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Abdellatif A, Bahria K, Slama N, Oukrif D, Shalaby A, Birkmayer G, Oumouna M, Benachour K. NADH intraperitoneal injection prevents massive pancreatic beta cell destruction in a streptozotocin-induced diabetes in rats. Histochem Cell Biol 2024; 161:239-253. [PMID: 37943325 DOI: 10.1007/s00418-023-02253-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/26/2023] [Indexed: 11/10/2023]
Abstract
Diabetes mellitus is a chronic metabolic disease characterized by persistent hyperglycemia, revealing a decrease in insulin efficiency. The sustained glucotoxic pancreatic microenvironment increases reactive oxygen species generation, resulting in chronic oxidative stress responsible for massive DNA damage. This triggers PARP-1 activation with both NAD+ and ATP depletion, affecting drastically pancreatic beta cells' energy storage and leading to their dysfunction and death. The aim of the present study is to highlight the main histological changes observed in pancreatic islets pre-treated with a unique NADH intraperitoneal injection in a streptozotocin-(STZ)-induced diabetes model. In order to adjust NADH doses, a preliminary study with three different doses, 500 mg/kg, 300 mg/kg, and 150 mg/kg, respectively, was conducted. Subsequently, and on the basis of the results of the aforementioned study, Wistar rats were randomly divided into four groups: non-diabetic control group, diabetics (STZ 45 mg/kg), NADH-treated group (150 mg/kg) 15 min before STZ administration, and NADH-treated group (150 mg/kg) 15 min after STZ administration. The effect of NADH was assessed by blood glucose level, TUNEL staining, histo-morphological analysis, and immunohistochemistry. The optimum protective dose of NADH was 150 mg/kg. NADH effectively decreased hyperglycemia and reduced diabetes induced by STZ. Histologically, NADH pre-treatment revealed a decrease in beta cell death favoring apoptosis over necrosis and therefore preventing inflammation with further beta cell destruction. Our data clearly demonstrate that NADH prior or post-treatment could effectively prevent the deleterious loss of beta cell mass in STZ-induced diabetes in rats and preserve the normal pancreatic islet's function.
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Affiliation(s)
- Amina Abdellatif
- Laboratory of Experimental Biology and Pharmacology, Faculty of Sciences, Dr Yahia Fares University, Medea, Algeria
| | - Karima Bahria
- Laboratory of Experimental Biology and Pharmacology, Faculty of Sciences, Dr Yahia Fares University, Medea, Algeria
| | - Nada Slama
- Laboratory of Experimental Biology and Pharmacology, Faculty of Sciences, Dr Yahia Fares University, Medea, Algeria
| | - Dahmane Oukrif
- Pathology Department, University College London, London, UK
| | - Asem Shalaby
- Pathology Department, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Oman
- Pathology Department, College of Medicine, Mansoura University, Mansoura, Egypt
| | - George Birkmayer
- Department of Medical Chemistry, University of Graz and Birkmayer Laboratories, Vienna, Austria
| | - Mustapha Oumouna
- Laboratory of Experimental Biology and Pharmacology, Faculty of Sciences, Dr Yahia Fares University, Medea, Algeria
| | - Karine Benachour
- Laboratory of Experimental Biology and Pharmacology, Faculty of Sciences, Dr Yahia Fares University, Medea, Algeria.
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2
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Ng J, Henriquez N, Kitchen N, Williams N, Novelli M, Oukrif D, MacRobert A, Bown S. Suppression of tumour growth from transplanted astrocytoma cells transfected with luciferase in mice by bioluminescence mediated, systemic, photodynamic therapy. Photodiagnosis Photodyn Ther 2024; 45:103923. [PMID: 38101502 DOI: 10.1016/j.pdpdt.2023.103923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 11/27/2023] [Accepted: 12/01/2023] [Indexed: 12/17/2023]
Abstract
BACKGROUND Grade 4 astrocytomas are usually incurable due to their diffusely infiltrative nature. Photodynamic therapy (PDT) is a promising therapeutic option, but external light delivery is impractical when cancer cells infiltrate unknown areas of normal brain. Hence the search for endogenous sources to generate light at cancer cells. In vitro, astrocytoma cells, transfected with firefly luciferase, can be killed by bioluminescence-mediated PDT (bPDT). This study asks if bPDT can suppress tumour growth In vivo, when all components of treatment are administered systemically. METHODS Transfected astrocytoma cells were injected subcutaneously or intra-cranially in athymic CD1 nu/nu mice. bPDT required ip bolus of mTHPC (photosensitiser) and delivery of the d-luciferin substrate over 7 days via an implanted osmotic pump. Control animals had no treatment, photosensitiser only or d-luciferin only. For subcutaneous tumours, size and BLI (light emitted after d-luciferin bolus) were measured before and every 2 days after PDT. For intracranial tumours, monitoring was weekly BLI. RESULTS For subcutaneous tumours, there was significant suppression of the tumour growth rate (P<0.05), and absolute tumour size (P<0.01) after bPDT. Proliferation of subcutaneous and intracranial tumours (monitored by BrdU uptake) was significantly reduced in treated mice. (P<0.001) CONCLUSIONS: This study reports bPDT suppression of tumour growth from luciferase transfected astrocytoma cells with all components of treatment given systemically, as required for effective management of recurrent astrocytomas in unknown sites. However, research on systemic bPDT is needed to establish whether effects on non-transfected tumours can be achieved without any unacceptable effects on normal tissues.
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Affiliation(s)
- Jane Ng
- UCL Queen Square Institute of Neurology, Queen Square, London WC1N 3BG, United Kingdom; National Medical Laser Centre (now Department of Targeted Intervention, Division of Surgery and Interventional Science), University College London, Charles Bell House 43-45 Foley Street, London W1W 7TS, United Kingdom
| | - Nico Henriquez
- UCL Queen Square Institute of Neurology, Queen Square, London WC1N 3BG, United Kingdom
| | - Neil Kitchen
- Victor Horsley Department of Neurosurgery, National Hospital for Neurology and Neurosurgery, UCLH NHS Trust, Queen Square, London WC1 3BG, United Kingdom of Great Britain and Northern Ireland, United Kingdom
| | - Norman Williams
- Division of Surgery & Interventional Science, University College London, Charles Bell House, 43-45 Foley Street London W1W 7TS, United Kingdom
| | - Marco Novelli
- Department of Cellular Pathology, University College Hospital, London, 60 Whitfield Street, London W1T 4EU, United Kingdom
| | - Dahmane Oukrif
- Department of Cellular Pathology, University College Hospital, London, 60 Whitfield Street, London W1T 4EU, United Kingdom
| | - Alexander MacRobert
- National Medical Laser Centre (now Department of Targeted Intervention, Division of Surgery and Interventional Science), University College London, Charles Bell House 43-45 Foley Street, London W1W 7TS, United Kingdom
| | - Stephen Bown
- National Medical Laser Centre (now Department of Targeted Intervention, Division of Surgery and Interventional Science), University College London, Charles Bell House 43-45 Foley Street, London W1W 7TS, United Kingdom.
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Vithayathil M, Modolell I, Ortiz-Fernandez-Sordo J, Oukrif D, Pappas A, Januszewicz W, O'Donovan M, Hadjinicolaou A, Bianchi M, Blasko A, White J, Kaye P, Novelli M, Wernisch L, Ragunath K, di Pietro M. Image-Enhanced Endoscopy and Molecular Biomarkers Vs Seattle Protocol to Diagnose Dysplasia in Barrett's Esophagus. Clin Gastroenterol Hepatol 2022; 20:2514-2523.e3. [PMID: 35183768 DOI: 10.1016/j.cgh.2022.01.060] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 01/21/2022] [Accepted: 01/28/2022] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS Dysplasia in Barrett's esophagus often is invisible on high-resolution white-light endoscopy (HRWLE). We compared the diagnostic accuracy for inconspicuous dysplasia of the combination of autofluorescence imaging (AFI)-guided probe-based confocal laser endomicroscopy (pCLE) and molecular biomarkers vs HRWLE with Seattle protocol biopsies. METHODS Barrett's esophagus patients with no dysplastic lesions were block-randomized to standard endoscopy (HRWLE with the Seattle protocol) or AFI-guided pCLE with targeted biopsies for molecular biomarkers (p53 and cyclin A by immunohistochemistry; aneuploidy by image cytometry), with crossover to the other arm after 6 to 12 weeks. The primary end point was the histologic diagnosis from all study biopsies (trial histology). A sensitivity analysis was performed for overall histology, which included diagnoses within 12 months from the first study endoscopy. Endoscopists were blinded to the referral endoscopy and histology results. The primary outcome was diagnostic accuracy for dysplasia by real-time pCLE vs HRWLE biopsies. RESULTS Of 154 patients recruited, 134 completed both arms. In the primary outcome analysis (trial histology analysis), AFI-guided pCLE had similar sensitivity for dysplasia compared with standard endoscopy (74.3%; 95% CI, 56.7-87.5 vs 80.0%; 95% CI, 63.1-91.6; P = .48). Multivariate logistic regression showed pCLE optical dysplasia, aberrant p53, and aneuploidy had the strongest correlation with dysplasia (secondary outcome). This 3-biomarker panel had higher sensitivity for any grade of dysplasia than the Seattle protocol (81.5% vs 51.9%; P < .001) in the overall histology analysis, but not in the trial histology analysis (91.4% vs 80.0%; P = .16), with an area under the receiver operating curve of 0.83. CONCLUSIONS Seattle protocol biopsies miss dysplasia in approximately half of patients with inconspicuous neoplasia. AFI-guided pCLE has similar accuracy to the current gold standard. The addition of molecular biomarkers could improve diagnostic accuracy.
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Affiliation(s)
- Mathew Vithayathil
- Medical Research Council Cancer Unit, University of Cambridge, United Kingdom
| | - Ines Modolell
- Department of Gastroenterology, University Hospital National Health Service Foundation Trust, United Kingdom
| | - Jacobo Ortiz-Fernandez-Sordo
- Nottingham Digestive Diseases Centre, National Institute of Health Research Nottingham Biomedical Research Centre, United Kingdom
| | - Dahmane Oukrif
- Department of Histopathology, University College London Hospital, Longdon, United Kingdom
| | - Apostolos Pappas
- Medical Research Council Cancer Unit, University of Cambridge, United Kingdom
| | - Wladyslaw Januszewicz
- Medical Research Council Cancer Unit, University of Cambridge, United Kingdom; Department of Gastroenterology, Hepatology and Clinical Oncology, Medical Centre for Postgraduate Education, Warsaw, Poland
| | - Maria O'Donovan
- Department of Histopathology, Cambridge University Hospital National Health Service Foundation Trust, United Kingdom
| | - Andreas Hadjinicolaou
- Medical Research Council Cancer Unit, University of Cambridge, United Kingdom; Department of Gastroenterology, University Hospital National Health Service Foundation Trust, United Kingdom
| | - Michele Bianchi
- Medical Research Council Cancer Unit, University of Cambridge, United Kingdom
| | - Adrienn Blasko
- Medical Research Council Cancer Unit, University of Cambridge, United Kingdom
| | - Jonathan White
- Nottingham Digestive Diseases Centre, National Institute of Health Research Nottingham Biomedical Research Centre, United Kingdom
| | - Philip Kaye
- Department of Histopathology, Nottingham University Hospitals National Health Service Trust, University of Nottingham, United Kingdom
| | - Marco Novelli
- Department of Histopathology, University College London Hospital, Longdon, United Kingdom
| | - Lorenz Wernisch
- BIOS Health, Ltd, Cambridge, United Kingdom; Medical Research Council Biostatistics Unit, University of Cambridge, United Kingdom
| | - Krish Ragunath
- Nottingham Digestive Diseases Centre, National Institute of Health Research Nottingham Biomedical Research Centre, United Kingdom
| | - Massimiliano di Pietro
- Medical Research Council Cancer Unit, University of Cambridge, United Kingdom; Department of Gastroenterology, University Hospital National Health Service Foundation Trust, United Kingdom.
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4
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Cross W, Lyskjær I, Lesluyes T, Hargreaves S, Strobl AC, Davies C, Waise S, Hames-Fathi S, Oukrif D, Ye H, Amary F, Tirabosco R, Gerrand C, Baker T, Barnes D, Steele C, Alexandrov L, Bond G, Cool P, Pillay N, Loo PV, Flanagan AM. A genetic model for central chondrosarcoma evolution correlates with patient outcome. Genome Med 2022; 14:99. [PMID: 36042521 PMCID: PMC9426036 DOI: 10.1186/s13073-022-01084-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 07/07/2022] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Central conventional chondrosarcoma (CS) is the most common subtype of primary malignant bone tumour in adults. Treatment options are usually limited to surgery, and prognosis is challenging. These tumours are characterised by the presence and absence of IDH1 and IDH2 mutations, and recently, TERT promoter alterations have been reported in around 20% of cases. The effect of these mutations on clinical outcome remains unclear. The purpose of this study was to determine if prognostic accuracy can be improved by the addition of genomic data, and specifically by examination of IDH1, IDH2, and TERT mutations. METHODS In this study, we combined both archival samples and data sourced from the Genomics England 100,000 Genomes Project (n = 356). Mutations in IDH1, IDH2, and TERT were profiled using digital droplet PCR (n = 346), whole genome sequencing (n=68), or both (n = 64). Complex events and other genetic features were also examined, along with methylation array data (n = 84). We correlated clinical features and patient outcomes with our genetic findings. RESULTS IDH2-mutant tumours occur in older patients and commonly present with high-grade or dedifferentiated disease. Notably, TERT mutations occur most frequently in IDH2-mutant tumours, although have no effect on survival in this group. In contrast, TERT mutations are rarer in IDH1-mutant tumours, yet they are associated with a less favourable outcome in this group. We also found that methylation profiles distinguish IDH1- from IDH2-mutant tumours. IDH wild-type tumours rarely exhibit TERT mutations and tend to be diagnosed in a younger population than those with tumours harbouring IDH1 and IDH2 mutations. A major genetic feature of this group is haploidisation and subsequent genome doubling. These tumours evolve less frequently to dedifferentiated disease and therefore constitute a lower risk group. CONCLUSIONS Tumours with IDH1 or IDH2 mutations or those that are IDHwt have significantly different genetic pathways and outcomes in relation to TERT mutation. Diagnostic testing for IDH1, IDH2, and TERT mutations could therefore help to guide clinical monitoring and prognostication.
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Affiliation(s)
- William Cross
- grid.83440.3b0000000121901201Research Department of Pathology, University College London, UCL Cancer Institute, London, UK
| | - Iben Lyskjær
- grid.83440.3b0000000121901201Research Department of Pathology, University College London, UCL Cancer Institute, London, UK ,grid.83440.3b0000000121901201Medical Genomics Research Group, University College London, UCL Cancer Institute, London, UK
| | - Tom Lesluyes
- grid.451388.30000 0004 1795 1830The Francis Crick Institute, London, UK
| | - Steven Hargreaves
- grid.83440.3b0000000121901201Research Department of Pathology, University College London, UCL Cancer Institute, London, UK
| | - Anna-Christina Strobl
- grid.416177.20000 0004 0417 7890Department of Histopathology, Royal National Orthopaedic Hospital, Stanmore, UK
| | - Christopher Davies
- grid.83440.3b0000000121901201Research Department of Pathology, University College London, UCL Cancer Institute, London, UK ,grid.416177.20000 0004 0417 7890Department of Histopathology, Royal National Orthopaedic Hospital, Stanmore, UK
| | - Sara Waise
- grid.451388.30000 0004 1795 1830The Francis Crick Institute, London, UK ,grid.5491.90000 0004 1936 9297Cancer Sciences Unit, University of Southampton, Southampton, UK
| | - Shadi Hames-Fathi
- grid.83440.3b0000000121901201Research Department of Pathology, University College London, UCL Cancer Institute, London, UK
| | - Dahmane Oukrif
- grid.83440.3b0000000121901201Research Department of Pathology, University College London, UCL Cancer Institute, London, UK
| | - Hongtao Ye
- grid.416177.20000 0004 0417 7890Department of Histopathology, Royal National Orthopaedic Hospital, Stanmore, UK
| | - Fernanda Amary
- grid.416177.20000 0004 0417 7890Department of Histopathology, Royal National Orthopaedic Hospital, Stanmore, UK
| | - Roberto Tirabosco
- grid.416177.20000 0004 0417 7890Department of Histopathology, Royal National Orthopaedic Hospital, Stanmore, UK
| | - Craig Gerrand
- grid.416177.20000 0004 0417 7890Bone Tumour Unit, Royal National Orthopaedic Hospital, Stanmore, UK
| | - Toby Baker
- grid.451388.30000 0004 1795 1830The Francis Crick Institute, London, UK
| | - David Barnes
- grid.6572.60000 0004 1936 7486Institute of Cancer and Genomic Sciences, Birmingham University, Birmingham, UK
| | - Christopher Steele
- grid.83440.3b0000000121901201Research Department of Pathology, University College London, UCL Cancer Institute, London, UK
| | - Ludmil Alexandrov
- grid.266100.30000 0001 2107 4242University of California, San Diego, USA
| | - Gareth Bond
- grid.6572.60000 0004 1936 7486Institute of Cancer and Genomic Sciences, Birmingham University, Birmingham, UK
| | | | - Paul Cool
- grid.412943.90000 0001 0507 535XRobert Jones & Agnes Hunt Orthopaedic Hospital NHS Foundation Trust, Oswestry, UK ,grid.9757.c0000 0004 0415 6205Keele University, Keele, UK
| | - Nischalan Pillay
- grid.83440.3b0000000121901201Research Department of Pathology, University College London, UCL Cancer Institute, London, UK ,grid.416177.20000 0004 0417 7890Department of Histopathology, Royal National Orthopaedic Hospital, Stanmore, UK
| | - Peter Van Loo
- grid.451388.30000 0004 1795 1830The Francis Crick Institute, London, UK
| | - Adrienne M. Flanagan
- grid.83440.3b0000000121901201Research Department of Pathology, University College London, UCL Cancer Institute, London, UK ,grid.416177.20000 0004 0417 7890Department of Histopathology, Royal National Orthopaedic Hospital, Stanmore, UK
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Hobor S, Bakir MA, Skrzypski M, Frankell AM, Bakker B, Watkins TB, Markovets A, Dry JR, Brown AP, van der Aart J, Oukrif D, Novelli M, Renshaw MJ, Hill W, Bos HVD, Spierings DC, Chmielecki J, Barrett C, Litchfield K, de Bruin E, Foijer F, Vousden KH, Hynds RE, Hiley CT, Kanu N, Zaccaria S, Gronroos EC, Swanton C. Abstract 6217: TP53 loss with whole genome doubling mediates heterogeneous intra-patient therapy response in EGFR-driven lung adenocarcinoma: A TRACERx study. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-6217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Introduction: Mutations in the epidermal growth factor receptor (EGFR) are often found in never-smokers who develop lung adenocarcinoma (LUAD) and resistance to receptor-targeted tyrosine kinase inhibitors (TKIs) generally occurs within five years of treatment. Mixed responses, where individual tumor lesions within the same patient respond differently to treatment, contribute to early treatment failure and indicate the involvement of multiple genomic alterations. TP53 loss of function has been associated with both tolerance to chromosomal instability (CIN) and with shortened progression free survival in EGFR-driven tumors. The aim of this study was to investigate the hypothesis that CIN, together with loss of p53 function, may lead to diverse genotypes that underlie the mixed responses observed in EGFR-driven LUAD.
