1
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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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2
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Teh S, Bowland K, Halper-Stromberg E, Kotwal A, Bennett A, Skaist A, Tang J, Cai F, Macoretta A, Liang H, Kamiyama H, Wheelan S, Lin MT, Hruban R, Hung CF, Goldstein M, Scharpf R, Roberts N, Eshleman J. CRISPR-Cas9 for selective targeting of somatic mutations in pancreatic cancers. NAR Cancer 2024; 6:zcae028. [PMID: 38915758 PMCID: PMC11195629 DOI: 10.1093/narcan/zcae028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 05/23/2024] [Accepted: 06/03/2024] [Indexed: 06/26/2024] Open
Abstract
Somatic mutations are desirable targets for selective elimination of cancer, yet most are found within noncoding regions. We have adapted the CRISPR-Cas9 gene editing tool as a novel, cancer-specific killing strategy by targeting the subset of somatic mutations that create protospacer adjacent motifs (PAMs), which have evolutionally allowed bacterial cells to distinguish between self and non-self DNA for Cas9-induced double strand breaks. Whole genome sequencing (WGS) of paired tumor minus normal (T-N) samples from three pancreatic cancer patients (Panc480, Panc504, and Panc1002) showed an average of 417 somatic PAMs per tumor produced from single base substitutions. Further analyses of 591 paired T-N samples from The International Cancer Genome Consortium found medians of ∼455 somatic PAMs per tumor in pancreatic, ∼2800 in lung, and ∼3200 in esophageal cancer cohorts. Finally, we demonstrated 69-99% selective cell death of three targeted pancreatic cancer cell lines using 4-9 sgRNAs designed using the somatic PAM discovery approach. We also showed no off-target activity from these tumor-specific sgRNAs in either the patient's normal cells or an irrelevant cancer using WGS. This study demonstrates the potential of CRISPR-Cas9 as a novel and selective anti-cancer strategy, and supports the genetic targeting of adult cancers.
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Affiliation(s)
- Selina Shiqing K Teh
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Kirsten Bowland
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Eitan Halper-Stromberg
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Akhil Kotwal
- Department of Radiation Oncology and Molecular Radiation Sciences, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Alexis Bennett
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Alyza Skaist
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jacqueline Tang
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Fidel Cai
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Antonella Macoretta
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Hong Liang
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | - Sarah Wheelan
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Scientific Review Branch, National Human Genome Research Institute, Bethesda, MD, USA
| | - Ming-Tseh Lin
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ralph H Hruban
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Chien-Fu Hung
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Michael Goldstein
- Department of Radiation Oncology and Molecular Radiation Sciences, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Robert B Scharpf
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Nicholas J Roberts
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - James R Eshleman
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
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3
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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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Hoppe S, Jonas C, Wenzel MC, Velazquez Camacho O, Arolt C, Zhao Y, Büttner R, Quaas A, Plum PS, Hillmer AM. Genomic and Transcriptomic Characteristics of Esophageal Adenocarcinoma. Cancers (Basel) 2021; 13:cancers13174300. [PMID: 34503107 PMCID: PMC8428370 DOI: 10.3390/cancers13174300] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 08/20/2021] [Accepted: 08/22/2021] [Indexed: 12/28/2022] Open
Abstract
Simple Summary Cancer of the esophagus is a deadly disease. There are two main subtypes, adenocarcinoma and squamous cell carcinoma, with adenocarcinoma of the esophagus (EAC) being more common in Western countries. Barrett’s esophagus (BE) describes a change in the esophageal surface near the stomach in response to reflux of gastric acid into the esophagus. BE increases the risk of developing EAC, and the incidence of EAC has risen dramatically over recent decades. One likely reason for the poor prognosis of EAC is based on the fact that each tumor has many genes affected by mutations, and most of these genes differ across patients, hampering the efficacy of therapies that target specific cancer driver proteins. In this review, we provide an overview of the gene mutations and gene activity changes in EAC and how these features can be used to divide patients into groups that might have different clinical characteristics. Abstract Esophageal adenocarcinoma (EAC) is a deadly disease with limited options for targeted therapy. With the help of next-generation sequencing studies over the last decade, we gained an understanding of the genomic architecture of EAC. The tumor suppressor gene TP53 is mutated in 70 to 80% of tumors followed by genomic alterations in CDKN2A, KRAS, ERBB2, ARID1A, SMAD4 and a long tail of less frequently mutated genes. EAC is characterized by a high burden of point mutations and genomic rearrangements, resulting in amplifications and deletions of genomic regions. The genomic complexity is likely hampering the efficacy of targeted therapies. Barrett’s esophagus (BE), a metaplastic response of the esophagus to gastro-esophageal reflux disease, is the main risk factor for the development of EAC. Almost all EACs are derived from BE. The sequence from BE to EAC provides an opportunity to study the genomic evolution towards EAC. While the overlap of point mutations between BE and EAC within the same patient is, at times, surprisingly low, there is a correlation between the complexity of the genomic copy number profile and the development of EAC. Transcriptomic analyses separated EAC into a basal and a classical subtype, with the basal subtype showing a higher level of resistance to chemotherapy. In this review, we provide an overview of the current knowledge of the genomic and transcriptomic characteristics of EAC and their relevance for the development of the disease and patient care.
