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Colling R, Indave I, Del Aguila J, Jimenez RC, Campbell F, Chechlińska M, Kowalewska M, Holdenrieder S, Trulson I, Worf K, Pollán M, Plans-Beriso E, Pérez-Gómez B, Craciun O, García-Ovejero E, Michałek IM, Maslova K, Rymkiewicz G, Didkowska J, Tan PH, Md Nasir ND, Myles N, Goldman-Lévy G, Lokuhetty D, Cree IA. A New Hierarchy of Research Evidence for Tumor Pathology: A Delphi Study to Define Levels of Evidence in Tumor Pathology. Mod Pathol 2024; 37:100357. [PMID: 37866639 DOI: 10.1016/j.modpat.2023.100357] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 10/03/2023] [Accepted: 10/15/2023] [Indexed: 10/24/2023]
Abstract
The hierarchy of evidence is a fundamental concept in evidence-based medicine, but existing models can be challenging to apply in laboratory-based health care disciplines, such as pathology, where the types of evidence and contexts are significantly different from interventional medicine. This project aimed to define a comprehensive and complementary framework of new levels of evidence for evaluating research in tumor pathology-introducing a novel Hierarchy of Research Evidence for Tumor Pathology collaboratively designed by pathologists with help from epidemiologists, public health professionals, oncologists, and scientists, specifically tailored for use by pathologists-and to aid in the production of the World Health Organization Classification of Tumors (WCT) evidence gap maps. To achieve this, we adopted a modified Delphi approach, encompassing iterative online surveys, expert oversight, and external peer review, to establish the criteria for evidence in tumor pathology, determine the optimal structure for the new hierarchy, and ascertain the levels of confidence for each type of evidence. Over a span of 4 months and 3 survey rounds, we collected 1104 survey responses, culminating in a 3-day hybrid meeting in 2023, where a new hierarchy was unanimously agreed upon. The hierarchy is organized into 5 research theme groupings closely aligned with the subheadings of the WCT, and it consists of 5 levels of evidence-level P1 representing evidence types that merit the greatest level of confidence and level P5 reflecting the greatest risk of bias. For the first time, an international collaboration of pathology experts, supported by the International Agency for Research on Cancer, has successfully united to establish a standardized approach for evaluating evidence in tumor pathology. We intend to implement this novel Hierarchy of Research Evidence for Tumor Pathology to map the available evidence, thereby enriching and informing the WCT effectively.
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Affiliation(s)
- Richard Colling
- Nuffield Department of Surgical Sciences, University of Oxford, John Radcliffe Hospital, Oxford, UK; Department of Cellular Pathology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK.
| | - Iciar Indave
- International Agency for Research on Cancer (IARC), World Health Organization, Lyon, France
| | - Javier Del Aguila
- International Agency for Research on Cancer (IARC), World Health Organization, Lyon, France
| | - Ramon Cierco Jimenez
- International Agency for Research on Cancer (IARC), World Health Organization, Lyon, France
| | - Fiona Campbell
- Population Health Sciences Institute, Newcastle University, Newcastle Upon Tyne, UK
| | - Magdalena Chechlińska
- Department of Cancer Biology, Maria Sklodowska-Curie National Research Institute of Oncology (MSCI), Warsaw, Poland
| | - Magdalena Kowalewska
- Department of Molecular and Translational Oncology, Maria Sklodowska-Curie National Research Institute of Oncology (MSCI), Warsaw, Poland
| | - Stefan Holdenrieder
- Institute of Laboratory Medicine, German Heart Centre Munich (DHM), Munich, Germany
| | - Inga Trulson
- Institute of Laboratory Medicine, German Heart Centre Munich (DHM), Munich, Germany
| | - Karolina Worf
- Institute of Laboratory Medicine, German Heart Centre Munich (DHM), Munich, Germany
| | - Marina Pollán
- National Center for Epidemiology, Instituto de Salud Carlos III (ISC III), Madrid, Spain; Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Elena Plans-Beriso
- National Center for Epidemiology, Instituto de Salud Carlos III (ISC III), Madrid, Spain
| | - Beatriz Pérez-Gómez
- National Center for Epidemiology, Instituto de Salud Carlos III (ISC III), Madrid, Spain; Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Oana Craciun
- National Center for Epidemiology, Instituto de Salud Carlos III (ISC III), Madrid, Spain
| | - Ester García-Ovejero
- National Center for Epidemiology, Instituto de Salud Carlos III (ISC III), Madrid, Spain
| | - Irmina Maria Michałek
- Department of Cancer Pathology, Maria Sklodowska-Curie National Research Institute of Oncology (MSCI), Warsaw, Poland
| | - Kateryna Maslova
- Department of Cancer Biology, Maria Sklodowska-Curie National Research Institute of Oncology (MSCI), Warsaw, Poland
| | - Grzegorz Rymkiewicz
- Department of Cancer Pathology, Maria Sklodowska-Curie National Research Institute of Oncology (MSCI), Warsaw, Poland
| | - Joanna Didkowska
- Polish National Cancer Registry, Department of Epidemiology and Cancer Prevention, Maria Sklodowska-Curie National Research Institute of Oncology (MSCI), Warsaw, Poland
| | | | | | - Nickolas Myles
- International Agency for Research on Cancer (IARC), World Health Organization, Lyon, France
| | - Gabrielle Goldman-Lévy
- International Agency for Research on Cancer (IARC), World Health Organization, Lyon, France
| | - Dilani Lokuhetty
- International Agency for Research on Cancer (IARC), World Health Organization, Lyon, France
| | - Ian A Cree
- International Agency for Research on Cancer (IARC), World Health Organization, Lyon, France
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Liu JTC, Chow SSL, Colling R, Downes MR, Farré X, Humphrey P, Janowczyk A, Mirtti T, Verrill C, Zlobec I, True LD. Engineering the future of 3D pathology. J Pathol Clin Res 2024; 10:e347. [PMID: 37919231 PMCID: PMC10807588 DOI: 10.1002/cjp2.347] [Citation(s) in RCA: 1] [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] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 10/06/2023] [Accepted: 10/15/2023] [Indexed: 11/04/2023]
Abstract
In recent years, technological advances in tissue preparation, high-throughput volumetric microscopy, and computational infrastructure have enabled rapid developments in nondestructive 3D pathology, in which high-resolution histologic datasets are obtained from thick tissue specimens, such as whole biopsies, without the need for physical sectioning onto glass slides. While 3D pathology generates massive datasets that are attractive for automated computational analysis, there is also a desire to use 3D pathology to improve the visual assessment of tissue histology. In this perspective, we discuss and provide examples of potential advantages of 3D pathology for the visual assessment of clinical specimens and the challenges of dealing with large 3D datasets (of individual or multiple specimens) that pathologists have not been trained to interpret. We discuss the need for artificial intelligence triaging algorithms and explainable analysis methods to assist pathologists or other domain experts in the interpretation of these novel, often complex, large datasets.
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Affiliation(s)
- Jonathan TC Liu
- Department of Mechanical EngineeringUniversity of WashingtonSeattleWAUSA
- Department of Laboratory Medicine & PathologyUniversity of Washington School of MedicineSeattleUSA
- Department of BioengineeringUniversity of WashingtonSeattleUSA
| | - Sarah SL Chow
- Department of Mechanical EngineeringUniversity of WashingtonSeattleWAUSA
| | | | | | | | - Peter Humphrey
- Department of UrologyYale School of MedicineNew HavenCTUSA
| | - Andrew Janowczyk
- Wallace H Coulter Department of Biomedical EngineeringEmory University and Georgia Institute of TechnologyAtlantaGAUSA
- Geneva University HospitalsGenevaSwitzerland
| | - Tuomas Mirtti
- Helsinki University Hospital and University of HelsinkiHelsinkiFinland
- Emory University School of MedicineAtlantaGAUSA
| | - Clare Verrill
- John Radcliffe HospitalUniversity of OxfordOxfordUK
- NIHR Oxford Biomedical Research CentreOxford University Hospitals NHS Foundation TrustOxfordUK
| | - Inti Zlobec
- Institute for Tissue Medicine and PathologyUniversity of BernBernSwitzerland
| | - Lawrence D True
- Department of Laboratory Medicine & PathologyUniversity of Washington School of MedicineSeattleUSA
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Figiel S, Yin W, Doultsinos D, Erickson A, Poulose N, Singh R, Magnussen A, Anbarasan T, Teague R, He M, Lundeberg J, Loda M, Verrill C, Colling R, Gill PS, Bryant RJ, Hamdy FC, Woodcock DJ, Mills IG, Cussenot O, Lamb AD. Spatial transcriptomic analysis of virtual prostate biopsy reveals confounding effect of tissue heterogeneity on genomic signatures. Mol Cancer 2023; 22:162. [PMID: 37789377 PMCID: PMC10546768 DOI: 10.1186/s12943-023-01863-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 09/18/2023] [Indexed: 10/05/2023] Open
Abstract
Genetic signatures have added a molecular dimension to prognostics and therapeutic decision-making. However, tumour heterogeneity in prostate cancer and current sampling methods could confound accurate assessment. Based on previously published spatial transcriptomic data from multifocal prostate cancer, we created virtual biopsy models that mimic conventional biopsy placement and core size. We then analysed the gene expression of different prognostic signatures (OncotypeDx®, Decipher®, Prostadiag®) using a step-wise approach with increasing resolution from pseudo-bulk analysis of the whole biopsy, to differentiation by tissue subtype (benign, stroma, tumour), followed by distinct tumour grade and finally clonal resolution. The gene expression profile of virtual tumour biopsies revealed clear differences between grade groups and tumour clones, compared to a benign control, which were not reflected in bulk analyses. This suggests that bulk analyses of whole biopsies or tumour-only areas, as used in clinical practice, may provide an inaccurate assessment of gene profiles. The type of tissue, the grade of the tumour and the clonal composition all influence the gene expression in a biopsy. Clinical decision making based on biopsy genomics should be made with caution while we await more precise targeting and cost-effective spatial analyses.
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Affiliation(s)
- Sandy Figiel
- Nuffield Department of Surgical Sciences, University of Oxford, Old Road Campus Research Building, Oxford, OX3 7DQ, UK
| | - Wencheng Yin
- Nuffield Department of Surgical Sciences, University of Oxford, Old Road Campus Research Building, Oxford, OX3 7DQ, UK
| | - Dimitrios Doultsinos
- Nuffield Department of Surgical Sciences, University of Oxford, Old Road Campus Research Building, Oxford, OX3 7DQ, UK
| | - Andrew Erickson
- Nuffield Department of Surgical Sciences, University of Oxford, Old Road Campus Research Building, Oxford, OX3 7DQ, UK
| | - Ninu Poulose
- Nuffield Department of Surgical Sciences, University of Oxford, Old Road Campus Research Building, Oxford, OX3 7DQ, UK
| | - Reema Singh
- Nuffield Department of Surgical Sciences, University of Oxford, Old Road Campus Research Building, Oxford, OX3 7DQ, UK
| | - Anette Magnussen
- Nuffield Department of Surgical Sciences, University of Oxford, Old Road Campus Research Building, Oxford, OX3 7DQ, UK
| | - Thineskrishna Anbarasan
- Nuffield Department of Surgical Sciences, University of Oxford, Old Road Campus Research Building, Oxford, OX3 7DQ, UK
- Department of Urology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Renuka Teague
- Nuffield Department of Surgical Sciences, University of Oxford, Old Road Campus Research Building, Oxford, OX3 7DQ, UK
- Department of Cellular Pathology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Mengxiao He
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Solna, Sweden
| | - Joakim Lundeberg
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Solna, Sweden
| | - Massimo Loda
- Nuffield Department of Surgical Sciences, University of Oxford, Old Road Campus Research Building, Oxford, OX3 7DQ, UK
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Clare Verrill
- Nuffield Department of Surgical Sciences, University of Oxford, Old Road Campus Research Building, Oxford, OX3 7DQ, UK
- Department of Cellular Pathology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- Oxford NIHR Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Richard Colling
- Nuffield Department of Surgical Sciences, University of Oxford, Old Road Campus Research Building, Oxford, OX3 7DQ, UK
- Department of Cellular Pathology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Pelvender S Gill
- Nuffield Department of Surgical Sciences, University of Oxford, Old Road Campus Research Building, Oxford, OX3 7DQ, UK
- Department of Cellular Pathology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Richard J Bryant
- Nuffield Department of Surgical Sciences, University of Oxford, Old Road Campus Research Building, Oxford, OX3 7DQ, UK
- Department of Urology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- Oxford NIHR Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Freddie C Hamdy
- Nuffield Department of Surgical Sciences, University of Oxford, Old Road Campus Research Building, Oxford, OX3 7DQ, UK
- Department of Urology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- Oxford NIHR Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Dan J Woodcock
- Nuffield Department of Surgical Sciences, University of Oxford, Old Road Campus Research Building, Oxford, OX3 7DQ, UK
| | - Ian G Mills
- Nuffield Department of Surgical Sciences, University of Oxford, Old Road Campus Research Building, Oxford, OX3 7DQ, UK
| | - Olivier Cussenot
- Nuffield Department of Surgical Sciences, University of Oxford, Old Road Campus Research Building, Oxford, OX3 7DQ, UK
| | - Alastair D Lamb
- Nuffield Department of Surgical Sciences, University of Oxford, Old Road Campus Research Building, Oxford, OX3 7DQ, UK.
- Department of Urology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK.
- Oxford NIHR Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK.
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Browning L, Winter L, Cooper RA, Ghosh A, Dytor T, Colling R, Fryer E, Rittscher J, Verrill C. Impact of the transition to digital pathology in a clinical setting on histopathologists in training: experiences and perceived challenges within a UK training region. J Clin Pathol 2023; 76:712-718. [PMID: 35906044 PMCID: PMC10511979 DOI: 10.1136/jcp-2022-208416] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 07/08/2022] [Indexed: 11/03/2022]
Abstract
AIMS With increasing utility of digital pathology (DP), it is important to consider the experiences of histopathologists in training, particularly in view of the varied access to DP across a training region and the consequent need to remain competent in reporting on glass slides (GS), which is also relevant for the Fellowship of the Royal College of Pathologists part 2 examination. Understanding the impact of DP on training is limited but could aid development of guidance to support the transition. We sought to investigate the perceptions of histopathologists in training around the introduction of DP for clinical diagnosis within a training region, and the potential training benefits and challenges. METHODS An anonymous online survey was circulated to 24 histopathologists in training within a UK training region, including a hospital which has been fully digitised since summer 2020. RESULTS 19 of 24 histopathologists in training responded (79%). The results indicate that DP offers many benefits to training, including ease of access to cases to enhance individual learning and teaching in general. Utilisation of DP for diagnosis appears variable; almost half of the (10 of 19) respondents with DP experience using it only for ancillary purposes such as measurements, reporting varying levels of confidence in using DP clinically. For those yet to undergo the transition, there was a perceived anxiety regarding digital reporting despite experience with DP in other contexts. CONCLUSIONS The survey evidences the need for provision of training and support for histopathologists in training during the transition to DP, and for consideration of their need to maintain competence and confidence with GS reporting.
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Affiliation(s)
- Lisa Browning
- NIHR Oxford Biomedical Research Centre, Oxford, UK
- Cellular Pathology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Lucinda Winter
- Cellular Pathology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | | | - Abhisek Ghosh
- Cellular Pathology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- Nuffield Department of Clinical Laboratory Sciences, University of Oxford, Oxford, UK
| | - Thomas Dytor
- Cellular Pathology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Richard Colling
- Cellular Pathology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Eve Fryer
- Cellular Pathology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Jens Rittscher
- NIHR Oxford Biomedical Research Centre, Oxford, UK
- Department of Engineering Science, University of Oxford, Oxford, UK
- Big Data Institute, University of Oxford, Oxford, UK
| | - Clare Verrill
- NIHR Oxford Biomedical Research Centre, Oxford, UK
- Cellular Pathology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
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Kelleher M, Colling R, Browning L, Roskell D, Roberts-Gant S, Shah KA, Hemsworth H, White K, Rees G, Dolton M, Soares MF, Verrill C. Department Wide Validation in Digital Pathology-Experience from an Academic Teaching Hospital Using the UK Royal College of Pathologists' Guidance. Diagnostics (Basel) 2023; 13:2144. [PMID: 37443538 DOI: 10.3390/diagnostics13132144] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 06/08/2023] [Accepted: 06/14/2023] [Indexed: 07/15/2023] Open
Abstract
AIM we describe our experience of validating departmental pathologists for digital pathology reporting, based on the UK Royal College of Pathologists (RCPath) "Best Practice Recommendations for Implementing Digital Pathology (DP)," at a large academic teaching hospital that scans 100% of its surgical workload. We focus on Stage 2 of validation (prospective experience) prior to full validation sign-off. METHODS AND RESULTS twenty histopathologists completed Stage 1 of the validation process and subsequently completed Stage 2 validation, prospectively reporting a total of 3777 cases covering eight specialities. All cases were initially viewed on digital whole slide images (WSI) with relevant parameters checked on glass slides, and discordances were reconciled before the case was signed out. Pathologists kept an electronic log of the cases, the preferred reporting modality used, and their experiences. At the end of each validation, a summary was compiled and reviewed with a mentor. This was submitted to the DP Steering Group who assessed the scope of cases and experience before sign-off for full validation. A total of 1.3% (49/3777) of the cases had a discordance between WSI and glass slides. A total of 61% (30/49) of the discordances were categorised as a minor error in a supplementary parameter without clinical impact. The most common reasons for diagnostic discordances across specialities included identification and grading of dysplasia, assessment of tumour invasion, identification of small prognostic or diagnostic objects, interpretation of immunohistochemistry/special stains, and mitotic count assessment. Pathologists showed similar mean diagnostic confidences (on Likert scale from 0 to 7) with a mean of 6.8 on digital and 6.9 on glass slide reporting. CONCLUSION we describe one of the first real-world experiences of a department-wide effort to implement, validate, and roll out digital pathology reporting by applying the RCPath Recommendations for Implementing DP. We have shown a very low rate of discordance between WSI and glass slides.