Experimental Procedures: We used genetically engineered mouse models (GEMMs), driven by EGFR with or without concomitant Trp53 loss and human isogenic cell lines to investigate cellular evolution and the effect of whole genome doubling on targeted therapy responses and mechanisms of resistance. Next generation sequencing and shallow whole genome single cell analyses, together with longitudinal imaging analysis from the Aura clinical trials (AURA2, AURA3 and the AURA extension cohort, Identifiers: NCT02094261, NCT02151981 and NCT01802632) was used to investigate the effect of p53 loss on tumor evolution.
Results: EGFR mutant tumors with clonal Trp53 loss or TP53 pathway disruption displayed increased Weighted Genome Integrity Index (wGII) and higher cell to cell variation in both the mouse and TRACERx data sets. We found that TP53 loss of function increased the incidence of mixed responses and resistance to targeted therapy in both mouse and human tumors leading to early treatment failure and reduced survival. Whole-exome sequencing (median depth of 92x, range: 58-169x) of nine erlotinib-resistant EGFR mouse tumors identified four EGFR bypassing mutations (oncogenic KRAS mutations; Q61H, Q61R, and two G12D mutations) and one likely driver mutation in FGFR2 (C286R). We could only identify one known resistance associated mutation, EGFRT790M, in EGFR mutant tumors with concomitant loss of Trp53. In depth analysis revealed no major copy number differences in treatment naÏve vs resistant EGFR mutant tumors. In contrast, 70% of all tumors with concomitant Trp53 loss had amplified a region of mouse chromosome 7, harboring MET and BRAF. Investigating an isogenic EGFR/TP53 mutant cell model system revealed whole genome doubling as advantageous in overcoming the selection pressure induced by targeted therapy.
Conclusion: We find that loss of TP53 in the context of mutated EGFR leads to an altered and plastic genomic landscape, with multiple copy number changes, which in turn facilitates therapy resistance.
Citation Format: Sebastijan Hobor, Maise Al Bakir, Marcin Skrzypski, Alexander M. Frankell, Bjorn Bakker, Thomas B. Watkins, Aleksandra Markovets, Jonathan R. Dry, Andrew P. Brown, Jasper van der Aart, Dahmane Oukrif, Marco Novelli, Matthew J. Renshaw, William Hill, Hilda van den Bos, Diana C. Spierings, Juliann Chmielecki, Carl Barrett, Kevin Litchfield, Elza de Bruin, Floris Foijer, Karen H. Vousden, TRACERx consortium, Robert E. Hynds, Crispin T. Hiley, Nnennaya Kanu, Simone Zaccaria, Eva C. Gronroos, Charles Swanton. TP53 loss with whole genome doubling mediates heterogeneous intra-patient therapy response in EGFR-driven lung adenocarcinoma: A TRACERx study [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 6217.
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Affiliation(s)
| | | | - Marcin Skrzypski
- 2Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, The Francis Crick Institute, London, United Kingdom
| | - Alexander M. Frankell
- 2Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, The Francis Crick Institute, London, United Kingdom
| | - Bjorn Bakker
- 3European Research Institute for the Biology of Ageing, University of Groningen, Groningen, Netherlands
| | | | - Aleksandra Markovets
- 4Translational Medicine, Oncology Research and Early Development, AstraZeneca Pharmaceuticals LP, Boston, MA
| | | | - Andrew P. Brown
- 6Late Stage Oncology R&D, AstraZeneca, Cambridge, United Kingdom
| | | | - Dahmane Oukrif
- 7University College London Medical School, London, United Kingdom
| | - Marco Novelli
- 7University College London Medical School, London, United Kingdom
| | | | - William Hill
- 1The Francis Crick Institute, London, United Kingdom
| | - Hilda van den Bos
- 3European Research Institute for the Biology of Ageing, University of Groningen, Groningen, Netherlands
| | - Diana C. Spierings
- 3European Research Institute for the Biology of Ageing, University of Groningen, Groningen, Netherlands
| | - Juliann Chmielecki
- 4Translational Medicine, Oncology Research and Early Development, AstraZeneca Pharmaceuticals LP, Boston, MA
| | - Carl Barrett
- 6Late Stage Oncology R&D, AstraZeneca, Cambridge, United Kingdom
| | - Kevin Litchfield
- 8Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, United Kingdom
| | - Elza de Bruin
- 6Late Stage Oncology R&D, AstraZeneca, Cambridge, United Kingdom
| | - Floris Foijer
- 3European Research Institute for the Biology of Ageing, University of Groningen, Groningen, Netherlands
| | | | - Robert E. Hynds
- 8Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, United Kingdom
| | - Crispin T. Hiley
- 8Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, United Kingdom
| | - Nnennaya Kanu
- 8Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, United Kingdom
| | - Simone Zaccaria
- 8Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, United Kingdom
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6
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Fittall MW, Lyskjaer I, Ellery P, Lombard P, Ijaz J, Strobl AC, Oukrif D, Tarabichi M, Sill M, Koelsche C, Mechtersheimer G, Demeulemeester J, Tirabosco R, Amary F, Campbell PJ, Pfister SM, Jones DT, Pillay N, Van Loo P, Behjati S, Flanagan AM. Drivers underpinning the malignant transformation of giant cell tumour of bone. J Pathol 2020; 252:433-440. [PMID: 32866294 PMCID: PMC8432151 DOI: 10.1002/path.5537] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 07/29/2020] [Accepted: 08/20/2020] [Indexed: 02/02/2023]
Abstract
The rare benign giant cell tumour of bone (GCTB) is defined by an almost unique mutation in the H3.3 family of histone genes H3‐3A or H3‐3B; however, the same mutation is occasionally found in primary malignant bone tumours which share many features with the benign variant. Moreover, lung metastases can occur despite the absence of malignant histological features in either the primary or metastatic lesions. Herein we investigated the genetic events of 17 GCTBs including benign and malignant variants and the methylation profiles of 122 bone tumour samples including GCTBs. Benign GCTBs possessed few somatic alterations and no other known drivers besides the H3.3 mutation, whereas all malignant tumours harboured at least one additional driver mutation and exhibited genomic features resembling osteosarcomas, including high mutational burden, additional driver event(s), and a high degree of aneuploidy. The H3.3 mutation was found to predate the development of aneuploidy. In contrast to osteosarcomas, malignant H3.3‐mutated tumours were enriched for a variety of alterations involving TERT, other than amplification, suggesting telomere dysfunction in the transformation of benign to malignant GCTB. DNA sequencing of the benign metastasising GCTB revealed no additional driver alterations; polyclonal seeding in the lung was identified, implying that the metastatic lesions represent an embolic event. Unsupervised clustering of DNA methylation profiles revealed that malignant H3.3‐mutated tumours are distinct from their benign counterpart, and other bone tumours. Differential methylation analysis identified CCND1, encoding cyclin D1, as a plausible cancer driver gene in these tumours because hypermethylation of the CCND1 promoter was specific for GCTBs. We report here the genomic and methylation patterns underlying the rare clinical phenomena of benign metastasising and malignant transformation of GCTB and show how the combination of genomic and epigenomic findings could potentially distinguish benign from malignant GCTBs, thereby predicting aggressive behaviour in challenging diagnostic cases. © 2020 The Authors. The Journal of Pathology published by John Wiley & Sons, Ltd. on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Matthew W Fittall
- The Francis Crick Institute, London, UK.,Department of Pathology (research), University College London Cancer Institute, London, UK.,Cancer, Ageing and Somatic Mutation, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Iben Lyskjaer
- Department of Pathology (research), University College London Cancer Institute, London, UK.,Department of Molecular Medicine, Aarhus Universitet, Aarhus, Denmark
| | - Peter Ellery
- Department of Pathology (research), University College London Cancer Institute, London, UK.,Department of Cellular Pathology, University College London NHS Trust, London, UK
| | - Patrick Lombard
- Department of Pathology (research), University College London Cancer Institute, London, UK
| | - Jannat Ijaz
- Cancer, Ageing and Somatic Mutation, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Anna-Christina Strobl
- Department of Histopathology, Royal National Orthopaedic Hospital NHS Trust, Stanmore, UK
| | - Dahmane Oukrif
- Department of Pathology (research), University College London Cancer Institute, London, UK
| | - Maxime Tarabichi
- The Francis Crick Institute, London, UK.,Cancer, Ageing and Somatic Mutation, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Martin Sill
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Christian Koelsche
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | | | - Jonas Demeulemeester
- The Francis Crick Institute, London, UK.,Department of Human Genetics, University of Leuven, Leuven, Belgium
| | - Roberto Tirabosco
- Department of Histopathology, Royal National Orthopaedic Hospital NHS Trust, Stanmore, UK
| | - Fernanda Amary
- Department of Histopathology, Royal National Orthopaedic Hospital NHS Trust, Stanmore, UK
| | - Peter J Campbell
- Cancer, Ageing and Somatic Mutation, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Stefan M Pfister
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany.,Department of Pediatric Hematology and Oncology, University Hospital Heidelberg, Heidelberg, Germany
| | - David Tw Jones
- Department of Pediatric Hematology and Oncology, University Hospital Heidelberg, Heidelberg, Germany.,Pediatric Glioma Research Group, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Nischalan Pillay
- Department of Pathology (research), University College London Cancer Institute, London, UK.,Department of Histopathology, Royal National Orthopaedic Hospital NHS Trust, Stanmore, UK
| | - Peter Van Loo
- The Francis Crick Institute, London, UK.,Department of Human Genetics, University of Leuven, Leuven, Belgium
| | - Sam Behjati
- Cancer, Ageing and Somatic Mutation, Wellcome Trust Sanger Institute, Hinxton, UK.,Department of Paediatrics, University of Cambridge, Cambridge, UK
| | - Adrienne M Flanagan
- Department of Pathology (research), University College London Cancer Institute, London, UK.,Department of Histopathology, Royal National Orthopaedic Hospital NHS Trust, Stanmore, UK
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7
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Antas P, Novellasdemunt L, Kucharska A, Massie I, Carvalho J, Oukrif D, Nye E, Novelli M, Li VSW. SH3BP4 Regulates Intestinal Stem Cells and Tumorigenesis by Modulating β-Catenin Nuclear Localization. Cell Rep 2020; 26:2266-2273.e4. [PMID: 30811977 PMCID: PMC6391711 DOI: 10.1016/j.celrep.2019.01.110] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Revised: 01/09/2019] [Accepted: 01/29/2019] [Indexed: 01/12/2023] Open
Abstract
Wnt signals at the base of mammalian crypts play a pivotal role in intestinal stem cell (ISC) homeostasis, whereas aberrant Wnt activation causes colon cancer. Precise control of Wnt signal strength is governed by a number of negative inhibitory mechanisms acting at distinct levels of the cascade. Here, we identify the Wnt negative regulatory role of Sh3bp4 in the intestinal crypt. We show that the loss of Sh3bp4 increases ISC and Paneth cell numbers in murine intestine and accelerates adenoma development in Apcmin mice. Mechanistically, human SH3BP4 inhibits Wnt signaling downstream of β-catenin phosphorylation and ubiquitination. This Wnt inhibitory role is dependent on the ZU5 domain of SH3BP4. We further demonstrate that SH3BP4 is expressed at the perinuclear region to restrict nuclear localization of β-catenin. Our data uncover the tumor-suppressive role of SH3BP4 that functions as a negative feedback regulator of Wnt signaling through modulating β-catenin’s subcellular localization. SH3BP4 is a Wnt inhibitor and is expressed in the intestinal crypt Deletion of Sh3bp4 increases stem cell numbers and accelerates tumor development SH3BP4 inhibits β-catenin nuclear localization at the perinuclear region
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Affiliation(s)
- Pedro Antas
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | | | - Anna Kucharska
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Isobel Massie
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Joana Carvalho
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Dahmane Oukrif
- Histopathology Department, University College London Hospitals NHS Foundation Trust, London, UK
| | - Emma Nye
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Marco Novelli
- Histopathology Department, University College London Hospitals NHS Foundation Trust, London, UK
| | - Vivian S W Li
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.
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8
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Gaifulina R, Caruana DJ, Oukrif D, Guppy NJ, Culley S, Brown R, Bell I, Rodriguez-Justo M, Lau K, Thomas GMH. Rapid and complete paraffin removal from human tissue sections delivers enhanced Raman spectroscopic and histopathological analysis. Analyst 2020; 145:1499-1510. [PMID: 31894759 PMCID: PMC7677988 DOI: 10.1039/c9an01030k] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 12/14/2019] [Indexed: 12/29/2022]
Abstract
Incomplete removal of paraffin and organic contaminants from tissues processed for diagnostic histology has been a profound barrier to the introduction of Raman spectroscopic techniques into clinical practice. We report a route to rapid and complete paraffin removal from a range of formalin-fixed paraffin embedded tissues using super mirror stainless steel slides. The method is equally effective on a range of human and animal tissues, performs equally well with archived and new samples and is compatible with standard pathology lab procedures. We describe a general enhancement of the Raman scatter and enhanced staining with antibodies used in immunohistochemistry for clinical diagnosis. We conclude that these novel slide substrates have the power to improve diagnosis through anatomical pathology by facilitating the simultaneous combination of improved, more sensitive immunohistochemical staining and simplified, more reliable Raman spectroscopic imaging, analysis and signal processing.
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Affiliation(s)
- Riana Gaifulina
- Department of Cell and Developmental Biology
, University College London
,
UK
.
; Tel: +44 (0)20 7679 6098
- Department of Chemistry
, University College London
,
UK
| | | | - Dahmane Oukrif
- Research Department of Pathology
, University College London
,
UK
| | - Naomi J. Guppy
- UCL Advanced Diagnostics
, University College Hospital
,
UK
| | - Siân Culley
- Department of Cell and Developmental Biology
, University College London
,
UK
.
; Tel: +44 (0)20 7679 6098
- MRC Laboratory for Molecular Cell Biology
, University College London
,
UK
| | - Robert Brown
- Spectroscopy Products Division
,
Renishaw plc
, UK
.
| | - Ian Bell
- Spectroscopy Products Division
,
Renishaw plc
, UK
.
| | - Manuel Rodriguez-Justo
- Department of Gastrointestinal Pathology
, University College Hospital and Department of Research Pathology/Cancer Institute
,
UCL
, UK
| | - Katherine Lau
- Spectroscopy Products Division
,
Renishaw plc
, UK
.
| | - Geraint M. H. Thomas
- Department of Cell and Developmental Biology
, University College London
,
UK
.
