 02115, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - David Zhou
- Department of Surgery, University of Rochester, Rochester, NY 14642, USA
| | - Lin Lin
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jules Lin
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Rishindra Reddy
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Andrew Chang
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - James D. Luketich
- Department of Cardiothoracic Surgery, University of Pittsburgh Medical Center, Pittsburgh, PA 15206, USA
| | - Arjun Pennathur
- Department of Cardiothoracic Surgery, University of Pittsburgh Medical Center, Pittsburgh, PA 15206, USA
| | - Shuji Ogino
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Brigham and Women’s Hospital, Boston, MA, 02115, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
- Department of Epidemiology, Harvard School of Public Health, Boston, MA 02115, USA
| | - Todd R. Golub
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Cancer Program, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA
| | - Stacey B. Gabriel
- Cancer Program, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Eric S. Lander
- Cancer Program, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - David G. Beer
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Tony E. Godfrey
- Department of Surgery, University of Rochester, Rochester, NY 14642, USA
| | - Gad Getz
- Cancer Program, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Adam J. Bass
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Cancer Program, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Brigham and Women’s Hospital, Boston, MA, 02115, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
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11
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Chimge NO, Frenkel B. The RUNX family in breast cancer: relationships with estrogen signaling. Oncogene 2013; 32:2121-30. [PMID: 23045283 PMCID: PMC5770236 DOI: 10.1038/onc.2012.328] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2012] [Revised: 06/20/2012] [Accepted: 06/20/2012] [Indexed: 12/22/2022]
Abstract
The three RUNX family members are lineage specific master regulators, which also have important, context-dependent roles in carcinogenesis as either tumor suppressors or oncogenes. Here we review evidence for such roles in breast cancer (BCa). RUNX1, the predominant RUNX family member in breast epithelial cells, has a tumor suppressor role reflected by many somatic mutations found in primary tumor biopsies. The classical tumor suppressor gene RUNX3 does not consist of such a mutation hot spot, but it too seems to inhibit BCa; it is often inactivated in human BCa tumors and its haploinsufficiency in mice leads to spontaneous BCa development. The tumor suppressor activities of RUNX1 and RUNX3 are mediated in part by antagonism of estrogen signaling, a feature recently attributed to RUNX2 as well. Paradoxically, however RUNX2, a master osteoblast regulator, has been implicated in various aspects of metastasis in general and bone metastasis in particular. Reciprocating the anti-estrogenic tumor suppressor activity of RUNX proteins, inhibition of RUNX2 by estrogens may help explain their context-dependent anti-metastatic roles. Such roles are reserved to non-osseous metastasis, because ERα is associated with increased, not decreased skeletal dissemination of BCa cells. Finally, based on diverse expression patterns in BCa subtypes, the successful use of future RUNX-based therapies will most likely require careful patient selection.
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Affiliation(s)
- N-O Chimge
- Department of Biochemistry and Molecular Biology, Institute for Genetic Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA
| | - B Frenkel
- Departments of Orthopaedic Surgery and Biochemistry and Molecular Biology, Institute for Genetic Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA
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12
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Fijneman RJA, Anderson RA, Richards E, Liu J, Tijssen M, Meijer GA, Anderson J, Rod A, O'Sullivan MG, Scott PM, Cormier RT. Runx1 is a tumor suppressor gene in the mouse gastrointestinal tract. Cancer Sci 2012; 103:593-9. [PMID: 22171576 DOI: 10.1111/j.1349-7006.2011.02189.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The Runx1 transcription factor plays an important role in tissue homeostasis through its effects on stem/progenitor cell populations and differentiation. The effect of Runx1 on epithelial differentiation of the secretory cell lineage of the colon was recently demonstrated. This study aimed to examine the role of Runx1 in tumor development in epithelial cells of the gastrointestinal tract. Conditional knockout mice that lacked Runx1 expression in epithelial cells of the GI tract were generated. These mice were crossed onto the Apc(Min) background, killed and their intestinal tumor phenotypes were compared with Apc(Min) Runx1 wild-type control mice. Apc-wild-type Runx1-mutant mice were also examined for tumor development. Colons from Runx1 knockout and wild-type mice were used for genome-wide mRNA expression analyses followed by gene-specific quantitative RT-PCR of whole colon and colon epithelium to identify Runx1 target genes. Runx1 deficiency in intestinal epithelial cells significantly enhanced tumorigenesis in Apc(Min) mice. Notably, epithelial Runx1 deficiency in Apc-wild-type mice was sufficient to cause tumor development. Absence of Runx1 was associated with global changes in the expression of genes involved in inflammation and intestinal metabolism, and with gene sets indicative of a metastatic phenotype and poor prognosis. Gene-specific analysis of Runx1-deficient colon epithelium revealed increased expression of genes linked to an expansion of the stem/progenitor cell population. These results identify Runx1 as a novel tumor suppressor gene for gastrointestinal tumors and support a role for Runx1 in maintaining the balance between the intestinal stem/progenitor cell population and epithelial differentiation of the GI tract.
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Affiliation(s)
- Remond J A Fijneman
- Department of Pathology, VU University Medical Center, Amsterdam, Netherlands
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