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Affiliation(s)
- Mai Kelleher
- Department of Cellular Pathology, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 9DU, UK
| | - Richard Colling
- Department of Cellular Pathology, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 9DU, UK
- Nuffield Department of Surgical Sciences, Oxford University, Oxford OX3 9DU, UK
| | - Lisa Browning
- Department of Cellular Pathology, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 9DU, UK
| | - Derek Roskell
- Department of Cellular Pathology, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 9DU, UK
| | - Sharon Roberts-Gant
- Department of Cellular Pathology, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 9DU, UK
| | - Ketan A Shah
- Department of Cellular Pathology, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 9DU, UK
| | - Helen Hemsworth
- Department of Cellular Pathology, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 9DU, UK
| | - Kieron White
- Department of Cellular Pathology, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 9DU, UK
| | - Gabrielle Rees
- Department of Cellular Pathology, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 9DU, UK
| | - Monica Dolton
- Nuffield Department of Surgical Sciences, Oxford University, Oxford OX3 9DU, UK
| | - Maria Fernanda Soares
- Department of Cellular Pathology, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 9DU, UK
| | - Clare Verrill
- Department of Cellular Pathology, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 9DU, UK
- Nuffield Department of Surgical Sciences, Oxford University, Oxford OX3 9DU, UK
- NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 9DU, UK
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Fane ME, Ecker BL, Kaur A, Marino GE, Alicea GM, Douglass SM, Chhabra Y, Webster MR, Marshall A, Colling R, Espinosa O, Coupe N, Maroo N, Campo L, Middleton MR, Corrie P, Xu X, Karakousis GC, Weeraratna AT. Correction: sFRP2 Supersedes VEGF as an Age-related Driver of Angiogenesis in Melanoma, Affecting Response to Anti-VEGF Therapy in Older Patients. Clin Cancer Res 2023; 29:2012. [PMID: 37183634 DOI: 10.1158/1078-0432.ccr-23-0871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
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Del Aguila Mejía J, Armon S, Campbell F, Colling R, Chechlinska M, Kowalewska M, Pollán M, Holdenrieder S, Tan PH, Cree I, Indave Ruiz BI. Understanding the use of evidence in the WHO Classification of Tumours: a protocol for an evidence gap map of the classification of tumours of the lung. BMJ Open 2022; 12:e061240. [PMID: 36220326 PMCID: PMC9558796 DOI: 10.1136/bmjopen-2022-061240] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 09/30/2022] [Indexed: 11/22/2022] Open
Abstract
INTRODUCTION There are gaps in the evidence base of tumour classification despite being essential for cancer diagnosis, treatment and patient care. The WHO in charge of the production of an updated international classification, the WHO Classification of Tumours (WCT), aims to adapt evidence gap map (EGM) methodology to inform future editions of the WCT, by providing a visual summary of the existing evidence. METHODS AND ANALYSIS Bibliographical references used in the WCT fifth edition of Tumours of the Lung (Thoracic Tumours volume) will be used as search results of a literature search. A descriptive analysis of the cited evidence for tumour types and descriptors will be drafted and plotted in EPPI-Reviewer to develop a visual evidence map. The resulting EGM will reflect the number of cited studies in the size of the spheres, and the level of evidence by applying a four-colour code (red=low level evidence, orange=moderate level, green=high level and blue=unclassifiable). Overview of the findings will be provided in narrative form and a report will discuss the overall stage of cited research in the WCT and will include analysis of gaps, under-researched categories of tumour descriptors and pockets of low-level evidence. ETHICS AND DISSEMINATION No ethics approval will be required as this is a study of previously published material. Findings of the EGM will be published and used to guide editors, stakeholders and researchers for future research planning and related decision-making, especially for the development of future editions of the WCT. PROSPERO REGISTRATION NUMBER CRD42022302327.
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Affiliation(s)
- Javier Del Aguila Mejía
- WHO/IARC Classification of Tumours Programme, International Agency for Research on Cancer, Lyon, France
| | - Subasri Armon
- WHO/IARC Classification of Tumours Programme, International Agency for Research on Cancer, Lyon, France
| | - Fiona Campbell
- Evidence Synthesis Group, Population Health Sciences Institute Newcastle University, Newcastle upon Tyne, UK
| | - Richard Colling
- Department of Cellular Pathology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Magdalena Chechlinska
- Department of Cancer Biology, Maria Sklodowska-Curie National Research Institute of Oncology, Warszawa, Poland
| | - Magdalena Kowalewska
- Department of Cancer Biology, Maria Sklodowska-Curie National Research Institute of Oncology, Warszawa, Poland
| | - Marina Pollán
- Centro Nacional de Epidemiología, Instituto de Salud Carlos III, Madrid, Spain
- CIBERESP, Madrid, Spain
| | - Stefan Holdenrieder
- Institute of Laboratory Medicine, Munich Biomarker Research Center, Deutsches Herzzentrum München, Munchen, Germany
| | - Puay Hoon Tan
- Division of Pathology, Singapore General Hospital, Singapore
| | - Ian Cree
- WHO/IARC Classification of Tumours Programme, International Agency for Research on Cancer, Lyon, France
| | - Blanca Iciar Indave Ruiz
- WHO/IARC Classification of Tumours Programme, International Agency for Research on Cancer, Lyon, France
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8
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Indave BI, Colling R, Campbell F, Tan PH, Cree IA. Evidence-levels in pathology for informing the WHO classification of tumours. Histopathology 2022; 81:420-425. [PMID: 36089568 DOI: 10.1111/his.14648] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/11/2022] [Accepted: 03/15/2022] [Indexed: 03/25/2024]
Affiliation(s)
- Blanca Iciar Indave
- WHO Classification of Tumours Programme, International Agency for Research on Cancer, World Health Organisation, Lyon, France
| | - Richard Colling
- Nuffield Department of Surgical Sciences, University of Oxford, John Radcliffe Hospital, Oxford, UK
- Department of Cellular Pathology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK
| | - Fiona Campbell
- School of Health and Related Research (ScHARR), University of Sheffield, Sheffield, UK
| | - Puay Hoon Tan
- Division of Pathology, Singapore General Hospital, Singapore
| | - Ian A Cree
- WHO Classification of Tumours Programme, International Agency for Research on Cancer, World Health Organisation, Lyon, France
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Erickson A, He M, Berglund E, Marklund M, Mirzazadeh R, Schultz N, Kvastad L, Andersson A, Bergenstråhle L, Bergenstråhle J, Larsson L, Alonso Galicia L, Shamikh A, Basmaci E, Díaz De Ståhl T, Rajakumar T, Doultsinos D, Thrane K, Ji AL, Khavari PA, Tarish F, Tanoglidi A, Maaskola J, Colling R, Mirtti T, Hamdy FC, Woodcock DJ, Helleday T, Mills IG, Lamb AD, Lundeberg J. Spatially resolved clonal copy number alterations in benign and malignant tissue. Nature 2022; 608:360-367. [PMID: 35948708 PMCID: PMC9365699 DOI: 10.1038/s41586-022-05023-2] [Citation(s) in RCA: 63] [Impact Index Per Article: 31.5] [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: 07/23/2021] [Accepted: 06/23/2022] [Indexed: 12/28/2022]
Abstract
Defining the transition from benign to malignant tissue is fundamental to improving early diagnosis of cancer1. Here we use a systematic approach to study spatial genome integrity in situ and describe previously unidentified clonal relationships. We used spatially resolved transcriptomics2 to infer spatial copy number variations in >120,000 regions across multiple organs, in benign and malignant tissues. We demonstrate that genome-wide copy number variation reveals distinct clonal patterns within tumours and in nearby benign tissue using an organ-wide approach focused on the prostate. Our results suggest a model for how genomic instability arises in histologically benign tissue that may represent early events in cancer evolution. We highlight the power of capturing the molecular and spatial continuums in a tissue context and challenge the rationale for treatment paradigms, including focal therapy.
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Affiliation(s)
- Andrew Erickson
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Mengxiao He
- Department of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Solna, Sweden
| | - Emelie Berglund
- Department of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Solna, Sweden
| | - Maja Marklund
- Department of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Solna, Sweden
| | - Reza Mirzazadeh
- Department of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Solna, Sweden
| | - Niklas Schultz
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Solna, Sweden
| | - Linda Kvastad
- Department of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Solna, Sweden
| | - Alma Andersson
- Department of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Solna, Sweden
| | - Ludvig Bergenstråhle
- Department of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Solna, Sweden
| | - Joseph Bergenstråhle
- Department of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Solna, Sweden
| | - Ludvig Larsson
- Department of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Solna, Sweden
| | - Leire Alonso Galicia
- Department of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Solna, Sweden
| | - Alia Shamikh
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Pathology and Cytology, Karolinska University Hospital, Stockholm, Sweden
| | - Elisa Basmaci
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Pathology and Cytology, Karolinska University Hospital, Stockholm, Sweden
| | - Teresita Díaz De Ståhl
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Pathology and Cytology, Karolinska University Hospital, Stockholm, Sweden
| | - Timothy Rajakumar
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | | | - Kim Thrane
- Department of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Solna, Sweden
| | - Andrew L Ji
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Paul A Khavari
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Firaz Tarish
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Solna, Sweden
| | - Anna Tanoglidi
- Department of Clinical Pathology, University Uppsala Hospital, Uppsala, Sweden
| | - Jonas Maaskola
- Department of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Solna, Sweden
| | - Richard Colling
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
- Department of Cellular Pathology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Tuomas Mirtti
- Department of Pathology, University of Helsinki & Helsinki University Hospital, Helsinki, Finland
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- iCAN-Digital Precision Cancer Medicine Flagship, Helsinki, Finland
| | - Freddie C Hamdy
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
- Department of Urology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Dan J Woodcock
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
- Big Data Institute, University of Oxford, Oxford, UK
| | - Thomas Helleday
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Solna, Sweden
- Weston Park Cancer Centre, Department of Oncology and Metabolism, University of Sheffield, Sheffield, UK
| | - Ian G Mills
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Alastair D Lamb
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK.
- Department of Urology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK.
| | - Joakim Lundeberg
- Department of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Solna, Sweden.
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10
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Browning L, White K, Siiankoski D, Colling R, Roskell D, Fryer E, Hemsworth H, Roberts-Gant S, Roelofsen R, Rittscher J, Verrill C. RFID analysis of the complexity of cellular pathology workflow—An opportunity for digital pathology. Front Med (Lausanne) 2022; 9:933933. [PMID: 35979219 PMCID: PMC9377528 DOI: 10.3389/fmed.2022.933933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Accepted: 07/07/2022] [Indexed: 12/02/2022] Open
Abstract
Digital pathology (DP) offers potential for time efficiency gains over an analog workflow however, to date, evidence supporting this claim is relatively lacking. Studies available concentrate on specific workflow points such as diagnostic reporting time, rather than overall efficiencies in slide logistics that might be expected. This is in part a result of the complexity and variation in analog working, and the challenge therefore in capturing this. We have utilized RFID technology to conduct a novel study capturing the movement of diagnostic cases within the analog pathway in a large teaching hospital setting, thus providing benchmark data for potential efficiency gains with DP. This technology overcomes the need to manually record data items and has facilitated the capture of both the physical journey of a case and the time associated with relevant components of the analog pathway predicted to be redundant in the digital setting. RFID tracking of 1,173 surgical pathology cases and over 30 staff in an analog cellular pathology workflow illustrates the complexity of the physical movement of slides within the department, which impacts on case traceability within the system. Detailed analysis of over 400 case journeys highlights redundant periods created by batching of slides at workflow points, including potentially 2–3 h for a case to become available for reporting after release from the lab, and variable lag-times prior to collection for reporting, and provides an illustration of patterns of lab and pathologist working within the analog setting. This study supports the challenge in evidencing efficiency gains to be anticipated with DP in the context of the variation and complexity of the analog pathway, but also evidences the efficiency gains that may be expected through a greater understanding of patterns of working and movement of cases. Such data may benefit other departments building a business case for DP.
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Affiliation(s)
- Lisa Browning
- Department of Cellular Pathology, Oxford University Hospitals NHS Trust, John Radcliffe Hospital, Oxford, United Kingdom
- NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
- *Correspondence: Lisa Browning
| | - Kieron White
- Department of Cellular Pathology, Oxford University Hospitals NHS Trust, John Radcliffe Hospital, Oxford, United Kingdom
| | - Darrin Siiankoski
- Department of Cellular Pathology, Oxford University Hospitals NHS Trust, John Radcliffe Hospital, Oxford, United Kingdom
| | - Richard Colling
- Department of Cellular Pathology, Oxford University Hospitals NHS Trust, John Radcliffe Hospital, Oxford, United Kingdom
- Nuffield Department of Surgical Sciences, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Derek Roskell
- Department of Cellular Pathology, Oxford University Hospitals NHS Trust, John Radcliffe Hospital, Oxford, United Kingdom
| | - Eve Fryer
- Department of Cellular Pathology, Oxford University Hospitals NHS Trust, John Radcliffe Hospital, Oxford, United Kingdom
| | - Helen Hemsworth
- Department of Cellular Pathology, Oxford University Hospitals NHS Trust, John Radcliffe Hospital, Oxford, United Kingdom
| | - Sharon Roberts-Gant
- Department of Cellular Pathology, Oxford University Hospitals NHS Trust, John Radcliffe Hospital, Oxford, United Kingdom
| | - Ruud Roelofsen
- Philips Digital and Computational Pathology, Precision Diagnosis Solutions, Best, Netherlands
| | - Jens Rittscher
- NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
- Department of Engineering Science, Institute of Biomedical Engineering, University of Oxford, Oxford, United Kingdom
| | - Clare Verrill
- Department of Cellular Pathology, Oxford University Hospitals NHS Trust, John Radcliffe Hospital, Oxford, United Kingdom
- NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
- Nuffield Department of Surgical Sciences, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
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11
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Erickson A, Berglund E, He M, Marklund M, Mirzazadeh R, Schultz N, Kvastad L, Andersson A, Bergenstråhle L, Bergenstråhle J, Larsson L, Shamikh A, Basmaci E, De Ståhl TD, Rajakumar T, Thrane K, Ji AL, Khavari PA, Tarish F, Tanoglidi A, Maaskola J, Colling R, Mirtti T, Hamdy F, Woodcock DJ, Helleday T, Mills IG, Lamb AD, Lundenberg J. Abstract 2171: The spatial landscape of clonal somatic mutations in benign and malignant tissue. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-2171] [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: Defining the transition from benign to malignant tissue is fundamental to improve early diagnosis of cancer. In order to obtain spatial information of clonal genetic events, prior studies have used methods such as laser capture microdissection, which results in assessment of small regions or even single cells. These studies have an inherent bias as a limited number of regions per tissue section can be retrieved and examined. Furthermore, because investigators have selected such regions based on morphology, previous studies have limited their analyses to histologically defined tumour areas while excluding regions populated by benign cells. The possibility to perform unsupervised genome and tissue-wide analysis would therefore provide an important contribution to delineate clonal events. We sought study spatial genome integrity in situ to gain molecular insight into clonal relationships.
Materials and Methods: We employed spatially resolved transcriptomics (Visium, 10x Genomics) to infer spatial copy number variations in >120 000 spatial regions across multiple organs, including three whole axial prostates and additional tissues from skin, breast and brain tumors. We used this information to deduce clonal relationships between regions harboring 5-20 cells.