; Tel: +44 (0)20 7679 6098
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9
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Spiro SG, Shah PL, Rintoul RC, George J, Janes S, Callister M, Novelli M, Shaw P, Kocjan G, Griffiths C, Falzon M, Booton R, Magee N, Peake M, Dhillon P, Sridharan K, Nicholson AG, Padley S, Taylor MN, Ahmed A, Allen J, Ngai Y, Chinyanganya N, Ashford-Turner V, Lewis S, Oukrif D, Rabbitts P, Counsell N, Hackshaw A. Sequential screening for lung cancer in a high-risk group: randomised controlled trial: LungSEARCH: a randomised controlled trial of Surveillance using sputum and imaging for the EARly detection of lung Cancer in a High-risk group. Eur Respir J 2019; 54:13993003.00581-2019. [PMID: 31537697 PMCID: PMC6796151 DOI: 10.1183/13993003.00581-2019] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 07/11/2019] [Indexed: 12/18/2022]
Abstract
BACKGROUND Low-dose computed tomography (LDCT) screening detects early-stage lung cancer and reduces mortality. We proposed a sequential approach targeted to a high-risk group as a potentially efficient screening strategy. METHODS LungSEARCH was a national multicentre randomised trial. Current/ex-smokers with mild/moderate chronic obstructive pulmonary disease (COPD) were allocated (1:1) to have 5 years surveillance or not. Screened participants provided annual sputum samples for cytology and cytometry, and if abnormal were offered annual LDCT and autofluorescence bronchoscopy (AFB). Those with normal sputum provided annual samples. The primary end-point was the percentage of lung cancers diagnosed at stage I/II (nonsmall cell) or limited disease (small cell). RESULTS 1568 participants were randomised during 2007-2011 from 10 UK centres. 85.2% of those screened provided an adequate baseline sputum sample. There were 42 lung cancers among 785 screened individuals and 36 lung cancers among 783 controls. 54.8% (23 out of 42) of screened individuals versus 45.2% (14 out of 31) of controls with known staging were diagnosed with early-stage disease (one-sided p=0.24). Relative risk was 1.21 (95% CI 0.75-1.95) or 0.82 (95% CI 0.52-1.31) for early-stage or advanced cancers, respectively. Overall sensitivity for sputum (in those randomised to surveillance) was low (40.5%) with a cumulative false-positive rate (FPR) of 32.8%. 55% of cancers had normal sputum results throughout. Among sputum-positive individuals who had AFB, sensitivity was 45.5% and cumulative FPR was 39.5%; the corresponding measures for those who had LDCT were 100% and 16.1%, respectively. CONCLUSIONS Our sequential strategy, using sputum cytology/cytometry to select high-risk individuals for AFB and LDCT, did not lead to a clear stage shift and did not improve the efficiency of lung cancer screening.
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Affiliation(s)
- Stephen G Spiro
- Dept of Respiratory Medicine, University College Hospital, London, UK.,These authors are joint lead authors
| | - Pallav L Shah
- Dept of Respiratory Medicine, Royal Brompton Hospital, Chelsea and Westminster Hospital and Imperial College London, London, UK
| | - Robert C Rintoul
- Dept of Oncology, Royal Papworth Hospital and University of Cambridge, Cambridge, UK
| | - Jeremy George
- UCL Respiratory, Dept of Medicine, University College London, London, UK
| | - Samuel Janes
- UCL Respiratory, Dept of Medicine, University College London, London, UK
| | - Matthew Callister
- Dept of Respiratory Medicine, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Marco Novelli
- Cellular Pathology, University College Hospital, London, UK
| | - Penny Shaw
- Radiology (Imaging), University College Hospital, London, UK
| | | | - Chris Griffiths
- Institute of Population Health Sciences, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Mary Falzon
- Cellular Pathology, University College Hospital, London, UK
| | - Richard Booton
- Lung Cancer and Thoracic Surgery Directorate, Manchester University NHS Trust and University of Manchester, Manchester, UK
| | - Nicholas Magee
- Respiratory Medicine, Belfast City Hospital, Belfast, UK
| | - Michael Peake
- Dept of Immunity, Infection and Inflammation, University of Leicester, Leicester, UK.,Centre for Cancer Outcomes, University College London Hospitals NHS Foundation Trust, London, UK
| | - Paul Dhillon
- Respiratory Medicine, University Hospitals Coventry and Warwickshire, Coventry, UK
| | - Kishore Sridharan
- Dept of Thoracic Medicine, Sunderland Royal Hospital, Sunderland, UK
| | - Andrew G Nicholson
- Dept of Histopathology, Royal Brompton Hospital and Harefield NHS Foundation Trust and National Heart and Lung Institute, London, UK
| | - Simon Padley
- Radiology, Royal Brompton Hospital and National Heart and Lung Institute, Imperial College London, London, UK
| | - Magali N Taylor
- Radiology (Imaging), University College Hospital, London, UK
| | - Asia Ahmed
- Radiology (Imaging), University College Hospital, London, UK
| | - Jack Allen
- Cancer Research UK and UCL Cancer Trials Centre, London, UK
| | - Yenting Ngai
- Cancer Research UK and UCL Cancer Trials Centre, London, UK
| | | | | | - Sarah Lewis
- Research and Development, Royal Papworth Hospital, Cambridge, UK
| | - Dahmane Oukrif
- Dept of Pathology, University College Hospital, London, UK
| | - Pamela Rabbitts
- Leeds Institute of Cancer and Pathology (LICAP), University of Leeds, Leeds, UK
| | | | - Allan Hackshaw
- Cancer Research UK and UCL Cancer Trials Centre, London, UK.,These authors are joint lead authors
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10
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Glaire MA, Domingo E, Sveen A, Bruun J, Nesbakken A, Nicholson G, Novelli M, Lawson K, Oukrif D, Kildal W, Danielsen HE, Kerr R, Kerr D, Tomlinson I, Lothe RA, Church DN. Correction: Tumour-infiltrating CD8 + lymphocytes and colorectal cancer recurrence by tumour and nodal stage. Br J Cancer 2019; 121:807. [PMID: 31548598 PMCID: PMC6888835 DOI: 10.1038/s41416-019-0590-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Affiliation(s)
- Mark A Glaire
- Cancer Genomics and Immunology Group, The Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Enric Domingo
- Cancer Genomics and Immunology Group, The Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
- Department of Oncology, University of Oxford, Oxford, UK
| | - Anita Sveen
- Department of Molecular Oncology, Institute for Cancer Research & K.G. Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, Oslo, Norway
| | - Jarle Bruun
- Department of Molecular Oncology, Institute for Cancer Research & K.G. Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, Oslo, Norway
| | - Arild Nesbakken
- Department of Gastroenterological Surgery & K.G. Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, Oslo, Norway
- Institute for Clinical Medicine, University of Oslo, Oslo, Norway
| | | | - Marco Novelli
- Department of Histopathology, UCL, Rockefeller Building, University Street, London, WC1E 6JJ, UK
| | - Kay Lawson
- Department of Histopathology, UCL, Rockefeller Building, University Street, London, WC1E 6JJ, UK
| | - Dahmane Oukrif
- Department of Histopathology, UCL, Rockefeller Building, University Street, London, WC1E 6JJ, UK
| | - Wanja Kildal
- Institute for Cancer Genetics and Informatics, Oslo University Hospital, Oslo, Norway
| | - Havard E Danielsen
- Institute for Cancer Genetics and Informatics, Oslo University Hospital, Oslo, Norway
- Department of Informatics, University of Oslo, Oslo, Norway
- Nuffield Division of Clinical Laboratory Sciences, University of Oxford, Oxford, OX3 9 DU, UK
| | - Rachel Kerr
- Oxford Cancer Centre, Churchill Hospital, Oxford University Hospitals Foundation NHS Trust, Oxford, UK
| | - David Kerr
- Nuffield Division of Clinical Laboratory Sciences, University of Oxford, Oxford, OX3 9 DU, UK
| | - Ian Tomlinson
- Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Ragnhild A Lothe
- Department of Molecular Oncology, Institute for Cancer Research & K.G. Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, Oslo, Norway
- Institute for Clinical Medicine, University of Oslo, Oslo, Norway
| | - David N Church
- Cancer Genomics and Immunology Group, The Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK.
- Oxford Cancer Centre, Churchill Hospital, Oxford University Hospitals Foundation NHS Trust, Oxford, UK.
- Oxford NIHR Comprehensive Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK.
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11
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Glaire MA, Domingo E, Sveen A, Bruun J, Nesbakken A, Nicholson G, Novelli M, Lawson K, Oukrif D, Kildal W, Danielsen HE, Kerr R, Kerr D, Tomlinson I, Lothe RA, Church DN. Tumour-infiltrating CD8 + lymphocytes and colorectal cancer recurrence by tumour and nodal stage. Br J Cancer 2019; 121:474-482. [PMID: 31388185 PMCID: PMC6738075 DOI: 10.1038/s41416-019-0540-4] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 07/10/2019] [Accepted: 07/18/2019] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Intratumoural T-cell infiltrate intensity cortes wrelaith clinical outcome in stage II/III colorectal cancer (CRC). We aimed to determine whether this association varies across this heterogeneous group. METHODS We performed a pooled analysis of 1804 CRCs from the QUASAR2 and VICTOR trials. Intratumoural CD8+ and CD3+ densities were quantified by immunohistochemistry in tissue microarray (TMA) cores, and their association with clinical outcome analysed by Cox regression. We validated our results using publicly available gene expression data in a pooled analysis of 1375 CRCs from seven independent series. RESULTS In QUASAR2, intratumoural CD8+ was a stronger predictor of CRC recurrence than CD3+ and showed similar discriminative ability to both markers in combination. Pooled multivariable analysis of both trials showed increasing CD8+ density was associated with reduced recurrence risk independent of confounders including DNA mismatch repair deficiency, POLE mutation and chromosomal instability (multivariable hazard ratio [HR] for each two-fold increase = 0.92, 95%CI = 0.87-0.97, P = 3.6 × 10-3). This association was not uniform across risk strata defined by tumour and nodal stage: absent in low-risk (pT3,N0) cases (HR = 1.03, 95%CI = 0.87-1.21, P = 0.75), modest in intermediate-risk (pT4,N0 or pT1-3,N1-2) cases (HR = 0.92, 95%CI = 0.86-1.0, P = 0.046) and strong in high-risk (pT4,N1-2) cases (HR = 0.87, 95%CI = 0.79-0.97, P = 9.4 × 10-3); PINTERACTION = 0.090. Analysis of tumour CD8A expression in the independent validation cohort revealed similar variation in prognostic value across risk strata (PINTERACTION = 0.048). CONCLUSIONS The prognostic value of intratumoural CD8+ cell infiltration in stage II/III CRC varies across tumour and nodal risk strata.
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Affiliation(s)
- Mark A Glaire
- Cancer Genomics and Immunology Group, The Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Enric Domingo
- Cancer Genomics and Immunology Group, The Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
- Department of Oncology, University of Oxford, Oxford, UK
| | - Anita Sveen
- Department of Molecular Oncology, Institute for Cancer Research & K.G. Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, Oslo, Norway
| | - Jarle Bruun
- Department of Molecular Oncology, Institute for Cancer Research & K.G. Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, Oslo, Norway
| | - Arild Nesbakken
- Department of Gastroenterological Surgery & K.G. Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, Oslo, Norway
- Institute for Clinical Medicine, University of Oslo, Oslo, Norway
| | | | - Marco Novelli
- Department of Histopathology, UCL, Rockefeller Building, University Street, London, WC1E 6JJ, UK
| | - Kay Lawson
- Department of Histopathology, UCL, Rockefeller Building, University Street, London, WC1E 6JJ, UK
| | - Dahmane Oukrif
- Department of Histopathology, UCL, Rockefeller Building, University Street, London, WC1E 6JJ, UK
| | - Wanja Kildal
- Institute for Cancer Genetics and Informatics, Oslo University Hospital, Oslo, Norway
| | - Havard E Danielsen
- Institute for Cancer Genetics and Informatics, Oslo University Hospital, Oslo, Norway
- Department of Informatics, University of Oslo, Oslo, Norway
- Nuffield Division of Clinical Laboratory Sciences, University of Oxford, Oxford, OX3 9 DU, UK
| | - Rachel Kerr
- Oxford Cancer Centre, Churchill Hospital, Oxford University Hospitals Foundation NHS Trust, Oxford, UK
| | - David Kerr
- Nuffield Division of Clinical Laboratory Sciences, University of Oxford, Oxford, OX3 9 DU, UK
| | - Ian Tomlinson
- Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Ragnhild A Lothe
- Department of Molecular Oncology, Institute for Cancer Research & K.G. Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, Oslo, Norway
- Institute for Clinical Medicine, University of Oslo, Oslo, Norway
| | - David N Church
- Cancer Genomics and Immunology Group, The Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK.
- Oxford Cancer Centre, Churchill Hospital, Oxford University Hospitals Foundation NHS Trust, Oxford, UK.
- Oxford NIHR Comprehensive Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK.
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12
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Steele CD, Tarabichi M, Oukrif D, Webster AP, Ye H, Fittall M, Lombard P, Martincorena I, Tarpey PS, Collord G, Haase K, Strauss SJ, Berisha F, Vaikkinen H, Dhami P, Jansen M, Behjati S, Amary MF, Tirabosco R, Feber A, Campbell PJ, Alexandrov LB, Van Loo P, Flanagan AM, Pillay N. Undifferentiated Sarcomas Develop through Distinct Evolutionary Pathways. Cancer Cell 2019; 35:441-456.e8. [PMID: 30889380 PMCID: PMC6428691 DOI: 10.1016/j.ccell.2019.02.002] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 11/12/2018] [Accepted: 02/06/2019] [Indexed: 01/01/2023]
Abstract
Undifferentiated sarcomas (USARCs) of adults are diverse, rare, and aggressive soft tissue cancers. Recent sequencing efforts have confirmed that USARCs exhibit one of the highest burdens of structural aberrations across human cancer. Here, we sought to unravel the molecular basis of the structural complexity in USARCs by integrating DNA sequencing, ploidy analysis, gene expression, and methylation profiling. We identified whole genome duplication as a prevalent and pernicious force in USARC tumorigenesis. Using mathematical deconvolution strategies to unravel the complex copy-number profiles and mutational timing models we infer distinct evolutionary pathways of these rare cancers. In addition, 15% of tumors exhibited raised mutational burdens that correlated with gene expression signatures of immune infiltration, and good prognosis.
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Affiliation(s)
- Christopher D Steele
- Research Department of Pathology, Cancer Institute, University College London, London WC1E 6BT, UK
| | - Maxime Tarabichi
- Cancer Genomics Laboratory, The Francis Crick Institute, London NW1 1BF, UK
| | - Dahmane Oukrif
- Research Department of Pathology, Cancer Institute, University College London, London WC1E 6BT, UK
| | - Amy P Webster
- Department of Cancer Biology, UCL Cancer Institute, University College London, London, UK
| | - Hongtao Ye
- Department of Cellular and Molecular Pathology, Royal National Orthopaedic Hospital NHS Trust, Stanmore, Middlesex HA7 4LP, UK
| | - Matthew Fittall
- Cancer Genomics Laboratory, The Francis Crick Institute, London NW1 1BF, UK
| | - Patrick Lombard
- Research Department of Pathology, Cancer Institute, University College London, London WC1E 6BT, UK
| | - Iñigo Martincorena
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Patrick S Tarpey
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Grace Collord
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Kerstin Haase
- Cancer Genomics Laboratory, The Francis Crick Institute, London NW1 1BF, UK
| | - Sandra J Strauss
- Research Department of Pathology, Cancer Institute, University College London, London WC1E 6BT, UK; Department of Oncology, University College London Hospital NHS Foundation Trust, London, NW1 2PG, UK
| | - Fitim Berisha
- Department of Cellular and Molecular Pathology, Royal National Orthopaedic Hospital NHS Trust, Stanmore, Middlesex HA7 4LP, UK
| | - Heli Vaikkinen
- Genomics and Genome Engineering Core Facility, CRUK-UCL Centre, Cancer Institute, University College London, London WC1E 6BT, UK; Research Department of Oncology, Cancer Institute, University College London, London WC1E 6BT, UK
| | - Pawan Dhami
- Genomics and Genome Engineering Core Facility, CRUK-UCL Centre, Cancer Institute, University College London, London WC1E 6BT, UK
| | - Marnix Jansen
- Research Department of Pathology, Cancer Institute, University College London, London WC1E 6BT, UK; Department of Cellular Pathology, University College London Hospital NHS Foundation Trust, London NW1 2BU, UK
| | - Sam Behjati
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK; Department of Paediatrics, University of Cambridge, Cambridge CB2 0QQ, UK
| | - M Fernanda Amary
- Department of Cellular and Molecular Pathology, Royal National Orthopaedic Hospital NHS Trust, Stanmore, Middlesex HA7 4LP, UK
| | - Roberto Tirabosco
- Department of Cellular and Molecular Pathology, Royal National Orthopaedic Hospital NHS Trust, Stanmore, Middlesex HA7 4LP, UK
| | - Andrew Feber
- Department of Targeted Intervention, Division of Surgery and Interventional Science, University College London, London WC1E 6BT, UK
| | - Peter J Campbell
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK; Department of Haematology, University of Cambridge, Hills Road, Cambridge CB2 2XY, UK
| | - Ludmil B Alexandrov
- Department of Cellular and Molecular Medicine, University of California, San Diego 92093, USA
| | - Peter Van Loo
- Cancer Genomics Laboratory, The Francis Crick Institute, London NW1 1BF, UK; Department of Human Genetics, University of Leuven, 3000 Leuven, Belgium
| | - Adrienne M Flanagan
- Research Department of Pathology, Cancer Institute, University College London, London WC1E 6BT, UK; Department of Cellular and Molecular Pathology, Royal National Orthopaedic Hospital NHS Trust, Stanmore, Middlesex HA7 4LP, UK
| | - Nischalan Pillay
- Research Department of Pathology, Cancer Institute, University College London, London WC1E 6BT, UK; Department of Cellular and Molecular Pathology, Royal National Orthopaedic Hospital NHS Trust, Stanmore, Middlesex HA7 4LP, UK.
