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Mi H, Sivagnanam S, Ho WJ, Zhang S, Bergman D, Deshpande A, Baras AS, Jaffee EM, Coussens LM, Fertig EJ, Popel AS. Computational methods and biomarker discovery strategies for spatial proteomics: a review in immuno-oncology. Brief Bioinform 2024; 25:bbae421. [PMID: 39179248 PMCID: PMC11343572 DOI: 10.1093/bib/bbae421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Revised: 07/11/2024] [Accepted: 08/09/2024] [Indexed: 08/26/2024] Open
Abstract
Advancements in imaging technologies have revolutionized our ability to deeply profile pathological tissue architectures, generating large volumes of imaging data with unparalleled spatial resolution. This type of data collection, namely, spatial proteomics, offers invaluable insights into various human diseases. Simultaneously, computational algorithms have evolved to manage the increasing dimensionality of spatial proteomics inherent in this progress. Numerous imaging-based computational frameworks, such as computational pathology, have been proposed for research and clinical applications. However, the development of these fields demands diverse domain expertise, creating barriers to their integration and further application. This review seeks to bridge this divide by presenting a comprehensive guideline. We consolidate prevailing computational methods and outline a roadmap from image processing to data-driven, statistics-informed biomarker discovery. Additionally, we explore future perspectives as the field moves toward interfacing with other quantitative domains, holding significant promise for precision care in immuno-oncology.
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Affiliation(s)
- Haoyang Mi
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, United States
| | - Shamilene Sivagnanam
- The Knight Cancer Institute, Oregon Health and Science University, Portland, OR 97201, United States
- Department of Cell, Development and Cancer Biology, Oregon Health and Science University, Portland, OR 97201, United States
| | - Won Jin Ho
- Department of Oncology, Johns Hopkins University School of Medicine, MD 21205, United States
- Convergence Institute, Johns Hopkins University, Baltimore, MD 21205, United States
| | - Shuming Zhang
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, United States
| | - Daniel Bergman
- Department of Oncology, Johns Hopkins University School of Medicine, MD 21205, United States
- Convergence Institute, Johns Hopkins University, Baltimore, MD 21205, United States
| | - Atul Deshpande
- Department of Oncology, Johns Hopkins University School of Medicine, MD 21205, United States
- Convergence Institute, Johns Hopkins University, Baltimore, MD 21205, United States
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD 21205, United States
| | - Alexander S Baras
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD 21205, United States
- Department of Pathology, Johns Hopkins University School of Medicine, MD 21205, United States
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, United States
| | - Elizabeth M Jaffee
- Department of Oncology, Johns Hopkins University School of Medicine, MD 21205, United States
- Convergence Institute, Johns Hopkins University, Baltimore, MD 21205, United States
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD 21205, United States
| | - Lisa M Coussens
- The Knight Cancer Institute, Oregon Health and Science University, Portland, OR 97201, United States
- Department of Cell, Development and Cancer Biology, Oregon Health and Science University, Portland, OR 97201, United States
- Brenden-Colson Center for Pancreatic Care, Oregon Health and Science University, Portland, OR 97201, United States
| | - Elana J Fertig
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, United States
- Department of Oncology, Johns Hopkins University School of Medicine, MD 21205, United States
- Convergence Institute, Johns Hopkins University, Baltimore, MD 21205, United States
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD 21205, United States
- Department of Applied Mathematics and Statistics, Johns Hopkins University Whiting School of Engineering, Baltimore, MD 21218, United States
| | - Aleksander S Popel
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, United States
- Department of Oncology, Johns Hopkins University School of Medicine, MD 21205, United States
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Raufeisen J, Xie K, Hörst F, Braunschweig T, Li J, Kleesiek J, Röhrig R, Egger J, Leibe B, Hölzle F, Hermans A, Puladi B. Cyto R-CNN and CytoNuke Dataset: Towards reliable whole-cell segmentation in bright-field histological images. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2024; 252:108215. [PMID: 38781811 DOI: 10.1016/j.cmpb.2024.108215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 04/19/2024] [Accepted: 05/06/2024] [Indexed: 05/25/2024]
Abstract
BACKGROUND AND OBJECTIVE Cell segmentation in bright-field histological slides is a crucial topic in medical image analysis. Having access to accurate segmentation allows researchers to examine the relationship between cellular morphology and clinical observations. Unfortunately, most segmentation methods known today are limited to nuclei and cannot segment the cytoplasm. METHODS We present a new network architecture Cyto R-CNN that is able to accurately segment whole cells (with both the nucleus and the cytoplasm) in bright-field images. We also present a new dataset CytoNuke, consisting of multiple thousand manual annotations of head and neck squamous cell carcinoma cells. Utilizing this dataset, we compared the performance of Cyto R-CNN to other popular cell segmentation algorithms, including QuPath's built-in algorithm, StarDist, Cellpose and a multi-scale Attention Deeplabv3+. To evaluate segmentation performance, we calculated AP50, AP75 and measured 17 morphological and staining-related features for all detected cells. We compared these measurements to the gold standard of manual segmentation using the Kolmogorov-Smirnov test. RESULTS Cyto R-CNN achieved an AP50 of 58.65% and an AP75 of 11.56% in whole-cell segmentation, outperforming all other methods (QuPath 19.46/0.91%; StarDist 45.33/2.32%; Cellpose 31.85/5.61%, Deeplabv3+ 3.97/1.01%). Cell features derived from Cyto R-CNN showed the best agreement to the gold standard (D¯=0.15) outperforming QuPath (D¯=0.22), StarDist (D¯=0.25), Cellpose (D¯=0.23) and Deeplabv3+ (D¯=0.33). CONCLUSION Our newly proposed Cyto R-CNN architecture outperforms current algorithms in whole-cell segmentation while providing more reliable cell measurements than any other model. This could improve digital pathology workflows, potentially leading to improved diagnosis. Moreover, our published dataset can be used to develop further models in the future.