Results: We demonstrate that genome-wide copy number variation reveals distinct clonal patterns within tumours and in nearby benign tissue. We perform an in-depth spatial analysis of cancers that includes an unprecedented interrogation of up to 50,000 tissue domains in a single patient, and 120,000 tissue domains across 10 patients. In a prostate section, we observed that many CNVs occurred in histologically benign luminal epithelial cells, most notably in chromosomes 8 and 10. This clone constituted a region of exclusively benign acinar cells branching off a duct lined by largely copy neutral cells. The changes in these cells were shared with the nearby intermediate risk prostate cancer cells in the same tissue section. We observed similar findings in another patient’s cutaneous squamous cell carcinoma (cSCC), wherein benign squamous epithelial had alterations in chromosomes 1 and 12 that were shared with nearby cSCC. Our results suggest a model for how genomic instability arises in histo-pathologically benign tissue that may represent early events in cancer evolution. Furthermore the spatial information allowed us to identify small clonal units not evident from morphology and hence would be overlooked by pathologists.
Conclusions: We present the first large-scale, comprehensive atlas of genomic evolution at high spatial resolution in prostate cancer. Our study adds an important new approach to the armamentarium of cancer molecular pathology. We highlight the power of an unsupervised approach to capture the molecular and spatial continuums in a tissue context and challenge the rationale for focal therapy in prostate cancer.
Citation Format: Andrew Erickson, Emelie Berglund, Mengxiao He, Maja Marklund, Reza Mirzazadeh, Niklas Schultz, Linda Kvastad, Alma Andersson, Ludvig Bergenstråhle, Joseph Bergenstråhle, Ludvig Larsson, Alia Shamikh, Elisa Basmaci, Teresita Diaz De Ståhl, Timothy Rajakumar, Kim Thrane, Andrew L. Ji, Paul A. Khavari, Firaz Tarish, Anna Tanoglidi, Jonas Maaskola, Richard Colling, Tuomas Mirtti, Freddie Hamdy, Dan J. Woodcock, Thomas Helleday, Ian G. Mills, Alastair D. Lamb, Joakim Lundenberg. The spatial landscape of clonal somatic mutations in benign and malignant tissue [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 2171.
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Affiliation(s)
| | - Emelie Berglund
- 2KTH Royal Institute of Technology, Science for Life Laboratory, Solna, Sweden
| | - Mengxiao He
- 2KTH Royal Institute of Technology, Science for Life Laboratory, Solna, Sweden
| | - Maja Marklund
- 2KTH Royal Institute of Technology, Science for Life Laboratory, Solna, Sweden
| | - Reza Mirzazadeh
- 2KTH Royal Institute of Technology, Science for Life Laboratory, Solna, Sweden
| | - Niklas Schultz
- 3Karolinska Institutet, Science for Life Laboratory, Solna, Sweden
| | - Linda Kvastad
- 2KTH Royal Institute of Technology, Science for Life Laboratory, Solna, Sweden
| | - Alma Andersson
- 2KTH Royal Institute of Technology, Science for Life Laboratory, Solna, Sweden
| | | | | | - Ludvig Larsson
- 2KTH Royal Institute of Technology, Science for Life Laboratory, Solna, Sweden
| | - Alia Shamikh
- 4Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Elisa Basmaci
- 4Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | | | | | - Kim Thrane
- 2KTH Royal Institute of Technology, Science for Life Laboratory, Solna, Sweden
| | - Andrew L. Ji
- 5Stanford University School of Medicine, Stanford, CA
| | | | - Firaz Tarish
- 3Karolinska Institutet, Science for Life Laboratory, Solna, Sweden
| | | | - Jonas Maaskola
- 2KTH Royal Institute of Technology, Science for Life Laboratory, Solna, Sweden
| | - Richard Colling
- 6University of Oxford and Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Tuomas Mirtti
- 7Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Freddie Hamdy
- 6University of Oxford and Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | | | - Thomas Helleday
- 8KTH Royal Institute of Technology, Science for Life Laboratory and University of Sheffield, Solna, Sweden
| | | | - Alastair D. Lamb
- 6University of Oxford and Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Joakim Lundenberg
- 2KTH Royal Institute of Technology, Science for Life Laboratory, Solna, Sweden
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12
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Erickson A, Berglund E, He M, Marklund M, Mirzazadeh R, Schultz N, Bergenstråhle L, Kvastad L, Andersson A, Bergenstråhle J, Larsson L, Shamikh A, Basmaci E, De Ståhl TD, Rajakumar T, Thrane K, Ji AL, Khavari PA, Tarish F, Tanoglidi A, Maaskola J, Colling R, Mirtti T, Hamdy FC, Woodcock DJ, Helleday T, Mills IG, Lamb AD, Lundeberg J. Abstract PR016: The spatial landscape of clonal somatic mutations in benign and malignant tissue. Cancer Res 2022. [DOI: 10.1158/1538-7445.evodyn22-pr016] [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: Defining the transition from benign to malignant tissue is fundamental to improve early diagnosis of cancer. In order to obtain spatial information of clonal genetic events, prior studies have used methods such as laser capture microdissection, which results in assessment of small regions or even single cells. These studies have an inherent bias as a limited number of regions per tissue section can be retrieved and examined. Furthermore, because investigators have selected such regions based on morphology, previous studies have limited their analyses to histologically defined tumor areas while excluding regions populated by benign cells. The possibility to perform unsupervised genome and tissue-wide analysis would therefore provide an important contribution to delineate clonal events. We sought study spatial genome integrity in situ to gain molecular insight into clonal relationships. Materials and Methods: We employed spatially resolved transcriptomics (Visium, 10x Genomics) to infer spatial copy number variations in >120 000 spatial regions across multiple organs, including three whole axial prostates and additional tissues from skin, breast and brain tumors. We additionally performed in silico assessment of spatial copy number inference. We used this information to deduce clonal relationships between regions harboring 5-20 cells. Results: We demonstrate that genome-wide copy number variation reveals distinct clonal patterns within tumors and in nearby benign tissue. We perform an in-depth spatial analysis of cancers that includes an unprecedented interrogation of up to 50,000 tissue domains in a single patient, and 120,000 tissue domains across 10 patients. In a prostate section, we observed that many CNVs occurred in histologically benign luminal epithelial cells, most notably in chromosomes 8 and 10. This clone constituted a region of exclusively benign acinar cells branching off a duct lined by largely copy neutral cells. The changes in these cells were shared with the nearby intermediate risk prostate cancer cells in the same tissue section. We observed similar findings in another patient’s cutaneous squamous cell carcinoma (cSCC), wherein benign squamous epithelial had alterations in chromosomes 1 and 12 that were shared with nearby cSCC. Our results suggest a model for how genomic instability arises in histo-pathologically benign tissue that may represent early events in cancer evolution. Furthermore the spatial information allowed us to identify small clonal units not evident from morphology and hence would be overlooked by pathologists. Conclusions: We present the first large-scale, comprehensive atlas of genomic evolution at high spatial resolution in prostate cancer. Our study adds an important new approach to the armamentarium of cancer molecular pathology. We highlight the power of an unsupervised approach to capture the molecular and spatial continuums in a tissue context and challenge the rationale for focal therapy in prostate cancer
Citation Format: Andrew Erickson, Emelie Berglund, Mengxiao He, Maja Marklund, Reza Mirzazadeh, Niklas Schultz, Ludvig Bergenstråhle, Linda Kvastad, Alma Andersson, Joseph Bergenstråhle, Ludvig Larsson, Alia Shamikh, Elisa Basmaci, Teresita Diaz De Ståhl, Timothy Rajakumar, Kim Thrane, Andrew L. Ji, Paul A. Khavari, Firaz Tarish, Anna Tanoglidi, Jonas Maaskola, Richard Colling, Tuomas Mirtti, Freddie C. Hamdy, Dan J. Woodcock, Thomas Helleday, Ian G. Mills, Alastair D. Lamb, Joakim Lundeberg. The spatial landscape of clonal somatic mutations in benign and malignant tissue [abstract]. In: Proceedings of the AACR Special Conference on the Evolutionary Dynamics in Carcinogenesis and Response to Therapy; 2022 Mar 14-17. Philadelphia (PA): AACR; Cancer Res 2022;82(10 Suppl):Abstract nr PR016.
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Affiliation(s)
- Andrew Erickson
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, United Kingdom,
| | - Emelie Berglund
- KTH Royal Institute of Technology, Science for Life Laboratory, Solna, Sweden,
| | - Mengxiao He
- KTH Royal Institute of Technology, Science for Life Laboratory, Solna, Sweden,
| | - Maja Marklund
- KTH Royal Institute of Technology, Science for Life Laboratory, Solna, Sweden,
| | - Reza Mirzazadeh
- KTH Royal Institute of Technology, Science for Life Laboratory, Solna, Sweden,
| | - Niklas Schultz
- Department of Oncology-Pathology, Science for Life Laboratory, Solna, Sweden,
| | | | - Linda Kvastad
- KTH Royal Institute of Technology, Science for Life Laboratory, Solna, Sweden,
| | - Alma Andersson
- KTH Royal Institute of Technology, Science for Life Laboratory, Solna, Sweden,
| | | | - Ludvig Larsson
- KTH Royal Institute of Technology, Science for Life Laboratory, Solna, Sweden,
| | - Alia Shamikh
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden,
| | - Elisa Basmaci
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden,
| | | | - Timothy Rajakumar
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, United Kingdom,
| | - Kim Thrane
- KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden,
| | - Andrew L. Ji
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA,
| | - Paul A. Khavari
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA,
| | - Firaz Tarish
- Department of Oncology-Pathology, Science for Life Laboratory, Stockholm, Sweden,
| | - Anna Tanoglidi
- Department of Clinical Pathology, University Uppsala Hospital, Uppsala, Sweden,
| | - Jonas Maaskola
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA,
| | - Richard Colling
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, United Kingdom,
| | - Tuomas Mirtti
- Department of Pathology, University of Helsinki & Helsinki University Hospital, Helsinki, Finland
| | - Freddie C. Hamdy
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, United Kingdom,
| | - Dan J. Woodcock
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, United Kingdom,
| | - Thomas Helleday
- Department of Oncology-Pathology, Science for Life Laboratory, Stockholm, Sweden,
| | - Ian G. Mills
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, United Kingdom,
| | - Alastair D. Lamb
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, United Kingdom,
| | - Joakim Lundeberg
- KTH Royal Institute of Technology, Science for Life Laboratory, Solna, Sweden,
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13
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Rakovic K, Colling R, Browning L, Dolton M, Horton MR, Protheroe A, Lamb AD, Bryant RJ, Scheffer R, Crofts J, Stanislaus E, Verrill C. The Use of Digital Pathology and Artificial Intelligence in Histopathological Diagnostic Assessment of Prostate Cancer: A Survey of Prostate Cancer UK Supporters. Diagnostics (Basel) 2022; 12:1225. [PMID: 35626380 PMCID: PMC9141178 DOI: 10.3390/diagnostics12051225] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 05/09/2022] [Accepted: 05/11/2022] [Indexed: 12/03/2022] Open
Abstract
There has been particular interest in the deployment of digital pathology (DP) and artificial intelligence (AI) in the diagnosis of prostate cancer, but little is known about the views of the public on their use. Prostate Cancer UK supporters were invited to an online survey which included quantitative and qualitative questions exploring views on the use of DP and AI in histopathological assessment. A total of 1276 responses to the survey were analysed (response rate 12.5%). Most respondents were supportive of DP (87%, 1113/1276) and of testing AI in clinical practice as a diagnostic adjunct (83%, 1058/1276). Respondents saw DP as potentially increasing workflow efficiency, facilitating research, education/training and fostering clinical discussions between clinician and patient. Some respondents raised concerns regarding data security, reliability and the need for human oversight. Among those who were unsure about AI, information was requested regarding its performance and others wanted to defer the decision to use it to an expert. Although most are in favour of its use, some are unsure, and their concerns could be addressed with more information or better communication. A small minority (<1%) are not in favour of the testing of the use of AI in histopathology for reasons which are not easily addressed.
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Affiliation(s)
- Kai Rakovic
- Institute of Cancer Sciences, University of Glasgow, Switchback Road, Glasgow G61 1QH, UK
- Department of Pathology, Queen Elizabeth University Hospital, Govan Road, Glasgow G51 4TF, UK
| | - Richard Colling
- Department of Cellular Pathology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headley Way, Oxford OX3 9DU, UK; (R.C.); (L.B.); (C.V.)
- Nuffield Department of Surgical Sciences, University of Oxford, John Radcliffe Hospital, Headley Way, Oxford OX3 9DU, UK; (M.D.); (A.D.L.); (R.J.B.); (R.S.); (J.C.); (E.S.)
| | - Lisa Browning
- Department of Cellular Pathology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headley Way, Oxford OX3 9DU, UK; (R.C.); (L.B.); (C.V.)
- NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headley Way, Oxford OX3 9DU, UK
| | - Monica Dolton
- Nuffield Department of Surgical Sciences, University of Oxford, John Radcliffe Hospital, Headley Way, Oxford OX3 9DU, UK; (M.D.); (A.D.L.); (R.J.B.); (R.S.); (J.C.); (E.S.)
| | | | - Andrew Protheroe
- Department of Oncology, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, UK;
- Oxford Cancer & Haematology Centre, Oxford University Hospitals NHS Foundation Trust, Churchill Hospital, Old Road, Oxford OX3 7LE, UK
| | - Alastair D. Lamb
- Nuffield Department of Surgical Sciences, University of Oxford, John Radcliffe Hospital, Headley Way, Oxford OX3 9DU, UK; (M.D.); (A.D.L.); (R.J.B.); (R.S.); (J.C.); (E.S.)
- Department of Urology, Oxford University Hospitals NHS Foundation Trust, Churchill Hospital, Old Road, Oxford OX3 7LE, UK
| | - Richard J. Bryant
- Nuffield Department of Surgical Sciences, University of Oxford, John Radcliffe Hospital, Headley Way, Oxford OX3 9DU, UK; (M.D.); (A.D.L.); (R.J.B.); (R.S.); (J.C.); (E.S.)
- Department of Urology, Oxford University Hospitals NHS Foundation Trust, Churchill Hospital, Old Road, Oxford OX3 7LE, UK
| | - Richard Scheffer
- Nuffield Department of Surgical Sciences, University of Oxford, John Radcliffe Hospital, Headley Way, Oxford OX3 9DU, UK; (M.D.); (A.D.L.); (R.J.B.); (R.S.); (J.C.); (E.S.)
| | - James Crofts
- Nuffield Department of Surgical Sciences, University of Oxford, John Radcliffe Hospital, Headley Way, Oxford OX3 9DU, UK; (M.D.); (A.D.L.); (R.J.B.); (R.S.); (J.C.); (E.S.)
| | - Ewart Stanislaus
- Nuffield Department of Surgical Sciences, University of Oxford, John Radcliffe Hospital, Headley Way, Oxford OX3 9DU, UK; (M.D.); (A.D.L.); (R.J.B.); (R.S.); (J.C.); (E.S.)
| | - Clare Verrill
- Department of Cellular Pathology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headley Way, Oxford OX3 9DU, UK; (R.C.); (L.B.); (C.V.)
- Nuffield Department of Surgical Sciences, University of Oxford, John Radcliffe Hospital, Headley Way, Oxford OX3 9DU, UK; (M.D.); (A.D.L.); (R.J.B.); (R.S.); (J.C.); (E.S.)
- NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headley Way, Oxford OX3 9DU, UK
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14
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Haghighat M, Browning L, Sirinukunwattana K, Malacrino S, Khalid Alham N, Colling R, Cui Y, Rakha E, Hamdy FC, Verrill C, Rittscher J. Automated quality assessment of large digitised histology cohorts by artificial intelligence. Sci Rep 2022; 12:5002. [PMID: 35322056 PMCID: PMC8943120 DOI: 10.1038/s41598-022-08351-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [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: 09/24/2021] [Accepted: 03/03/2022] [Indexed: 02/07/2023] Open
Abstract
Research using whole slide images (WSIs) of histopathology slides has increased exponentially over recent years. Glass slides from retrospective cohorts, some with patient follow-up data are digitised for the development and validation of artificial intelligence (AI) tools. Such resources, therefore, become very important, with the need to ensure that their quality is of the standard necessary for downstream AI development. However, manual quality control of large cohorts of WSIs by visual assessment is unfeasible, and whilst quality control AI algorithms exist, these focus on bespoke aspects of image quality, e.g. focus, or use traditional machine-learning methods, which are unable to classify the range of potential image artefacts that should be considered. In this study, we have trained and validated a multi-task deep neural network to automate the process of quality control of a large retrospective cohort of prostate cases from which glass slides have been scanned several years after production, to determine both the usability of the images at the diagnostic level (considered in this study to be the minimal standard for research) and the common image artefacts present. Using a two-layer approach, quality overlays of WSIs were generated from a quality assessment (QA) undertaken at patch-level at \documentclass[12pt]{minimal}
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\begin{document}$$5\times$$\end{document}5× magnification. From these quality overlays the slide-level quality scores were predicted and then compared to those generated by three specialist urological pathologists, with a Pearson correlation of 0.89 for overall ‘usability’ (at a diagnostic level), and 0.87 and 0.82 for focus and H&E staining quality scores respectively. To demonstrate its wider potential utility, we subsequently applied our QA pipeline to the TCGA prostate cancer cohort and to a colorectal cancer cohort, for comparison. Our model, designated as PathProfiler, indicates comparable predicted usability of images from the cohorts assessed (86–90% of WSIs predicted to be usable), and perhaps more significantly is able to predict WSIs that could benefit from an intervention such as re-scanning or re-staining for quality improvement. We have shown in this study that AI can be used to automate the process of quality control of large retrospective WSI cohorts to maximise their utility for research.