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13
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Domingo E, Camps C, Kaisaki PJ, Parsons MJ, Mouradov D, Pentony MM, Makino S, Palmieri M, Ward RL, Hawkins NJ, Gibbs P, Askautrud H, Oukrif D, Wang H, Wood J, Tomlinson E, Bark Y, Kaur K, Johnstone EC, Palles C, Church DN, Novelli M, Danielsen HE, Sherlock J, Kerr D, Kerr R, Sieber O, Taylor JC, Tomlinson I. Mutation burden and other molecular markers of prognosis in colorectal cancer treated with curative intent: results from the QUASAR 2 clinical trial and an Australian community-based series. Lancet Gastroenterol Hepatol 2018; 3:635-643. [PMID: 30042065 PMCID: PMC6088509 DOI: 10.1016/s2468-1253(18)30117-1] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 03/06/2018] [Accepted: 03/27/2018] [Indexed: 12/24/2022]
Abstract
BACKGROUND Molecular indicators of colorectal cancer prognosis have been assessed in several studies, but most analyses have been restricted to a handful of markers. We aimed to identify prognostic biomarkers for colorectal cancer by sequencing panels of multiple driver genes. METHODS In stage II or III colorectal cancers from the QUASAR 2 open-label randomised phase 3 clinical trial and an Australian community-based series, we used targeted next-generation sequencing of 82 and 113 genes, respectively, including the main colorectal cancer drivers. We investigated molecular pathways of tumorigenesis, and analysed individual driver gene mutations, combinations of mutations, or global measures such as microsatellite instability (MSI) and mutation burden (total number of non-synonymous mutations and coding indels) for associations with relapse-free survival in univariable and multivariable models, principally Cox proportional hazards models. FINDINGS In QUASAR 2 (511 tumours), TP53, KRAS, BRAF, and GNAS mutations were independently associated with shorter relapse-free survival (p<0·035 in all cases), and total somatic mutation burden with longer survival (hazard ratio [HR] 0·81 [95% CI 0·68-0·96]; p=0·014). MSI was not independently associated with survival (HR 1·12 [95% CI 0·57-2·19]; p=0·75). We successfully validated these associations in the Australian sample set (296 tumours). In a combined analysis of both the QUASAR 2 and the Australian sample sets, mutation burden was also associated with longer survival (HR 0·84 [95% CI 0·74-0·94]; p=0·004) after exclusion of MSI-positive and POLE mutant tumours. In an extended analysis of 1732 QUASAR 2 and Australian colorectal cancers for which KRAS, BRAF, and MSI status were available, KRAS and BRAF mutations were specifically associated with poor prognosis in MSI-negative cancers. MSI-positive cancers with KRAS or BRAF mutations had better prognosis than MSI-negative cancers that were wild-type for KRAS or BRAF. Mutations in the genes NF1 and NRAS from the MAPK pathway co-occurred, and mutations in the DNA damage-response genes TP53 and ATM were mutually exclusive. We compared a prognostic model based on the gold standard of clinicopathological variables and MSI with our new model incorporating clinicopathological variables, mutation burden, and driver mutations in KRAS, BRAF, and TP53. In both QUASAR 2 and the Australian cohort, our new model was significantly better (p=0·00004 and p=0·0057, respectively, based on a likelihood ratio test). INTERPRETATION Multigene panels identified two previously unreported prognostic associations in colorectal cancer involving TP53 mutation and total mutation burden, and confirmed associations with KRAS and BRAF. Even a modest-sized gene panel can provide important information for use in clinical practice and outperform MSI-based prognostic models. FUNDING UK Technology Strategy Board, National Institute for Health Research Oxford Biomedical Research Centre, Cancer Australia Project, Cancer Council Victoria, Ludwig Institute for Cancer Research, Victorian Government.
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Affiliation(s)
- Enric Domingo
- Oxford Centre for Cancer Gene Research, Wellcome Trust Centre for Human Genetics, Oxford, UK; Genomic Medicine Theme, National Institute for Health Research Oxford Biomedical Research Centre, Wellcome Trust Centre for Human Genetics, Oxford, UK; Department of Oncology, University of Oxford, Oxford, UK.
| | - Carme Camps
- Genomic Medicine Theme, National Institute for Health Research Oxford Biomedical Research Centre, Wellcome Trust Centre for Human Genetics, Oxford, UK
| | - Pamela J Kaisaki
- Genomic Medicine Theme, National Institute for Health Research Oxford Biomedical Research Centre, Wellcome Trust Centre for Human Genetics, Oxford, UK
| | - Marie J Parsons
- Systems Biology and Personalised Medicine Division, Walter and Eliza Hall Institute of Medial Research, Parkville, VIC, Australia; Department of Surgery, University of Melbourne, Parkville, VIC, Australia
| | - Dmitri Mouradov
- Systems Biology and Personalised Medicine Division, Walter and Eliza Hall Institute of Medial Research, Parkville, VIC, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Melissa M Pentony
- Genomic Medicine Theme, National Institute for Health Research Oxford Biomedical Research Centre, Wellcome Trust Centre for Human Genetics, Oxford, UK
| | - Seiko Makino
- Oxford Centre for Cancer Gene Research, Wellcome Trust Centre for Human Genetics, Oxford, UK
| | - Michelle Palmieri
- Systems Biology and Personalised Medicine Division, Walter and Eliza Hall Institute of Medial Research, Parkville, VIC, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Robyn L Ward
- Office of the Deputy Vice-Chancellor (Research), University of Queensland, Brisbane, QLD, Australia
| | | | - Peter Gibbs
- Systems Biology and Personalised Medicine Division, Walter and Eliza Hall Institute of Medial Research, Parkville, VIC, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia; Department of Medical Oncology, Royal Melbourne Hospital, Parkville, VIC, Australia
| | - Hanne Askautrud
- Institute for Cancer Genetics and Informatics, Oslo University Hospital, Oslo, Norway
| | - Dahmane Oukrif
- Department of Histopathology, University College London, London, UK
| | - Haitao Wang
- Department of Oncology, University of Oxford, Oxford, UK
| | - Joe Wood
- Thermo Fisher Scientific, Paisley, UK
| | - Evie Tomlinson
- Department of Oncology, University of Oxford, Oxford, UK
| | - Yasmine Bark
- Department of Oncology, University of Oxford, Oxford, UK
| | - Kulvinder Kaur
- Genomic Medicine Theme, National Institute for Health Research Oxford Biomedical Research Centre, Wellcome Trust Centre for Human Genetics, Oxford, UK
| | | | - Claire Palles
- Oxford Centre for Cancer Gene Research, Wellcome Trust Centre for Human Genetics, Oxford, UK
| | - David N Church
- Oxford Centre for Cancer Gene Research, Wellcome Trust Centre for Human Genetics, Oxford, UK; Genomic Medicine Theme, National Institute for Health Research Oxford Biomedical Research Centre, Wellcome Trust Centre for Human Genetics, Oxford, UK
| | - Marco Novelli
- Department of Histopathology, University College London, London, UK
| | - Havard E Danielsen
- Institute for Cancer Genetics and Informatics, Oslo University Hospital, Oslo, Norway; Nuffield Department of Clinical and Laboratory Science, Radcliffe Department of Medicine, John Radcliffe Hospital, Oxford, UK
| | | | - David Kerr
- Nuffield Department of Clinical and Laboratory Science, Radcliffe Department of Medicine, John Radcliffe Hospital, Oxford, UK
| | - Rachel Kerr
- Department of Oncology, University of Oxford, Oxford, UK
| | - Oliver Sieber
- Systems Biology and Personalised Medicine Division, Walter and Eliza Hall Institute of Medial Research, Parkville, VIC, Australia; Department of Surgery, University of Melbourne, Parkville, VIC, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia; School of Biomedical Sciences, Monash University, Clayton, VIC, Australia
| | - Jenny C Taylor
- Genomic Medicine Theme, National Institute for Health Research Oxford Biomedical Research Centre, Wellcome Trust Centre for Human Genetics, Oxford, UK
| | - Ian Tomlinson
- Oxford Centre for Cancer Gene Research, Wellcome Trust Centre for Human Genetics, Oxford, UK; Genomic Medicine Theme, National Institute for Health Research Oxford Biomedical Research Centre, Wellcome Trust Centre for Human Genetics, Oxford, UK; Cancer Genetics and Evolution Laboratory, Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham, UK
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14
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Glaire M, Domingo E, Nicholson G, Novelli M, Lawson K, Oukrif D, Kidal W, Danielsen HE, Kerr R, Kerr DJ, Tomlinson I, Church DN. Tumour-infiltrating CD8 + lymphocytes as a prognostic marker in colorectal cancer: A retrospective, pooled analysis of the QUASAR2 and VICTOR trials. J Clin Oncol 2018. [DOI: 10.1200/jco.2018.36.15_suppl.3515] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Mark Glaire
- University of Oxford, Oxford, United Kingdom
| | - Enric Domingo
- Department of Oncology, University of Oxford, Oxford, United Kingdom
| | - George Nicholson
- Department of Statistics, University of Oxford, Oxford, United Kingdom
| | - Marco Novelli
- Department of Histopathology, UCL, London, United Kingdom
| | - Kay Lawson
- Department of Histopathology, UCL, London, United Kingdom
| | - Dahmane Oukrif
- Department of Histopathology, UCL, London, United Kingdom
| | - Wanja Kidal
- Institute for Cancer Genetics and Informatics, Oslo, Norway
| | - Havard Emil Danielsen
- Oslo University Hospital, Institute for Cancer Genetics and Informatics, Oslo, Norway
| | - Rachel Kerr
- University of Oxford, Oxford, United Kingdom
| | | | - Ian Tomlinson
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
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15
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Pye H, Butt MA, Funnell L, Reinert HW, Puccio I, Rehman Khan SU, Saouros S, Marklew JS, Stamati I, Qurashi M, Haidry R, Sehgal V, Oukrif D, Gandy M, Whitaker HC, Rodriguez-Justo M, Novelli M, Hamoudi R, Yahioglu G, Deonarain MP, Lovat LB. Using antibody directed phototherapy to target oesophageal adenocarcinoma with heterogeneous HER2 expression. Oncotarget 2018; 9:22945-22959. [PMID: 29796164 PMCID: PMC5955430 DOI: 10.18632/oncotarget.25159] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 03/28/2018] [Indexed: 12/22/2022] Open
Abstract
Early oesophageal adenocarcinoma (OA) and pre-neoplastic dysplasia may be treated with endoscopic resection and ablative techniques such as photodynamic therapy (PDT). Though effective, discrete areas of disease may be missed leading to recurrence. PDT further suffers from the side effects of off-target photosensitivity. A tumour specific and light targeted therapeutic agent with optimised pharmacokinetics could be used to destroy residual cancerous cells left behind after resection. A small molecule antibody-photosensitizer conjugate was developed targeting human epidermal growth factor receptor 2 (HER2). This was tested in an in vivo mouse model of human OA using a xenograft flank model with clinically relevant low level HER2 expression and heterogeneity. In vitro we demonstrate selective binding of the conjugate to tumour versus normal tissue. Light dependent cytotoxicity of the phototherapy agent in vitro was observed. In an in vivo OA mouse xenograft model the phototherapy agent had desirable pharmacokinetic properties for tumour uptake and blood clearance time. PDT treatment caused tumour growth arrest in all the tumours despite the tumours having a clinically defined low/negative HER2 expression level. This new phototherapy agent shows therapeutic potential for treatment of both HER2 positive and borderline/negative OA.
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Affiliation(s)
- Hayley Pye
- Department for Tissue and Energy, Division of Surgery and Interventional Science, University College London, London, UK
| | - Mohammed Adil Butt
- Department for Tissue and Energy, Division of Surgery and Interventional Science, University College London, London, UK.,Upper Gastrointestinal Service, University College London Hospitals NHS Foundation Trust, London, UK
| | - Laura Funnell
- Department for Tissue and Energy, Division of Surgery and Interventional Science, University College London, London, UK
| | - Halla W Reinert
- Department for Tissue and Energy, Division of Surgery and Interventional Science, University College London, London, UK
| | - Ignazio Puccio
- Department for Tissue and Energy, Division of Surgery and Interventional Science, University College London, London, UK
| | - Saif U Rehman Khan
- Department for Tissue and Energy, Division of Surgery and Interventional Science, University College London, London, UK
| | - Savvas Saouros
- Antikor BioPharma, Stevenage, UK.,Imperial College London, London, UK
| | | | | | - Maryam Qurashi
- Department for Tissue and Energy, Division of Surgery and Interventional Science, University College London, London, UK.,Imperial College London, London, UK
| | - Rehan Haidry
- Upper Gastrointestinal Service, University College London Hospitals NHS Foundation Trust, London, UK
| | - Vinay Sehgal
- Department for Tissue and Energy, Division of Surgery and Interventional Science, University College London, London, UK.,Upper Gastrointestinal Service, University College London Hospitals NHS Foundation Trust, London, UK
| | - Dahmane Oukrif
- Department of Pathology, University College London, London, UK
| | - Michael Gandy
- Department for Tissue and Energy, Division of Surgery and Interventional Science, University College London, London, UK
| | - Hayley C Whitaker
- Department for Tissue and Energy, Division of Surgery and Interventional Science, University College London, London, UK
| | | | - Marco Novelli
- Department of Pathology, University College London, London, UK
| | - Rifat Hamoudi
- Department for Tissue and Energy, Division of Surgery and Interventional Science, University College London, London, UK.,Sharjah Institute for Medical Research, College of Medicine, University of Sharjah, Sharjah, UAE
| | - Gokhan Yahioglu
- Antikor BioPharma, Stevenage, UK.,Imperial College London, London, UK
| | - Mahendra P Deonarain
- Department for Tissue and Energy, Division of Surgery and Interventional Science, University College London, London, UK.,Antikor BioPharma, Stevenage, UK.,Imperial College London, London, UK
| | - Laurence B Lovat
- Department for Tissue and Energy, Division of Surgery and Interventional Science, University College London, London, UK.,Upper Gastrointestinal Service, University College London Hospitals NHS Foundation Trust, London, UK
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16
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Abbosh C, Birkbak NJ, Wilson GA, Jamal-Hanjani M, Constantin T, Salari R, Le Quesne J, Moore DA, Veeriah S, Rosenthal R, Marafioti T, Kirkizlar E, Watkins TBK, McGranahan N, Ward S, Martinson L, Riley J, Fraioli F, Al Bakir M, Grönroos E, Zambrana F, Endozo R, Bi WL, Fennessy FM, Sponer N, Johnson D, Laycock J, Shafi S, Czyzewska-Khan J, Rowan A, Chambers T, Matthews N, Turajlic S, Hiley C, Lee SM, Forster MD, Ahmad T, Falzon M, Borg E, Lawrence D, Hayward M, Kolvekar S, Panagiotopoulos N, Janes SM, Thakrar R, Ahmed A, Blackhall F, Summers Y, Hafez D, Naik A, Ganguly A, Kareht S, Shah R, Joseph L, Quinn AM, Crosbie PA, Naidu B, Middleton G, Langman G, Trotter S, Nicolson M, Remmen H, Kerr K, Chetty M, Gomersall L, Fennell DA, Nakas A, Rathinam S, Anand G, Khan S, Russell P, Ezhil V, Ismail B, Irvin-Sellers M, Prakash V, Lester JF, Kornaszewska M, Attanoos R, Adams H, Davies H, Oukrif D, Akarca AU, Hartley JA, Lowe HL, Lock S, Iles N, Bell H, Ngai Y, Elgar G, Szallasi Z, Schwarz RF, Herrero J, Stewart A, Quezada SA, Peggs KS, Van Loo P, Dive C, Lin CJ, Rabinowitz M, Aerts HJWL, Hackshaw A, Shaw JA, Zimmermann BG, Swanton C. Corrigendum: Phylogenetic ctDNA analysis depicts early-stage lung cancer evolution. Nature 2018; 554:264. [PMID: 29258292 DOI: 10.1038/nature25161] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
This corrects the article DOI: 10.1038/nature22364.
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17
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Abbosh C, Birkbak NJ, Wilson GA, Jamal-Hanjani M, Constantin T, Salari R, Le Quesne J, Moore DA, Veeriah S, Rosenthal R, Marafioti T, Kirkizlar E, Watkins TBK, McGranahan N, Ward S, Martinson L, Riley J, Fraioli F, Al Bakir M, Grönroos E, Zambrana F, Endozo R, Bi WL, Fennessy FM, Sponer N, Johnson D, Laycock J, Shafi S, Czyzewska-Khan J, Rowan A, Chambers T, Matthews N, Turajlic S, Hiley C, Lee SM, Forster MD, Ahmad T, Falzon M, Borg E, Lawrence D, Hayward M, Kolvekar S, Panagiotopoulos N, Janes SM, Thakrar R, Ahmed A, Blackhall F, Summers Y, Hafez D, Naik A, Ganguly A, Kareht S, Shah R, Joseph L, Marie Quinn A, Crosbie PA, Naidu B, Middleton G, Langman G, Trotter S, Nicolson M, Remmen H, Kerr K, Chetty M, Gomersall L, Fennell DA, Nakas A, Rathinam S, Anand G, Khan S, Russell P, Ezhil V, Ismail B, Irvin-Sellers M, Prakash V, Lester JF, Kornaszewska M, Attanoos R, Adams H, Davies H, Oukrif D, Akarca AU, Hartley JA, Lowe HL, Lock S, Iles N, Bell H, Ngai Y, Elgar G, Szallasi Z, Schwarz RF, Herrero J, Stewart A, Quezada SA, Peggs KS, Van Loo P, Dive C, Lin CJ, Rabinowitz M, Aerts HJWL, Hackshaw A, Shaw JA, Zimmermann BG, Swanton C. Phylogenetic ctDNA analysis depicts early-stage lung cancer evolution. Nature 2017; 545:446-451. [PMID: 28445469 PMCID: PMC5812436 DOI: 10.1038/nature22364] [Citation(s) in RCA: 1092] [Impact Index Per Article: 156.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 04/13/2017] [Indexed: 12/13/2022]
Abstract
The early detection of relapse following primary surgery for non-small-cell lung cancer and the characterization of emerging subclones, which seed metastatic sites, might offer new therapeutic approaches for limiting tumour recurrence. The ability to track the evolutionary dynamics of early-stage lung cancer non-invasively in circulating tumour DNA (ctDNA) has not yet been demonstrated. Here we use a tumour-specific phylogenetic approach to profile the ctDNA of the first 100 TRACERx (Tracking Non-Small-Cell Lung Cancer Evolution Through Therapy (Rx)) study participants, including one patient who was also recruited to the PEACE (Posthumous Evaluation of Advanced Cancer Environment) post-mortem study. We identify independent predictors of ctDNA release and analyse the tumour-volume detection limit. Through blinded profiling of postoperative plasma, we observe evidence of adjuvant chemotherapy resistance and identify patients who are very likely to experience recurrence of their lung cancer. Finally, we show that phylogenetic ctDNA profiling tracks the subclonal nature of lung cancer relapse and metastasis, providing a new approach for ctDNA-driven therapeutic studies.