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Affiliation(s)
- Johannes Raufeisen
- Department of Oral and Maxillofacial Surgery, University Hospital RWTH Aachen, Pauwelsstr. 30, 52074 Aachen, Germany; Institute of Medical Informatics, University Hospital RWTH Aachen, Pauwelsstr. 30, 52074 Aachen, Germany; Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf (CIO ABCD), Pauwelsstraße 30, 52074 Aachen, Germany
| | - Kunpeng Xie
- Department of Oral and Maxillofacial Surgery, University Hospital RWTH Aachen, Pauwelsstr. 30, 52074 Aachen, Germany; Institute of Medical Informatics, University Hospital RWTH Aachen, Pauwelsstr. 30, 52074 Aachen, Germany; Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf (CIO ABCD), Pauwelsstraße 30, 52074 Aachen, Germany
| | - Fabian Hörst
- Institute for Artificial Intelligence in Medicine (IKIM), University Hospital Essen (AöR), Girardetstraße 2, 45131 Essen, Germany; Cancer Research Center Cologne Essen (CCCE), West German Cancer Center Essen, University Hospital Essen (AöR), Hufelandstr. 55, 45147 Essen, Germany
| | - Till Braunschweig
- Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf (CIO ABCD), Pauwelsstraße 30, 52074 Aachen, Germany; Institute of Pathology, University Hospital RWTH Aachen, Pauwelsstr. 30, 52074 Aachen, Germany; Institute of Pathology, LMU Munich, Thalkirchner Str. 36, 80337 Munich, Germany
| | - Jianning Li
- Institute for Artificial Intelligence in Medicine (IKIM), University Hospital Essen (AöR), Girardetstraße 2, 45131 Essen, Germany; Cancer Research Center Cologne Essen (CCCE), West German Cancer Center Essen, University Hospital Essen (AöR), Hufelandstr. 55, 45147 Essen, Germany
| | - Jens Kleesiek
- Institute for Artificial Intelligence in Medicine (IKIM), University Hospital Essen (AöR), Girardetstraße 2, 45131 Essen, Germany; Cancer Research Center Cologne Essen (CCCE), West German Cancer Center Essen, University Hospital Essen (AöR), Hufelandstr. 55, 45147 Essen, Germany; Department of Physics, TU Dortmund University, August-Schmidt-Str. 4, 44227 Dortmund, Germany
| | - Rainer Röhrig
- Institute of Medical Informatics, University Hospital RWTH Aachen, Pauwelsstr. 30, 52074 Aachen, Germany; Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf (CIO ABCD), Pauwelsstraße 30, 52074 Aachen, Germany
| | - Jan Egger
- Institute for Artificial Intelligence in Medicine (IKIM), University Hospital Essen (AöR), Girardetstraße 2, 45131 Essen, Germany; Cancer Research Center Cologne Essen (CCCE), West German Cancer Center Essen, University Hospital Essen (AöR), Hufelandstr. 55, 45147 Essen, Germany; Center for Virtual and Extended Reality in Medicine (ZvRM), University Hospital Essen, University Medicine Essen, Hufelandstraße 55, 45147 Essen, Germany
| | - Bastian Leibe
- Visual Computing Institute (Computer Vision), RWTH Aachen University, Mies-van-der-Rohe Str. 15, 52074 Aachen, Germany
| | - Frank Hölzle
- Department of Oral and Maxillofacial Surgery, University Hospital RWTH Aachen, Pauwelsstr. 30, 52074 Aachen, Germany; Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf (CIO ABCD), Pauwelsstraße 30, 52074 Aachen, Germany
| | - Alexander Hermans
- Visual Computing Institute (Computer Vision), RWTH Aachen University, Mies-van-der-Rohe Str. 15, 52074 Aachen, Germany
| | - Behrus Puladi
- Department of Oral and Maxillofacial Surgery, University Hospital RWTH Aachen, Pauwelsstr. 30, 52074 Aachen, Germany; Institute of Medical Informatics, University Hospital RWTH Aachen, Pauwelsstr. 30, 52074 Aachen, Germany; Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf (CIO ABCD), Pauwelsstraße 30, 52074 Aachen, Germany.
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3
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Page DB, Broeckx G, Jahangir CA, Verbandt S, Gupta RR, Thagaard J, Khiroya R, Kos Z, Abduljabbar K, Acosta Haab G, Acs B, Akturk G, Almeida JS, Alvarado-Cabrero I, Azmoudeh-Ardalan F, Badve S, Baharun NB, Bellolio ER, Bheemaraju V, Blenman KRM, Botinelly Mendonça Fujimoto L, Bouchmaa N, Burgues O, Cheang MCU, Ciompi F, Cooper LAD, Coosemans A, Corredor G, Dantas Portela FL, Deman F, Demaria S, Dudgeon SN, Elghazawy M, Ely S, Femandez-Martín C, Fineberg S, Fox SB, Gallagher WM, Giltnane JM, Gnjatic S, Gonzalez-Ericsson PI, Grigoriadis A, Halama N, Hanna MG, Harbhajanka A, Hardas A, Hart SN, Hartman J, Hewitt S, Hida AI, Horlings HM, Husain Z, Hytopoulos E, Irshad S, Janssen EAM, Kahila M, Kataoka TR, Kawaguchi K, Kharidehal D, Khramtsov AI, Kiraz U, Kirtani P, Kodach LL, Korski K, Kovács A, Laenkholm AV, Lang-Schwarz C, Larsirnont D, Lennerz JK, Lerousseau M, Li X, Ly A, Madabhushi A, Maley SK, Narasimhamurthy VM, Marks DK, McDonald ES, Mehrotra R, Michiels S, Minhas FUAA, Mittal S, Moore DA, Mushtaq S, Nighat H, Papathomas T, Penault-Llorca F, Perera RD, Pinard CJ, Pinto-Cardenas JC, Pruneri G, Pusztai L, Rahman A, Rajpoot NM, Rapoport BL, Rau TT, Reis-Filho JS, Ribeiro JM, Rimm D, Vincent-Salomon A, Salto-Tellez M, Saltz J, Sayed S, Siziopikou KP, Sotiriou C, Stenzinger A, Sughayer MA, Sur D, Symmans F, Tanaka S, Taxter T, Tejpar S, Teuwen J, Thompson EA, Tramm T, Tran WT, van der Laak J, van Diest PJ, Verghese GE, Viale G, Vieth M, Wahab N, Walter T, Waumans Y, Wen HY, Yang W, Yuan Y, Adams S, Bartlett JMS, Loibl S, Denkert C, Savas P, Loi S, Salgado R, Specht Stovgaard E. Spatial analyses of immune cell infiltration in cancer: current methods and future directions: A report of the International Immuno-Oncology Biomarker Working Group on Breast Cancer. J Pathol 2023; 260:514-532. [PMID: 37608771 PMCID: PMC11288334 DOI: 10.1002/path.6165] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 06/19/2023] [Indexed: 08/24/2023]
Abstract
Modern histologic imaging platforms coupled with machine learning methods have provided new opportunities to map the spatial distribution of immune cells in the tumor microenvironment. However, there exists no standardized method for describing or analyzing spatial immune cell data, and most reported spatial analyses are rudimentary. In this review, we provide an overview of two approaches for reporting and analyzing spatial data (raster versus vector-based). We then provide a compendium of spatial immune cell metrics that have been reported in the literature, summarizing prognostic associations in the context of a variety of cancers. We conclude by discussing two well-described clinical biomarkers, the breast cancer stromal tumor infiltrating lymphocytes score and the colon cancer Immunoscore, and describe investigative opportunities to improve clinical utility of these spatial biomarkers. © 2023 The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- David B Page
- Earle A Chiles Research Institute, Providence Cancer Institute, Portland, OR, USA
| | - Glenn Broeckx
- Department of Pathology, GZA-ZNA Hospitals, Antwerp, Belgium
- Centre for Oncological Research (CORE), MIPPRO, Faculty of Medicine, Antwerp University, Antwerp, Belgium
| | - Chowdhury Arif Jahangir
- UCD School of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland
| | - Sara Verbandt
- Digestive Oncology, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Rajarsi R Gupta
- Department of Biomedical Informatics, Stony Brook University, Stony Brook, NY, USA
| | - Jeppe Thagaard
- Technical University of Denmark, Kongens Lyngby, Denmark
- Visiopharm A/S, Hørshoim, Denmark
| | - Reena Khiroya
- Department of Cellular Pathology, University College Hospital, London, UK
| | - Zuzana Kos
- Department of Pathology and Laboratory Medicine, BC Cancer Vancouver Centre, University of British Columbia, Vancouver, BC, Canada
| | - Khalid Abduljabbar
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | | | - Balazs Acs
- Department of Oncology and Pathology, Karolinska Institutet Stockholm, Sweden
- Clinical Pathology and Cancer Diagnostics, Karolinska University Hospital, Stockholm, Sweden
| | - Guray Akturk
- Translational Molecular Biomarkers, Merck & Co Inc, Kenilworth, NJ, USA
| | - Jonas S Almeida