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Affiliation(s)
- Sascha Hoppe
- Institute of Pathology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany; (S.H.); (C.J.); (M.C.W.); (O.V.C.); (C.A.); (R.B.); (A.Q.); (P.S.P.)
| | - Christoph Jonas
- Institute of Pathology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany; (S.H.); (C.J.); (M.C.W.); (O.V.C.); (C.A.); (R.B.); (A.Q.); (P.S.P.)
| | - Marten Christian Wenzel
- Institute of Pathology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany; (S.H.); (C.J.); (M.C.W.); (O.V.C.); (C.A.); (R.B.); (A.Q.); (P.S.P.)
| | - Oscar Velazquez Camacho
- Institute of Pathology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany; (S.H.); (C.J.); (M.C.W.); (O.V.C.); (C.A.); (R.B.); (A.Q.); (P.S.P.)
| | - Christoph Arolt
- Institute of Pathology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany; (S.H.); (C.J.); (M.C.W.); (O.V.C.); (C.A.); (R.B.); (A.Q.); (P.S.P.)
| | - Yue Zhao
- Department of General, Visceral, Cancer and Transplantation Surgery, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany;
| | - Reinhard Büttner
- Institute of Pathology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany; (S.H.); (C.J.); (M.C.W.); (O.V.C.); (C.A.); (R.B.); (A.Q.); (P.S.P.)
| | - Alexander Quaas
- Institute of Pathology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany; (S.H.); (C.J.); (M.C.W.); (O.V.C.); (C.A.); (R.B.); (A.Q.); (P.S.P.)
| | - Patrick Sven Plum
- Institute of Pathology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany; (S.H.); (C.J.); (M.C.W.); (O.V.C.); (C.A.); (R.B.); (A.Q.); (P.S.P.)
- Department of General, Visceral, Cancer and Transplantation Surgery, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany;
| | - Axel Maximilian Hillmer
- Institute of Pathology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany; (S.H.); (C.J.); (M.C.W.); (O.V.C.); (C.A.); (R.B.); (A.Q.); (P.S.P.)
- Center for Molecular Medicine Cologne, University of Cologne, 50931 Cologne, Germany
- Correspondence:
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5
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Izadi F, Sharpe BP, Breininger SP, Secrier M, Gibson J, Walker RC, Rahman S, Devonshire G, Lloyd MA, Walters ZS, Fitzgerald RC, Rose-Zerilli MJJ, Underwood TJ. Genomic Analysis of Response to Neoadjuvant Chemotherapy in Esophageal Adenocarcinoma. Cancers (Basel) 2021; 13:3394. [PMID: 34298611 PMCID: PMC8308111 DOI: 10.3390/cancers13143394] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 06/28/2021] [Accepted: 07/01/2021] [Indexed: 01/04/2023] Open
Abstract
Neoadjuvant therapy followed by surgery is the standard of care for locally advanced esophageal adenocarcinoma (EAC). Unfortunately, response to neoadjuvant chemotherapy (NAC) is poor (20-37%), as is the overall survival benefit at five years (9%). The EAC genome is complex and heterogeneous between patients, and it is not yet understood whether specific mutational patterns may result in chemotherapy sensitivity or resistance. To identify associations between genomic events and response to NAC in EAC, a comparative genomic analysis was performed in 65 patients with extensive clinical and pathological annotation using whole-genome sequencing (WGS). We defined response using Mandard Tumor Regression Grade (TRG), with responders classified as TRG1-2 (n = 27) and non-responders classified as TRG4-5 (n =38). We report a higher non-synonymous mutation burden in responders (median 2.08/Mb vs. 1.70/Mb, p = 0.036) and elevated copy number variation in non-responders (282 vs. 136/patient, p < 0.001). We identified copy number variants unique to each group in our cohort, with cell cycle (CDKN2A, CCND1), c-Myc (MYC), RTK/PIK3 (KRAS, EGFR) and gastrointestinal differentiation (GATA6) pathway genes being specifically altered in non-responders. Of note, NAV3 mutations were exclusively present in the non-responder group with a frequency of 22%. Thus, lower mutation burden, higher chromosomal instability and specific copy number alterations are associated with resistance to NAC.
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Affiliation(s)
- Fereshteh Izadi
- School of Cancer Sciences, Cancer Research UK Centre, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton SO16 6YD, UK; (F.I.); (B.P.S.); (S.P.B.); (J.G.); (R.C.W.); (S.R.); (M.A.L.); (Z.S.W.); (M.J.J.R.-Z.)
- Centre for NanoHealth, Swansea University Medical School, Singleton Campus, Swansea SA2 8PP, UK
| | - Benjamin P. Sharpe
- School of Cancer Sciences, Cancer Research UK Centre, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton SO16 6YD, UK; (F.I.); (B.P.S.); (S.P.B.); (J.G.); (R.C.W.); (S.R.); (M.A.L.); (Z.S.W.); (M.J.J.R.-Z.)
- Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Stella P. Breininger
- School of Cancer Sciences, Cancer Research UK Centre, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton SO16 6YD, UK; (F.I.); (B.P.S.); (S.P.B.); (J.G.); (R.C.W.); (S.R.); (M.A.L.); (Z.S.W.); (M.J.J.R.-Z.)
| | - Maria Secrier
- UCL Genetics Institute, Division of Biosciences, University College London, Gower Street, London WC1E 6BT, UK;
| | - Jane Gibson
- School of Cancer Sciences, Cancer Research UK Centre, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton SO16 6YD, UK; (F.I.); (B.P.S.); (S.P.B.); (J.G.); (R.C.W.); (S.R.); (M.A.L.); (Z.S.W.); (M.J.J.R.-Z.)
- Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Robert C. Walker
- School of Cancer Sciences, Cancer Research UK Centre, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton SO16 6YD, UK; (F.I.); (B.P.S.); (S.P.B.); (J.G.); (R.C.W.); (S.R.); (M.A.L.); (Z.S.W.); (M.J.J.R.-Z.)
| | - Saqib Rahman
- School of Cancer Sciences, Cancer Research UK Centre, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton SO16 6YD, UK; (F.I.); (B.P.S.); (S.P.B.); (J.G.); (R.C.W.); (S.R.); (M.A.L.); (Z.S.W.); (M.J.J.R.-Z.)
| | - Ginny Devonshire
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK;
| | - Megan A. Lloyd
- School of Cancer Sciences, Cancer Research UK Centre, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton SO16 6YD, UK; (F.I.); (B.P.S.); (S.P.B.); (J.G.); (R.C.W.); (S.R.); (M.A.L.); (Z.S.W.); (M.J.J.R.-Z.)
| | - Zoë S. Walters
- School of Cancer Sciences, Cancer Research UK Centre, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton SO16 6YD, UK; (F.I.); (B.P.S.); (S.P.B.); (J.G.); (R.C.W.); (S.R.); (M.A.L.); (Z.S.W.); (M.J.J.R.-Z.)
- Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Rebecca C. Fitzgerald
- MRC Cancer Unit, Hutchison/MRC Research Centre, University of Cambridge, Cambridge CB2 OXZ, UK;
| | - Matthew J. J. Rose-Zerilli
- School of Cancer Sciences, Cancer Research UK Centre, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton SO16 6YD, UK; (F.I.); (B.P.S.); (S.P.B.); (J.G.); (R.C.W.); (S.R.); (M.A.L.); (Z.S.W.); (M.J.J.R.-Z.)
- Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Tim J. Underwood
- School of Cancer Sciences, Cancer Research UK Centre, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton SO16 6YD, UK; (F.I.); (B.P.S.); (S.P.B.); (J.G.); (R.C.W.); (S.R.); (M.A.L.); (Z.S.W.); (M.J.J.R.-Z.)
- Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, UK
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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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7
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Kumar S, Buon L, Talluri S, Roncador M, Liao C, Zhao J, Shi J, Chakraborty C, Gonzalez G, Tai YT, Prabhala R, Samur MK, Munshi NC, Shammas MA. Integrated genomics and comprehensive validation reveal drivers of genomic evolution in esophageal adenocarcinoma. Commun Biol 2021; 4:617. [PMID: 34031527 PMCID: PMC8144613 DOI: 10.1038/s42003-021-02125-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 04/16/2021] [Indexed: 12/13/2022] Open
Abstract
Esophageal adenocarcinoma (EAC) is associated with a marked genomic instability, which underlies disease progression and development of resistance to treatment. In this study, we used an integrated genomics approach to identify a genomic instability signature. Here we show that elevated expression of this signature correlates with poor survival in EAC as well as three other cancers. Knockout and overexpression screens establish the relevance of these genes to genomic instability. Indepth evaluation of three genes (TTK, TPX2 and RAD54B) confirms their role in genomic instability and tumor growth. Mutational signatures identified by whole genome sequencing and functional studies demonstrate that DNA damage and homologous recombination are common mechanisms of genomic instability induced by these genes. Our data suggest that the inhibitors of TTK and possibly other genes identified in this study have potential to inhibit/reduce growth and spontaneous as well as chemotherapy-induced genomic instability in EAC and possibly other cancers. Subodh Kumar et al. identify a gene signature correlated with genomic instability and poor survival in esophageal adenocarcinoma (EAC), using a combination of integrative genomic analysis of patient data and laboratory validation in cell line models and mice. They find that inhibitors of some of the identified proteins, including TTK, could be used to reduce genomic evolution as well as inhibit growth of EAC cells.
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Affiliation(s)
- Subodh Kumar
- Dana Farber Cancer Institute, Boston, MA, USA.,Veterans Administration Healthcare System, Boston, MA, USA
| | - Leutz Buon
- Dana Farber Cancer Institute, Boston, MA, USA
| | - Srikanth Talluri
- Dana Farber Cancer Institute, Boston, MA, USA.,Veterans Administration Healthcare System, Boston, MA, USA
| | | | - Chengcheng Liao
- Dana Farber Cancer Institute, Boston, MA, USA.,Veterans Administration Healthcare System, Boston, MA, USA
| | - Jiangning Zhao
- Dana Farber Cancer Institute, Boston, MA, USA.,Veterans Administration Healthcare System, Boston, MA, USA
| | - Jialan Shi
- Dana Farber Cancer Institute, Boston, MA, USA.,Veterans Administration Healthcare System, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | | | - Gabriel Gonzalez
- Veterans Administration Healthcare System, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Yu-Tzu Tai
- Dana Farber Cancer Institute, Boston, MA, USA
| | - Rao Prabhala
- Dana Farber Cancer Institute, Boston, MA, USA.,Veterans Administration Healthcare System, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | | | - Nikhil C Munshi
- Dana Farber Cancer Institute, Boston, MA, USA.,Veterans Administration Healthcare System, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Masood A Shammas
- Dana Farber Cancer Institute, Boston, MA, USA. .,Veterans Administration Healthcare System, Boston, MA, USA.