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MESH Headings
- Biopsy/methods
- Carcinoma, Non-Small-Cell Lung/blood
- Carcinoma, Non-Small-Cell Lung/genetics
- Carcinoma, Non-Small-Cell Lung/pathology
- Carcinoma, Non-Small-Cell Lung/surgery
- Cell Lineage/genetics
- Cell Tracking
- Clone Cells/metabolism
- Clone Cells/pathology
- DNA Mutational Analysis
- DNA, Neoplasm/blood
- DNA, Neoplasm/genetics
- Disease Progression
- Drug Resistance, Neoplasm/genetics
- Early Detection of Cancer/methods
- Evolution, Molecular
- Humans
- Limit of Detection
- Lung Neoplasms/blood
- Lung Neoplasms/genetics
- Lung Neoplasms/pathology
- Lung Neoplasms/surgery
- Multiplex Polymerase Chain Reaction
- Neoplasm Metastasis/diagnosis
- Neoplasm Metastasis/genetics
- Neoplasm Metastasis/pathology
- Neoplasm Recurrence, Local/diagnosis
- Neoplasm Recurrence, Local/genetics
- Neoplasm Recurrence, Local/pathology
- Postoperative Care/methods
- Reproducibility of Results
- Tumor Burden
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Affiliation(s)
- Christopher Abbosh
- Cancer Research UK Lung Cancer Centre of Excellence London and Manchester, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
| | - Nicolai J Birkbak
- Cancer Research UK Lung Cancer Centre of Excellence London and Manchester, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
- Translational Cancer Therapeutics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Gareth A Wilson
- Cancer Research UK Lung Cancer Centre of Excellence London and Manchester, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
- Translational Cancer Therapeutics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Mariam Jamal-Hanjani
- Cancer Research UK Lung Cancer Centre of Excellence London and Manchester, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
| | - Tudor Constantin
- Natera Inc., 201 Industrial Road, San Carlos, California 94070, USA
| | - Raheleh Salari
- Natera Inc., 201 Industrial Road, San Carlos, California 94070, USA
| | - John Le Quesne
- Cancer Studies, University of Leicester, Leicester LE2 7LX, UK
| | - David A Moore
- Cancer Studies, University of Leicester, Leicester LE2 7LX, UK
| | - Selvaraju Veeriah
- Cancer Research UK Lung Cancer Centre of Excellence London and Manchester, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
| | - Rachel Rosenthal
- Cancer Research UK Lung Cancer Centre of Excellence London and Manchester, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
| | - Teresa Marafioti
- Cancer Research UK Lung Cancer Centre of Excellence London and Manchester, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
- Department of Pathology, University College London Hospitals, 21 University Street, London WC1 6JJ, UK
| | - Eser Kirkizlar
- Natera Inc., 201 Industrial Road, San Carlos, California 94070, USA
| | - Thomas B K Watkins
- Cancer Research UK Lung Cancer Centre of Excellence London and Manchester, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
- Translational Cancer Therapeutics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Nicholas McGranahan
- Cancer Research UK Lung Cancer Centre of Excellence London and Manchester, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
- Translational Cancer Therapeutics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Sophia Ward
- Cancer Research UK Lung Cancer Centre of Excellence London and Manchester, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
- Translational Cancer Therapeutics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
- Advanced Sequencing Facility, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Luke Martinson
- Cancer Studies, University of Leicester, Leicester LE2 7LX, UK
| | - Joan Riley
- Cancer Studies, University of Leicester, Leicester LE2 7LX, UK
| | - Francesco Fraioli
- Department of Nuclear Medicine, University College London Hospitals, 235 Euston Road, Fitzrovia, London, NW1 2BU, UK
| | - Maise Al Bakir
- Translational Cancer Therapeutics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Eva Grönroos
- Translational Cancer Therapeutics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Francisco Zambrana
- Cancer Research UK Lung Cancer Centre of Excellence London and Manchester, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
| | - Raymondo Endozo
- Department of Nuclear Medicine, University College London Hospitals, 235 Euston Road, Fitzrovia, London, NW1 2BU, UK
| | - Wenya Linda Bi
- Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
- Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Fiona M Fennessy
- Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
- Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Nicole Sponer
- Natera Inc., 201 Industrial Road, San Carlos, California 94070, USA
| | - Diana Johnson
- Cancer Research UK Lung Cancer Centre of Excellence London and Manchester, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
| | - Joanne Laycock
- Cancer Research UK Lung Cancer Centre of Excellence London and Manchester, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
| | - Seema Shafi
- Cancer Research UK Lung Cancer Centre of Excellence London and Manchester, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
| | - Justyna Czyzewska-Khan
- Cancer Research UK Lung Cancer Centre of Excellence London and Manchester, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
| | - Andrew Rowan
- Translational Cancer Therapeutics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Tim Chambers
- Translational Cancer Therapeutics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
- Advanced Sequencing Facility, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Nik Matthews
- Advanced Sequencing Facility, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
- Tumour Profiling Unit Genomics Facility, The Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK
| | - Samra Turajlic
- Translational Cancer Therapeutics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
- Renal and Skin Units, The Royal Marsden Hospital, London SW3 6JJ, UK
| | - Crispin Hiley
- Cancer Research UK Lung Cancer Centre of Excellence London and Manchester, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
- Translational Cancer Therapeutics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Siow Ming Lee
- Cancer Research UK Lung Cancer Centre of Excellence London and Manchester, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
- Department of Oncology, University College London Hospitals, 250 Euston Road, London NW1 2BU, UK
| | - Martin D Forster
- Cancer Research UK Lung Cancer Centre of Excellence London and Manchester, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
- Department of Oncology, University College London Hospitals, 250 Euston Road, London NW1 2BU, UK
| | - Tanya Ahmad
- Department of Oncology, University College London Hospitals, 250 Euston Road, London NW1 2BU, UK
| | - Mary Falzon
- Department of Pathology, University College London Hospitals, 21 University Street, London WC1 6JJ, UK
| | - Elaine Borg
- Department of Pathology, University College London Hospitals, 21 University Street, London WC1 6JJ, UK
| | - David Lawrence
- Department of Cardiothoracic Surgery, University College London Hospitals, 235 Euston Road, Fitzrovia, London NW1 2BU, UK
| | - Martin Hayward
- Department of Cardiothoracic Surgery, University College London Hospitals, 235 Euston Road, Fitzrovia, London NW1 2BU, UK
| | - Shyam Kolvekar
- Department of Cardiothoracic Surgery, University College London Hospitals, 235 Euston Road, Fitzrovia, London NW1 2BU, UK
| | - Nikolaos Panagiotopoulos
- Department of Cardiothoracic Surgery, University College London Hospitals, 235 Euston Road, Fitzrovia, London NW1 2BU, UK
| | - Sam M Janes
- Cancer Research UK Lung Cancer Centre of Excellence London and Manchester, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
- Department of Respiratory Medicine, University College London Hospitals, 235 Euston Road, Fitzrovia, London NW1 2BU, UK
- Lungs for Living Research Centre, UCL Respiratory, Division of Medicine, Rayne Building, University College London, 5 University Street, London WC1E 6JF, UK
| | - Ricky Thakrar
- Department of Respiratory Medicine, University College London Hospitals, 235 Euston Road, Fitzrovia, London NW1 2BU, UK
| | - Asia Ahmed
- Department of Radiology, University College London Hospitals, 235 Euston Road, Fitzrovia, London NW1 2BU, UK
| | - Fiona Blackhall
- Institute of Cancer Studies, University of Manchester, Oxford Road, Manchester M13 9PL, UK
- The Christie Hospital, Manchester M20 4BX, UK
| | | | - Dina Hafez
- Natera Inc., 201 Industrial Road, San Carlos, California 94070, USA
| | - Ashwini Naik
- Natera Inc., 201 Industrial Road, San Carlos, California 94070, USA
| | - Apratim Ganguly
- Natera Inc., 201 Industrial Road, San Carlos, California 94070, USA
| | - Stephanie Kareht
- Natera Inc., 201 Industrial Road, San Carlos, California 94070, USA
| | - Rajesh Shah
- Department of Cardiothoracic Surgery, University Hospital South Manchester, Manchester M23 9LT, UK
| | - Leena Joseph
- Department of Pathology, University Hospital South Manchester, Manchester M23 9LT, UK
| | - Anne Marie Quinn
- Department of Pathology, University Hospital South Manchester, Manchester M23 9LT, UK
| | - Phil A Crosbie
- North West Lung Centre, University Hospital South Manchester, Manchester M23 9LT, UK
| | - Babu Naidu
- Department of Thoracic Surgery, Birmingham Heartlands Hospital, Birmingham B9 5SS, UK
- Institute of Inflammation and Ageing, University of Birmingham, Birmingham B15 2TT, UK. University College London Hospitals NHS Foundation Trust, London, UK
| | - Gary Middleton
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham B15 2TT, UK
| | - Gerald Langman
- Department of Cellular Pathology, Birmingham Heartlands Hospital, Birmingham B9 5SS, UK
| | - Simon Trotter
- Department of Cellular Pathology, Birmingham Heartlands Hospital, Birmingham B9 5SS, UK
| | - Marianne Nicolson
- Department of Medical Oncology, Aberdeen University Medical School and Aberdeen Royal Infirmary, Aberdeen AB25 2ZN, UK
| | - Hardy Remmen
- Department of Cardiothoracic Surgery, Aberdeen University Medical School and Aberdeen Royal Infirmary, Aberdeen AB25 2ZD, UK
| | - Keith Kerr
- Department of Pathology, Aberdeen University Medical School and Aberdeen Royal Infirmary, Aberdeen AB25 2ZD, UK
| | - Mahendran Chetty
- Department of Respiratory Medicine, Aberdeen University Medical School and Aberdeen Royal Infirmary, Aberdeen AB25 2ZN, UK
| | - Lesley Gomersall
- Department of Radiology, Aberdeen University Medical School and Aberdeen Royal Infirmary, Aberdeen AB25 2ZN, UK
| | - Dean A Fennell
- Cancer Studies, University of Leicester, Leicester LE2 7LX, UK
| | - Apostolos Nakas
- Department of Thoracic Surgery, Glenfield Hospital, Leicester LE3 9QP, UK
| | - Sridhar Rathinam
- Department of Thoracic Surgery, Glenfield Hospital, Leicester LE3 9QP, UK
| | - Girija Anand
- Department of Radiotherapy, North Middlesex University Hospital, London N18 1QX, UK
| | - Sajid Khan
- Department of Respiratory Medicine, Royal Free Hospital, Pond Street, London NW3 2QG, UK
- Department of Respiratory Medicine, Barnet and Chase Farm Hospitals, Wellhouse Lane, Barnet EN5 3DJ, UK
| | - Peter Russell
- Department of Respiratory Medicine, The Princess Alexandra Hospital, Hamstel Road, Harlow CM20 1QX, UK
| | - Veni Ezhil
- Department of Clinical Oncology, St.Luke's Cancer Centre, Royal Surrey County Hospital, Guildford GU2 7XX, UK
| | - Babikir Ismail
- Department of Pathology, Ashford and St. Peter's Hospital, Guildford Road, Chertsey, Surrey KT16 0PZ, UK
| | - Melanie Irvin-Sellers
- Department of Respiratory Medicine, Ashford and St. Peter's Hospital, Guildford Road, Chertsey, Surrey KT16 0PZ, UK
| | - Vineet Prakash
- Department of Radiology, Ashford and St. Peter's Hospital, Guildford Road, Chertsey, Surrey KT16 0PZ, UK
| | - Jason F Lester
- Department of Clinical Oncology, Velindre Hospital, Cardiff CF14 2TL, UK
| | | | - Richard Attanoos
- Department of Cellular Pathology, University Hospital of Wales and Cardiff University, Heath Park, Cardiff, UK
| | - Haydn Adams
- Department of Radiology, University Hospital Llandough, Cardiff CF64 2XX, UK
| | - Helen Davies
- Department of Respiratory Medicine, University Hospital Llandough, Cardiff CF64 2XX, UK
| | - Dahmane Oukrif
- Cancer Research UK Lung Cancer Centre of Excellence London and Manchester, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
| | - Ayse U Akarca
- Cancer Research UK Lung Cancer Centre of Excellence London and Manchester, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
| | - John A Hartley
- University College London Experimental Cancer Medicine Centre GCLP Facility, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
| | - Helen L Lowe
- University College London Experimental Cancer Medicine Centre GCLP Facility, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
| | - Sara Lock
- Department of Respiratory Medicine, The Whittington Hospital NHS Trust, London, N19 5NF, UK
| | - Natasha Iles
- University College London, Cancer Research UK and UCL Cancer Trials Centre, London W1T 4TJ, UK
| | - Harriet Bell
- University College London, Cancer Research UK and UCL Cancer Trials Centre, London W1T 4TJ, UK
| | - Yenting Ngai
- University College London, Cancer Research UK and UCL Cancer Trials Centre, London W1T 4TJ, UK
| | - Greg Elgar
- Translational Cancer Therapeutics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
- Advanced Sequencing Facility, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Zoltan Szallasi
- Centre for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, 2800 Lyngby, Denmark
- Computational Health Informatics Program (CHIP), Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
- MTA-SE-NAP, Brain Metastasis Research Group, 2nd Department of Pathology, Semmelweis University, 1091 Budapest, Hungary
| | - Roland F Schwarz
- Berlin Institute for Medical Systems Biology, Max Delbrueck Center for Molecular Medicine, Berlin, Germany
| | - Javier Herrero
- Bill Lyons Informatics Centre, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
| | - Aengus Stewart
- Department of Bioinformatics and Biostatistics, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Sergio A Quezada
- Cancer Immunology Unit, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
| | - Karl S Peggs
- Cancer Immunology Unit, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
- Research Department of Haematology, University College Cancer Institute, London WC1E 6DD, UK
| | - Peter Van Loo
- Cancer Genomics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
- Department of Human Genetics, University of Leuven, B-3000 Leuven, Belgium
| | - Caroline Dive
- Cancer Research UK Lung Cancer Centre of Excellence London and Manchester, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
- Cancer Research UK Manchester Institute, University of Manchester, Wilmslow Road, Manchester M20 4BX, UK
| | - C Jimmy Lin
- Natera Inc., 201 Industrial Road, San Carlos, California 94070, USA
| | | | - Hugo J W L Aerts
- Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
- Harvard Medical School, Boston, Massachusetts 02115, USA
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215-5450, USA
| | - Allan Hackshaw
- University College London, Cancer Research UK and UCL Cancer Trials Centre, London W1T 4TJ, UK
| | - Jacqui A Shaw
- Cancer Studies, University of Leicester, Leicester LE2 7LX, UK
| | | | - Charles Swanton
- Cancer Research UK Lung Cancer Centre of Excellence London and Manchester, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
- Translational Cancer Therapeutics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
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18
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Butt MA, Pye H, Haidry RJ, Oukrif D, Khan SUR, Puccio I, Gandy M, Reinert HW, Bloom E, Rashid M, Yahioglu G, Deonarain MP, Hamoudi R, Rodriguez-Justo M, Novelli MR, Lovat LB. Upregulation of mucin glycoprotein MUC1 in the progression to esophageal adenocarcinoma and therapeutic potential with a targeted photoactive antibody-drug conjugate. Oncotarget 2017; 8:25080-25096. [PMID: 28212575 PMCID: PMC5421911 DOI: 10.18632/oncotarget.15340] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Accepted: 01/24/2017] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Mucin glycoprotein 1 (MUC1) is a glycosylated transmembrane protein on epithelial cells. We investigate MUC1 as a therapeutic target in Barrett's epithelium (BE) and esophageal adenocarcinoma (EA) and provide proof of concept for a light based therapy targeting MUC1. RESULTS MUC1 was present in 21% and 30% of significantly enriched pathways comparing BE and EA to squamous epithelium respectively. MUC1 gene expression was x2.3 and x2.2 higher in BE (p=<0.001) and EA (p=0.03). MUC1 immunohistochemical expression increased during progression to EA and followed tumor invasion. HuHMFG1 based photosensitive antibody drug conjugates (ADC) showed cell internalization, MUC1 selective and light-dependent cytotoxicity (p=0.0006) and superior toxicity over photosensitizer alone (p=0.0022). METHODS Gene set enrichment analysis (GSEA) evaluated pathways during BE and EA development and quantified MUC1 gene expression. Immunohistochemistry and flow cytometry evaluated the anti-MUC1 antibody HuHMFG1 in esophageal cells of varying pathological grade. Confocal microscopy examined HuHMFG1 internalization and HuHMFG1 ADCs were created to deliver a MUC1 targeted phototoxic payload. CONCLUSIONS MUC1 is a promising target in EA. Molecular and light based targeting of MUC1 with a photosensitive ADC is effective in vitro and after development may enable treatment of locoregional tumors endoscopically.