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Affiliation(s)
- Maryam Haghighat
- Department of Engineering Science, Institute of Biomedical Engineering (IBME), University of Oxford, Oxford, UK. .,CSIRO, Brisbane, QLD, Australia.
| | - Lisa Browning
- Department of Cellular Pathology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK.,NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, Oxfordshire, UK
| | - Korsuk Sirinukunwattana
- Department of Engineering Science, Institute of Biomedical Engineering (IBME), University of Oxford, Oxford, UK
| | - Stefano Malacrino
- Nuffield Department of Surgical Sciences, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Nasullah Khalid Alham
- Department of Engineering Science, Institute of Biomedical Engineering (IBME), University of Oxford, Oxford, UK
| | - Richard Colling
- Department of Cellular Pathology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK.,Nuffield Department of Surgical Sciences, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Ying Cui
- Nuffield Department of Surgical Sciences, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Emad Rakha
- School of Medicine, University of Nottingham, Nottingham, UK
| | - Freddie C Hamdy
- NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, Oxfordshire, UK.,Nuffield Department of Surgical Sciences, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Clare Verrill
- Department of Cellular Pathology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK.,NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, Oxfordshire, UK.,Nuffield Department of Surgical Sciences, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Jens Rittscher
- Department of Engineering Science, Institute of Biomedical Engineering (IBME), University of Oxford, Oxford, UK. .,NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, Oxfordshire, UK.
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15
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Coulter C, McKay F, Hallowell N, Browning L, Colling R, Macklin P, Sorell T, Aslam M, Bryson G, Treanor D, Verrill C. Understanding the ethical and legal considerations of Digital Pathology. J Pathol Clin Res 2022; 8:101-115. [PMID: 34796679 PMCID: PMC8822384 DOI: 10.1002/cjp2.251] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 09/12/2021] [Accepted: 10/12/2021] [Indexed: 12/21/2022]
Abstract
Digital Pathology (DP) is a platform which has the potential to develop a truly integrated and global pathology community. The generation of DP data at scale creates novel challenges for the histopathology community in managing, processing, and governing the use of these data. The current understanding of, and confidence in, the legal and ethical aspects of DP by pathologists is unknown. We developed an electronic survey (e-survey), comprising 22 questions, with input from the Royal College of Pathologists (RCPath) Digital Pathology Working Group. The e-survey was circulated via e-mail and social media (Twitter) through the RCPath Digital Pathology Working Group network, RCPath Trainee Committee network, the Pathology image data Lake for Analytics, Knowledge and Education (PathLAKE) digital pathology consortium, National Pathology Imaging Co-operative (NPIC), local contacts, and to the membership of both The Pathological Society of Great Britain and Ireland and the British Division of the International Academy of Pathology (BDIAP). Between 14 July 2020 and 6 September 2020, we collected 198 responses representing a cross section of histopathologists, including individuals with experience of DP research. We ascertained that, in the UK, DP is being used for diagnosis, research, and teaching, and that the platform is enabling data sharing. Our survey demonstrated that there is often a lack of confidence and understanding of the key issues of consent, legislation, and ethical guidelines. Of 198 respondents, 82 (41%) did not know when the use of digital scanned slide images would fall under the relevant legislation and 93 (47%) were 'Not confident at all' in their interpretation of consent for scanned slide images in research. With increasing uptake of DP, a working knowledge of these areas is essential but histopathologists often express a lack of confidence in these topics. The need for specific training in these areas is highlighted by the findings of this study.
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Affiliation(s)
- Cheryl Coulter
- Department of Cellular Pathology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK.,Nuffield Division of Clinical Laboratory Sciences, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Francis McKay
- The Wellcome Centre for Ethics and Humanities and the Ethox Centre, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Nina Hallowell
- The Wellcome Centre for Ethics and Humanities and the Ethox Centre, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Lisa Browning
- Department of Cellular Pathology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK.,NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK
| | - Richard Colling
- Department of Cellular Pathology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK.,Nuffield Department of Surgical Sciences, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Philip Macklin
- Department of Cellular Pathology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK
| | - Tom Sorell
- Department of Politics and International Studies, University of Warwick, Coventry, UK
| | - Muhammad Aslam
- Department of Histopathology, Glangwilli Hospital, Hywel Dda University Health Board, Carmarthen, Wales, UK
| | - Gareth Bryson
- Department of Pathology, Queen Elizabeth University Hospital, NHS Greater Glasgow and Clyde, Glasgow, Scotland, UK
| | - Darren Treanor
- Department of Pathology, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Clare Verrill
- Department of Cellular Pathology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK.,NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK.,Nuffield Department of Surgical Sciences, University of Oxford, John Radcliffe Hospital, Oxford, UK
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16
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Erickson A, Berglund E, He M, Marklund M, Mirzazadeh R, Schultz N, Bergenstråhle L, Kvastad L, Andersson A, Bergenstråhle J, Larsson L, Rajakumar T, Thrane K, Ji A, Tarish F, Tanoglidi A, Maaskola J, Colling R, Mirtti T, Hamdy F, Woodcock D, Helleday T, Mills I, Lamb A, Lundenberg J. The spatial landscape of clonal somatic mutations in benign and malignant prostate epithelia. Eur Urol 2022. [DOI: 10.1016/s0302-2838(22)00563-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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17
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Chelebian E, Avenel C, Kartasalo K, Marklund M, Tanoglidi A, Mirtti T, Colling R, Erickson A, Lamb AD, Lundeberg J, Wählby C. Morphological Features Extracted by AI Associated with Spatial Transcriptomics in Prostate Cancer. Cancers (Basel) 2021; 13:4837. [PMID: 34638322 PMCID: PMC8507756 DOI: 10.3390/cancers13194837] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 09/21/2021] [Accepted: 09/22/2021] [Indexed: 11/16/2022] Open
Abstract
Prostate cancer is a common cancer type in men, yet some of its traits are still under-explored. One reason for this is high molecular and morphological heterogeneity. The purpose of this study was to develop a method to gain new insights into the connection between morphological changes and underlying molecular patterns. We used artificial intelligence (AI) to analyze the morphology of seven hematoxylin and eosin (H&E)-stained prostatectomy slides from a patient with multi-focal prostate cancer. We also paired the slides with spatially resolved expression for thousands of genes obtained by a novel spatial transcriptomics (ST) technique. As both spaces are highly dimensional, we focused on dimensionality reduction before seeking associations between them. Consequently, we extracted morphological features from H&E images using an ensemble of pre-trained convolutional neural networks and proposed a workflow for dimensionality reduction. To summarize the ST data into genetic profiles, we used a previously proposed factor analysis. We found that the regions were automatically defined, outlined by unsupervised clustering, associated with independent manual annotations, in some cases, finding further relevant subdivisions. The morphological patterns were also correlated with molecular profiles and could predict the spatial variation of individual genes. This novel approach enables flexible unsupervised studies relating morphological and genetic heterogeneity using AI to be carried out.
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Affiliation(s)
- Eduard Chelebian
- Science for Life Laboratory, Department of Information Technology, Uppsala University, 752 37 Uppsala, Sweden;
| | - Christophe Avenel
- Science for Life Laboratory, Department of Information Technology, Uppsala University, 752 37 Uppsala, Sweden;
| | - Kimmo Kartasalo
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, 171 77 Stockholm, Sweden;
| | - Maja Marklund
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, 171 65 Solna, Sweden; (M.M.); (J.L.)
| | - Anna Tanoglidi
- Department of Clinical Pathology, Uppsala University Hospital, 752 37 Uppsala, Sweden;
| | - Tuomas Mirtti
- Department of Pathology, Research Program in Systems Oncology, University of Helsinki, Helsinki University Hospital, 00100 Helsinki, Finland;
| | - Richard Colling
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford OX3 7DQ, UK; (R.C.); (A.E.); (A.D.L.)
- Department of Cellular Pathology, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 9DU, UK
| | - Andrew Erickson
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford OX3 7DQ, UK; (R.C.); (A.E.); (A.D.L.)
| | - Alastair D. Lamb
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford OX3 7DQ, UK; (R.C.); (A.E.); (A.D.L.)
- Department of Urology, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 7LE, UK
| | - Joakim Lundeberg
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, 171 65 Solna, Sweden; (M.M.); (J.L.)
| | - Carolina Wählby
- Science for Life Laboratory, Department of Information Technology, Uppsala University, 752 37 Uppsala, Sweden;
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18
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Colling R, Colling H, Browning L, Verrill C. Validation of grading of non-invasive urothelial carcinoma by digital pathology for routine diagnosis. BMC Cancer 2021; 21:995. [PMID: 34488682 PMCID: PMC8420048 DOI: 10.1186/s12885-021-08698-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 02/16/2021] [Accepted: 08/13/2021] [Indexed: 11/30/2022] Open
Abstract
Background Pathological grading of non-invasive urothelial carcinoma has a direct impact upon management. This study evaluates the reproducibility of grading these tumours on glass slides and digital pathology. Methods Forty eight non-invasive urothelial bladder carcinomas were graded by three uropathologists on glass and on a digital platform using the 1973 WHO and 2004 ISUP/WHO systems. Results Consensus grades for glass and digital grading gave Cohen’s kappa scores of 0.78 (2004) and 0.82 (1973). Of 142 decisions made on the key therapeutic borderline of low grade versus high grade urothelial carcinoma (2004) by the three pathologists, 85% were in agreement. For the 1973 grading system, agreement overall was 90%. Conclusions Agreement on grading on glass slide and digital screen assessment is similar or in some cases improved, suggesting at least non-inferiority of DP for grading of non-invasive urothelial carcinoma.
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Affiliation(s)
- Richard Colling
- Nuffield Department of Surgical Sciences, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DU, UK. .,Department of Cellular Pathology, Oxford University Hospitals NHS Trust, John Radcliffe Hospital, Oxford, OX3 9DU, UK.
| | - Hayleigh Colling
- Nuffield Department of Surgical Sciences, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DU, UK
| | - Lisa Browning
- Department of Cellular Pathology, Oxford University Hospitals NHS Trust, John Radcliffe Hospital, Oxford, OX3 9DU, UK.,NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, Oxfordshire, UK
| | - Clare Verrill
- Nuffield Department of Surgical Sciences, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DU, UK.,Department of Cellular Pathology, Oxford University Hospitals NHS Trust, John Radcliffe Hospital, Oxford, OX3 9DU, UK.,NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, Oxfordshire, UK
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19
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Browning L, Colling R, Verrill C. WHO/ISUP grading of clear cell renal cell carcinoma and papillary renal cell carcinoma; validation of grading on the digital pathology platform and perspectives on reproducibility of grade. Diagn Pathol 2021; 16:75. [PMID: 34419085 PMCID: PMC8380382 DOI: 10.1186/s13000-021-01130-2] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 07/12/2021] [Indexed: 11/10/2022] Open
Abstract
Background There are recognised potential pitfalls in digital diagnosis in urological pathology, including the grading of dysplasia. The World Health Organisation/International Society of Urological Pathology (WHO/ISUP) grading system for renal cell carcinoma (RCC) is prognostically important in clear cell RCC (CCRCC) and papillary RCC (PRCC), and is included in risk stratification scores for CCRCC, thus impacting on patient management. To date there are no systematic studies examining the concordance of WHO/ISUP grading between digital pathology (DP) and glass slide (GS) images. We present a validation study examining intraobserver agreement in WHO/ISUP grade of CCRCC and PRCC. Methods Fifty CCRCCs and 10 PRCCs were graded (WHO/ISUP system) by three specialist uropathologists on three separate occasions (DP once then two GS assessments; GS1 and GS2) separated by wash-out periods of at least two-weeks. The grade was recorded for each assessment, and compared using Cohen’s and Fleiss’s kappa. Results There was 65 to 78% concordance of WHO/ISUP grading on DP and GS1. Furthermore, for the individual pathologists, the comparative kappa scores for DP versus GS1, and GS1 versus GS2, were 0.70 and 0.70, 0.57 and 0.73, and 0.71 and 0.74, and with no apparent tendency to upgrade or downgrade on DP versus GS. The interobserver kappa agreement was less, at 0.58 on DP and 0.45 on GS. Conclusion Our results demonstrate that the assessment of WHO/ISUP grade on DP is noninferior to that on GS. There is an apparent slight improvement in agreement between pathologists on RCC grade when assessed on DP, which may warrant further study.
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Affiliation(s)
- Lisa Browning
- Department of Cellular Pathology, Oxford University Hospitals NHS Trust, John Radcliffe Hospital, Headley Way, OX3 9DU, Oxford, UK. .,NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, Oxfordshire, UK.
| | - Richard Colling
- Department of Cellular Pathology, Oxford University Hospitals NHS Trust, John Radcliffe Hospital, Headley Way, OX3 9DU, Oxford, UK.,Nuffield Department of Surgical Sciences, University of Oxford, John Radcliffe Hospital, OX3 9DU, Oxford, UK
| | - Clare Verrill
- Department of Cellular Pathology, Oxford University Hospitals NHS Trust, John Radcliffe Hospital, Headley Way, OX3 9DU, Oxford, UK.,NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, Oxfordshire, UK.,Nuffield Department of Surgical Sciences, University of Oxford, John Radcliffe Hospital, OX3 9DU, Oxford, UK
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20
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Young LAJ, Ceresa CDL, Mózes FE, Ellis J, Valkovič L, Colling R, Coussios CC, Friend PJ, Rodgers CT. Noninvasive assessment of steatosis and viability of cold-stored human liver grafts by MRI. Magn Reson Med 2021; 86:3246-3258. [PMID: 34272767 PMCID: PMC7613197 DOI: 10.1002/mrm.28930] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 03/04/2021] [Revised: 06/25/2021] [Accepted: 06/28/2021] [Indexed: 12/02/2022]
Abstract
Purpose A shortage of suitable donor livers is driving increased use of higher risk livers for transplantation. However, current biomarkers are not sensitive and specific enough to predict posttransplant liver function. This is limiting the expansion of the donor pool. Therefore, better noninvasive tests are required to determine which livers will function following implantation and hence can be safely transplanted. This study assesses the temperature sensitivity of proton density fat fraction and relaxometry parameters and examines their potential for assessment of liver function ex vivo. Methods Six ex vivo human livers were scanned during static cold storage following normothermic machine perfusion. Proton density fat fraction, T1, T2, and T2* were measured repeatedly during cooling on ice. Temperature corrections were derived from these measurements for the parameters that showed significant variation with temperature. Results Strong linear temperature sensitivities were observed for proton density fat fraction (R2 = 0.61, P < .001) and T1 (R2 = 0.78, P < .001). Temperature correction according to a linear model reduced the coefficient of repeatability in these measurements by 41% and 36%, respectively. No temperature dependence was observed in T2 or T2* measurements. Comparing livers deemed functional and nonfunctional during normothermic machine perfusion by hemodynamic and biochemical criteria, T1 differed significantly: 516 ± 50 ms for functional versus 679 ± 60 ms for non-functional, P = .02. Conclusion Temperature correction is essential for robust measurement of proton density fat fraction and T1 in cold-stored human livers. These parameters may provide a noninvasive measure of viability for transplantation.