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8
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Liao C, Zhao J, Kumar S, Chakraborty C, Talluri S, Munshi NC, Shammas MA. RAD51 Inhibitor Reverses Etoposide-Induced Genomic Toxicity and Instability in Esophageal Adenocarcinoma Cells. ARCHIVES OF CLINICAL TOXICOLOGY 2020; 2:3-9. [PMID: 32968740 PMCID: PMC7508453 DOI: 10.46439/toxicology.2.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Aim: In normal cells, homologous recombination (HR) is strictly regulated and precise and plays an important role in preserving genomic integrity by accurately repairing DNA damage. RAD51 is the recombinase which mediates homologous base pairing and strand exchange during DNA repair by HR. We have previously reported that HR is spontaneously elevated (or dysregulated) in esophageal adenocarcinoma (EAC) and contributes to ongoing genomic changes and instability. The purpose of this study was to evaluate the impact of RAD51 inhibitor on genomic toxicity caused by etoposide, a chemotherapeutic agent. Methods: EAC cell lines (FLO-1 and OE19) were cultured in the presence of RAD51 inhibitor and/or etoposide, and impact on cell viability, apoptosis and genomic integrity/stability investigated. Genomic integrity/stability was monitored by evaluating cells for γ-H2AX (a marker for DNA breaks), phosphorylated RPA32 (a marker of DNA end resection which is a distinct step in the initiation of HR) and micronuclei (a marker of genomic instability). Results: Treatment with etoposide, a chemotherapeutic agent, was associated with marked genomic toxicity (as evident from increase in DNA breaks) and genomic instability in both EAC cell lines. Consistently, the treatment was also associated with apoptotic cell death. A small molecule inhibitor of RAD51 increased cytotoxicity while reducing genomic toxicity and instability caused by etoposide, in both EAC cell lines. Conclusion: RAD51 inhibitors have potential to increase cytotoxicity while reducing harmful genomic impact of chemotherapy.
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Affiliation(s)
- Chengcheng Liao
- Dana Farber Cancer Institute, USA.,Veterans Administration Boston Healthcare System, USA
| | | | - Subodh Kumar
- Dana Farber Cancer Institute, USA.,Veterans Administration Boston Healthcare System, USA
| | | | - Srikanth Talluri
- Dana Farber Cancer Institute, USA.,Veterans Administration Boston Healthcare System, USA
| | - Nikhil C Munshi
- Dana Farber Cancer Institute, USA.,Veterans Administration Boston Healthcare System, USA.,Harvard Medical School, USA
| | - Masood A Shammas
- Dana Farber Cancer Institute, USA.,Veterans Administration Boston Healthcare System, USA
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9
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Roper N, Gao S, Maity TK, Banday AR, Zhang X, Venugopalan A, Cultraro CM, Patidar R, Sindiri S, Brown AL, Goncearenco A, Panchenko AR, Biswas R, Thomas A, Rajan A, Carter CA, Kleiner DE, Hewitt SM, Khan J, Prokunina-Olsson L, Guha U. APOBEC Mutagenesis and Copy-Number Alterations Are Drivers of Proteogenomic Tumor Evolution and Heterogeneity in Metastatic Thoracic Tumors. Cell Rep 2019; 26:2651-2666.e6. [PMID: 30840888 PMCID: PMC6461561 DOI: 10.1016/j.celrep.2019.02.028] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 01/02/2019] [Accepted: 02/07/2019] [Indexed: 12/13/2022] Open
Abstract
Intratumor mutational heterogeneity has been documented in primary non-small-cell lung cancer. Here, we elucidate mechanisms of tumor evolution and heterogeneity in metastatic thoracic tumors (lung adenocarcinoma and thymic carcinoma) using whole-exome and transcriptome sequencing, SNP array for copy-number alterations (CNAs), and mass-spectrometry-based quantitative proteomics of metastases obtained by rapid autopsy. APOBEC mutagenesis, promoted by increased expression of APOBEC3 region transcripts and associated with a high-risk APOBEC3 germline variant, correlated with mutational tumor heterogeneity. TP53 mutation status was associated with APOBEC hypermutator status. Interferon pathways were enriched in tumors with high APOBEC mutagenesis and IFN-γ-induced expression of APOBEC3B in lung adenocarcinoma cells, suggesting that the immune microenvironment may promote mutational heterogeneity. CNAs occurring late in tumor evolution correlated with downstream transcriptomic and proteomic heterogeneity, although global proteomic heterogeneity was significantly greater than transcriptomic and CNA heterogeneity. These results illustrate key mechanisms underlying multi-dimensional heterogeneity in metastatic thoracic tumors.