- National Cancer Institute, Division of Cancer Epidemiology and Genetics (DCEG), Rockville, MD, USA
| | | | | | - Sunil Badve
- Pathology and Laboratory Medicine, Emory University School of Medicine, Emory University Winship Cancer Institute, Atlanta, GA, USA
| | | | - Enrique R Bellolio
- Departamento de Anatomia Patológica, Facultad de Medicina, Universidad de La Frontera, Temuco, Chile
| | | | - Kim RM Blenman
- Internal Medicine Section of Medical Oncology and Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
- Computer Science, Yale School of Engineering and Applied Science, New Haven, CT, USA
| | | | - Najat Bouchmaa
- Institute of Biological Sciences, Faculty of Medical Sciences, Mohammed VI Polytechnic University (UM6P), Ben-Guerir, Morocco
| | - Octavio Burgues
- Pathology Department Hospital Cliníco Universitario de Valencia/lncliva, Valencia, Spain
| | - Maggie Chon U Cheang
- Head of Integrative Genomics Analysis in Clinical Trials, ICR-CTSU, Division of Clinical Studies, Institute of Cancer Research, London, UK
| | - Francesco Ciompi
- Radboud University Medical Center, Department of Pathology, Nijmegen, The Netherlands
| | - Lee AD Cooper
- Department of Pathology, Northwestern Feinberg School of Medicine, Chicago, IL, USA
| | - An Coosemans
- Department of Oncology, Laboratory of Tumor Immunology and Immunotherapy, KU Leuven, Leuven, Belgium
| | - Germán Corredor
- Biomedical Engineering Department Emory University, Atlanta, GA, USA
| | | | - Frederik Deman
- Department of Pathology, GZA-ZNA Hospitals, Antwerp, Belgium
| | - Sandra Demaria
- Department of Radiation Oncology, Weill Cornell Medical College, New York, NY, USA
- Department of Pathology, Weill Cornell Medicine, New York, NY, USA
| | - Sarah N Dudgeon
- Conputational Biology and Bioinformatics, Yale University, New Haven, CT, USA
| | - Mahmoud Elghazawy
- University of Surrey, Guildford, UK
- Ain Shams University, Cairo, Egypt
| | - Scott Ely
- Translational Pathology, Translational Sciences and Diagnostics/Translational Medicine/R&D, Bristol Myers Squibb, Princeton, NJ, USA
| | - Claudio Femandez-Martín
- Instituto Universitario de Investigación en Tecnología Centrada en el SerHumano, HUMAN-tech, Universitat Politècnica de València, Valencia, Spain
| | - Susan Fineberg
- Montefiore Medical Center and the Albert Einstein College of Medicine, New York, NY, USA
| | - Stephen B Fox
- Department of Pathology, Peter MacCallum Cancer Centre and Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - William M Gallagher
- UCD School of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland
| | | | - Sacha Gnjatic
- Department of Oncological Sciences, Medicine Hem/One, and Pathology, Tisch Cancer Institute – Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Anita Grigoriadis
- Cancer Bioinformatics, School of Cancer & Pharmaceutical Sciences, Faculty of Life Sciences and Medicine, King’s College London, London, UK
- Breast Cancer Now Research Unit School of Cancer and Pharmaceutical Sciences, Faculty of Life Sciences and Medicine, King’s College London, London, UK
| | - Niels Halama
- Translational Immunotherapy, German Cancer Research Center, Heidelberg, Germany
| | | | | | - Alexandros Hardas
- Pathobiology & Population Sciences, The Royal Veterinary College, London, UK
| | - Steven N Hart
- Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Johan Hartman
- Clinical Pathology and Cancer Diagnostics, Karolinska University Hospital, Stockholm, Sweden
- Department of Oncology-Pathology, Karolinska Institutet Stockholm, Sweden
| | - Stephen Hewitt
- Department of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Akira I Hida
- Department of Pathology, Matsuyama Shimin Hospital, Matsuyama, Japan
| | - Hugo M Horlings
- Division of Pathology, Netherlands Cancer Institute (NKI), Amsterdam, The Netherlands
| | | | | | - Sheeba Irshad
- Kings College London & Guy’s & St Thomas’ NHS Trust, London, UK
| | - Emiel AM Janssen
- Department of Pathology, Stavanger University Hospital, Stavanger, Norway
- Department of Chemistry, Bioscience and Environmental Technology, University of Stavanger, Stavanger, Norway
| | - Mohamed Kahila
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
| | | | - Kosuke Kawaguchi
- Department of Breast Surgery, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Durga Kharidehal
- Department of Pathology, Narayana Medical College, Nellore, India
| | - Andrey I Khramtsov
- Pathology and Laboratory Medicine, Ann & Robert H. Lurie Children’s Hospital of Chicago, Chicago, IL, USA
| | - Umay Kiraz
- Department of Pathology, Stavanger University Hospital, Stavanger, Norway
- Department of Chemistry, Bioscience and Environmental Technology, University of Stavanger, Stavanger, Norway
| | - Pawan Kirtani
- Department of Histopathology, Aakash Healthcare Super Speciality Hospital, New Delhi, India
| | - Liudmila L Kodach
- Department of Pathology, Netherlands Cancer Institute – Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
| | - Konstanty Korski
- Data, Analytics and Imaging, Product Development, F.Hoffmann-La Roche AG, Basel, Switzerland
| | - Anikó Kovács
- Department of Clinical Pathology, Sahlgrenska University Hospital, Gothenburg Sweden
- Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg Gothenburg, Sweden
| | - Anne-Vibeke Laenkholm
- Surgical Pathology, Zealand University Hospital, Roskilde, Denmark
- Surgical Pathology, University of Copenhagen, Copenhagen, Denmark
| | - Corinna Lang-Schwarz
- Institute of Pathology, Klinikum Bayreuth GmbH, Friedrich-Alexander-University Erlangen-Nuremberg, Bayreuth, Germany
| | - Denis Larsirnont
- Institut Jules Bordet Université, Libre de Bruxelles, Brussels, Belgium
| | - Jochen K Lennerz
- Center for Integrated Diagnostics, Massachusetts General Hospital/Harvard Medical School, Boston, MA, USA
| | - Marvin Lerousseau
- Centre for Computational Biology (CBIO), Mines Paris, PSL University, Paris, France
- Institut Curie, PSL University, Paris, France
- INSERM, U900, Paris, France
| | - Xiaoxian Li
- Pathology and Laboratory Medicine, Emory University, Atlanta, GA, USA
| | - Amy Ly
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Anant Madabhushi
- Biomedical Engineering, Radiology and Imaging Sciences, Biomedical Informatics, Pathology, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Sai K Maley
- NRG Oncology/NSABP Foundation, Pittsburgh, PA, USA
| | | | - Douglas K Marks
- Perlmutter Cancer Center, NYU Langone Health, New York NY, USA
| | - Elizabeth S McDonald
- Breast Cancer Translational Research Group, University of Pennsylvania, Philadelphia, PA, USA
| | - Ravi Mehrotra
- Indian Cancer Genome Atlas, Pune, India
- Centre for Health, Innovation and Policy Foundation, Noida, India
| | - Stefan Michiels
- Office of Biostatistics and Epidemiology, Gustave Roussy, Oncostat Ul 018, Inserm, University Paris-Saclay, Ligue Contre le Cancer labeled Team, Villejuif France
| | - Fayyaz ul Amir Afsar Minhas
- Tissue Image Analytics Centre, Warwick Cancer Research Centre, PathLAKE Consortium, Department of Computer Science, University of Warwick, Coventry, UK
| | - Shachi Mittal
- Department of Chemical Engineering, Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - David A Moore
- CRUK Lung Cancer Centre of Excellence, UCLH, London, UK
| | - Shamim Mushtaq
- Department of Biochemistry, Ziauddin University, Karachi, Pakistan
| | - Hussain Nighat
- Pathology and Laboratory Medicine, All India Institute of Medical Sciences, Raipur, India
| | - Thomas Papathomas
- Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, UK
- Department of Clinical Pathology, Drammen Sykehus, Vestre Viken HF, Drammen, Norway
| | - Frederique Penault-Llorca
- Centre Jean Perrin, INSERM U1240, Imagerie Moléculaire et Stratégies Théranostiques, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Rashindrie D Perera
- School of Electrical, Mechanical and Infrastructure Engineering, University of Melbourne, Melbourne, VIC, Australia
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Christopher J Pinard
- Radiogenomics Laboratory, Sunnybrook Health Sciences Centre, Toronto, ON, Canada