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Affiliation(s)
- Mohammed Adil Butt
- Department for Tissue & Energy, University College London, London, UK
- Upper Gastrointestinal Service, University College London Hospitals NHS Foundation Trust, London, UK
| | - Hayley Pye
- Department for Tissue & Energy, University College London, London, UK
| | - Rehan J. Haidry
- Upper Gastrointestinal Service, University College London Hospitals NHS Foundation Trust, London, UK
| | - Dahmane Oukrif
- Department of Pathology, University College London, London, UK
| | | | - Ignazio Puccio
- Department for Tissue & Energy, University College London, London, UK
| | - Michael Gandy
- Department for Tissue & Energy, University College London, London, UK
| | - Halla W. Reinert
- Department for Tissue & Energy, University College London, London, UK
| | - Ellie Bloom
- Department for Tissue & Energy, University College London, London, UK
| | | | - Gokhan Yahioglu
- Antikor BioPharma, Stevenage Bioscience Catalyst, Hertfordshire, UK
- Department of Chemistry, Imperial College London, London, UK
| | - Mahendra P. Deonarain
- Department for Tissue & Energy, University College London, London, UK
- Antikor BioPharma, Stevenage Bioscience Catalyst, Hertfordshire, UK
- Department of Chemistry, Imperial College London, London, UK
| | - Rifat Hamoudi
- Department for Tissue & Energy, University College London, London, UK
| | | | | | - Laurence B. Lovat
- Department for Tissue & Energy, University College London, London, UK
- Upper Gastrointestinal Service, University College London Hospitals NHS Foundation Trust, London, UK
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19
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Karpathakis A, Dibra H, Pipinikas C, Feber A, Morris T, Francis J, Oukrif D, Mandair D, Pericleous M, Mohmaduvesh M, Serra S, Ogunbiyi O, Novelli M, Luong T, Asa SL, Kulke M, Toumpanakis C, Meyer T, Caplin M, Beck S, Thirlwell C. Progressive epigenetic dysregulation in neuroendocrine tumour liver metastases. Endocr Relat Cancer 2017; 24:L21-L25. [PMID: 28049633 DOI: 10.1530/erc-16-0419] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2016] [Accepted: 12/20/2016] [Indexed: 02/03/2023]
Affiliation(s)
- Anna Karpathakis
- University College LondonLondon, UK
- 2The Royal Free HospitalLondon, UK
| | | | | | | | | | | | | | - Dalvinder Mandair
- University College LondonLondon, UK
- 2The Royal Free HospitalLondon, UK
| | | | | | - Stefano Serra
- UHN Princess Margaret Cancer CentreToronto, Ontario, Canada
| | | | | | | | - Sylvia L Asa
- UHN Princess Margaret Cancer CentreToronto, Ontario, Canada
| | - Matthew Kulke
- DanaFaber Cancer InstituteBoston, Massachusetts, USA
| | | | - Tim Meyer
- University College LondonLondon, UK
- 2The Royal Free HospitalLondon, UK
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20
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López-García C, Sansregret L, Domingo E, McGranahan N, Hobor S, Birkbak NJ, Horswell S, Grönroos E, Favero F, Rowan AJ, Matthews N, Begum S, Phillimore B, Burrell R, Oukrif D, Spencer-Dene B, Kovac M, Stamp G, Stewart A, Danielsen H, Novelli M, Tomlinson I, Swanton C. BCL9L Dysfunction Impairs Caspase-2 Expression Permitting Aneuploidy Tolerance in Colorectal Cancer. Cancer Cell 2017; 31:79-93. [PMID: 28073006 PMCID: PMC5225404 DOI: 10.1016/j.ccell.2016.11.001] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Revised: 08/05/2016] [Accepted: 10/28/2016] [Indexed: 01/03/2023]
Abstract
Chromosomal instability (CIN) contributes to cancer evolution, intratumor heterogeneity, and drug resistance. CIN is driven by chromosome segregation errors and a tolerance phenotype that permits the propagation of aneuploid genomes. Through genomic analysis of colorectal cancers and cell lines, we find frequent loss of heterozygosity and mutations in BCL9L in aneuploid tumors. BCL9L deficiency promoted tolerance of chromosome missegregation events, propagation of aneuploidy, and genetic heterogeneity in xenograft models likely through modulation of Wnt signaling. We find that BCL9L dysfunction contributes to aneuploidy tolerance in both TP53-WT and mutant cells by reducing basal caspase-2 levels and preventing cleavage of MDM2 and BID. Efforts to exploit aneuploidy tolerance mechanisms and the BCL9L/caspase-2/BID axis may limit cancer diversity and evolution.
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Affiliation(s)
- Carlos López-García
- Translational Cancer Therapeutics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Laurent Sansregret
- Translational Cancer Therapeutics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Enric Domingo
- Oxford Centre for Cancer Gene Research, The Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, OX3 7BN UK; Department of Oncology, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Nicholas McGranahan
- Translational Cancer Therapeutics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Translational Cancer Therapeutics Laboratory, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC2E 6DD, UK
| | - Sebastijan Hobor
- Translational Cancer Therapeutics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Nicolai Juul Birkbak
- Translational Cancer Therapeutics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Translational Cancer Therapeutics Laboratory, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC2E 6DD, UK
| | - Stuart Horswell
- Bioinformatics Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Eva Grönroos
- Translational Cancer Therapeutics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Francesco Favero
- Translational Cancer Therapeutics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Cancer System Biology, Centre for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby 2800, Denmark
| | - Andrew J Rowan
- Translational Cancer Therapeutics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Nicholas Matthews
- Advanced Sequencing Facility, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Sharmin Begum
- Advanced Sequencing Facility, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Benjamin Phillimore
- Advanced Sequencing Facility, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Rebecca Burrell
- Translational Cancer Therapeutics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Dahmane Oukrif
- Research Department of Pathology, University College London Medical School, University Street, London WC1E 6JJ, UK
| | - Bradley Spencer-Dene
- Experimental Histopathology Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Michal Kovac
- Oxford Centre for Cancer Gene Research, The Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, OX3 7BN UK
| | - Gordon Stamp
- Experimental Histopathology Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Aengus Stewart
- Bioinformatics Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Havard Danielsen
- Institute for Cancer Genetics and Informatics, Norwegian Radium Hospital, Oslo University Hospital, Ullernchausseen 70, 0379 Oslo, Norway
| | - Marco Novelli
- Research Department of Pathology, University College London Medical School, University Street, London WC1E 6JJ, UK
| | - Ian Tomlinson
- Oxford Centre for Cancer Gene Research, The Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, OX3 7BN UK
| | - Charles Swanton
- Translational Cancer Therapeutics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Translational Cancer Therapeutics Laboratory, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC2E 6DD, UK.
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21
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Domingo E, Freeman-Mills L, Rayner E, Glaire M, Briggs S, Vermeulen L, Fessler E, Medema JP, Boot A, Morreau H, van Wezel T, Liefers GJ, Lothe RA, Danielsen SA, Sveen A, Nesbakken A, Zlobec I, Lugli A, Koelzer VH, Berger MD, Castellví-Bel S, Muñoz J, de Bruyn M, Nijman HW, Novelli M, Lawson K, Oukrif D, Frangou E, Dutton P, Tejpar S, Delorenzi M, Kerr R, Kerr D, Tomlinson I, Church DN. Somatic POLE proofreading domain mutation, immune response, and prognosis in colorectal cancer: a retrospective, pooled biomarker study. Lancet Gastroenterol Hepatol 2016; 1:207-216. [PMID: 28404093 DOI: 10.1016/s2468-1253(16)30014-0] [Citation(s) in RCA: 201] [Impact Index Per Article: 25.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Revised: 05/26/2016] [Accepted: 05/31/2016] [Indexed: 12/16/2022]
Abstract
BACKGROUND Precision cancer medicine depends on defining distinct tumour subgroups using biomarkers that may occur at very modest frequencies. One such subgroup comprises patients with exceptionally mutated (ultramutated) cancers caused by mutations that impair DNA polymerase epsilon (POLE) proofreading. METHODS We examined the association of POLE proofreading domain mutation with clinicopathological variables and immune response in colorectal cancers from clinical trials (VICTOR, QUASAR2, and PETACC-3) and colorectal cancer cohorts (Leiden University Medical Centre 1 and 2, Oslo 1 and 2, Bern, AMC-AJCC-II, and Epicolon-1). We subsequently investigated its association with prognosis in stage II/III colorectal cancer by Cox regression of pooled individual patient data from more than 4500 cases from these studies. FINDINGS Pathogenic somatic POLE mutations were detected in 66 (1·0%) of 6517 colorectal cancers, and were mutually exclusive with mismatch repair deficiency (MMR-D) in the 6277 cases for whom both markers were determined (none of 66 vs 833 [13·4%] of 6211; p<0·0001). Compared with cases with wild-type POLE, cases with POLE mutations were younger at diagnosis (median 54·5 years vs 67·2 years; p<0·0001), were more frequently male (50 [75·8%] of 66 vs 3577 [55·5%] of 6445; p=0·0010), more frequently had right-sided tumour location (44 [68·8%] of 64 vs 2463 [39·8%] of 6193; p<0·0001), and were diagnosed at an earlier disease stage (p=0·006, χ2 test for trend). Compared with mismatch repair proficient (MMR-P) POLE wild-type tumours, POLE-mutant colorectal cancers displayed increased CD8+ lymphocyte infiltration and expression of cytotoxic T-cell markers and effector cytokines, similar in extent to that observed in immunogenic MMR-D cancers. Both POLE mutation and MMR-D were associated with significantly reduced risk of recurrence compared with MMR-P colorectal cancers in multivariable analysis (HR 0·34 [95% CI 0·11-0·76]; p=0·0060 and 0·72 [0·60-0·87]; p=0·00035), although the difference between the groups was not significant. INTERPRETATION POLE proofreading domain mutations identify a subset of immunogenic colorectal cancers with excellent prognosis. This association underscores the importance of rare biomarkers in precision cancer medicine, but also raises important questions about how to identify and implement them in practice. FUNDING Cancer Research UK, Academy of Medical Sciences, Health Foundation, EU, ERC, NIHR, Wellcome Trust, Dutch Cancer Society, Dutch Digestive Foundation.
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Affiliation(s)
- Enric Domingo
- Molecular and Population Genetics Laboratory, University of Oxford, Oxford, UK; Oxford Centre for Cancer Gene Research and NIHR Comprehensive Biomedical Research Centre, The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK; Department of Oncology, University of Oxford, Oxford, UK
| | - Luke Freeman-Mills
- Molecular and Population Genetics Laboratory, University of Oxford, Oxford, UK
| | - Emily Rayner
- Molecular and Population Genetics Laboratory, University of Oxford, Oxford, UK
| | - Mark Glaire
- Cancer Genomics and Immunology Group, University of Oxford, Oxford, UK
| | - Sarah Briggs
- Molecular and Population Genetics Laboratory, University of Oxford, Oxford, UK
| | - Louis Vermeulen
- Academic Medical Center Amsterdam, Center for Experimental Molecular Medicine, Amsterdam, Netherlands
| | - Evelyn Fessler
- Academic Medical Center Amsterdam, Center for Experimental Molecular Medicine, Amsterdam, Netherlands
| | - Jan Paul Medema
- Academic Medical Center Amsterdam, Center for Experimental Molecular Medicine, Amsterdam, Netherlands
| | - Arnoud Boot
- Department of Pathology, Leiden, Netherlands
| | | | | | | | - Ragnhild A Lothe
- K G Jebsen Colorectal Cancer Research Centre, Oslo, Norway; Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Stine A Danielsen
- K G Jebsen Colorectal Cancer Research Centre, Oslo, Norway; Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Anita Sveen
- K G Jebsen Colorectal Cancer Research Centre, Oslo, Norway; Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Arild Nesbakken
- K G Jebsen Colorectal Cancer Research Centre, Oslo, Norway; Department of Gastrointestinal Surgery, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Inti Zlobec
- Institute of Pathology, University of Bern, Bern, Switzerland
| | | | - Viktor H Koelzer
- Molecular and Population Genetics Laboratory, University of Oxford, Oxford, UK; Institute of Pathology, University of Bern, Bern, Switzerland
| | - Martin D Berger
- Department of Medical Oncology, University Hospital of Bern, Bern, Switzerland
| | - Sergi Castellví-Bel
- Gastroenterology Department, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), University of Barcelona, Barcelona, Spain
| | - Jenifer Muñoz
- Gastroenterology Department, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), University of Barcelona, Barcelona, Spain
| | - Marco de Bruyn
- Department of Obstetrics and Gynecology, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Hans W Nijman
- Department of Obstetrics and Gynecology, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | | | - Kay Lawson
- Department of Histopathology, UCL, London, UK
| | | | - Eleni Frangou
- Centre for Statistics in Medicine, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Peter Dutton
- Centre for Statistics in Medicine, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Sabine Tejpar
- Department of Molecular Digestive Oncology, University of Leuven, Leuven, Belgium
| | - Mauro Delorenzi
- Ludwig Center for Cancer Research, University of Lausanne, Epalinges, Switzerland; Department of Oncology, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland; SIB Swiss Institute Bioinformatics, Lausanne, Switzerland
| | - Rachel Kerr
- Department of Oncology, University of Oxford, Oxford, UK; Oxford Cancer Centre, Churchill Hospital, Oxford Radcliffe Hospitals NHS Trust, University of Oxford, Oxford, UK
| | - David Kerr
- Oxford Cancer Centre, Churchill Hospital, Oxford Radcliffe Hospitals NHS Trust, University of Oxford, Oxford, UK; Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Ian Tomlinson
- Molecular and Population Genetics Laboratory, University of Oxford, Oxford, UK; Oxford Centre for Cancer Gene Research and NIHR Comprehensive Biomedical Research Centre, The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - David N Church
- Cancer Genomics and Immunology Group, University of Oxford, Oxford, UK; Oxford Cancer Centre, Churchill Hospital, Oxford Radcliffe Hospitals NHS Trust, University of Oxford, Oxford, UK.
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22
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Karpathakis A, Dibra H, Pipinikas C, Feber A, Morris T, Francis J, Oukrif D, Mandair D, Pericleous M, Mohmaduvesh M, Serra S, Ogunbiyi O, Novelli M, Luong T, Asa SL, Kulke M, Toumpanakis C, Meyer T, Caplin M, Meyerson M, Beck S, Thirlwell C. Prognostic Impact of Novel Molecular Subtypes of Small Intestinal Neuroendocrine Tumor. Clin Cancer Res 2016; 22:250-8. [PMID: 26169971 DOI: 10.1158/1078-0432.ccr-15-0373] [Citation(s) in RCA: 121] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Accepted: 06/25/2015] [Indexed: 12/16/2022]
Abstract
PURPOSE Small intestinal neuroendocrine tumors (SINET) are the commonest malignancy of the small intestine; however, underlying pathogenic mechanisms remain poorly characterized. Whole-genome and -exome sequencing has demonstrated that SINETs are mutationally quiet, with the most frequent known mutation in the cyclin-dependent kinase inhibitor 1B gene (CDKN1B) occurring in only ∼8% of tumors, suggesting that alternative mechanisms may drive tumorigenesis. The aim of this study is to perform genome-wide molecular profiling of SINETs in order to identify pathogenic drivers based on molecular profiling. This study represents the largest unbiased integrated genomic, epigenomic, and transcriptomic analysis undertaken in this tumor type. EXPERIMENTAL DESIGN Here, we present data from integrated molecular analysis of SINETs (n = 97), including whole-exome or targeted CDKN1B sequencing (n = 29), HumanMethylation450 BeadChip (Illumina) array profiling (n = 69), methylated DNA immunoprecipitation sequencing (n = 16), copy-number variance analysis (n = 47), and Whole-Genome DASL (Illumina) expression array profiling (n = 43). RESULTS Based on molecular profiling, SINETs can be classified into three groups, which demonstrate significantly different progression-free survival after resection of primary tumor (not reached at 10 years vs. 56 months vs. 21 months, P = 0.04). Epimutations were found at a recurrence rate of up to 85%, and 21 epigenetically dysregulated genes were identified, including CDX1 (86%), CELSR3 (84%), FBP1 (84%), and GIPR (74%). CONCLUSIONS This is the first comprehensive integrated molecular analysis of SINETs. We have demonstrated that these tumors are highly epigenetically dysregulated. Furthermore, we have identified novel molecular subtypes with significant impact on progression-free survival.
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Affiliation(s)
- Anna Karpathakis
- University College London, London, United Kingdom. The Royal Free Hospital, London, United Kingdom
| | | | | | - Andrew Feber
- University College London, London, United Kingdom
| | | | - Joshua Francis
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts. Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | | | - Dalvinder Mandair
- University College London, London, United Kingdom. The Royal Free Hospital, London, United Kingdom
| | | | | | - Stefano Serra
- UHN Princess Margaret Cancer Centre, Toronto, Canada
| | | | | | | | - Sylvia L Asa
- UHN Princess Margaret Cancer Centre, Toronto, Canada
| | - Matthew Kulke
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | | | - Tim Meyer
- University College London, London, United Kingdom. The Royal Free Hospital, London, United Kingdom
| | | | - Matthew Meyerson
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts. Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Stephan Beck
- University College London, London, United Kingdom
| | - Christina Thirlwell
- University College London, London, United Kingdom. The Royal Free Hospital, London, United Kingdom.