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Affiliation(s)
- Nitin Roper
- Thoracic and GI Malignancies Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20814, USA
| | - Shaojian Gao
- Thoracic and GI Malignancies Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20814, USA
| | - Tapan K Maity
- Thoracic and GI Malignancies Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20814, USA
| | - A Rouf Banday
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20814, USA
| | - Xu Zhang
- Thoracic and GI Malignancies Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20814, USA
| | - Abhilash Venugopalan
- Thoracic and GI Malignancies Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20814, USA
| | - Constance M Cultraro
- Thoracic and GI Malignancies Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20814, USA
| | - Rajesh Patidar
- Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20814, USA
| | - Sivasish Sindiri
- Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20814, USA
| | - Anna-Leigh Brown
- National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD 20814, USA
| | - Alexander Goncearenco
- National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD 20814, USA
| | - Anna R Panchenko
- National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD 20814, USA
| | - Romi Biswas
- Thoracic and GI Malignancies Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20814, USA
| | - Anish Thomas
- Thoracic and GI Malignancies Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20814, USA
| | - Arun Rajan
- Thoracic and GI Malignancies Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20814, USA
| | - Corey A Carter
- Walter Reed National Military Medical Center, Bethesda, MD 20814, USA
| | - David E Kleiner
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20814, USA
| | - Stephen M Hewitt
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20814, USA
| | - Javed Khan
- Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20814, USA
| | - Ludmila Prokunina-Olsson
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20814, USA
| | - Udayan Guha
- Thoracic and GI Malignancies Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20814, USA.
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10
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Kosovec JE, Zaidi AH, Pounardjian TS, Jobe BA. The Potential Clinical Utility of Circulating Tumor DNA in Esophageal Adenocarcinoma: From Early Detection to Therapy. Front Oncol 2018; 8:610. [PMID: 30619750 PMCID: PMC6297385 DOI: 10.3389/fonc.2018.00610] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 11/28/2018] [Indexed: 12/11/2022] Open
Abstract
Esophageal adenocarcinoma (EAC) is a lethal cancer requiring improved screening strategies and treatment options due to poor detection methods, aggressive progression, and therapeutic resistance. Emerging circulating tumor DNA (ctDNA) technologies may offer a unique non-invasive strategy to better characterize the highly heterogeneous cancer and more clearly establish the genetic modulations leading to disease progression. The presented review describes the potential advantages of ctDNA methodologies as compared to current clinical strategies to improve clinical detection, enhance disease surveillance, evaluate prognosis, and personalize treatment. Specifically, we describe the ctDNA-targetable genetic markers of prognostic significance to stratify patients into risk of progression from benign to malignant disease and potentially offer cost-effective screening of established cancer. We also describe the application of ctDNA to more effectively characterize the heterogeneity and particular mutagenic resistance mechanisms in real-time to improve prognosis and therapeutic monitoring strategies. Lastly, we discuss the inconsistent clinical responses to currently approved therapies for EAC and the role of ctDNA to explore the dynamic regulation of novel targeted and immunotherapies to personalize therapy and improve patient outcomes. Although there are clear limitations of ctDNA technologies for immediate clinical deployment, this review presents the prospective role of such applications to potentially overcome many of the notable hurdles to treating EAC patients. A deeper understanding of complex EAC tumor biology may result in the progress toward improved clinical outcomes.
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Affiliation(s)
- Juliann E Kosovec
- Esophageal and Lung Institute, Allegheny Health Network, Pittsburgh, PA, United States
| | - Ali H Zaidi
- Esophageal and Lung Institute, Allegheny Health Network, Pittsburgh, PA, United States
| | - Tamar S Pounardjian
- Esophageal and Lung Institute, Allegheny Health Network, Pittsburgh, PA, United States
| | - Blair A Jobe
- Esophageal and Lung Institute, Allegheny Health Network, Pittsburgh, PA, United States
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11
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Ziogas DE, Kyrochristos ID, Roukos DH. Discovering novel valid biomarkers and drugs in patient-centric genomic trials: the new epoch of precision surgical oncology. Drug Discov Today 2018; 23:1848-1872. [DOI: 10.1016/j.drudis.2018.07.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2018] [Revised: 07/10/2018] [Accepted: 07/26/2018] [Indexed: 12/16/2022]
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12
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Khan KH, Cunningham D, Werner B, Vlachogiannis G, Spiteri I, Heide T, Mateos JF, Vatsiou A, Lampis A, Damavandi MD, Lote H, Huntingford IS, Hedayat S, Chau I, Tunariu N, Mentrasti G, Trevisani F, Rao S, Anandappa G, Watkins D, Starling N, Thomas J, Peckitt C, Khan N, Rugge M, Begum R, Hezelova B, Bryant A, Jones T, Proszek P, Fassan M, Hahne JC, Hubank M, Braconi C, Sottoriva A, Valeri N. Longitudinal Liquid Biopsy and Mathematical Modeling of Clonal Evolution Forecast Time to Treatment Failure in the PROSPECT-C Phase II Colorectal Cancer Clinical Trial. Cancer Discov 2018; 8:1270-1285. [PMID: 30166348 PMCID: PMC6380469 DOI: 10.1158/2159-8290.cd-17-0891] [Citation(s) in RCA: 163] [Impact Index Per Article: 27.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 05/01/2018] [Accepted: 07/05/2018] [Indexed: 12/14/2022]
Abstract