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Affiliation(s)
- Liam A J Young
- Oxford Centre for Clinical Magnetic Resonance Research, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Carlo D L Ceresa
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, United Kingdom
| | - Ferenc E Mózes
- Oxford Centre for Clinical Magnetic Resonance Research, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Jane Ellis
- Oxford Centre for Clinical Magnetic Resonance Research, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Ladislav Valkovič
- Oxford Centre for Clinical Magnetic Resonance Research, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom.,Department of Imaging Methods, Institute of Measurement Science, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Richard Colling
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, United Kingdom
| | | | - Peter J Friend
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, United Kingdom
| | - Christopher T Rodgers
- Oxford Centre for Clinical Magnetic Resonance Research, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom.,Wolfson Brain Imaging Centre, Department of Clinical Neurosciences, University of Cambridge, Cambridge, United Kingdom
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21
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Ghosh A, Sirinukunwattana K, Khalid Alham N, Browning L, Colling R, Protheroe A, Protheroe E, Jones S, Aberdeen A, Rittscher J, Verrill C. The Potential of Artificial Intelligence to Detect Lymphovascular Invasion in Testicular Cancer. Cancers (Basel) 2021; 13:cancers13061325. [PMID: 33809521 PMCID: PMC7998792 DOI: 10.3390/cancers13061325] [Citation(s) in RCA: 9] [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: 02/14/2021] [Revised: 03/08/2021] [Accepted: 03/12/2021] [Indexed: 11/16/2022] Open
Abstract
Testicular cancer is the most common cancer in men aged from 15 to 34 years. Lymphovascular invasion refers to the presence of tumours within endothelial-lined lymphatic or vascular channels, and has been shown to have prognostic significance in testicular germ cell tumours. In non-seminomatous tumours, lymphovascular invasion is the most powerful prognostic factor for stage 1 disease. For the pathologist, searching multiple slides for lymphovascular invasion can be highly time-consuming. The aim of this retrospective study was to develop and assess an artificial intelligence algorithm that can identify areas suspicious for lymphovascular invasion in histological digital whole slide images. Areas of possible lymphovascular invasion were annotated in a total of 184 whole slide images of haematoxylin and eosin (H&E) stained tissue from 19 patients with testicular germ cell tumours, including a mixture of seminoma and non-seminomatous cases. Following consensus review by specialist uropathologists, we trained a deep learning classifier for automatic segmentation of areas suspicious for lymphovascular invasion. The classifier identified 34 areas within a validation set of 118 whole slide images from 10 patients, each of which was reviewed by three expert pathologists to form a majority consensus. The precision was 0.68 for areas which were considered to be appropriate to flag, and 0.56 for areas considered to be definite lymphovascular invasion. An artificial intelligence tool which highlights areas of possible lymphovascular invasion to reporting pathologists, who then make a final judgement on its presence or absence, has been demonstrated as feasible in this proof-of-concept study. Further development is required before clinical deployment.
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Affiliation(s)
- Abhisek Ghosh
- Department of Cellular Pathology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford OX3 9DU, UK; (L.B.); (R.C.); (C.V.)
- Nuffield Department of Clinical and Laboratory Sciences, Oxford University, John Radcliffe Hospital, Oxford OX3 9DU, UK
- Correspondence:
| | - Korsuk Sirinukunwattana
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford OX3 7LF, UK; (K.S.); (N.K.A.); (J.R.)
- Oxford NIHR Biomedical Research Centre, Oxford University, Oxford OX3 9DU, UK
- Institute of Biomedical Engineering, Department of Engineering Science, University of Oxford, Oxford OX3 7DQ, UK
- Ground Truth Labs, Oxford OX4 2HN, UK;
| | - Nasullah Khalid Alham
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford OX3 7LF, UK; (K.S.); (N.K.A.); (J.R.)
- Oxford NIHR Biomedical Research Centre, Oxford University, Oxford OX3 9DU, UK
| | - Lisa Browning
- Department of Cellular Pathology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford OX3 9DU, UK; (L.B.); (R.C.); (C.V.)
- Oxford NIHR Biomedical Research Centre, Oxford University, Oxford OX3 9DU, UK
| | - Richard Colling
- Department of Cellular Pathology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford OX3 9DU, UK; (L.B.); (R.C.); (C.V.)
- Nuffield Department of Surgical Sciences, Oxford University, Oxford OX3 9DU, UK;
| | - Andrew Protheroe
- Department of Oncology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford OX3 9DU, UK; (A.P.); (E.P.)
| | - Emily Protheroe
- Department of Oncology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford OX3 9DU, UK; (A.P.); (E.P.)
| | - Stephanie Jones
- Nuffield Department of Surgical Sciences, Oxford University, Oxford OX3 9DU, UK;
| | | | - Jens Rittscher
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford OX3 7LF, UK; (K.S.); (N.K.A.); (J.R.)
- Oxford NIHR Biomedical Research Centre, Oxford University, Oxford OX3 9DU, UK
| | - Clare Verrill
- Department of Cellular Pathology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford OX3 9DU, UK; (L.B.); (R.C.); (C.V.)
- Oxford NIHR Biomedical Research Centre, Oxford University, Oxford OX3 9DU, UK
- Nuffield Department of Surgical Sciences, Oxford University, Oxford OX3 9DU, UK;
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22
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Velasco A, Tokat F, Bonde J, Trim N, Bauer E, Meeney A, de Leng W, Chong G, Dalstein V, Kis LL, Lorentzen JA, Tomić S, Thwaites K, Putzová M, Birnbaum A, Qazi R, Primmer V, Dockhorn-Dworniczak B, Hernández-Losa J, Soares FA, Gertler AA, Kalman M, Wong C, Carraro DM, Sousa AC, Reis RM, Fox SB, Fassan M, Brevet M, Merkelbach-Bruse S, Colling R, Soilleux E, Teo RYW, D'Haene N, Nolet S, Ristimäki A, Väisänen T, Chapusot C, Soruri A, Unger T, Wecgowiec J, Biscuola M, Frattini M, Long A, Campregher PV, Matias-Guiu X. Multi-center real-world comparison of the fully automated Idylla™ microsatellite instability assay with routine molecular methods and immunohistochemistry on formalin-fixed paraffin-embedded tissue of colorectal cancer. Virchows Arch 2020; 478:851-863. [PMID: 33170334 PMCID: PMC8099763 DOI: 10.1007/s00428-020-02962-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 09/14/2020] [Accepted: 10/30/2020] [Indexed: 12/24/2022]
Abstract
Microsatellite instability (MSI) is present in 15–20% of primary colorectal cancers. MSI status is assessed to detect Lynch syndrome, guide adjuvant chemotherapy, determine prognosis, and use as a companion test for checkpoint blockade inhibitors. Traditionally, MSI status is determined by immunohistochemistry or molecular methods. The Idylla™ MSI Assay is a fully automated molecular method (including automated result interpretation), using seven novel MSI biomarkers (ACVR2A, BTBD7, DIDO1, MRE11, RYR3, SEC31A, SULF2) and not requiring matched normal tissue. In this real-world global study, 44 clinical centers performed Idylla™ testing on a total of 1301 archived colorectal cancer formalin-fixed, paraffin-embedded (FFPE) tissue sections and compared Idylla™ results against available results from routine diagnostic testing in those sites. MSI mutations detected with the Idylla™ MSI Assay were equally distributed over the seven biomarkers, and 84.48% of the MSI-high samples had ≥ 5 mutated biomarkers, while 98.25% of the microsatellite-stable samples had zero mutated biomarkers. The concordance level between the Idylla™ MSI Assay and immunohistochemistry was 96.39% (988/1025); 17/37 discordant samples were found to be concordant when a third method was used. Compared with routine molecular methods, the concordance level was 98.01% (789/805); third-method analysis found concordance for 8/16 discordant samples. The failure rate of the Idylla™ MSI Assay (0.23%; 3/1301) was lower than that of referenced immunohistochemistry (4.37%; 47/1075) or molecular assays (0.86%; 7/812). In conclusion, lower failure rates and high concordance levels were found between the Idylla™ MSI Assay and routine tests.
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Affiliation(s)
- Ana Velasco
- Departments of Pathology and Molecular Genetics, Hospital U Arnau de Vilanova and Hospital U de Bellvitge, University of Lleida, IRBLLEIDA, IDIBELL, CIBERONC, Av. Alcalde Rovira Roure, 80 25198, Lleida, Spain.
| | - Fatma Tokat
- Department of Pathology, Acıbadem Mehmet Ali Aydınlar University, Istanbul, Turkey
| | - Jesper Bonde
- Molecular Pathology Laboratory, Department of Pathology, afs. 134, Hvidovre Hospital, Hvidovre, Denmark
| | - Nicola Trim
- Molecular Pathology Diagnostic Service, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | - Elisabeth Bauer
- Städtisches Klinikum Karlsruhe gGmbH, Institut für Pathologie, Karlsruhe, Germany
| | - Adam Meeney
- Ophthalmic Pathology Laboratory Histopathology, Royal Hallamshire Hospital, Glossop Road, Sheffield, UK
| | - Wendy de Leng
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - George Chong
- Molecular Pathology Centre, Jewish General Hospital-McGill University, Montreal, Quebec, Canada
| | - Véronique Dalstein
- Laboratoire de Biopathologie, Unité INSERM UMR-S 1250, CHU Reims, Reims, France
| | - Lorand L Kis
- Department of Clinical Pathology and Cytology, Karolinska University Hospital, Stockholm, Sweden
| | - Jon A Lorentzen
- Molecular Pathology Unit, Department of Pathology, Oslo University Hospital, Oslo, Norway
| | - Snjezana Tomić
- Department of Pathology, Forensic Medicine and Cytology, University Hospital Split, Split, Croatia
| | - Keeley Thwaites
- Histopathology Department, Barking, Havering and Redbridge University Hospitals NHS Trust, Queen's Hospital, Romford, UK
| | - Martina Putzová
- Bioptická laboratoř s.r.o., Laboratory of Molecular Genetics, Plzeň, Czech Republic.,ÚBLG FN Motol, Praha, Czech Republic.,LF UK, Plzeň, Czech Republic
| | | | - Romena Qazi
- Department of Pathology, Shaukat Khanum Memorial Cancer Hospital & Research Centre, Johr Town, Lahore, Pakistan
| | - Vanessa Primmer
- Pathologisch-Bakteriologisches Institut Kaiser-Franz-Josef-Spital, Vienna, Austria
| | | | - Javier Hernández-Losa
- Department of Pathology, Hospital Universitari Vall d'Hebron, Barcelona, Spain.,Spanish Biomedical Research Network Centre in Oncology (CIBERONC), Madrid, Spain
| | | | - Asaf A Gertler
- Department of Pathology, Hadassah Medical Center, Jerusalem, Israel
| | - Michal Kalman
- Department of Pathologic Anatomy, Jessenius Faculty of Medicine, Comenius University in Bratislava, Martin, Slovak Republic.,Martin's Biopsy Center Ltd., Martin, Slovak Republic
| | - Chris Wong
- Hong Kong Molecular Pathology Diagnostic Centre, Hong Kong Special Administrative Region of the People's Republic of China, Hong Kong, People's Republic of China
| | - Dirce M Carraro
- Genomics and Molecular Biology Group, International Research Center/CIPE, A. C. Camargo Cancer Center, São Paulo, SP, Brazil
| | - Ana C Sousa
- GenoMed, Diagnósticos de Medicina Molecular, SA, Lisbon, Portugal
| | - Rui M Reis
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, SP, Brazil.,Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal.,ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Stephen B Fox
- Pathology, Peter MacCallum Cancer Centre and University of Melbourne, Vic, Australia
| | - Matteo Fassan
- Surgical Pathology Unit, Department of Medicine (DIMED), University of Padua, Padua, Italy
| | - Marie Brevet
- Department of Pathology, Hospices Civils de Lyon, Université Lyon 1, Bron, France & Cypath, Villeurbanne, France
| | | | - Richard Colling
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | | | - Ryan Yee Wei Teo
- Department of Pathology, Tan Tock Seng Hospital, Novena, Republic of Singapore
| | - Nicky D'Haene
- Department of Pathology, Erasme Hospital, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Serge Nolet
- Département de Pathologie et Biologie Cellulaire, Université de Montréal, Montreal, Québec, Canada
| | - Ari Ristimäki
- Department of Pathology, Research Programs Unit and HUSLAB, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Timo Väisänen
- Oulu University Hospital and Department of Pathology, Cancer and Translational Medicine Research Unit, University of Oulu, Oulu, Finland
| | | | - Afsaneh Soruri
- Institut für Pathologie und Molekularpathologie, Pforzheim, Germany
| | - Tina Unger
- Institut für Pathologie, University of Leipzig, Leipzig, Germany
| | - Johanna Wecgowiec
- Institut für Pathologie, Evangelisches Krankenhaus BETHESDA Zu Duisburg GmbH, Duisburg, Germany
| | - Michele Biscuola
- Department of Pathology, Molecular Pathology Laboratory, Hospital Universitario Virgen del Rocío-IBIS, Seville, Spain
| | - Milo Frattini
- Laboratory of Molecular Pathology, Institute of Pathology, Locarno, Switzerland
| | - Anna Long
- Cellular Pathology, Newcastle Upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | | | - Xavier Matias-Guiu
- Departments of Pathology and Molecular Genetics, Hospital U Arnau de Vilanova and Hospital U de Bellvitge, University of Lleida, IRBLLEIDA, IDIBELL, CIBERONC, Av. Alcalde Rovira Roure, 80 25198, Lleida, Spain
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Fane ME, Ecker BL, Kaur A, Marino GE, Alicea GM, Douglass SM, Chhabra Y, Webster MR, Marshall A, Colling R, Espinosa O, Coupe N, Maroo N, Campo L, Middleton MR, Corrie P, Xu X, Karakousis GC, Weeraratna AT. sFRP2 Supersedes VEGF as an Age-related Driver of Angiogenesis in Melanoma, Affecting Response to Anti-VEGF Therapy in Older Patients. Clin Cancer Res 2020; 26:5709-5719. [PMID: 33097493 PMCID: PMC7642114 DOI: 10.1158/1078-0432.ccr-20-0446] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 06/30/2020] [Accepted: 08/27/2020] [Indexed: 12/22/2022]
Abstract
PURPOSE Angiogenesis is thought to be critical for tumor metastasis. However, inhibiting angiogenesis using antibodies such as bevacizumab (Avastin), has had little impact on melanoma patient survival. We have demonstrated that both angiogenesis and metastasis are increased in older individuals, and therefore sought to investigate whether there was an age-related difference in response to bevacizumab, and if so, what the underlying mechanism could be. EXPERIMENTAL DESIGN We analyzed data from the AVAST-M trial of 1,343 patients with melanoma treated with bevacizumab to determine whether there is an age-dependent response to bevacizumab. We also examined the age-dependent expression of VEGF and its cognate receptors in patients with melanoma, while using syngeneic melanoma animal models to target VEGF in young versus old mice. We also examined the age-related proangiogenic factor secreted frizzled-related protein 2 (sFRP2) and whether it could modulate response to anti-VEGF therapy. RESULTS We show that older patients respond poorly to bevacizumab, whereas younger patients show improvement in both disease-free survival and overall survival. We find that targeting VEGF does not ablate angiogenesis in an aged mouse model, while sFRP2 promotes angiogenesis in vitro and in young mice. Targeting sFRP2 in aged mice successfully ablates angiogenesis, while the effects of targeting VEGF in young mice can be overcome by increasing sFRP2. CONCLUSIONS VEGF is decreased during aging, thereby reducing response to bevacizumab. Despite the decrease in VEGF, angiogenesis is increased because of an increase in sFRP2 in the aged tumor microenvironment. These results stress the importance of considering age as a factor for designing targeted therapies.
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Affiliation(s)
- Mitchell E Fane
- Department of Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland.,Department of Oncology, Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Brett L Ecker
- Department of Surgery, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Amanpreet Kaur
- Department of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Gloria E Marino
- Department of Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland.,Department of Oncology, Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Gretchen M Alicea
- Department of Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland.,Department of Oncology, Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Stephen M Douglass
- Department of Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland.,Department of Oncology, Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Yash Chhabra
- Department of Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland.,Department of Oncology, Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Marie R Webster
- The Lankenau Institute for Medical Research, Wynnewood, Pennsylvania
| | - Andrea Marshall
- Warwick Clinical Trials Unit, University of Warwick, Coventry, United Kingdom
| | - Richard Colling
- Department of Cellular Pathology, Oxford University Hospitals, University of Oxford, Oxford, United Kingdom
| | - Olivia Espinosa
- Department of Cellular Pathology, Oxford University Hospitals, University of Oxford, Oxford, United Kingdom
| | - Nicholas Coupe
- Department of Oncology, University of Oxford, Oxford, United Kingdom
| | - Neera Maroo
- Department of Oncology, University of Oxford, Oxford, United Kingdom
| | - Leticia Campo
- Department of Oncology, University of Oxford, Oxford, United Kingdom
| | - Mark R Middleton
- Department of Oncology, University of Oxford, Oxford, United Kingdom
| | - Pippa Corrie
- Department of Oncology, University of Oxford, Oxford, United Kingdom
| | - Xiaowei Xu
- Department of Pathology, University of Pennsylvania, Philadelphia, Pennsylvania
| | | | - Ashani T Weeraratna
- Department of Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland. .,Department of Oncology, Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
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25
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Browning L, Colling R, Rakha E, Rajpoot N, Rittscher J, James JA, Salto-Tellez M, Snead DRJ, Verrill C. Digital pathology and artificial intelligence will be key to supporting clinical and academic cellular pathology through COVID-19 and future crises: the PathLAKE consortium perspective. J Clin Pathol 2020; 74:443-447. [PMID: 32620678 PMCID: PMC8223667 DOI: 10.1136/jclinpath-2020-206854] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 06/15/2020] [Indexed: 12/19/2022]
Abstract
The measures to control the COVID-19 outbreak will likely remain a feature of our working lives until a suitable vaccine or treatment is found. The pandemic has had a substantial impact on clinical services, including cancer pathways. Pathologists are working remotely in many circumstances to protect themselves, colleagues, family members and the delivery of clinical services. The effects of COVID-19 on research and clinical trials have also been significant with changes to protocols, suspensions of studies and redeployment of resources to COVID-19. In this article, we explore the specific impact of COVID-19 on clinical and academic pathology and explore how digital pathology and artificial intelligence can play a key role to safeguarding clinical services and pathology-based research in the current climate and in the future.