- Department of Clinical Studies, Ontario Veterinary College, University of Guelph, Guelph, ON, Canada
- Department of Oncology, Lakeshore Animal Health Partners, Mississauga, ON, Canada
- Centre for Advancing Responsible and Ethical Artificial Intelligence (CARE-AI), University of Guelph, Guelph, ON, Canada
| | | | - Giancarlo Pruneri
- Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
- Faculty of Medicine and Surgery, University of Milan, Milan, Italy
| | - Laios Pusztai
- Yale Cancer Center, New Haven, CT, USA
- Department of Medical Oncology, Yale School of Medicine, New Haven, CT, USA
| | - Arman Rahman
- UCD School of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland
| | | | - Bernardo Leon Rapoport
- The Medical Oncology Centre ofRosebank Johannesburg, South Africa
- Department of Immunology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | - Tilman T Rau
- Institute of Pathology, University Hospital Düsseldorf and Heinrich-Heine-University Düsseldorf Düsseldorf Germany
| | - Jorge S Reis-Filho
- Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York NY, USA
| | - Joana M Ribeiro
- Département de Médecine Oncologique, Institute Gustave Roussy, Villejuif France
| | - David Rimm
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
- Department of Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Anne Vincent-Salomon
- Department of Diagnostic and Theranostic Medicine, Institut Curie, University Paris-Sciences et Lettres, Paris, France
| | - Manuel Salto-Tellez
- Integrated Pathology Unit Institute of Cancer Research, London, UK
- Precision Medicine Centre, Queen’s University Belfast Belfast UK
| | - Joel Saltz
- Department of Biomedical Informatics, Stony Brook Medicine, New York NY, USA
| | - Shahin Sayed
- Department of Pathology, Aga Khan University, Nairobi, Kenya
| | - Kalliopi P Siziopikou
- Department of Pathology, Section of Breast Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Christos Sotiriou
- Breast Cancer Translational Research Laboratory J.-C. Heuson, Institut Jules Bordet Hôpital Universitaire de Bruxelles (HUB), Université Libre de Bruxelles (ULB), Brussels, Belgium
- Medical Oncology Department Institut Jules Bordet Hôpital Universitaire de Bruxelles (HUB), Université Libre de Bruxelles, Brussels, Belgium
| | - Albrecht Stenzinger
- Institute of Pathology, University Hospital Heidelberg Centers for Personalized Medicine (ZPM), Heidelberg Germany
| | | | - Daniel Sur
- Department of Medical Oncology, University of Medicine and Pharmacy “luliu Hatieganu”, Cluj-Napoca, Romania
| | - Fraser Symmans
- University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | | | - Sabine Tejpar
- Digestive Oncology, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Jonas Teuwen
- Al for Oncology Lab, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | | | - Trine Tramm
- Pathology, and Institute of Clinical Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - William T Tran
- Department of Radiation Oncology, University of Toronto and Sunnybrook Health Sciences Centre, Toronto, ON, Canada
| | - Jeroen van der Laak
- Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Paul J van Diest
- Department of Pathology, University Medical Center Utrecht Utrecht The Netherlands
- Johns Hopkins Oncology Center, Baltimore, MD, USA
| | - Gregory E Verghese
- Cancer Bioinformatics, School of Cancer & Pharmaceutical Sciences, Faculty of Life Sciences and Medicine, King’s College London, London, UK
- Breast Cancer Now Research Unit School of Cancer and Pharmaceutical Sciences, Faculty of Life Sciences and Medicine, King’s College London, London, UK
| | - Giuseppe Viale
- Department of Pathology, European Institute of Oncology & University of Milan, Milan, Italy
| | - Michael Vieth
- Institute of Pathology, Kiinikum Bayreuth GmbH, Friedrich-Alexander-University Erlangen-Nuremberg, Bayreuth, Germany
| | - Noorul Wahab
- Tissue Image Analytics Centre, Department of Computer Science, University of Warwick Coventry, UK
| | - Thomas Walter
- Centre for Computational Biology (CBIO), Mines Paris, PSL University, Paris, France
- Institut Curie, PSL University, Paris, France
- INSERM, U900, Paris, France
| | | | - Hannah Y Wen
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Wentao Yang
- Fudan Medical University Shanghai Cancer Center, Shanghai, PR China
| | - Yinyin Yuan
- Translational Molecular Pathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sylvia Adams
- Perlmutter Cancer Center, NYU Langone Health, New York NY, USA
- Department of Medicine, NYU Grossman School of Medicine, Manhattan, NY, USA
| | | | - Sibylle Loibl
- Department of Medicine and Research, German Breast Group, Neu-lsenburg Germany
| | - Carsten Denkert
- Institut für Pathologie, Philipps-Universität Marburg und Universitätsklinikum Marburg, Marburg, Germany
| | - Peter Savas
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Medical Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - Sherene Loi
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC Australia
| | - Roberto Salgado
- Department of Pathology, GZA-ZNA Hospitals, Antwerp, Belgium
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Elisabeth Specht Stovgaard
- Department of Pathology, Herlev and Gentofte Hospital, Herlev, Denmark
- Faculty of Health and Medical Sciences, Copenhagen University, Copenhagen, Denmark
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4
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Xie J, Pu X, He J, Qiu Y, Lu C, Gao W, Wang X, Lu H, Shi J, Xu Y, Madabhushi A, Fan X, Chen J, Xu J. Survival prediction on intrahepatic cholangiocarcinoma with histomorphological analysis on the whole slide images. Comput Biol Med 2022; 146:105520. [DOI: 10.1016/j.compbiomed.2022.105520] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 04/07/2022] [Accepted: 04/11/2022] [Indexed: 01/06/2023]
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5
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Rahman J, Panda S, Panigrahi S, Mohanty N, Swarnkar T, Mishra U. Perspective of nuclear fractal dimension in diagnosis and prognosis of oral squamous cell carcinoma. J Oral Maxillofac Pathol 2022; 26:127. [PMID: 35571291 PMCID: PMC9106250 DOI: 10.4103/jomfp.jomfp_470_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 10/24/2021] [Indexed: 12/03/2022] Open
Abstract
Background: Owing to the restricted predictive value of conventional prognostic factors and the inconsistent treatment strategies, several oral squamous cell carcinoma (OSCC) patients are still over-treated or under-treated. In recent years, computer-assisted nuclear fractal dimension (nFD) has emerged as an objective approach to predict the outcome of OSCC. Objective: This study is an attempt to find out the differences in nFD values of epithelial cells of normal tissue, fibroepithelial hyperplasia, verrucous carcinoma, and OSCC. Further effort to evaluate the predictive potential of nFD of tumor cells for cervical lymph node metastasis (cLNM) was also assessed. Methodology: Formalin-fixed paraffin-embedded blocks of OSCC tissues of patients treated with neck dissection were collected. Photomicrographs of H-&E-stained sections were subjected to the image analysis by ImageJ and Python programming to calculate nFD. The association of categorical variables with nFD was studied using cross-tabulation procedure and the Fisher exact test. Receiver operating curve analysis was performed to find out cutoff value of nFD. A logistic regression model was developed to test the individual and combined predictive potential of grading and nFD for cLNM. Results: A significant difference between the mean nFD of healthy cells and malignant epithelial cells was observed (P = 0.01). nFD was not found to be an independent predictor of cLNM, although nFD and grading together demonstrated significant predictive potential (P = 0.004). Conclusion: nFD combined with grading can predict lymph node metastasis in OSCC. To the best of our knowledge, this is the first study of its kind.