Sequential profiling of plasma cell-free DNA (cfDNA) holds immense promise for early detection of patient progression. However, how to exploit the predictive power of cfDNA as a liquid biopsy in the clinic remains unclear. RAS pathway aberrations can be tracked in cfDNA to monitor resistance to anti-EGFR monoclonal antibodies in patients with metastatic colorectal cancer. In this prospective phase II clinical trial of single-agent cetuximab in RAS wild-type patients, we combine genomic profiling of serial cfDNA and matched sequential tissue biopsies with imaging and mathematical modeling of cancer evolution. We show that a significant proportion of patients defined as RAS wild-type based on diagnostic tissue analysis harbor aberrations in the RAS pathway in pretreatment cfDNA and, in fact, do not benefit from EGFR inhibition. We demonstrate that primary and acquired resistance to cetuximab are often of polyclonal nature, and these dynamics can be observed in tissue and plasma. Furthermore, evolutionary modeling combined with frequent serial sampling of cfDNA allows prediction of the expected time to treatment failure in individual patients. This study demonstrates how integrating frequently sampled longitudinal liquid biopsies with a mathematical framework of tumor evolution allows individualized quantitative forecasting of progression, providing novel opportunities for adaptive personalized therapies.Significance: Liquid biopsies capture spatial and temporal heterogeneity underpinning resistance to anti-EGFR monoclonal antibodies in colorectal cancer. Dense serial sampling is needed to predict the time to treatment failure and generate a window of opportunity for intervention. Cancer Discov; 8(10); 1270-85. ©2018 AACR. See related commentary by Siravegna and Corcoran, p. 1213 This article is highlighted in the In This Issue feature, p. 1195.
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Affiliation(s)
- Khurum H Khan
- Department of Medicine, The Royal Marsden NHS Trust, London and Sutton, United Kingdom
- Division of Molecular Pathology, The Institute of Cancer Research, London and Sutton, United Kingdom
| | - David Cunningham
- Department of Medicine, The Royal Marsden NHS Trust, London and Sutton, United Kingdom
| | - Benjamin Werner
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, United Kingdom
| | - Georgios Vlachogiannis
- Division of Molecular Pathology, The Institute of Cancer Research, London and Sutton, United Kingdom
| | - Inmaculada Spiteri
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, United Kingdom
| | - Timon Heide
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, United Kingdom
| | - Javier Fernandez Mateos
- Division of Molecular Pathology, The Institute of Cancer Research, London and Sutton, United Kingdom
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, United Kingdom
| | - Alexandra Vatsiou
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, United Kingdom
| | - Andrea Lampis
- Division of Molecular Pathology, The Institute of Cancer Research, London and Sutton, United Kingdom
| | - Mahnaz Darvish Damavandi
- Division of Molecular Pathology, The Institute of Cancer Research, London and Sutton, United Kingdom
| | - Hazel Lote
- Division of Molecular Pathology, The Institute of Cancer Research, London and Sutton, United Kingdom
| | - Ian Said Huntingford
- Division of Molecular Pathology, The Institute of Cancer Research, London and Sutton, United Kingdom
| | - Somaieh Hedayat
- Division of Molecular Pathology, The Institute of Cancer Research, London and Sutton, United Kingdom
| | - Ian Chau
- Department of Medicine, The Royal Marsden NHS Trust, London and Sutton, United Kingdom
| | - Nina Tunariu
- Department of Radiology, The Royal Marsden NHS Trust, Londonand Sutton, United Kingdom
| | - Giulia Mentrasti
- Division of Molecular Pathology, The Institute of Cancer Research, London and Sutton, United Kingdom
| | - Francesco Trevisani
- Division of Molecular Pathology, The Institute of Cancer Research, London and Sutton, United Kingdom
| | - Sheela Rao
- Department of Medicine, The Royal Marsden NHS Trust, London and Sutton, United Kingdom
| | - Gayathri Anandappa
- Department of Medicine, The Royal Marsden NHS Trust, London and Sutton, United Kingdom
- Division of Molecular Pathology, The Institute of Cancer Research, London and Sutton, United Kingdom
| | - David Watkins
- Department of Medicine, The Royal Marsden NHS Trust, London and Sutton, United Kingdom
| | - Naureen Starling
- Department of Medicine, The Royal Marsden NHS Trust, London and Sutton, United Kingdom
| | - Janet Thomas
- Department of Medicine, The Royal Marsden NHS Trust, London and Sutton, United Kingdom
| | - Clare Peckitt
- Department of Medicine, The Royal Marsden NHS Trust, London and Sutton, United Kingdom
| | - Nasir Khan
- Department of Radiology, The Royal Marsden NHS Trust, Londonand Sutton, United Kingdom
| | - Massimo Rugge
- Department of Medicine and Surgical Pathology, University of Padua, Padua, Italy
| | - Ruwaida Begum
- Department of Medicine, The Royal Marsden NHS Trust, London and Sutton, United Kingdom
| | - Blanka Hezelova
- Department of Medicine, The Royal Marsden NHS Trust, London and Sutton, United Kingdom
| | - Annette Bryant
- Department of Medicine, The Royal Marsden NHS Trust, London and Sutton, United Kingdom
| | - Thomas Jones
- Clinical Genomics, The Centre for Molecular Pathology, The Royal Marsden NHS Trust, London and Sutton, United Kingdom
| | - Paula Proszek
- Clinical Genomics, The Centre for Molecular Pathology, The Royal Marsden NHS Trust, London and Sutton, United Kingdom
| | - Matteo Fassan
- Department of Medicine and Surgical Pathology, University of Padua, Padua, Italy
| | - Jens C Hahne
- Division of Molecular Pathology, The Institute of Cancer Research, London and Sutton, United Kingdom
| | - Michael Hubank
- Clinical Genomics, The Centre for Molecular Pathology, The Royal Marsden NHS Trust, London and Sutton, United Kingdom
| | - Chiara Braconi
- Department of Medicine, The Royal Marsden NHS Trust, London and Sutton, United Kingdom
- Division of Cancer Therapeutics, The Institute of Cancer Research, London and Sutton, United Kingdom
| | - Andrea Sottoriva
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, United Kingdom.