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Affiliation(s)
- Lisa Browning
- Cellular Pathology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK.,NIHR Oxford Biomedical Research Centre, Oxford, Oxfordshire, UK
| | - Richard Colling
- Nuffield Department of Surgical Sciences, Oxford University, Oxford, Oxfordshire, UK
| | - Emad Rakha
- School of Medicine, University of Nottingham, Nottingham, Nottinghamshire, UK
| | - Nasir Rajpoot
- Tissue Image Analytics Laboratory, Department of Computer Science, University of Warwick, Coventry, West Midlands, UK.,Department of Pathology, University Hospitals Coventry and Warwickshire NHS Trust, Coventry, West Midlands, UK
| | - Jens Rittscher
- NIHR Oxford Biomedical Research Centre, Oxford, Oxfordshire, UK.,Department of Engineering Science and Big Data Institute, Oxford University, Oxford, Oxfordshire, UK
| | - Jacqueline A James
- Precision Medicine Centre of Excellence, Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, Belfast, UK.,Cellular Pathology, Belfast Health and Social Care Trust, Belfast, Belfast, UK
| | - Manuel Salto-Tellez
- Precision Medicine Centre of Excellence, Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, Belfast, UK.,Cellular Pathology, Belfast Health and Social Care Trust, Belfast, Belfast, UK
| | - David R J Snead
- Department of Pathology, University Hospitals Coventry and Warwickshire NHS Trust, Coventry, West Midlands, UK
| | - Clare Verrill
- NIHR Oxford Biomedical Research Centre, Oxford, Oxfordshire, UK .,Nuffield Department of Surgical Sciences, Oxford University, Oxford, Oxfordshire, UK
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26
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Browning L, Fryer E, Roskell D, White K, Colling R, Rittscher J, Verrill C. Role of digital pathology in diagnostic histopathology in the response to COVID-19: results from a survey of experience in a UK tertiary referral hospital. J Clin Pathol 2020; 74:129-132. [PMID: 32616541 PMCID: PMC7841475 DOI: 10.1136/jclinpath-2020-206786] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [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: 05/21/2020] [Accepted: 06/05/2020] [Indexed: 12/21/2022]
Abstract
The COVID-19 pandemic has challenged our diagnostic services at a time when many histopathology departments already faced a diminishing workforce and increasing workload. Digital pathology (DP) has been hailed as a potential solution to at least some of the challenges faced. We present a survey of pathologists within a UK National Health Service cellular pathology department with access to DP, in which we ascertain the role of DP in clinical services during this current pandemic and explore challenges encountered. This survey indicates an increase in uptake of diagnostic DP during this period, with increased remote access. Half of respondents agreed that DP had facilitated maintenance of diagnostic practice. While challenges have been encountered, these are remediable, and none have impacted on the uptake of DP during this period. We conclude that in our institution, DP has demonstrated current and future potential to increase resilience in diagnostic practice and have highlighted some of the challenges that need to be considered.
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Affiliation(s)
- Lisa Browning
- Department of Cellular Pathology, Oxford University Hospitals NHS Foundation Trust, Oxford, Oxfordshire, UK .,NIHR Oxford Biomedical Research Centre, Oxford, Oxfordshire, UK
| | - Eve Fryer
- Department of Cellular Pathology, Oxford University Hospitals NHS Foundation Trust, Oxford, Oxfordshire, UK
| | - Derek Roskell
- Department of Cellular Pathology, Oxford University Hospitals NHS Foundation Trust, Oxford, Oxfordshire, UK
| | - Kieron White
- Department of Cellular Pathology, Oxford University Hospitals NHS Foundation Trust, Oxford, Oxfordshire, UK
| | - Richard Colling
- Department of Cellular Pathology, Oxford University Hospitals NHS Foundation Trust, Oxford, Oxfordshire, UK.,Nuffield Department of Surgical Sciences, University of Oxford, Oxford, Oxfordshire, UK
| | - Jens Rittscher
- NIHR Oxford Biomedical Research Centre, Oxford, Oxfordshire, UK.,Department of Engineering Science, University of Oxford, Oxford, Oxfordshire, UK
| | - Clare Verrill
- Department of Cellular Pathology, Oxford University Hospitals NHS Foundation Trust, Oxford, Oxfordshire, UK.,NIHR Oxford Biomedical Research Centre, Oxford, Oxfordshire, UK.,Nuffield Department of Surgical Sciences, University of Oxford, Oxford, Oxfordshire, UK
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27
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Macklin PS, Verrill CL, Roberts ISD, Colling R, Sullivan ME, Webster GM, Cranston DW, Tapping CR, Browning L. Tumour seeding of the renal tumour biopsy tract – a histologically under‐recognised feature? Histopathology 2020; 76:763-766. [DOI: 10.1111/his.14004] [Citation(s) in RCA: 2] [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: 12/24/2022]
Affiliation(s)
- Philip S Macklin
- Department of Cellular Pathology John Radcliffe Hospital Oxford UK
| | - Clare L Verrill
- Department of Cellular Pathology John Radcliffe Hospital Oxford UK
- Nuffield Department of Surgical Sciences University of Oxford Oxford UK
- National Institute for Health Research (NIHR) Oxford Biomedical Research Centre (BRC) Oxford UK
| | - Ian S D Roberts
- Department of Cellular Pathology John Radcliffe Hospital Oxford UK
| | - Richard Colling
- Department of Cellular Pathology John Radcliffe Hospital Oxford UK
- Nuffield Department of Surgical Sciences University of Oxford Oxford UK
| | | | | | | | | | - Lisa Browning
- Department of Cellular Pathology John Radcliffe Hospital Oxford UK
- National Institute for Health Research (NIHR) Oxford Biomedical Research Centre (BRC) Oxford UK
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28
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Browning L, Colling R, Rittscher J, Winter L, McEntyre N, Verrill C. Implementation of digital pathology into diagnostic practice: perceptions and opinions of histopathology trainees and implications for training. J Clin Pathol 2019; 73:223-227. [PMID: 31597682 DOI: 10.1136/jclinpath-2019-206137] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 09/13/2019] [Accepted: 09/19/2019] [Indexed: 11/04/2022]
Abstract
There is increasing interest in the utility of digital pathology in the diagnostic setting. Successful transition requires guidance and training, but additionally an understanding of opinions and attitudes of histopathologists to ensure that potential barriers are addressed. Histopathology trainees as a group are likely to be at the forefront of this revolution, and have specific and as yet largely neglected training needs in this context. We designed an online survey for trainees within our region to capture their opinions and attitudes to digital pathology in the diagnostic setting, and to assess their perceived training needs. This survey indicates overall that these trainees have similar aspirations with regard to the predicted utility of digital pathology and the challenges faced as have been recognised among consultant histopathologists. While their training needs are also largely similar, there are specific additional considerations based around training in multiple centres with varying exposure to digital pathology.
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Affiliation(s)
- Lisa Browning
- Department of Cellular Pathology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Richard Colling
- Department of Cellular Pathology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK.,Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Jens Rittscher
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK.,Big Data Institute, Oxford University, Oxford, UK
| | - Lucinda Winter
- Department of Cellular Pathology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Nicholas McEntyre
- Department of Cellular Pathology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Clare Verrill
- Department of Cellular Pathology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK.,Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
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29
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Macklin PS, Pillay N, Lee JL, Pitman H, Scott S, Wang J, Craig C, Jones JL, Oien KA, Colling R, Coupland SE, Verrill C. CM-Path Molecular Diagnostics Forum-consensus statement on the development and implementation of molecular diagnostic tests in the United Kingdom. Br J Cancer 2019; 121:738-743. [PMID: 31575975 PMCID: PMC6889373 DOI: 10.1038/s41416-019-0588-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [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: 04/06/2019] [Revised: 09/03/2019] [Accepted: 09/06/2019] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Pathology has evolved from a purely morphological description of cellular alterations in disease to our current ability to interrogate tissues with multiple 'omics' technologies. By utilising these techniques and others, 'molecular diagnostics' acts as the cornerstone of precision/personalised medicine by attempting to match the underlying disease mechanisms to the most appropriate targeted therapy. METHODS Despite the promises of molecular diagnostics, significant barriers have impeded its widespread clinical adoption. Thus, the National Cancer Research Institute (NCRI) Cellular Molecular Pathology (CM-Path) initiative convened a national Molecular Diagnostics Forum to facilitate closer collaboration between clinicians, academia, industry, regulators and other key stakeholders in an attempt to overcome these. RESULTS We agreed on a consensus 'roadmap' that should be followed during development and implementation of new molecular diagnostic tests. We identified key barriers to efficient implementation and propose possible solutions to these. In addition, we discussed the recent reconfiguration of molecular diagnostic services in NHS England and its likely impacts. CONCLUSIONS We anticipate that this consensus statement will provide practical advice to those involved in the development of novel molecular diagnostic tests. Although primarily focusing on test adoption within the United Kingdom, we also refer to international guidelines to maximise the applicability of our recommendations.
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Affiliation(s)
- Philip S Macklin
- Department of Cellular Pathology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK.
| | | | - Jessica L Lee
- Strategy and Initiatives, National Cancer Research Institute, London, UK
| | - Helen Pitman
- CM-Path Programme Manager, National Cancer Research Institute, London, UK
| | - Sophie Scott
- Medical Science Liaison (Europe), Guardant Health, London, UK
| | - Jayson Wang
- Molecular Pathology Lead, Department of Cellular Pathology, St George's University Hospitals NHS Foundation Trust, London, UK
| | | | - J Louise Jones
- Genomics England, London, UK
- Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Karin A Oien
- Department of Pathology, The Queen Elizabeth University Hospital, Glasgow, UK
| | - Richard Colling
- Department of Cellular Pathology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Sarah E Coupland
- North West Cancer Research Centre, University of Liverpool, Liverpool, UK
| | - Clare Verrill
- Department of Cellular Pathology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK.
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK.
- National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, Oxford, UK.
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30
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Colling R, Pitman H, Oien K, Rajpoot N, Macklin P, Snead D, Sackville T, Verrill C. Artificial intelligence in digital pathology: a roadmap to routine use in clinical practice. J Pathol 2019; 249:143-150. [PMID: 31144302 DOI: 10.1002/path.5310] [Citation(s) in RCA: 119] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 05/02/2019] [Accepted: 05/10/2019] [Indexed: 12/28/2022]
Abstract
The use of artificial intelligence will transform clinical practice over the next decade and the early impact of this will likely be the integration of image analysis and machine learning into routine histopathology. In the UK and around the world, a digital revolution is transforming the reporting practice of diagnostic histopathology and this has sparked a proliferation of image analysis software tools. While this is an exciting development that could discover novel predictive clinical information and potentially address international pathology workforce shortages, there is a clear need for a robust and evidence-based framework in which to develop these new tools in a collaborative manner that meets regulatory approval. With these issues in mind, the NCRI Cellular Molecular Pathology (CM-Path) initiative and the British In Vitro Diagnostics Association (BIVDA) have set out a roadmap to help academia, industry, and clinicians develop new software tools to the point of approved clinical use. © 2019 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Affiliation(s)
- Richard Colling
- Nuffield Department of Surgical Sciences, University of Oxford, John Radcliffe Hospital, Oxford UK
| | | | - Karin Oien
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Nasir Rajpoot
- Department of Computer Science, University of Warwick, Coventry, UK
| | - Philip Macklin
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - David Snead
- PathLAKE (Director) and Histopathology, University Hospitals Coventry and Warwickshire NHS Trust, University Hospital, Coventry, UK
| | | | - Clare Verrill
- PathLAKE (Principal Investigator), Nuffield Department of Surgical Sciences and Oxford NIHR Biomedical Research Centre, University of Oxford, John Radcliffe Hospital, Oxford, UK
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31
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Cardus B, Colling R, Hamblin A, Soilleux E. Comparison of methodologies for the detection of BRAF mutations in bone marrow trephine specimens. J Clin Pathol 2019; 72:406-411. [DOI: 10.1136/jclinpath-2019-205734] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 02/07/2019] [Accepted: 02/08/2019] [Indexed: 02/06/2023]
Abstract
AimsBRAF V600E detection assists in the diagnosis of hairy cell leukaemia (HCL); however, testing practices vary. We evaluated the clinical utility of 5 BRAF mutation testing strategies for use on bone marrow trephines (BMT).Methods11 HCL, 5 HCL ‘mimic’, 2 treated HCL and 10 normal BMT specimens were tested for mutant BRAF, comparing Sanger sequencing, pyrosequencing, amplicon-based next generation sequencing (NGS), automated (Idylla) PCR and immunohistochemistry (IHC).ResultsPCR and IHC were cheaper and identified V600E in 100 % of HCL cases. Pyrosequencing detected the mutation in 91%, NGS in 55% of cases and Sanger sequencing in 27%. All assays gave wild-type BRAF results in HCL mimics and normal BMT samples.ConclusionsPCR and IHC were most sensitive and cost-effective, but these have limited scope for multiplexing and are likely to be replaced by NGS gene panels or whole genome sequencing in the medium to long term.
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32
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Linder N, Taylor JC, Colling R, Pell R, Alveyn E, Joseph J, Protheroe A, Lundin M, Lundin J, Verrill C. Deep learning for detecting tumour-infiltrating lymphocytes in testicular germ cell tumours. J Clin Pathol 2018; 72:157-164. [DOI: 10.1136/jclinpath-2018-205328] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 10/23/2018] [Accepted: 11/03/2018] [Indexed: 01/02/2023]
Abstract
AimsTo evaluate if a deep learning algorithm can be trained to identify tumour-infiltrating lymphocytes (TILs) in tissue samples of testicular germ cell tumours and to assess whether the TIL counts correlate with relapse status of the patient.MethodsTILs were manually annotated in 259 tumour regions from 28 whole-slide images (WSIs) of H&E-stained tissue samples. A deep learning algorithm was trained on half of the regions and tested on the other half. The algorithm was further applied to larger areas of tumour WSIs from 89 patients and correlated with clinicopathological data.ResultsA correlation coefficient of 0.89 was achieved when comparing the algorithm with the manual TIL count in the test set of images in which TILs were present (n=47). In the WSI regions from the 89 patient samples, the median TIL density was 1009/mm2. In seminomas, none of the relapsed patients belonged to the highest TIL density tertile (>2011/mm2). TIL quantifications performed visually by three pathologists on the same tumours were not significantly associated with outcome. The average interobserver agreement between the pathologists when assigning a patient into TIL tertiles was 0.32 (Kappa test) compared with 0.35 between the algorithm and the experts, respectively. A higher TIL density was associated with a lower clinical tumour stage, seminoma histology and lack of lymphovascular invasion.ConclusionsDeep learning–based image analysis can be used for detecting TILs in testicular germ cell cancer more objectively and it has potential for use as a prognostic marker for disease relapse.
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33
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Schuh A, Dreau H, Knight SJL, Ridout K, Mizani T, Vavoulis D, Colling R, Antoniou P, Kvikstad EM, Pentony MM, Hamblin A, Protheroe A, Parton M, Shah KA, Orosz Z, Athanasou N, Hassan B, Flanagan AM, Ahmed A, Winter S, Harris A, Tomlinson I, Popitsch N, Church D, Taylor JC. Clinically actionable mutation profiles in patients with cancer identified by whole-genome sequencing. Cold Spring Harb Mol Case Stud 2018; 4:a002279. [PMID: 29610388 PMCID: PMC5880257 DOI: 10.1101/mcs.a002279] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [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: 08/30/2017] [Accepted: 02/09/2018] [Indexed: 02/07/2023] Open
Abstract
Next-generation sequencing (NGS) efforts have established catalogs of mutations relevant to cancer development. However, the clinical utility of this information remains largely unexplored. Here, we present the results of the first eight patients recruited into a clinical whole-genome sequencing (WGS) program in the United Kingdom. We performed PCR-free WGS of fresh frozen tumors and germline DNA at 75× and 30×, respectively, using the HiSeq2500 HTv4. Subtracted tumor VCFs and paired germlines were subjected to comprehensive analysis of coding and noncoding regions, integration of germline with somatically acquired variants, and global mutation signatures and pathway analyses. Results were classified into tiers and presented to a multidisciplinary tumor board. WGS results helped to clarify an uncertain histopathological diagnosis in one case, led to informed or supported prognosis in two cases, leading to de-escalation of therapy in one, and indicated potential treatments in all eight. Overall 26 different tier 1 potentially clinically actionable findings were identified using WGS compared with six SNVs/indels using routine targeted NGS. These initial results demonstrate the potential of WGS to inform future diagnosis, prognosis, and treatment choice in cancer and justify the systematic evaluation of the clinical utility of WGS in larger cohorts of patients with cancer.