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Affiliation(s)
- Juber Rahman
- Department of Oral Pathology and Microbiology, Institute of Dental Sciences, Siksha 'O' Anusandhan Deemed to be University, Bhubaneswar, Odisha, India
| | - Swagatika Panda
- Department of Oral Pathology and Microbiology, Institute of Dental Sciences, Siksha 'O' Anusandhan Deemed to be University, Bhubaneswar, Odisha, India
| | - Santisudha Panigrahi
- Department of Computer Science and Engineering, Institute of Technical Education and Research, Siksha 'O' Anusandhan Deemed to be University, Bhubaneswar, Odisha, India
| | - Neeta Mohanty
- Department of Oral Pathology and Microbiology, Institute of Dental Sciences, Siksha 'O' Anusandhan Deemed to be University, Bhubaneswar, Odisha, India
| | - Tripti Swarnkar
- Department of Computer Science and Engineering, Institute of Technical Education and Research, Siksha 'O' Anusandhan Deemed to be University, Bhubaneswar, Odisha, India
| | - Umashankar Mishra
- Department of Management, School of Commerce and Management, Central university of Rajasthan, Ajmer, India
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6
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Wortman JC, He TF, Solomon S, Zhang RZ, Rosario A, Wang R, Tu TY, Schmolze D, Yuan Y, Yost SE, Li X, Levine H, Atwal G, Lee PP, Yu CC. Spatial distribution of B cells and lymphocyte clusters as a predictor of triple-negative breast cancer outcome. NPJ Breast Cancer 2021; 7:84. [PMID: 34210991 PMCID: PMC8249408 DOI: 10.1038/s41523-021-00291-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 06/03/2021] [Indexed: 02/07/2023] Open
Abstract
While tumor infiltration by CD8+ T cells is now widely accepted to predict outcomes, the clinical significance of intratumoral B cells is less clear. We hypothesized that spatial distribution rather than density of B cells within tumors may provide prognostic significance. We developed statistical techniques (fractal dimension differences and a box-counting method 'occupancy') to analyze the spatial distribution of tumor-infiltrating lymphocytes (TILs) in human triple-negative breast cancer (TNBC). Our results indicate that B cells in good outcome tumors (no recurrence within 5 years) are spatially dispersed, while B cells in poor outcome tumors (recurrence within 3 years) are more confined. While most TILs are located within the stroma, increased numbers of spatially dispersed lymphocytes within cancer cell islands are associated with a good prognosis. B cells and T cells often form lymphocyte clusters (LCs) identified via density-based clustering. LCs consist either of T cells only or heterotypic mixtures of B and T cells. Pure B cell LCs were negligible in number. Compared to tertiary lymphoid structures (TLS), LCs have fewer lymphocytes at lower densities. Both types of LCs are more abundant and more spatially dispersed in good outcomes compared to poor outcome tumors. Heterotypic LCs in good outcome tumors are smaller and more numerous compared to poor outcome. Heterotypic LCs are also closer to cancer islands in a good outcome, with LC size decreasing as they get closer to cancer cell islands. These results illuminate the significance of the spatial distribution of B cells and LCs within tumors.
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Affiliation(s)
- Juliana C Wortman
- Department of Physics and Astronomy, University of California, Irvine, Irvine, CA, USA
| | - Ting-Fang He
- Department of Immuno-Oncology, City of Hope Comprehensive Cancer Center and Beckman Research Institute, Duarte, CA, USA
| | - Shawn Solomon
- Department of Immuno-Oncology, City of Hope Comprehensive Cancer Center and Beckman Research Institute, Duarte, CA, USA
| | - Robert Z Zhang
- Department of Immuno-Oncology, City of Hope Comprehensive Cancer Center and Beckman Research Institute, Duarte, CA, USA
| | - Anthony Rosario
- Department of Immuno-Oncology, City of Hope Comprehensive Cancer Center and Beckman Research Institute, Duarte, CA, USA
| | - Roger Wang
- Department of Immuno-Oncology, City of Hope Comprehensive Cancer Center and Beckman Research Institute, Duarte, CA, USA
| | - Travis Y Tu
- Department of Immuno-Oncology, City of Hope Comprehensive Cancer Center and Beckman Research Institute, Duarte, CA, USA
| | - Daniel Schmolze
- Department of Pathology, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Yuan Yuan
- Department of Medical Oncology and Therapeutics Research, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Susan E Yost
- Department of Medical Oncology and Therapeutics Research, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Xuefei Li
- Department of Bioengineering and the Center for Theoretical Biological Physics, Rice University, Houston, TX, USA
| | - Herbert Levine
- Department of Bioengineering and the Center for Theoretical Biological Physics, Rice University, Houston, TX, USA
- Department of Bioengineering and Department of Physics, Northeastern University, Boston, MA, USA
| | - Gurinder Atwal
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Peter P Lee
- Department of Immuno-Oncology, City of Hope Comprehensive Cancer Center and Beckman Research Institute, Duarte, CA, USA.
| | - Clare C Yu
- Department of Physics and Astronomy, University of California, Irvine, Irvine, CA, USA.
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7
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Yu CC, Wortman JC, He TF, Solomon S, Zhang RZ, Rosario A, Wang R, Tu TY, Schmolze D, Yuan Y, Yost SE, Li X, Levine H, Atwal G, Lee PP. Physics approaches to the spatial distribution of immune cells in tumors. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2021; 84:022601. [PMID: 33232952 DOI: 10.1088/1361-6633/abcd7b] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The goal of immunotherapy is to mobilize the immune system to kill cancer cells. Immunotherapy is more effective and, in general, the prognosis is better, when more immune cells infiltrate the tumor. We explore the question of whether the spatial distribution rather than just the density of immune cells in the tumor is important in forecasting whether cancer recurs. After reviewing previous work on this issue, we introduce a novel application of maximum entropy to quantify the spatial distribution of discrete point-like objects. We apply our approach to B and T cells in images of tumor tissue taken from triple negative breast cancer patients. We find that the immune cells are more spatially dispersed in good clinical outcome (no recurrence of cancer within at least 5 years of diagnosis) compared to poor clinical outcome (recurrence within 3 years of diagnosis). Our results highlight the importance of spatial distribution of immune cells within tumors with regard to clinical outcome, and raise new questions on their role in cancer recurrence.