| | - Nicola Valeri
- Department of Medicine, The Royal Marsden NHS Trust, London and Sutton, United Kingdom.
- Division of Molecular Pathology, The Institute of Cancer Research, London and Sutton, United Kingdom
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13
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In-depth characterization of the cisplatin mutational signature in human cell lines and in esophageal and liver tumors. Genome Res 2018; 28:654-665. [PMID: 29632087 PMCID: PMC5932606 DOI: 10.1101/gr.230219.117] [Citation(s) in RCA: 104] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2017] [Accepted: 03/13/2018] [Indexed: 12/18/2022]
Abstract
Cisplatin reacts with DNA and thereby likely generates a characteristic pattern of somatic mutations, called a mutational signature. Despite widespread use of cisplatin in cancer treatment and its role in contributing to secondary malignancies, its mutational signature has not been delineated. We hypothesize that cisplatin's mutational signature can serve as a biomarker to identify cisplatin mutagenesis in suspected secondary malignancies. Knowledge of which tissues are at risk of developing cisplatin-induced secondary malignancies could lead to guidelines for noninvasive monitoring for secondary malignancies after cisplatin chemotherapy. We performed whole genome sequencing of 10 independent clones of cisplatin-exposed MCF-10A and HepG2 cells and delineated the patterns of single and dinucleotide mutations in terms of flanking sequence, transcription strand bias, and other characteristics. We used the mSigAct signature presence test and nonnegative matrix factorization to search for cisplatin mutagenesis in hepatocellular carcinomas and esophageal adenocarcinomas. All clones showed highly consistent patterns of single and dinucleotide substitutions. The proportion of dinucleotide substitutions was high: 8.1% of single nucleotide substitutions were part of dinucleotide substitutions, presumably due to cisplatin's propensity to form intra- and interstrand crosslinks between purine bases in DNA. We identified likely cisplatin exposure in nine hepatocellular carcinomas and three esophageal adenocarcinomas. All hepatocellular carcinomas for which clinical data were available and all esophageal cancers indeed had histories of cisplatin treatment. We experimentally delineated the single and dinucleotide mutational signature of cisplatin. This signature enabled us to detect previous cisplatin exposure in human hepatocellular carcinomas and esophageal adenocarcinomas with high confidence.
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14
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Piro G, Carbone C, Santoro R, Tortora G, Melisi D. Predictive biomarkers for the treatment of resectable esophageal and esophago-gastric junction adenocarcinoma: from hypothesis generation to clinical validation. Expert Rev Mol Diagn 2018; 18:357-370. [PMID: 29544370 DOI: 10.1080/14737159.2018.1454312] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
INTRODUCTION Esophageal and esophago-gastric junction (EGJ) adenocarcinomas remain a major health problem worldwide with a worryingly increasing incidence. Recent trials indicate survivals benefit for preoperative or perioperative chemoradiotherapy compared to surgery alone. Beside standard chemoradiotherapy regimens, new therapeutic approaches with targeted therapies have been proposed for the treatment of resectable disease. However, clinical outcomes remain extremely poor due to drug resistance phenomena. The failure of these approaches could be partially ascribed to their incorrect application in patients. Therefore, the identification of strong biomarkers for optimal patient management is urgently needed. Areas covered: This review aims to summarize and critically discuss the most relevant findings regarding predictive biomarker development for neoadjuvant treatment of resectable esophageal and esophago-gastric junction adenocarcinoma patients. Expert commentary: Optimizing the currently available therapeutic modalities through a more accurate selection of patients may avoid the use of ineffective and potentially toxic treatments. During the last decade, the advent of high-throughput '-omics' technologies has set the basis for a new biomarker discovery approach from 'molecule by molecule' screening towards a large-scale systematic screening process with exponential increases in putative biomarkers, which often failed to provide adequate clinical validation.