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Pipinikas CP, Dibra H, Karpathakis A, Feber A, Novelli M, Oukrif D, Fusai G, Valente R, Caplin M, Meyer T, Teschendorff A, Bell C, Morris TJ, Salomoni P, Luong TV, Davidson B, Beck S, Thirlwell C. Epigenetic dysregulation and poorer prognosis in DAXX-deficient pancreatic neuroendocrine tumours. Endocr Relat Cancer 2015; 22:L13-8. [PMID: 25900181 PMCID: PMC4496774 DOI: 10.1530/erc-15-0108] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/21/2015] [Indexed: 12/17/2022]
Affiliation(s)
- Christodoulos P Pipinikas
- Medical Genomics Laboratory, University College London Cancer Institute, University College London72 Huntley Street, London, WC1E 6BT, UK
| | - Harpreet Dibra
- Medical Genomics Laboratory, University College London Cancer Institute, University College London72 Huntley Street, London, WC1E 6BT, UK
| | - Anna Karpathakis
- Medical Genomics Laboratory, University College London Cancer Institute, University College London72 Huntley Street, London, WC1E 6BT, UK
| | - Andrew Feber
- Medical Genomics Laboratory, University College London Cancer Institute, University College London72 Huntley Street, London, WC1E 6BT, UK
| | - Marco Novelli
- Medical Genomics Laboratory, University College London Cancer Institute, University College London72 Huntley Street, London, WC1E 6BT, UK
| | - Dahmane Oukrif
- Medical Genomics Laboratory, University College London Cancer Institute, University College London72 Huntley Street, London, WC1E 6BT, UK
| | - Guiseppe Fusai
- Medical Genomics Laboratory, University College London Cancer Institute, University College London72 Huntley Street, London, WC1E 6BT, UK
| | - Roberto Valente
- Medical Genomics Laboratory, University College London Cancer Institute, University College London72 Huntley Street, London, WC1E 6BT, UK
| | - Martyn Caplin
- Medical Genomics Laboratory, University College London Cancer Institute, University College London72 Huntley Street, London, WC1E 6BT, UK
| | - Tim Meyer
- Medical Genomics Laboratory, University College London Cancer Institute, University College London72 Huntley Street, London, WC1E 6BT, UK Medical Genomics Laboratory, University College London Cancer Institute, University College London72 Huntley Street, London, WC1E 6BT, UK
| | - Andrew Teschendorff
- Medical Genomics Laboratory, University College London Cancer Institute, University College London72 Huntley Street, London, WC1E 6BT, UK Medical Genomics Laboratory, University College London Cancer Institute, University College London72 Huntley Street, London, WC1E 6BT, UK
| | - Christopher Bell
- Medical Genomics Laboratory, University College London Cancer Institute, University College London72 Huntley Street, London, WC1E 6BT, UK
| | - Tiffany J Morris
- Medical Genomics Laboratory, University College London Cancer Institute, University College London72 Huntley Street, London, WC1E 6BT, UK
| | - Paolo Salomoni
- Medical Genomics Laboratory, University College London Cancer Institute, University College London72 Huntley Street, London, WC1E 6BT, UK
| | - Tu-Vinh Luong
- Medical Genomics Laboratory, University College London Cancer Institute, University College London72 Huntley Street, London, WC1E 6BT, UK
| | - Brian Davidson
- Medical Genomics Laboratory, University College London Cancer Institute, University College London72 Huntley Street, London, WC1E 6BT, UK
| | - Stephan Beck
- Medical Genomics Laboratory, University College London Cancer Institute, University College London72 Huntley Street, London, WC1E 6BT, UK
| | - Christina Thirlwell
- Medical Genomics Laboratory, University College London Cancer Institute, University College London72 Huntley Street, London, WC1E 6BT, UK Medical Genomics Laboratory, University College London Cancer Institute, University College London72 Huntley Street, London, WC1E 6BT, UK
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24
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Mouradov D, Domingo E, Gibbs P, Jorissen RN, Li S, Soo PY, Lipton L, Desai J, Danielsen HE, Oukrif D, Novelli M, Yau C, Holmes CC, Jones IT, McLaughlin S, Molloy P, Hawkins NJ, Ward R, Midgely R, Kerr D, Tomlinson IPM, Sieber OM. Survival in stage II/III colorectal cancer is independently predicted by chromosomal and microsatellite instability, but not by specific driver mutations. Am J Gastroenterol 2013; 108:1785-93. [PMID: 24042191 DOI: 10.1038/ajg.2013.292] [Citation(s) in RCA: 104] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/11/2013] [Accepted: 08/05/2013] [Indexed: 12/11/2022]
Abstract
OBJECTIVES Microsatellite instability (MSI) is an established marker of good prognosis in colorectal cancer (CRC). Chromosomal instability (CIN) is strongly negatively associated with MSI and has been shown to be a marker of poor prognosis in a small number of studies. However, a substantial group of "double-negative" (MSI-/CIN-) CRCs exists. The prognosis of these patients is unclear. Furthermore, MSI and CIN are each associated with specific molecular changes, such as mutations in KRAS and BRAF, that have been associated with prognosis. It is not known which of MSI, CIN, and the specific gene mutations are primary predictors of survival. METHODS We evaluated the prognostic value (disease-free survival, DFS) of CIN, MSI, mutations in KRAS, NRAS, BRAF, PIK3CA, FBXW7, and TP53, and chromosome 18q loss-of-heterozygosity (LOH) in 822 patients from the VICTOR trial of stage II/III CRC. We followed up promising associations in an Australian community-based cohort (N=375). RESULTS In the VICTOR patients, no specific mutation was associated with DFS, but individually MSI and CIN showed significant associations after adjusting for stage, age, gender, tumor location, and therapy. A combined analysis of the VICTOR and community-based cohorts showed that MSI and CIN were independent predictors of DFS (for MSI, hazard ratio (HR)=0.58, 95% confidence interval (CI) 0.36-0.93, and P=0.021; for CIN, HR=1.54, 95% CI 1.14-2.08, and P=0.005), and joint CIN/MSI testing significantly improved the prognostic prediction of MSI alone (P=0.028). Higher levels of CIN were monotonically associated with progressively poorer DFS, and a semi-quantitative measure of CIN was a better predictor of outcome than a simple CIN+/- variable. All measures of CIN predicted DFS better than the recently described Watanabe LOH ratio. CONCLUSIONS MSI and CIN are independent predictors of DFS for stage II/III CRC. Prognostic molecular tests for CRC relapse should currently use MSI and a quantitative measure of CIN rather than specific gene mutations.
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Affiliation(s)
- Dmitri Mouradov
- 1] Ludwig Colon Cancer Initiative Laboratory, Ludwig Institute for Cancer Research, Parkville, Victoria, Australia [2] Faculty of Medicine, Dentistry and Health Sciences, Department of Medical Biology, University of Melbourne, Royal Melbourne Hospital, Parkville, Victoria, Australia
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25
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Domingo E, Ramamoorthy R, Oukrif D, Rosmarin D, Presz M, Wang H, Pulker H, Lockstone H, Hveem T, Cranston T, Danielsen H, Novelli M, Davidson B, Xu ZZ, Molloy P, Johnstone E, Holmes C, Midgley R, Kerr D, Sieber O, Tomlinson I. Use of multivariate analysis to suggest a new molecular classification of colorectal cancer. J Pathol 2013; 229:441-8. [PMID: 23165447 PMCID: PMC3588155 DOI: 10.1002/path.4139] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2012] [Revised: 09/20/2012] [Accepted: 10/10/2012] [Indexed: 01/12/2023]
Abstract
Abstract Molecular classification of colorectal cancer (CRC) is currently based on microsatellite instability (MSI), KRAS or BRAF mutation and, occasionally, chromosomal instability (CIN). Whilst useful, these categories may not fully represent the underlying molecular subgroups. We screened 906 stage II/III CRCs from the VICTOR clinical trial for somatic mutations. Multivariate analyses (logistic regression, clustering, Bayesian networks) identified the primary molecular associations. Positive associations occurred between: CIN and TP53 mutation; MSI and BRAF mutation; and KRAS and PIK3CA mutations. Negative associations occurred between: MSI and CIN; MSI and NRAS mutation; and KRAS mutation, and each of NRAS, TP53 and BRAF mutations. Some complex relationships were elucidated: KRAS and TP53 mutations had both a direct negative association and a weaker, confounding, positive association via TP53–CIN–MSI–BRAF–KRAS. Our results suggested a new molecular classification of CRCs: (1) MSI+ and/or BRAF-mutant; (2) CIN+ and/or TP53– mutant, with wild-type KRAS and PIK3CA; (3) KRAS- and/or PIK3CA-mutant, CIN+, TP53-wild-type; (4) KRAS– and/or PIK3CA-mutant, CIN–, TP53-wild-type; (5) NRAS-mutant; (6) no mutations; (7) others. As expected, group 1 cancers were mostly proximal and poorly differentiated, usually occurring in women. Unexpectedly, two different types of CIN+ CRC were found: group 2 cancers were usually distal and occurred in men, whereas group 3 showed neither of these associations but were of higher stage. CIN+ cancers have conventionally been associated with all three of these variables, because they have been tested en masse. Our classification also showed potentially improved prognostic capabilities, with group 3, and possibly group 1, independently predicting disease-free survival. Copyright © 2012 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Affiliation(s)
- Enric Domingo
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, UK
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26
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Bird-Lieberman EL, Dunn JM, Coleman HG, Lao-Sirieix P, Oukrif D, Moore CE, Varghese S, Johnston BT, Arthur K, McManus DT, Novelli MR, O'Donovan M, Cardwell CR, Lovat LB, Murray LJ, Fitzgerald RC. Population-based study reveals new risk-stratification biomarker panel for Barrett's esophagus. Gastroenterology 2012; 143:927-35.e3. [PMID: 22771507 DOI: 10.1053/j.gastro.2012.06.041] [Citation(s) in RCA: 134] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2012] [Revised: 06/20/2012] [Accepted: 06/22/2012] [Indexed: 12/17/2022]
Abstract
BACKGROUND & AIMS The risk of progression of Barrett's esophagus (BE) to esophageal adenocarcinoma (EAC) is low and difficult to calculate. Accurate tools to determine risk are needed to optimize surveillance and intervention. We assessed the ability of candidate biomarkers to predict which cases of BE will progress to EAC or high-grade dysplasia and identified those that can be measured in formalin-fixed tissues. METHODS We analyzed data from a nested case-control study performed using the population-based Northern Ireland BE Register (1993-2005). Cases who progressed to EAC (n = 89) or high-grade dysplasia ≥ 6 months after diagnosis with BE were matched to controls (nonprogressors, n = 291), for age, sex, and year of BE diagnosis. Established biomarkers (abnormal DNA content, p53, and cyclin A expression) and new biomarkers (levels of sialyl Lewis(a), Lewis(x), and Aspergillus oryzae lectin [AOL] and binding of wheat germ agglutinin) were assessed in paraffin-embedded tissue samples from patients with a first diagnosis of BE. Conditional logistic regression analysis was applied to assess odds of progression for patients with dysplastic and nondysplastic BE, based on biomarker status. RESULTS Low-grade dysplasia and all biomarkers tested, other than Lewis(x), were associated with risk of EAC or high-grade dysplasia. In backward selection, a panel comprising low-grade dysplasia, abnormal DNA ploidy, and AOL most accurately identified progressors and nonprogressors. The adjusted odds ratio for progression of patients with BE with low-grade dysplasia was 3.74 (95% confidence interval, 2.43-5.79) for each additional biomarker and the risk increased by 2.99 for each additional factor (95% confidence interval, 1.72-5.20) in patients without dysplasia. CONCLUSIONS Low-grade dysplasia, abnormal DNA ploidy, and AOL can be used to identify patients with BE most likely to develop EAC or high-grade dysplasia.
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Galandiuk S, Rodriguez-Justo M, Jeffery R, Nicholson AM, Cheng Y, Oukrif D, Elia G, Leedham SJ, Mcdonald SAC, Wright NA, Graham TA. Field cancerization in the intestinal epithelium of patients with Crohn's ileocolitis. Gastroenterology 2012; 142:855-864.e8. [PMID: 22178590 PMCID: PMC4446968 DOI: 10.1053/j.gastro.2011.12.004] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/20/2011] [Revised: 11/23/2011] [Accepted: 12/03/2012] [Indexed: 12/16/2022]
Abstract
BACKGROUND & AIMS Tumors that develop in patients with Crohn's disease tend be multifocal, so field cancerization (the replacement of normal cells with nondysplastic but tumorigenic clones) might contribute to intestinal carcinogenesis. We investigated patterns of tumor development from pretumor intestinal cell clones. METHODS We performed genetic analyses of multiple areas of intestine from 10 patients with Crohn's disease and intestinal neoplasia. Two patients had multifocal neoplasia; longitudinal sections were collected from 3 patients. Individual crypts were microdissected and genotyped; clonal dependency analysis was used to determine the order and timing of mutations that led to tumor development. RESULTS The same mutations in KRAS, CDKN2A(p16), and TP53 that were observed in neoplasias were also present in nontumor, nondysplastic, and dysplastic epithelium. In 2 patients, carcinogenic mutations were detected in nontumor epithelium 4 years before tumors developed. The same mutation (TP53 p.R248W) was detected at multiple sites along the entire length of the colon from 1 patient; it was the apparent founder mutation for synchronous tumors and multiple dysplastic areas. Disruption of TP53, CDKN2A, and KRAS were all seen as possible initial events in tumorigenesis; the sequence of mutations (the tumor development pathway) differed among lesions. CONCLUSIONS Pretumor clones can grow extensively in the intestinal epithelium of patients with Crohn's disease. Segmental resections for neoplasia in patients with Crohn's disease might therefore leave residual pretumor disease, and dysplasia might be an unreliable biomarker for cancer risk. Characterization of the behavior of pretumor clones might be used to predict the development of intestinal neoplasia.
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Affiliation(s)
- Susan Galandiuk
- Histopathology Laboratory, Cancer Research UK London Research Institute, London, England.
| | | | - Rosemary Jeffery
- Histopathology Laboratory, Cancer Research UK London Research Institute, London, England
| | - Anna M. Nicholson
- Centre for Digestive Diseases, Blizard Institute of Cell and Molecular Science, Barts and the London School of Medicine and Dentistry, London, England
| | - Yong Cheng
- Histopathology Laboratory, Cancer Research UK London Research Institute, London, England,Department of Gastrointestinal Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, Peoples Republic of China
| | - Dahmane Oukrif
- Department of Histopathology, University College London Hospital, London, England
| | - George Elia
- Centre for Tumour Biology, Institute of Cancer and CR-UK Clinical Centre, Barts and the London School of Medicine and Dentistry, London, England
| | - Simon J. Leedham
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, England
| | - Stuart A. C. Mcdonald
- Histopathology Laboratory, Cancer Research UK London Research Institute, London, England,Centre for Digestive Diseases, Blizard Institute of Cell and Molecular Science, Barts and the London School of Medicine and Dentistry, London, England
| | - Nicholas A. Wright
- Histopathology Laboratory, Cancer Research UK London Research Institute, London, England,Centre for Digestive Diseases, Blizard Institute of Cell and Molecular Science, Barts and the London School of Medicine and Dentistry, London, England
| | - Trevor A. Graham
- Histopathology Laboratory, Cancer Research UK London Research Institute, London, England
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Dunn JM, Banks MR, Oukrif D, Mackenzie GD, Thorpe S, Rodriguez-Justo M, Winstanley A, Bown SG, Novelli MR, Lovat LB. Radiofrequency ablation is effective for the treatment of high-grade dysplasia in Barrett's esophagus after failed photodynamic therapy. Endoscopy 2011; 43:627-30. [PMID: 21717379 DOI: 10.1055/s-0030-1256443] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Endoscopic radiofrequency ablation (RFA) is an effective treatment for high-grade dysplasia in Barrett's esophagus in ablation-naïve patients, but no studies have evaluated its use in patients in whom ablative therapy has previously failed. We describe 14 patients with residual high-grade dysplasia following aminolevulinic acid or Photofrin (porfimer sodium) photodynamic therapy (PDT). An overall complete reversal of dysplasia was achieved in 86 % with a combination of RFA and rescue endoscopic mucosal resection. The median total follow-up is 19 months. The rate of strictures was 7 % (1/14) and there was a low rate of buried glands (0.5 % follow-up biopsies). These data suggest RFA is both safe and effective for eradication of high-grade dysplasia in patients in whom PDT has failed.
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Affiliation(s)
- J M Dunn
- National Medical Laser Centre, Department of Surgery, University College London, London, UK
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29
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Dunn JM, Mackenzie GD, Oukrif D, Mosse CA, Banks MR, Thorpe S, Sasieni P, Bown SG, Novelli MR, Rabinovitch PS, Lovat LB. Image cytometry accurately detects DNA ploidy abnormalities and predicts late relapse to high-grade dysplasia and adenocarcinoma in Barrett's oesophagus following photodynamic therapy. Br J Cancer 2010; 102:1608-17. [PMID: 20461081 PMCID: PMC2883155 DOI: 10.1038/sj.bjc.6605688] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Background and aims: DNA ploidy abnormalities (aneuploidy/tetraploidy) measured by flow cytometry (FC) are strong predictors of future cancer development in untreated Barrett's oesophagus, independent of histology grade. Image cytometric DNA analysis (ICDA) is an optical technique allowing visualisation of abnormal nuclei that may be undertaken on archival tissue. Our aim was to determine the accuracy of ICDA vs FC, and evaluate DNA ploidy as a prognostic biomarker after histologically successful treatment with photodynamic therapy (PDT). Methods: Nuclei were extracted from 40 μm sections of paraffin-embedded biopsies and processed for ICDA at UCL and FC at UW using standardised protocols. Subsequently, DNA ploidy was evaluated by ICDA on a cohort of 30 patients clear of dysplasia 1 year after aminolaevulinic acid PDT for high-grade dysplasia (HGD). The results were correlated with long-term outcome. Results: In the comparative study, 93% (41 out of 44) of cases were classified identically. Errors occurred in the near-diploid region by ICDA and the tetraploid region by FC. In the cohort study, there were 13 cases of late relapse (7 cancer, 6 HGD) and 17 patients who remained free of dysplasia after a mean follow-up of 44 months. Aneuploidy post-PDT was highly predictive for recurrent HGD or cancer with a hazard ratio of 8.2 (1.8–37.8) (log-rank P=0.001). Conclusions: ICDA is accurate for the detection of DNA ploidy abnormalities when compared with FC. After histologically successful PDT, patients with residual aneuploidy are significantly more likely to develop HGD or cancer than those who become diploid. DNA ploidy by ICDA is a valuable prognostic biomarker after ablative therapy.