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Affiliation(s)
- Clare C Yu
- Department of Physics and Astronomy, University of California, Irvine, Irvine, CA 92697, United States of America
- Department of Immuno-Oncology, City of Hope Comprehensive Cancer Center and Beckman Research Institute, 1500 East Duarte Road, Duarte, CA 91010, United States of America
| | - Juliana C Wortman
- Department of Physics and Astronomy, University of California, Irvine, Irvine, CA 92697, United States of America
| | - Ting-Fang He
- Department of Immuno-Oncology, City of Hope Comprehensive Cancer Center and Beckman Research Institute, 1500 East Duarte Road, Duarte, CA 91010, United States of America
| | - Shawn Solomon
- Department of Immuno-Oncology, City of Hope Comprehensive Cancer Center and Beckman Research Institute, 1500 East Duarte Road, Duarte, CA 91010, United States of America
| | - Robert Z Zhang
- Department of Immuno-Oncology, City of Hope Comprehensive Cancer Center and Beckman Research Institute, 1500 East Duarte Road, Duarte, CA 91010, United States of America
| | - Anthony Rosario
- Department of Immuno-Oncology, City of Hope Comprehensive Cancer Center and Beckman Research Institute, 1500 East Duarte Road, Duarte, CA 91010, United States of America
| | - Roger Wang
- Department of Immuno-Oncology, City of Hope Comprehensive Cancer Center and Beckman Research Institute, 1500 East Duarte Road, Duarte, CA 91010, United States of America
| | - Travis Y Tu
- Department of Immuno-Oncology, City of Hope Comprehensive Cancer Center and Beckman Research Institute, 1500 East Duarte Road, Duarte, CA 91010, United States of America
| | - Daniel Schmolze
- Department of Pathology, City of Hope Comprehensive Cancer Center, 1500 East Duarte Road, Duarte, CA 91010, United States of America
| | - Yuan Yuan
- Department of Medical Oncology and Therapeutics Research, City of Hope Comprehensive Cancer Center, 1500 East Duarte Road, Duarte, CA 91010, United States of America
| | - Susan E Yost
- Department of Medical Oncology and Therapeutics Research, City of Hope Comprehensive Cancer Center, 1500 East Duarte Road, Duarte, CA 91010, United States of America
| | - Xuefei Li
- Department of Bioengineering and the Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, United States of America
| | - Herbert Levine
- Department of Bioengineering and the Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, United States of America
- Department of Bioengineering and Department of Physics, Northeastern University, Boston, MA 02115, United States of America
| | - Gurinder Atwal
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, United States of America
| | - Peter P Lee
- Department of Immuno-Oncology, City of Hope Comprehensive Cancer Center and Beckman Research Institute, 1500 East Duarte Road, Duarte, CA 91010, United States of America
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8
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Lu C, Koyuncu C, Corredor G, Prasanna P, Leo P, Wang X, Janowczyk A, Bera K, Lewis J, Velcheti V, Madabhushi A. Feature-driven local cell graph (FLocK): New computational pathology-based descriptors for prognosis of lung cancer and HPV status of oropharyngeal cancers. Med Image Anal 2020; 68:101903. [PMID: 33352373 DOI: 10.1016/j.media.2020.101903] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 10/26/2020] [Accepted: 11/09/2020] [Indexed: 01/02/2023]
Abstract
Local spatial arrangement of nuclei in histopathology images of different cancer subtypes has been shown to have prognostic value. In order to capture localized nuclear architectural information, local cell cluster graph-based measurements have been proposed. However, conventional ways of cell graph construction only utilize nuclear spatial proximity, and do not differentiate between different cell types while constructing the graph. In this paper, we present feature-driven local cell cluster graph (FLocK), a new approach to constructing local cell graphs by simultaneously considering spatial proximity and attributes of the individual nuclei (e.g. shape, size, texture). In addition, we have designed a new set of quantitative graph-derived metrics to be extracted from FLocKs, in turn capturing the interplay between different proximally located clusters of nuclei. We have evaluated the efficacy of FLocK features extracted from H&E stained tissue images in two clinical applications: to classify short-term vs. long-term survival among patients of early stage non-small cell lung cancer (ES-NSCLC), and also to predict human papillomavirus (HPV) status of oropharyngeal squamous cell carcinoma (OP-SCCs). In the classification of long-term vs. short-term survival among patients of ES-NSCLC (training cohort, n = 434), the top 10 discriminative FLocK features related to the variation of FLocK size and intersected FLocK distance were identified, via Minimum Redundancy and Maximum Relevance (MRMR) selection, in 100 runs of 10-fold cross-validation, and in conjunction with a linear discriminant classifier yielded a mean AUC of 0.68 for predicting survival in the training cohort. This is better than other state-of-art histomorphometric and deep learning classifiers (cell cluster graphs (AUC = 0.62), global cell graph (AUC = 0.56), nuclear shape (AUC = 0.54), nuclear orientation (AUC = 0.61), AlexNet (AUC = 0.55), ResNet (AUC = 0.56)). The FLocK-based classifier yielded an AUC of 0.70 in an independent testing cohort (n = 150). The patients identified as "high-risk" had significantly poorer overall survival in the testing cohort, with a hazard ratio (95% confidence interval) of 2.24 (1.24-4.05), p = 0.01144). In the classification of HPV status of OP-SCC, the top three FLocK features pertaining to the portion of intersected FLocKs were used to construct a classifier, which yielded an AUC of 0.80 in the training cohort (n = 50), and an accuracy of 0.78 in an independent testing cohort (n = 35). The combination of FLocK measurements with cell cluster graphs, nuclear orientation, and nuclear shape improved the training AUC to 0.87, 0.91 and 0.85, respectively. Deep learning approaches yielded marginally better performance than the FLocK-based classifier in this application, with AUC = 0.78 for AlexNet, AUC = 0.81 for ResNet, and AUC = 0.76 for FLocK-based classifier in the testing cohort. However, the combination of two hand-crafted features: FLocK and nuclear orientation yielded a better performance (AUC = 0.84). FLocK provides a unique and quantitative way to analyze histology images of solid tumors and interrogate tumor morphology from a different aspect than existing histomorphometrics. The source code can be accessed at https://github.com/hacylu/FLocK.
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Affiliation(s)
- Cheng Lu
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, OH, USA
| | - Can Koyuncu
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, OH, USA
| | - German Corredor
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, OH, USA
| | - Prateek Prasanna
- Department of Biomedical Informatics, Stony Brook University, New York, NY, USA
| | - Patrick Leo
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, OH, USA
| | - XiangXue Wang
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, OH, USA
| | - Andrew Janowczyk
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, OH, USA; Precision Oncology Center, Lausanne University Hospital, Switzerland
| | - Kaustav Bera
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, OH, USA
| | - James Lewis
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | | | - Anant Madabhushi
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, OH, USA; Louis Stokes Cleveland Veterans Administration Medical Center, Cleveland, OH, USA.