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Affiliation(s)
- Anna Schuh
- Oxford Molecular Diagnostics Centre, Department of Oncology, University of Oxford, Oxford OX3 9DU, United Kingdom
- Oxford NIHR Biomedical Research Centre, Oxford OX4 2PG, United Kingdom
| | - Helene Dreau
- Oxford Molecular Diagnostics Centre, Department of Oncology, University of Oxford, Oxford OX3 9DU, United Kingdom
- Nuffield Department of Clinical Laboratory Sciences, University of Oxford, Oxford OX3 9DU, United Kingdom
| | - Samantha J L Knight
- Oxford NIHR Biomedical Research Centre, Oxford OX4 2PG, United Kingdom
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Kate Ridout
- Oxford NIHR Biomedical Research Centre, Oxford OX4 2PG, United Kingdom
- Nuffield Department of Clinical Laboratory Sciences, University of Oxford, Oxford OX3 9DU, United Kingdom
| | - Tuba Mizani
- Oxford Molecular Diagnostics Centre, Department of Oncology, University of Oxford, Oxford OX3 9DU, United Kingdom
- Oxford NIHR Biomedical Research Centre, Oxford OX4 2PG, United Kingdom
| | - Dimitris Vavoulis
- Oxford NIHR Biomedical Research Centre, Oxford OX4 2PG, United Kingdom
- Nuffield Department of Clinical Laboratory Sciences, University of Oxford, Oxford OX3 9DU, United Kingdom
| | - Richard Colling
- Oxford Molecular Diagnostics Centre, Department of Oncology, University of Oxford, Oxford OX3 9DU, United Kingdom
- Nuffield Department of Clinical Laboratory Sciences, University of Oxford, Oxford OX3 9DU, United Kingdom
| | - Pavlos Antoniou
- Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge CB2 0QQ, United Kingdom
| | - Erika M Kvikstad
- Oxford NIHR Biomedical Research Centre, Oxford OX4 2PG, United Kingdom
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Melissa M Pentony
- Oxford NIHR Biomedical Research Centre, Oxford OX4 2PG, United Kingdom
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Angela Hamblin
- Department of Haematology, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 9DU, United Kingdom
| | - Andrew Protheroe
- Oxford Cancer and Haematology Centre, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 7LE, United Kingdom
| | - Marina Parton
- Breast Unit, Royal Marsden NHS Foundation Trust and Kingston NHS Foundation Trust, London SW3 6JJ, United Kingdom
| | - Ketan A Shah
- Department of Cellular Pathology, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 9DU, United Kingdom
| | - Zsolt Orosz
- Breast Unit, Royal Marsden NHS Foundation Trust and Kingston NHS Foundation Trust, London SW3 6JJ, United Kingdom
- Department of Cellular Pathology, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 9DU, United Kingdom
| | - Nick Athanasou
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford OX3 7LD, United Kingdom
| | - Bass Hassan
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom
| | - Adrienne M Flanagan
- University College London, Cancer Institute and Royal National Orthopaedic NHS Hospital, London WC1E 6BT, United Kingdom
| | - Ahmed Ahmed
- Nuffield Department of Obstetrics and Gynaecology, University of Oxford, Oxford OX3 9DU, United Kingdom
| | - Stuart Winter
- Department of Ear Nose and Throat-Head and Neck Surgery, Oxford University Hospitals, Oxford OX3 9DU, United Kingdom
| | - Adrian Harris
- Department of Oncology, University of Oxford, Oxford OX3 7DQ, United Kingdom
| | - Ian Tomlinson
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Niko Popitsch
- The Children's Cancer Research Institute (CCRI), 1090 Vienna, Austria
| | - David Church
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Jenny C Taylor
- Oxford NIHR Biomedical Research Centre, Oxford OX4 2PG, United Kingdom
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
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Roxanis I, Colling R, Kartsonaki C, Green AR, Rakha EA. The significance of tumour microarchitectural features in breast cancer prognosis: a digital image analysis. Breast Cancer Res 2018; 20:11. [PMID: 29402299 PMCID: PMC5799893 DOI: 10.1186/s13058-018-0934-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [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: 08/04/2017] [Accepted: 01/10/2018] [Indexed: 12/02/2022] Open
Abstract
Background As only a minor portion of the information present in histological sections is accessible by eye, recognition and quantification of complex patterns and relationships among constituents relies on digital image analysis. In this study, our working hypothesis was that, with the application of digital image analysis technology, visually unquantifiable breast cancer microarchitectural features can be rigorously assessed and tested as prognostic parameters for invasive breast carcinoma of no special type. Methods Digital image analysis was performed using public domain software (ImageJ) on tissue microarrays from a cohort of 696 patients, and validated with a commercial platform (Visiopharm). Quantified features included elements defining tumour microarchitecture, with emphasis on the extent of tumour-stroma interface. The differential prognostic impact of tumour nest microarchitecture in the four immunohistochemical surrogates for molecular classification was analysed. Prognostic parameters included axillary lymph node status, breast cancer-specific survival, and time to distant metastasis. Associations of each feature with prognostic parameters were assessed using logistic regression and Cox proportional models adjusting for age at diagnosis, grade, and tumour size. Results An arrangement in numerous small nests was associated with axillary lymph node involvement. The association was stronger in luminal tumours (odds ratio (OR) = 1.39, p = 0.003 for a 1-SD increase in nest number, OR = 0.75, p = 0.006 for mean nest area). Nest number was also associated with survival (hazard ratio (HR) = 1.15, p = 0.027), but total nest perimeter was the parameter most significantly associated with survival in luminal tumours (HR = 1.26, p = 0.005). In the relatively small cohort of triple-negative tumours, mean circularity showed association with time to distant metastasis (HR = 1.71, p = 0.027) and survival (HR = 1.8, p = 0.02). Conclusions We propose that tumour arrangement in few large nests indicates a decreased metastatic potential. By contrast, organisation in numerous small nests provides the tumour with increased metastatic potential to regional lymph nodes. An outstretched pattern in small nests bestows tumours with a tendency for decreased breast cancer-specific survival. Although further validation studies are required before the argument for routine quantification of microarchitectural features is established, our approach is consistent with the demand for cost-effective methods for triaging breast cancer patients that are more likely to benefit from chemotherapy.
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Affiliation(s)
- I Roxanis
- Department of Cellular Pathology, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Headley Way, Headington, Oxford, OX3 9DU, UK. .,Present Address: Institute of Cancer Research, London and Royal Free London NHS Foundation Trust, London, UK.
| | - R Colling
- Department of Cellular Pathology, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Headley Way, Headington, Oxford, OX3 9DU, UK
| | - C Kartsonaki
- Nuffield Department of Population Health, University of Oxford, Big Data Institute Building, Old Road Campus, Roosevelt Drive, Oxford, OX3 7LF, UK
| | - A R Green
- Academic Pathology, Division of Cancer and Stem Cells, The University of Nottingham, Room 2-052-S Academic Unit of Oncology, Nottingham City Hospital, Nottingham, NG5 1PB, UK
| | - E A Rakha
- Department of Cellular Pathology, University of Nottingham and Nottingham University Hospitals NHS Trust, City Hospital Campus, Nottingham, NG5 1PB, UK
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Yeung TM, Wang LM, Colling R, Kraus R, Cahill R, Hompes R, Mortensen NJ. Intraoperative identification and analysis of lymph nodes at laparoscopic colorectal cancer surgery using fluorescence imaging combined with rapid OSNA pathological assessment. Surg Endosc 2017. [PMID: 28643063 PMCID: PMC5772117 DOI: 10.1007/s00464-017-5644-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [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] [Indexed: 12/15/2022]
Abstract
Background Standard surgical practice for colorectal cancer involves resection of the primary lesion and all draining lymph nodes. Accurate intraoperative assessment of nodal status could allow stratified resectional extent. One-step nucleic acid (OSNA) can provide a rapid method of interrogating nodal tissue, whilst near-infrared (NIR) laparoscopy together with indocyanine green (ICG) can identify relevant nodal tissue intraoperatively. Methods ICG was administered around the tumour endoscopically prior to the operation. Fluorescent nodes identified by NIR were marked and submitted for whole-node OSNA analysis. Further fresh lymph nodes dissected from the standard resection specimen were examined and analysed by both conventional histology and OSNA. In addition, the status of the fluorescent nodes was compared to that of non-ICG nodes to assess their predictive value. Results Sixteen patients were recruited with a total final lymph node count of 287. 78 fresh lymph nodes were identified on fresh dissection for both histological and OSNA assessment with an analytical concordance rate of 98.7% (77/78). OSNA sensitivity was 1 (0.81–1, 95% CI) and specificity 0.98 (0.91–1, 95% CI). Six patients had a total of nine nodes identified intraoperatively by ICG fluorescence. Of these nine nodes, one was positive for metastasis on OSNA. OSNA analysis of the ICG-labelled node matched the final histological nodal stage in 3/6 patients (two being N0 and one N1). The final pathological nodal stage of the other three was N1 or N2, while the ICG nodes were negative. Conclusion OSNA is highly concordant with standard histology, although only a minority of nodes identifiable by full pathological analysis were found for OSNA on fresh dissection. OSNA can be combined with NIR and ICG lymphatic mapping to provide intraoperative assessment of nodal tissue in patients with colorectal cancer.
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Affiliation(s)
- Trevor M Yeung
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, OX3 9DU, UK. .,Department of Colorectal Surgery, Oxford University Hospitals NHS Foundation Trust, Oxford, UK.
| | - Lai Mun Wang
- Department of Cellular Pathology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Richard Colling
- Department of Cellular Pathology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Rebecca Kraus
- Department of Colorectal Surgery, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Ronan Cahill
- Mater Misericordiae University Hospital and UCD School of Medicine & Medical Science, Oxford, UK
| | - Roel Hompes
- Department of Colorectal Surgery, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Neil J Mortensen
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, OX3 9DU, UK.,Department of Colorectal Surgery, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
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N Kalimuthu S, Serra S, Hafezi-Bakhtiari S, Colling R, Wang LM, Chetty R. Mucin-rich variant of traditional serrated adenoma: a distinct morphological variant. Histopathology 2017; 71:208-216. [PMID: 28295534 DOI: 10.1111/his.13212] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 03/08/2017] [Indexed: 12/28/2022]
Abstract
AIMS Traditional serrated adenomas (TSAs) account for 5% of serrated polyps, and have a villiform architecture, eosinophilic cells with a brush border, and indented, flat-topped luminal serrations. However, some are composed of mucin-filled goblet cells (GCs): mucin-rich TSA (MrTSA). The aim of this study was to determine whether this variant has unique features as compared with classic TSA (cTSA). METHODS AND RESULTS One hundred and fifty-six TSAs were retrieved from the period 2010-2016. Patient demographics, site of polyps and 16 microscopic variables were evaluated. TSAs containing ≥50% GCs were classified as MrTSAs. Ectopic crypt foci (ECFs) were quantified as low (1-10) or high (>10), counted at ×200 magnification, and the average was taken for 10 fields. Twenty-four fulfilled the criteria for MrTSA. In males, MrTSAs (65%) were more prevalent than cTSAs (55%). There was no age difference, and both variants had a predilection for the left colon, although, in the right colon, MrTSAs were more frequent (39%) than cTSAs (10%) (P = 0.012). Adenomatous dysplasia was present in four of 24 MrTSAs (low grade, 3; high grade, 1). The most distinctive features of MrTSAs were: a variable growth pattern [endophytic (9%), mixed (30%), or villiform/exophytic (61%)], and a lower frequency of ECFs (P = 0.001) and more intraepithelial lymphocytes (P < 0.05) than in cTSAs. MrTSAs retain characteristic luminal serrations, at least focally. Inflamed MrTSAs can mimic inflammatory polyps and hamartomatous polyps (when there are >95% GCs). CONCLUSIONS MrTSA is characterized by >50% GCs, and fewer ECFs than cTSA, but with preservation of archetypal luminal serrations. Awareness of this variant will prevent misdiagnosis, given the association of TSA with the accelerated pathway to colorectal cancer.
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Affiliation(s)
- Sangeetha N Kalimuthu
- Department of Pathology, Laboratory Medicine Program, University Health Network, University of Toronto, Toronto, ON, Canada
| | - Stefano Serra
- Department of Pathology, Laboratory Medicine Program, University Health Network, University of Toronto, Toronto, ON, Canada
| | - Sara Hafezi-Bakhtiari
- Department of Pathology, Laboratory Medicine Program, University Health Network, University of Toronto, Toronto, ON, Canada
| | - Richard Colling
- Department of Cellular Pathology, Oxford University Hospitals, Oxford, UK
| | - Lai Mun Wang
- Department of Cellular Pathology, Oxford University Hospitals, Oxford, UK
| | - Runjan Chetty
- Department of Pathology, Laboratory Medicine Program, University Health Network, University of Toronto, Toronto, ON, Canada
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Colling R, Yeung T, Hompes R, Kraus R, Cahill R, Mortensen N, Wang LM. OSNA testing for lymph node staging in colorectal cancer. J Clin Pathol 2017; 70:638-639. [DOI: 10.1136/jclinpath-2016-204299] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 02/13/2017] [Accepted: 03/10/2017] [Indexed: 01/11/2023]
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Colling R, Wang LM, Soilleux E. Validating a fully automated real-time PCR-based system for use in the molecular diagnostic analysis of colorectal carcinoma: a comparison with NGS and IHC. J Clin Pathol 2017; 70:610-614. [PMID: 28292978 DOI: 10.1136/jclinpath-2017-204356] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Revised: 02/10/2017] [Accepted: 02/13/2017] [Indexed: 12/21/2022]
Abstract
BACKGROUND Molecular testing is increasingly needed in colorectal carcinoma (CRC) and the current clinically relevant mutations are in BRAF, KRAS and NRAS. This study aimed to further validate a new alternative polymerase chain reaction (PCR) platform (Idylla, Biocartis) against existing next-generation sequencing (NGS) and immunohistochemistry (IHC) assays. METHODS 56 Idylla tests were performed on 43 CRC cases, in a total of 74 comparisons against an NGS panel (Ion Torrent) and the VE1 (anti-BRAF) antibody IHC. Discrepant cases were also compared with either conventional (Cobas) or droplet digital PCR (Bio-Rad). RESULTS Idylla showed an overall concordance of 100% (95% CI 93% to 100%) with comparator molecular testing and indications were that Idylla is likely to be more sensitive than routine NGS. BRAF IHC showed 90% concordance with NGS (95% CI 70% to 97%). CONCLUSIONS This study validates Idylla in formalin-fixed, paraffin-embedded CRC tissue. BRAF IHC, however, is an unreliable substitute for molecular testing in CRC.