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Affiliation(s)
- Geny Piro
- a Digestive Molecular Clinical Oncology Research Unit, Department of Medicine , Università degli studi di Verona , Verona , Italy.,b Laboratory of Oncology and Molecular Therapy, Department of Medicine , Università degli studi di Verona , Verona , Italy.,d Comprehensive Cancer Centre , Azienda Ospedaliera Universitaria Integrata , Verona , Italy
| | - Carmine Carbone
- a Digestive Molecular Clinical Oncology Research Unit, Department of Medicine , Università degli studi di Verona , Verona , Italy.,d Comprehensive Cancer Centre , Azienda Ospedaliera Universitaria Integrata , Verona , Italy
| | - Raffaela Santoro
- a Digestive Molecular Clinical Oncology Research Unit, Department of Medicine , Università degli studi di Verona , Verona , Italy.,d Comprehensive Cancer Centre , Azienda Ospedaliera Universitaria Integrata , Verona , Italy
| | - Giampaolo Tortora
- b Laboratory of Oncology and Molecular Therapy, Department of Medicine , Università degli studi di Verona , Verona , Italy.,c Medical Oncology Unit , Azienda Ospedaliera Universitaria Integrata , Verona , Italy.,d Comprehensive Cancer Centre , Azienda Ospedaliera Universitaria Integrata , Verona , Italy
| | - Davide Melisi
- a Digestive Molecular Clinical Oncology Research Unit, Department of Medicine , Università degli studi di Verona , Verona , Italy.,c Medical Oncology Unit , Azienda Ospedaliera Universitaria Integrata , Verona , Italy.,d Comprehensive Cancer Centre , Azienda Ospedaliera Universitaria Integrata , Verona , Italy
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15
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Testa U, Castelli G, Pelosi E. Esophageal Cancer: Genomic and Molecular Characterization, Stem Cell Compartment and Clonal Evolution. MEDICINES (BASEL, SWITZERLAND) 2017; 4:E67. [PMID: 28930282 PMCID: PMC5622402 DOI: 10.3390/medicines4030067] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 09/05/2017] [Accepted: 09/07/2017] [Indexed: 12/20/2022]
Abstract
Esophageal cancer (EC) is the eighth most common cancer and is the sixth leading cause of death worldwide. The incidence of histologic subtypes of EC, esophageal adenocarcinoma (EAC) and esophageal squamous carcinoma (ESCC), display considerable geographic variation. EAC arises from metaplastic Barrett's esophagus (BE) in the context of chronic inflammation secondary to exposure to acid and bile. The main risk factors for developing ESCC are cigarette smoking and alcohol consumption. The main somatic genetic abnormalities showed a different genetic landscape in EAC compared to ESCC. EAC is a heterogeneous cancer dominated by copy number alterations, a high mutational burden, co-amplification of receptor tyrosine kinase, frequent TP53 mutations. The cellular origins of BE and EAC are still not understood: animal models supported a cellular origin either from stem cells located in the basal layer of esophageal epithelium or from progenitors present in the cardia region. Many studies support the existence of cancer stem cells (CSCs) able to initiate and maintain EAC or ESCC. The exact identification of these CSCs, as well as their role in the pathogenesis of EAC and ESCC remain still to be demonstrated. The reviewed studies suggest that current molecular and cellular characterization of EAC and ESCC should serve as background for development of new treatment strategies.
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Affiliation(s)
- Ugo Testa
- Department of Hematology, Oncology and Molecular Medicine, Istituto Superiore di Sanità, 00141 Rome, Italy.
| | - Germana Castelli
- Department of Hematology, Oncology and Molecular Medicine, Istituto Superiore di Sanità, 00141 Rome, Italy.
| | - Elvira Pelosi
- Department of Hematology, Oncology and Molecular Medicine, Istituto Superiore di Sanità, 00141 Rome, Italy.
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16
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Contino G, Vaughan TL, Whiteman D, Fitzgerald RC. The Evolving Genomic Landscape of Barrett's Esophagus and Esophageal Adenocarcinoma. Gastroenterology 2017; 153:657-673.e1. [PMID: 28716721 PMCID: PMC6025803 DOI: 10.1053/j.gastro.2017.07.007] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/11/2017] [Revised: 06/21/2017] [Accepted: 07/11/2017] [Indexed: 12/13/2022]
Abstract
We have recently gained unprecedented insight into genetic factors that determine risk for Barrett's esophagus (BE) and progression to esophageal adenocarcinoma (EA). Next-generation sequencing technologies have allowed us to identify somatic mutations that initiate BE and track genetic changes during development of tumors and invasive cancer. These technologies led to identification of mechanisms of tumorigenesis that challenge the current multistep model of progression to EA. Newer, cost-effective technologies create opportunities to rapidly translate the analysis of DNA into tools that can identify patients with BE at high risk for cancer, detect dysplastic lesions more reliably, and uncover mechanisms of carcinogenesis.
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Affiliation(s)
- Gianmarco Contino
- Medical Research Council Cancer Unit, Hutchison/Medical Research Council Research Centre, University of Cambridge, Cambridge, UK.
| | - Thomas L Vaughan
- Cancer Epidemiology Program, Fred Hutchinson Cancer Research Center, Seattle, Washington; Department of Epidemiology, School of Public Health, University of Washington, Seattle, Washington
| | - David Whiteman
- Cancer Control, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Rebecca C Fitzgerald
- Medical Research Council Cancer Unit, Hutchison/Medical Research Council Research Centre, University of Cambridge, Cambridge, UK
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