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9
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Bera K, Katz I, Madabhushi A. Reimagining T Staging Through Artificial Intelligence and Machine Learning Image Processing Approaches in Digital Pathology. JCO Clin Cancer Inform 2020; 4:1039-1050. [PMID: 33166198 PMCID: PMC7713520 DOI: 10.1200/cci.20.00110] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/21/2020] [Indexed: 02/06/2023] Open
Abstract
Tumor stage and grade, visually assessed by pathologists from evaluation of pathology images in conjunction with radiographic imaging techniques, have been linked to outcome, progression, and survival for a number of cancers. The gold standard of staging in oncology has been the TNM (tumor-node-metastasis) staging system. Though histopathological grading has shown prognostic significance, it is subjective and limited by interobserver variability even among experienced surgical pathologists. Recently, artificial intelligence (AI) approaches have been applied to pathology images toward diagnostic-, prognostic-, and treatment prediction-related tasks in cancer. AI approaches have the potential to overcome the limitations of conventional TNM staging and tumor grading approaches, providing a direct prognostic prediction of disease outcome independent of tumor stage and grade. Broadly speaking, these AI approaches involve extracting patterns from images that are then compared against previously defined disease signatures. These patterns are typically categorized as either (1) handcrafted, which involve domain-inspired attributes, such as nuclear shape, or (2) deep learning (DL)-based representations, which tend to be more abstract. DL approaches have particularly gained considerable popularity because of the minimal domain knowledge needed for training, mostly only requiring annotated examples corresponding to the categories of interest. In this article, we discuss AI approaches for digital pathology, especially as they relate to disease prognosis, prediction of genomic and molecular alterations in the tumor, and prediction of treatment response in oncology. We also discuss some of the potential challenges with validation, interpretability, and reimbursement that must be addressed before widespread clinical deployment. The article concludes with a brief discussion of potential future opportunities in the field of AI for digital pathology and oncology.
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Affiliation(s)
- Kaustav Bera
- Case Western Reserve University, Department of Biomedical Engineering, Cleveland, OH
- Maimonides Medical Center, Department of Internal Medicine, Brooklyn, NY
| | - Ian Katz
- Southern Sun Pathology, Sydney, Australia, and University of Queensland, Brisbane, Australia
| | - Anant Madabhushi
- Case Western Reserve University, Department of Biomedical Engineering, Cleveland, OH
- Louis Stokes Veterans Affairs Medical Center, Cleveland, OH
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10
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Wortman JC, He TF, Rosario A, Wang R, Schmolze D, Yuan Y, Yost SE, Li X, Levine H, Atwal G, Lee P, Yu CC. Occupancy and Fractal Dimension Analyses of the Spatial Distribution of Cytotoxic (CD8+) T Cells Infiltrating the Tumor Microenvironment in Triple Negative Breast Cancer. ACTA ACUST UNITED AC 2020. [DOI: 10.1142/s1793048020500022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Favorable outcomes have been associated with high densities of tumor infiltrating lymphocytes (TILs) such as cytotoxic ([Formula: see text]) T cells. However, the clinical significance of the spatial distribution of TILs is less well understood. We have developed novel statistical techniques to characterize the spatial distribution of TILs at various length scales. These include a box counting method that we call “occupancy” and novel applications of fractal dimensions. We apply these techniques to the spatial distribution of [Formula: see text] T cells in the tumor microenvironment of tissue resected from 35 triple negative breast cancer patients. We find that there is a distinct difference in the spatial distribution of [Formula: see text] T cells between good clinical outcome (no recurrence within at least 5 years of diagnosis) and poor clinical outcome (recurrence within 3 years of diagnosis). The statistical significance of the difference between good and poor outcome in the occupancy, fractal dimension (FD), and FD difference of [Formula: see text] T cells is comparable to that of the [Formula: see text] T cell density. Even when we randomly exclude some of the cells so that the images have the same cell density, we still find that the fractal dimension at short length scales is correlated with cancer recurrence, implying that the actual spatial distribution of [Formula: see text] cells, and not just the [Formula: see text] cell density, is associated with clinical outcome. The occupancy and FD difference indicate that the [Formula: see text] T cells are more spatially dispersed in good outcome and more aggregated in poor outcome. We discuss possible interpretations.
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Affiliation(s)
- Juliana C. Wortman
- Department of Physics and Astronomy, University of California, Irvine 92697, CA, USA
| | - Ting-Fang He
- Cancer Immunotherapeutics & Tumor Immunology, City of Hope Comprehensive Cancer Center and Beckman Research Institute, 1500 East Duarte Road, Duarte 91010, CA, USA
| | - Anthony Rosario
- Cancer Immunotherapeutics & Tumor Immunology, City of Hope Comprehensive Cancer Center and Beckman Research Institute, 1500 East Duarte Road, Duarte 91010, CA, USA
| | - Roger Wang
- Cancer Immunotherapeutics & Tumor Immunology, City of Hope Comprehensive Cancer Center and Beckman Research Institute, 1500 East Duarte Road, Duarte 91010, CA, USA
| | - Daniel Schmolze
- Department of Pathology, City of Hope Comprehensive Cancer Center and Beckman Research Institute, 1500 East Duarte Road, Duarte 91010, CA, USA
| | - Yuan Yuan
- Department of Medical Oncology and Molecular Therapeutics, City of Hope Comprehensive Cancer Center and Beckman Research Institute, 1500 East Duarte Road, Duarte 91010, CA, USA
| | - Susan E. Yost
- Department of Medical Oncology and Molecular Therapeutics, City of Hope Comprehensive Cancer Center and Beckman Research Institute, 1500 East Duarte Road, Duarte 91010, CA, USA
| | - Xuefei Li
- Department of Bioengineering and the Center for Theoretical Biological Physics, Rice University, Houston 77030, TX, USA
| | - Herbert Levine
- Department of Bioengineering and the Center for Theoretical Biological Physics, Rice University, Houston 77030, TX, USA
| | - Gurinder Atwal
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Peter Lee
- Cancer Immunotherapeutics & Tumor Immunology, City of Hope Comprehensive Cancer Center and Beckman Research Institute, 1500 East Duarte Road, Duarte 91010, CA, USA
| | - Clare C. Yu
- Department of Physics and Astronomy, University of California, Irvine 92697, CA, USA
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11
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Mambetsariev I, Mirzapoiazova T, Lennon F, Jolly MK, Li H, Nasser MW, Vora L, Kulkarni P, Batra SK, Salgia R. Small Cell Lung Cancer Therapeutic Responses Through Fractal Measurements: From Radiology to Mitochondrial Biology. J Clin Med 2019; 8:jcm8071038. [PMID: 31315252 PMCID: PMC6679065 DOI: 10.3390/jcm8071038] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 07/03/2019] [Accepted: 07/11/2019] [Indexed: 12/29/2022] Open
Abstract
Small cell lung cancer (SCLC) is an aggressive neuroendocrine disease with an overall 5 year survival rate of ~7%. Although patients tend to respond initially to therapy, therapy-resistant disease inevitably emerges. Unfortunately, there are no validated biomarkers for early-stage SCLC to aid in early detection. Here, we used readouts of lesion image characteristics and cancer morphology that were based on fractal geometry, namely fractal dimension (FD) and lacunarity (LC), as novel biomarkers for SCLC. Scanned tumors of patients before treatment had a high FD and a low LC compared to post treatment, and this effect was reversed after treatment, suggesting that these measurements reflect the initial conditions of the tumor, its growth rate, and the condition of the lung. Fractal analysis of mitochondrial morphology showed that cisplatin-treated cells showed a discernibly decreased LC and an increased FD, as compared with control. However, treatment with mdivi-1, the small molecule that attenuates mitochondrial division, was associated with an increase in FD as compared with control. These data correlated well with the altered metabolic functions of the mitochondria in the diseased state, suggesting that morphological changes in the mitochondria predicate the tumor’s future ability for mitogenesis and motogenesis, which was also observed on the CT scan images. Taken together, FD and LC present ideal tools to differentiate normal tissue from malignant SCLC tissue as a potential diagnostic biomarker for SCLC.