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Affiliation(s)
- Richard Colling
- Department of Cellular Pathology, Oxford University Hospitals NHS Trust, John Radcliffe Hospital, Oxford, UK.,Oxford Molecular Diagnostics Centre, Molecular Haematology, Oxford University Hospitals NHS Trust, John Radcliffe Hospital, Oxford, UK.,Department of Oncology, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Lai Mun Wang
- Department of Cellular Pathology, Oxford University Hospitals NHS Trust, John Radcliffe Hospital, Oxford, UK.,Department of Laboratory Medicine, Changi General Hospital, Singapore, Singapore.,Ludwig Institute for Cancer Research, University of Oxford, Old Road Campus Research Building, Oxford, UK
| | - Elizabeth Soilleux
- Department of Cellular Pathology, Oxford University Hospitals NHS Trust, John Radcliffe Hospital, Oxford, UK.,Nuffield Division of Clinical Laboratory Sciences, University of Oxford, John Radcliffe Hospital, Oxford, UK
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Solassol J, Vendrell J, Märkl B, Haas C, Bellosillo B, Montagut C, Smith M, O’Sullivan B, D’Haene N, Le Mercier M, Grauslund M, Melchior LC, Burt E, Cotter F, Stieber D, Schmitt FDL, Motta V, Lauricella C, Colling R, Soilleux E, Fassan M, Mescoli C, Collin C, Pagès JC, Sillekens P. Multi-Center Evaluation of the Fully Automated PCR-Based Idylla™ KRAS Mutation Assay for Rapid KRAS Mutation Status Determination on Formalin-Fixed Paraffin-Embedded Tissue of Human Colorectal Cancer. PLoS One 2016; 11:e0163444. [PMID: 27685259 PMCID: PMC5042411 DOI: 10.1371/journal.pone.0163444] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [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: 06/13/2016] [Accepted: 09/07/2016] [Indexed: 12/18/2022] Open
Abstract
Since the advent of monoclonal antibodies against epidermal growth factor receptor (EGFR) in colorectal cancer therapy, the determination of RAS mutational status is needed for therapeutic decision-making. Most prevalent in colorectal cancer are KRAS exon 2 mutations (40% prevalence); lower prevalence is observed for KRAS exon 3 and 4 mutations (6%) and NRAS exon 2, 3, and 4 mutations (5%). The Idylla™ KRAS Mutation Test on the molecular diagnostics Idylla™ platform is a simple (<2 minutes hands-on time), highly reliable, and rapid (approximately 2 hours turnaround time) in vitro diagnostic sample-to-result solution. This test enables qualitative detection of 21 mutations in codons 12, 13, 59, 61, 117, and 146 of the KRAS oncogene being clinically relevant according to the latest clinical guidelines. Here, the performance of the Idylla™ KRAS Mutation Assay, for Research Use Only, was assessed on archived formalin-fixed paraffin-embedded (FFPE) tissue sections by comparing its results with the results previously obtained by routine reference approaches for KRAS genotyping. In case of discordance, samples were assessed further by additional methods. Among the 374 colorectal cancer FFPE samples tested, the overall concordance between the Idylla™ KRAS Mutation Assay and the confirmed reference routine test results was found to be 98.9%. The Idylla™ KRAS Mutation Assay enabled detection of 5 additional KRAS-mutated samples not detected previously with reference methods. As conclusion the Idylla™ KRAS Mutation Test can be applied as routine tool in any clinical setting, without needing molecular infrastructure or expertise, to guide the personalized treatment of colorectal cancer patients.
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Affiliation(s)
- Jérôme Solassol
- Laboratory of Biopathology, Institut du Cancer de Montpellier, Montpellier, France
| | - Julie Vendrell
- Laboratory of Biopathology, Institut du Cancer de Montpellier, Montpellier, France
| | - Bruno Märkl
- Institute of Pathology, Klinikum Augsburg, Augsburg, Germany
| | - Christian Haas
- Institute of Pathology, Klinikum Augsburg, Augsburg, Germany
| | - Beatriz Bellosillo
- Pathology Department, Hospital del Mar, IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
| | - Clara Montagut
- Oncology Department, Hospital del Mar, IMIM, Barcelona, Spain
| | - Matthew Smith
- Queen Elizabeth Hospital, Birmingham, United Kingdom
| | | | - Nicky D’Haene
- Department of Pathology, Hôpital Erasme - Université Libre de Bruxelles, Brussels, Belgium
| | - Marie Le Mercier
- Department of Pathology, Hôpital Erasme - Université Libre de Bruxelles, Brussels, Belgium
| | - Morten Grauslund
- Department of Pathology, Rigshospitalet Copenhagen, Copenhagen, Denmark
| | | | - Emma Burt
- Royal London Hospital, London, United Kingdom
| | | | - Daniel Stieber
- Molecular Genetic Unit, Laboratoire National de Santé, Dudelange, Luxembourg
| | | | - Valentina Motta
- Molecular Pathology Unit, Department of Laboratory Medicine, Niguarda Cancer Center, ASST - Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | - Calogero Lauricella
- Molecular Pathology Unit, Department of Laboratory Medicine, Niguarda Cancer Center, ASST - Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | - Richard Colling
- Department of Cellular Pathology, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Elizabeth Soilleux
- Department of Cellular Pathology, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Matteo Fassan
- Department of Medicine (DIMED), Surgical Pathology Unit, University of Padua, Padua, Italy
| | - Claudia Mescoli
- Department of Medicine (DIMED), Surgical Pathology Unit, University of Padua, Padua, Italy
| | - Christine Collin
- Platform of Somatic Tumor Molecular Genetics, Centre Hospitalier Régional Universitaire de Tours, Tours, France
| | - Jean-Christophe Pagès
- Platform of Somatic Tumor Molecular Genetics, Centre Hospitalier Régional Universitaire de Tours, Tours, France
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Colling R, Royston D, Soilleux E. Transformation of CLL to ALCL: the role of clonality studies in diagnostic molecular haematopathology. J Hematop 2016; 9:143-147. [PMID: 27766121 PMCID: PMC5047934 DOI: 10.1007/s12308-016-0280-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 07/15/2016] [Indexed: 12/03/2022] Open
Abstract
Clonality studies greatly assist in the diagnosis of challenging haematopathology cases. These robust and standardised tests aid the detection of clonal lymphoid populations and may assist in lymphocyte subtyping. In this case report, a gentleman presented with a high-grade transformation of a B cell neoplasm which histologically and immunophenotypically mimicked a T cell anaplastic large-cell lymphoma. With the aid of T cell and B cell receptor clonality studies, it was demonstrated that this tumour was in fact of B cell lineage. This report exemplifies the role of these increasingly used and relatively new molecular tests in unusual and difficult lymphoma presentations and highlights potential pitfalls in the interpretation of their results.
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Affiliation(s)
- Richard Colling
- Department of Cellular Pathology, Oxford University Hospitals NHS Trust, Oxford, UK
- Department of Oncology, University of Oxford, Oxford, UK
| | - Daniel Royston
- Department of Cellular Pathology, Oxford University Hospitals NHS Trust, Oxford, UK
- Nuffield Division of Clinical Laboratory Sciences, University of Oxford, Oxford, UK
| | - Elizabeth Soilleux
- Department of Cellular Pathology, Oxford University Hospitals NHS Trust, Oxford, UK
- Nuffield Division of Clinical Laboratory Sciences, University of Oxford, Oxford, UK
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Colling R, Wang LM, Soilleux E. Automated PCR detection of BRAF mutations in colorectal adenocarcinoma: a diagnostic test accuracy study. J Clin Pathol 2015; 69:398-402. [PMID: 26537294 DOI: 10.1136/jclinpath-2015-203345] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 10/10/2015] [Indexed: 11/03/2022]
Abstract
BACKGROUND Testing for BRAF mutations in colorectal carcinoma (CRC) is important in the screening pathway for Lynch syndrome and is of prognostic value to guide management. This is a diagnostic accuracy study of the Idylla system, a novel and automated alternative PCR system. METHODS 100 consecutive formalin-fixed, paraffin-embedded CRC resection cases were tested for BRAF mutations using the Idylla automated platform and compared with standard (Cobas) PCR. RESULTS The sensitivity of the Idylla BRAF test was 100% and the specificity was 96%. Only one discordant Idylla positive/standard PCR negative result occurred and on Droplet Digital PCR demonstrated a mutation not identified by traditional PCR in this case. CONCLUSION This study has validated the Idylla system for BRAF testing in CRC and demonstrated a possibly greater sensitivity, in addition to cost effectiveness and shorter turnaround time, when compared with standard PCR.
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Affiliation(s)
- Richard Colling
- Department of Cellular Pathology, Oxford University Hospitals NHS Trust, Oxford, UK
| | - Lai Mun Wang
- Department of Cellular Pathology, Oxford University Hospitals NHS Trust, Oxford, UK
| | - Elizabeth Soilleux
- Department of Cellular Pathology, Oxford University Hospitals NHS Trust, Oxford, UK Nuffield Division of Clinical Laboratory Sciences, University of Oxford, Oxford, UK
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Colling R, Verrill C, Fryer E, Kartsonaki C, Wang LM, Chapman R, Rajabally N, Fleming K. Bile duct basement membrane thickening in primary sclerosing cholangitis. Histopathology 2015; 68:819-24. [DOI: 10.1111/his.12857] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2015] [Accepted: 08/29/2015] [Indexed: 12/15/2022]
Affiliation(s)
- Richard Colling
- Cellular Pathology; John Radcliffe Hospital; Oxford University Hospitals NHS Trust; Oxford UK
| | - Clare Verrill
- Cellular Pathology; John Radcliffe Hospital; Oxford University Hospitals NHS Trust; Oxford UK
| | - Eve Fryer
- Cellular Pathology; John Radcliffe Hospital; Oxford University Hospitals NHS Trust; Oxford UK
| | | | - Lai M Wang
- Cellular Pathology; John Radcliffe Hospital; Oxford University Hospitals NHS Trust; Oxford UK
| | - Roger Chapman
- Medical Sciences Division; University of Oxford; Oxford UK
| | - Naayil Rajabally
- Department of Hepatology; Oxford University Hospitals NHS Trust; Oxford UK
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Colling R, Fryer E, Cobbold J, Collier J, Collantes E, Wang LM, Hubscher S, Wyatt J, Fleming K. A template for a clinico-pathological audit of medical liver biopsies. J Clin Pathol 2015. [DOI: 10.1136/jclinpath-2015-203023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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Colling R, Church DN, Carmichael J, Murphy L, East J, Risby P, Kerr R, Chetty R, Wang LM. Screening for Lynch syndrome and referral to clinical genetics by selective mismatch repair protein immunohistochemistry testing: an audit and cost analysis. J Clin Pathol 2015. [DOI: 10.1136/jclinpath-2015-203083] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Lynch syndrome (LS) accounts for around 3% of colorectal cancers (CRCs) and is caused by germline mutations in mismatch repair (MMR) genes. Recently, screening strategies to identify patients with LS have become popular. We audited CRCs screened with MMR immunohistochemistry (IHC) in 2013. 209 tumours had MMR IHC performed at a cost of £12 540. 47/209 (21%) cases showed IHC loss of expression in at least one MMR protein. 28/44 cases with loss of MLH1 had additional BRAF V600E testing, at a cost of £5040. MMR IHC reduced the number of potential clinical genetics referrals from 209 to 47. BRAF mutation testing, performed in a subset of cases with MLH1 loss, further reduced this to 21. At a cost of £1340 per referral, this model of LS screening for clinical genetics referral had significant potential savings (£234 340) and can be easily implemented in parallel with MMR IHC done for prognostication in CRCs.
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Chetty R, Hafezi-Bakhtiari S, Serra S, Colling R, Wang LM. Traditional serrated adenomas (TSAs) admixed with other serrated (so-called precursor) polyps and conventional adenomas: a frequent occurrence. J Clin Pathol 2015; 68:270-3. [PMID: 25589791 DOI: 10.1136/jclinpath-2014-202827] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
BACKGROUND Traditional serrated adenoma (TSA) is a very characteristic type of serrated polyp that has a predilection for the left colon. Recent molecular advances have shown two molecular phenotypes of TSA: one associated with BRAF mutations and the other with KRAS mutations. The former is associated with hyperplastic polyps (HPs) and sessile serrated adenomas (SSAs), while the latter is associated with more conventional adenomatous dysplasia. AIMS The association of TSAs with so-called precursor lesions (HPs and SSAs) is not well recognised and the purpose of this study was to explore the coexistent presence of HPs, SSAs and adenomatous polyps within a large cohort of TSAs. METHODS In total 149 TSAs were examined for the presence of HP, SSA and adenomatous polyps. RESULTS Seen in 83 men and 65 women ranging in age from 32 to 89 years and 127 were left sided with 22 in the right colon. Seventy-eight of the 149 TSAs showed evidence of another polyp (52.34%): 32 were low-grade tubular/tubulovillous adenomas (TAs/TVAs; 41%), 28 were HPs (36%) and 18 were SSAs (23%). Eleven of the 22 right-sided TSAs were associated with a precursor lesion (1 HP and 7 SSA). In addition, five TSAs showed more than one polyp type: TSA with TA/TVA and HP (3); TSA with TA/TVA and SSA (2). The TAs/TVAs were adjacent to the TSA but occurred as a separate discrete polyp, while HPs and SSAs were intermingled with the TSA and present at the base and surface of the lesion. CONCLUSIONS More than 50% of TSAs are associated with a precursor lesion or adjacent TA/TVA. Their recognition is important as this may have surveillance and management ramifications.
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Affiliation(s)
- Runjan Chetty
- Department of Pathology, Laboratory Medicine Program, University Health Network and University of Toronto, Toronto, Ontario, Canada
| | - Sara Hafezi-Bakhtiari
- Department of Pathology, Laboratory Medicine Program, University Health Network and University of Toronto, Toronto, Ontario, Canada
| | - Stefano Serra
- Department of Pathology, Laboratory Medicine Program, University Health Network and University of Toronto, Toronto, Ontario, Canada
| | - Richard Colling
- Department of Cellular Pathology, Oxford University Hospitals, Oxford, UK
| | - Lai Mun Wang
- Department of Pathology, Laboratory Medicine Program, University Health Network and University of Toronto, Toronto, Ontario, Canada
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Abstract
Medical liver biopsy reporting is challenging, and maintaining competency with small case numbers is potentially difficult. This study evaluates the discrepancies identified in cases referred to a specialist centre between the specialist reports and those of the referring general departments. Fifty consecutive recently referred cases were selected, and original and final reports were compared. Discrepancies were classified as per the Royal College of Pathologists guidelines and scored for potential clinical impact. The overall rate of discrepancy was 38% with most of these due to differences in interpretation of morphology. Seventy per cent of these discrepancies were judged to have major clinical impact (26% of all referred cases). This study highlights the need for robust systems of quality control of liver biopsies in a general setting.
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Hafezi-Bakhtiari S, Wang LM, Colling R, Serra S, Chetty R. Histological overlap between colorectal villous/tubulovillous and traditional serrated adenomas. Histopathology 2014; 66:308-13. [PMID: 25257227 DOI: 10.1111/his.12555] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Accepted: 09/19/2014] [Indexed: 12/25/2022]
Abstract
AIMS To ascertain the degree of histological overlap between conventional villous/tubulovillous (VA/TVAs) and traditional serrated adenomas (TSA). METHODS AND RESULTS A total of 180 polyps from the left colon/rectum diagnosed as VA/TVAs were retrieved randomly and reviewed by five pathologists looking specifically at luminal serration, cytoplasmic eosinophilia and the presence of ectopic crypt foci (ECF). For comparative purposes, 100 tubular adenomas and 80 TSAs were also examined. Twenty VA/TVAs were reclassified as TSA. Luminal serration as noted in TSA was not seen in any of the remaining 160 polyps, ECFs were noted in 55 of the 160 VA/TVAs (34%), while cytoplasmic eosinophilia (constituting <50% of the adenoma) was noted in only 10 of 160 cases (6.2%). CONCLUSIONS Ectopic crypt foci and cytoplasmic eosinophilia are encountered in sporadic VA/TVAs but not to the same extent and degree as in TSA. ECFs were found in one-third of cases, but cytoplasmic eosinophilia is rare. The pattern of luminal serration in TSA is very characteristic and not recapitulated in VA/TVA. The occurrence of all three histological features together occurs only in TSA. ECFs are not a sine qua non for TSA and are encountered commonly in VA/TVAs. VA/TVAs often contain occasional glands typical of TSA.
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Affiliation(s)
- Sara Hafezi-Bakhtiari
- Department of Pathology, Laboratory Medicine Program, University Health Network and University of Toronto, Toronto, ON, Canada
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Wong NACS, Wingate J, Colling R. A study of α5 chain of collagen IV, caldesmon, placental alkaline phosphatase and smoothelin as immunohistochemical markers of gastrointestinal smooth muscle neoplasms. J Clin Pathol 2013; 67:105-11. [DOI: 10.1136/jclinpath-2013-201797] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Colling R, Lopes T, Das N, Mathew J. Endometrial metastasis of colorectal cancer with coincident endometrial adenocarcinoma. BMJ Case Rep 2010; 2010:2010/nov04_1/bcr0920092229. [PMID: 22791861 DOI: 10.1136/bcr.09.2009.2229] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
Metastasis to the uterine corpus is uncommon and secondary colorectal tumours of the endometrium are rare. We describe a uterine tumour with components of both primary endometrial and metastatic colorectal carcinomata. In this case, a 72-year-old obese woman presented with a 2-week history of postmenopausal bleeding per vaginum and weight loss. She had an abdominoperineal resection 3 years previously for a Dukes stage B rectal carcinoma. A transvaginal ultrasonography showed a thickened endometrium. Histology immunophenotyping showed a CK7+, CK20+, CA125- and CEA+ colorectal metastasis (a profile consistent with her previous cancer) associated with a primary CK7+, CK20-, CA125+ and CEA- endometroid endometrial adenocarcinoma. We conclude this represents endometrial metastasis of colorectal carcinoma with coincident primary endometrial adenocarcinoma. We speculate as to whether the endometrial carcinoma arose de novo or was induced by the colorectal metastasis, or whether the primary endometrial tumour provided a fertile site for the colorectal metastasis.
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Affiliation(s)
- Richard Colling
- Department of Diagnostic and Molecular Pathology, Royal Cornwall Hospitals Trust, Truro, UK
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