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Affiliation(s)
- J M Dunn
- Department of Surgery, National Medical Laser Centre, University College London, 67-73 Riding House Street, London W1W 7EJ, UK
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30
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Thirlwell C, Will OCC, Domingo E, Graham TA, McDonald SAC, Oukrif D, Jeffrey R, Gorman M, Rodriguez-Justo M, Chin-Aleong J, Clark SK, Novelli MR, Jankowski JA, Wright NA, Tomlinson IPM, Leedham SJ. Clonality assessment and clonal ordering of individual neoplastic crypts shows polyclonality of colorectal adenomas. Gastroenterology 2010; 138:1441-54, 1454.e1-7. [PMID: 20102718 DOI: 10.1053/j.gastro.2010.01.033] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/27/2009] [Revised: 11/24/2009] [Accepted: 01/07/2010] [Indexed: 01/28/2023]
Abstract
BACKGROUND & AIMS According to the somatic mutation theory, monoclonal colorectal lesions arise from sequential mutations in the progeny of a single stem cell. However, studies in a sex chromosome mixoploid mosaic (XO/XY) patient indicated that colorectal adenomas were polyclonal. We assessed adenoma clonality on an individual crypt basis and completed a genetic dependency analysis in carcinomas-in-adenomas to assess mutation order and timing. METHODS Polyp samples were analyzed from the XO/XY individual, patients with familial adenomatous polyposis and attenuated familial adenomatous polyposis, patients with small sporadic adenomas, and patients with sporadic carcinoma-in-adenomas. Clonality was analyzed using X/Y chromosome fluorescence in situ hybridization, analysis of 5q loss of heterozygosity in XO/XY tissue, and sequencing of adenomatous polyposis coli. Individual crypts and different phenotypic areas of carcinoma-in-adenoma lesions were analyzed for mutations in adenomatous polyposis coli, p53, and K-RAS; loss of heterozygosity at 5q, 17p, and 18q; and aneuploidy. Phylogenetic trees were constructed. RESULTS All familial adenomatous polyposis-associated adenomas and some sporadic lesions had polyclonal genetic defects. Some independent clones appeared to be maintained in advanced adenomas. No clear obligate order of genetic events was established. Top-down growth of dysplastic tissue into neighboring crypts was a possible mechanism of clonal competition. CONCLUSIONS Human colorectal microadenomas are polyclonal and may arise from a combination of host genetic features, mucosal exposures, and active crypt interactions. Analyses of tumor phylogenies show that most lesions undergo intermittent genetic homogenization, but heterotypic mutation patterns indicate that independent clonal evolution can occur throughout adenoma development. Based on observations of clonal ordering the requirement and timing of genetic events during neoplastic progression may be more variable than previously thought.
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Woodhams J, Lou PJ, Selbo PK, Mosse A, Oukrif D, MacRobert A, Novelli M, Peng Q, Berg K, Bown SG. Intracellular re-localisation by photochemical internalisation enhances the cytotoxic effect of gelonin — Quantitative studies in normal rat liver. J Control Release 2010; 142:347-53. [DOI: 10.1016/j.jconrel.2009.11.017] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2009] [Accepted: 11/16/2009] [Indexed: 10/20/2022]
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Leedham SJ, Graham TA, Oukrif D, McDonald SAC, Rodriguez-Justo M, Harrison RF, Shepherd NA, Novelli MR, Jankowski JAZ, Wright NA. Clonality, founder mutations, and field cancerization in human ulcerative colitis-associated neoplasia. Gastroenterology 2009; 136:542-50.e6. [PMID: 19103203 DOI: 10.1053/j.gastro.2008.10.086] [Citation(s) in RCA: 129] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/30/2008] [Revised: 10/07/2008] [Accepted: 10/30/2008] [Indexed: 12/14/2022]
Abstract
BACKGROUND & AIMS The clonality of colitis-associated neoplasia has not been fully determined. One previous report showed polyclonal origins with subsequent monoclonal outgrowth. We aimed to assess the clonality and mutation burden of individual crypts in colitis-associated neoplasias to try to identify gatekeeping founder mutations, and explore the clonality of synchronous lesions to look for field effects. METHODS Individual crypts (range, 8-21 crypts) were microdissected from across 17 lesions from 10 patients. Individual crypt adenomatous polyposis coli (APC), p53, K-RAS, and 17p loss of heterozygosity mutation burden was established using polymerase chain reaction and sequencing analysis. Serial sections underwent immunostaining for p53, beta-catenin, and image cytometry to detect aneuploidy. RESULTS In most lesions an oncogenic mutation could be identified in all crypts across the lesion showing monoclonality. This founder mutation was a p53 lesion in the majority of neoplasms but 4 tumors had an initiating K-RAS mutation. Some nondysplastic crypts surrounding areas of dysplasia were found to contain clonal p53 mutations and in one case 3 clonal tumors arose from a patch of nondysplastic crypts containing a K-RAS mutation. CONCLUSIONS This study used mutation burden analysis of individual crypts across colitis-associated neoplasms to show lesion monoclonality. This study confirmed p53 mutation as initiating mutation in the majority of lesions, but also identified K-RAS activation as an alternative gatekeeping mutation. Local and segmental field cancerization was found by showing pro-oncogenic mutations in nondysplastic crypts surrounding neoplasms, although field changes are unlikely to involve the entire colon because widely separated tumors were genetically distinct.
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Affiliation(s)
- Simon J Leedham
- Histopathology Unit, Cancer Research UK, London, United Kingdom.
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33
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Preston SL, Leedham SJ, Oukrif D, Deheregoda M, Goodlad RA, Poulsom R, Alison MR, Wright NA, Novelli M. The development of duodenal microadenomas in FAP patients: the human correlate of the Min mouse. J Pathol 2008; 214:294-301. [PMID: 18085615 DOI: 10.1002/path.2294] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
UNLABELLED The morphological changes associated with the adenoma-carcinoma sequence are well documented in the colorectum. Small intestinal carcinogenesis is thought to progress through a similar adenoma-to-carcinoma pathway, but there is a relative dearth of studies examining the associated morphological changes. The best-known mouse model of intestinal neoplasia, the multiple intestinal neoplasia (Min) mouse, has been criticized as a genetic model of intestinal neoplasia, as the majority of its tumours occur in the small intestine. We examined pancreatico-duodenal resection specimens from seven familial adenomatous polyposis (FAP) patients. Serial sections of these were stained with haematoxylin and eosin for beta-catenin and its downstream target CD44, for BMPR1a, lysozyme, carbonic anhydrase II, and with MIB-1. Individual dysplastic crypts were isolated and mutations in the FAP (APC) gene compared between the top and bottom of the crypt. We found that: (a) duodenal microadenomas are extremely common in FAP patients; (b) these grow in the core of duodenal villi, forming lesions similar to those described in the Min mouse; (c) many lesions arise as monocryptal adenomas and grow by a process of crypt fission and branching; (d) migrating adenomatous cells lose their dysplastic phenotype as they migrate up the crypt villous axis; and (e) Paneth cells lose positional information. IN CONCLUSION (a) the morphological similarity of adenomas in the Min mouse and human suggest the Min mouse is a good model of FAP; (b) duodenal adenomas in FAP originate in monocryptal adenomas and follow the 'bottom-up' rather than the 'top-down' model of morphogenesis; (c) early microadenomas show evidence of cellular differentiation; (d) defects in the positioning of Paneth cells suggests disruption of the EphB2:EphB3 receptor system.
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Affiliation(s)
- S L Preston
- Histopathology Unit, London Research Institute, Cancer Research UK, London, UK
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McDonald SAC, Greaves LC, Gutierrez-Gonzalez L, Rodriguez-Justo M, Deheragoda M, Leedham SJ, Taylor RW, Lee CY, Preston SL, Lovell M, Hunt T, Elia G, Oukrif D, Harrison R, Novelli MR, Mitchell I, Stoker DL, Turnbull DM, Jankowski JAZ, Wright NA. Mechanisms of field cancerization in the human stomach: the expansion and spread of mutated gastric stem cells. Gastroenterology 2008; 134:500-10. [PMID: 18242216 DOI: 10.1053/j.gastro.2007.11.035] [Citation(s) in RCA: 189] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/04/2007] [Accepted: 11/08/2007] [Indexed: 12/13/2022]
Abstract
BACKGROUND & AIMS How mutations are established and spread through the human stomach is unclear because the clonal structure of gastric mucosal units is unknown. Here we investigate, using mitochondrial DNA (mtDNA) mutations as a marker of clonal expansion, the clonality of the gastric unit and show how mutations expand in normal mucosa and gastric mucosa showing intestinal metaplasia. This has important implications in gastric carcinogenesis. METHODS Mutated units were identified by a histochemical method to detect activity of cytochrome c oxidase. Negative units were laser-capture microdissected, and mutations were identified by polymerase chain reaction sequencing. Differentiated epithelial cells were identified by immunohistochemistry for lineage markers. RESULTS We show that mtDNA mutations establish themselves in stem cells within normal human gastric body units, and are passed on to all their differentiated progeny, thereby providing evidence for clonal conversion to a new stem cell-derived unit-monoclonal conversion, encompassing all gastric epithelial lineages. The presence of partially mutated units indicates that more than one stem cell is present in each unit. Mutated units can divide by fission to form patches, with each unit sharing an indentical, mutant mtDNA genotype. Furthermore, we show that intestinal metaplastic crypts are clonal, possess multiple stem cells, and that fission is a mechanism by which intestinal metaplasia spreads. CONCLUSIONS These data show that human gastric body units are clonal, contain multiple multipotential stem cells, and provide definitive evidence for how mutations spread within the human stomach, and show how field cancerization develops.
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Affiliation(s)
- Stuart A C McDonald
- Histopathology Unit, London Research Institute, Cancer Research UK, London, United Kingdom.
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Greaves LC, Preston SL, Tadrous PJ, Taylor RW, Barron MJ, Oukrif D, Leedham SJ, Deheragoda M, Sasieni P, Novelli MR, Jankowski JAZ, Turnbull DM, Wright NA, McDonald SAC. Mitochondrial DNA mutations are established in human colonic stem cells, and mutated clones expand by crypt fission. Proc Natl Acad Sci U S A 2006; 103:714-9. [PMID: 16407113 PMCID: PMC1325106 DOI: 10.1073/pnas.0505903103] [Citation(s) in RCA: 223] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The understanding of the fixation of mutations within human tissues and their subsequent clonal expansion is a considerable problem, of which little is known. We have previously shown that nononcogenic mutations in the mitochondrial genome occur in one of a number of morphologically normal colonic crypt stem cells, the progeny of which later occupy the whole crypt. We propose that these wholly mutated crypts then clonally expand by crypt fission, where each crypt divides into two mutated daughter crypts. Here we show that (i) mutated crypts in the process of fission share the same mutated mitochondrial genotype not present in neighboring cytochrome c oxidase-positive crypts (the odds of this being a random event are >or=2.48 x 10(9):1); (ii) neighboring mutated crypts have the same genotype, which is different from adjacent cytochrome c oxidase-positive crypts; (iii) mutated crypts are clustered together throughout the colon; and (iv) patches of cytochrome c oxidase-deficient crypts increase in size with age. We thus demonstrate definitively that crypt fission is the mechanism by which mutations spread in the normal human colon. This has important implications for the biology of the normal adult human colon and possibly for the growth and spread of colorectal neoplasms.
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Affiliation(s)
- Laura C Greaves
- Mitochondrial Research Group, School of Neurology, Neurobiology and Psychiatry, University of Newcastle upon Tyne, Newcastle upon Tyne NE2 4HH, United Kingdom
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Direkze NC, Hodivala-Dilke K, Jeffery R, Hunt T, Poulsom R, Oukrif D, Alison MR, Wright NA. Bone marrow contribution to tumor-associated myofibroblasts and fibroblasts. Cancer Res 2005; 64:8492-5. [PMID: 15574751 DOI: 10.1158/0008-5472.can-04-1708] [Citation(s) in RCA: 409] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The role of myofibroblasts in tissue repair and fibrosis is well documented, but the source of these myofibroblasts is unclear. There is evidence of a circulating population of fibrocytes that can home to areas of injury and contribute to myofibroblast populations. Previously, we have shown that the bone marrow is a source of myofibroblasts for many tissues including the gut, lung, and kidney and that this phenomenon is exacerbated by injury. We now show that the bone marrow can contribute to myofibroblast and fibroblast populations in tumor stroma in a mouse model of pancreatic insulinoma. Mice transgenic for the rat insulin promoter II gene linked to the large-T antigen of SV40 (RIPTag) develop solid beta-cell tumors of the pancreas. Approximately 25% of myofibroblasts in these pancreatic tumors were donor-derived, and these were concentrated toward the edge of the tumor. Thus, the development of tumor stroma is at least in part a systemic response that may ultimately yield methods of targeting new therapy.
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Affiliation(s)
- Natalie C Direkze
- Cancer Research United Kingdom, London Research Institute, London, UK.
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Novelli M, Cossu A, Oukrif D, Quaglia A, Lakhani S, Poulsom R, Sasieni P, Carta P, Contini M, Pasca A, Palmieri G, Bodmer W, Tanda F, Wright N. X-inactivation patch size in human female tissue confounds the assessment of tumor clonality. Proc Natl Acad Sci U S A 2003; 100:3311-4. [PMID: 12610207 PMCID: PMC152288 DOI: 10.1073/pnas.0437825100] [Citation(s) in RCA: 102] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Most models of tumorigenesis assume that tumors are monoclonal in origin. This conclusion is based largely on studies using X chromosome-linked markers in females. One important factor, often ignored in such studies, is the distribution of X-inactivated cells in tissues. Because lyonization occurs early in development, many of the progeny of a single embryonic stem cell are grouped together in the adult, forming patches. As polyclonality can be demonstrated only at the borders of X-inactivation patches, the patch size is crucial in determining the chance of demonstrating polyclonality and hence the number of tumors that need to be examined to exclude polyclonality. Previously studies using X-linked genes such as glucose-6-phosphate dehydrogenase have been handicapped by the need to destroy the tissues to study the haplotypes of glucose-6-phosphate dehydrogenase [Fialkow, P.-J. (1976) Biochim. Biophys. Acta 458, 283-321] or to determine the restriction fragment length polymorphisms of X chromosome-linked genes [Vogelstein, B., Fearon, E. R., Hamilton, S. R. & Feinberg, A. P. (1985) Science 227, 642-645]. Here we visualize X-inactivation patches in human females directly. Results show that the patch size is relatively large in both the human colon and breast, confounding assessment of tumor clonality with traditional X-inactivation studies.
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Affiliation(s)
- Marco Novelli
- Department of Histopathology, Rockefeller Building, University Street, University College London Hospitals, London WC1E 6JJ, United Kingdom.
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Mobasheri A, Oukrif D, Dawodu SP, Sinha M, Greenwell P, Stewart D, Djamgoz MB, Foster CS, Martín-Vasallo P, Mobasheri R. Isoforms of Na+, K+-ATPase in human prostate; specificity of expression and apical membrane polarization. Histol Histopathol 2001; 16:141-54. [PMID: 11193188 DOI: 10.14670/hh-16.141] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The cellular distribution of Na+, K+-ATPase subunit isoforms was mapped in the secretory epithelium of the human prostate gland by immunostaining with antibodies to the alpha and beta subunit isoforms of the enzyme. Immunolabeling of the alpha1, beta1 and beta2 isoforms was observed in the apical and lateral plasma membrane domains of prostatic epithelial cells in contrast to human kidney where the alpha1 and beta1 isoforms of Na+, K+-ATPase were localized in the basolateral membrane of both proximal and distal convoluted tubules. Using immunohistochemistry and PCR we found no evidence of Na+, K+-ATPase alpha2 and alpha3 isoform expression suggesting that prostatic Na+, K+-ATPase consists of alpha1/beta1 and alpha1/beta2 isozymes. Our immunohistochemical findings are consistent with previously proposed models placing prostatic Na+, K+-ATPase in the apical plasma membrane domain. Abundant expression of Na+, K+-ATPase in epithelial cells lining tubulo-alveoli in the human prostate gland confirms previous conclusions drawn from biochemical, pharmacological and physiological data and provides further evidence for the critical role of this enzyme in prostatic cell physiology and ion homeostasis. Na+, K+-ATPase most likely maintains an inwardly directed Na+ gradient essential for nutrient uptake and active citrate secretion by prostatic epithelial cells. Na+, K+-ATPase may also regulate lumenal Na+ and K+, major counter-ions for citrate.
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Affiliation(s)
- A Mobasheri
- Department of Veterinary Preclinical Sciences, University of Liverpool, United Kingdom.
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