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Affiliation(s)
- Isa Mambetsariev
- City of Hope, Dept. of Medical Oncology and Therapeutics Research, Duarte, CA 91010, USA
| | - Tamara Mirzapoiazova
- City of Hope, Dept. of Medical Oncology and Therapeutics Research, Duarte, CA 91010, USA
| | | | - Mohit Kumar Jolly
- Center for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India
| | - Haiqing Li
- City of Hope, Center for Informatics, Duarte, CA 91010, USA
- City of Hope, Dept. of Computational & Quantitative Medicine, Duarte, CA 91010, USA
| | - Mohd W Nasser
- University of Nebraska Medical Center, Dept. of Biochemistry and Molecular Biology, Omaha, NE 68198, USA
| | - Lalit Vora
- City of Hope, Dept. of Diagnostic Radiology, Duarte, CA 91010, USA
| | - Prakash Kulkarni
- City of Hope, Dept. of Medical Oncology and Therapeutics Research, Duarte, CA 91010, USA
| | - Surinder K Batra
- University of Nebraska Medical Center, Dept. of Biochemistry and Molecular Biology, Omaha, NE 68198, USA
| | - Ravi Salgia
- City of Hope, Dept. of Medical Oncology and Therapeutics Research, Duarte, CA 91010, USA.
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12
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Metze K, Adam R, Florindo JB. The fractal dimension of chromatin - a potential molecular marker for carcinogenesis, tumor progression and prognosis. Expert Rev Mol Diagn 2019; 19:299-312. [DOI: 10.1080/14737159.2019.1597707] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Konradin Metze
- Department of Pathology, Faculty of Medical Sciences, State University of Campinas (UNICAMP), Campinas, Brazil
| | - Randall Adam
- Department of Pathology, Faculty of Medical Sciences, State University of Campinas (UNICAMP), Campinas, Brazil
| | - João Batista Florindo
- Department of Applied Mathematics, Institute of Mathematics, Statistics and Scientific Computing, State University of Campinas, Campinas, Brazil
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13
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Nuclear shape and orientation features from H&E images predict survival in early-stage estrogen receptor-positive breast cancers. J Transl Med 2018; 98:1438-1448. [PMID: 29959421 PMCID: PMC6214731 DOI: 10.1038/s41374-018-0095-7] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2018] [Revised: 04/23/2018] [Accepted: 05/07/2018] [Indexed: 02/07/2023] Open
Abstract
Early-stage estrogen receptor-positive (ER+) breast cancer (BCa) is the most common type of BCa in the United States. One critical question with these tumors is identifying which patients will receive added benefit from adjuvant chemotherapy. Nuclear pleomorphism (variance in nuclear shape and morphology) is an important constituent of breast grading schemes, and in ER+ cases, the grade is highly correlated with disease outcome. This study aimed to investigate whether quantitative computer-extracted image features of nuclear shape and orientation on digitized images of hematoxylin-stained and eosin-stained tissue of lymph node-negative (LN-), ER+ BCa could help stratify patients into discrete (<10 years short-term vs. >10 years long-term survival) outcome groups independent of standard clinical and pathological parameters. We considered a tissue microarray (TMA) cohort of 276 ER+, LN- patients comprising 150 patients with long-term and 126 patients with short-term overall survival, wherein 177 randomly chosen cases formed the modeling set, and 99 remaining cases the test set. Segmentation of individual nuclei was performed using multiresolution watershed; subsequently, 615 features relating to nuclear shape/texture and orientation disorder were extracted from each TMA spot. The Wilcoxon's rank-sum test identified the 15 most prognostic quantitative histomorphometric features within the modeling set. These features were then subsequently combined via a linear discriminant analysis classifier and evaluated on the test set to assign a probability of long-term vs. short-term disease-specific survival. In univariate survival analysis, patients identified by the image classifier as high risk had significantly poorer survival outcome: hazard ratio (95% confident interval) = 2.91(1.23-6.92), p = 0.02786. Multivariate analysis controlling for T-stage, histology grade, and nuclear grade showed the classifier to be independently predictive of poorer survival: hazard ratio (95% confident interval) = 3.17(0.33-30.46), p = 0.01039. Our results suggest that quantitative histomorphometric features of nuclear shape and orientation are strongly and independently predictive of patient survival in ER+, LN- BCa.
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Abstract
PURPOSE OF REVIEW There is confusion in all of healthcare, including oculofacial surgery, as to what is 'complex' and what is 'merely complicated'. Although in common usage, these terms tend to be interchangeable, the distinction is more than trivial. A different and somewhat unfamiliar toolset is needed to successfully navigate complex problems. This review will explore a methodology for the physician to understand what is complex in oculofacial surgery, the tools needed to optimize performance in a complex healthcare system and successfully manage patients with complex diseases. RECENT FINDINGS A specific understanding of complexity science in oculofacial surgery is only in its nascent beginnings at this point. Nevertheless, recent advances in closely related fields can provide concrete applications. The practice of oculofacial surgery is optimized within a healthcare network of supporting professionals. Moreover, a newer understanding of the 'complex' nature of disease common to oculofacial surgery, such as neoplasia and inflammation, will direct the physician to recognize the most appropriate therapies. SUMMARY Oculofacial surgery, like all of medicine, is a fluid mixture of problems that are complex and those that are merely complicated. As a different toolset is needed to deal with each, physicians need to recognize these differences and acquire those tools.
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Lu C, Lewis JS, Dupont WD, Plummer WD, Janowczyk A, Madabhushi A. An oral cavity squamous cell carcinoma quantitative histomorphometric-based image classifier of nuclear morphology can risk stratify patients for disease-specific survival. Mod Pathol 2017; 30:1655-1665. [PMID: 28776575 PMCID: PMC6128166 DOI: 10.1038/modpathol.2017.98] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 06/02/2017] [Accepted: 06/02/2017] [Indexed: 12/31/2022]
Abstract
Oral cavity squamous cell carcinoma is the most common type of head and neck carcinoma. Its incidence is increasing worldwide, and it is associated with major morbidity and mortality. It is often unclear which patients have aggressive, treatment refractory tumors vs those whose tumors will be more responsive to treatment. Better identification of patients with high- vs low-risk cancers could help provide more tailored treatment approaches and could improve survival rates while decreasing treatment-related morbidity. This study investigates computer-extracted image features of nuclear shape and texture on digitized images of H&E-stained tissue sections for risk stratification of oral cavity squamous cell carcinoma patients compared with standard clinical and pathologic parameters. With a tissue microarray cohort of 115 retrospectively identified oral cavity squamous cell carcinoma patients, 50 were randomly chosen as the modeling set, and the remaining 65 constituted the test set. Following nuclear segmentation and feature extraction, the Wilcoxon rank sum test was used to identify the five most prognostic quantitative histomorphometric features from the modeling set. These top ranked features were then combined via a machine learning classifier to construct the oral cavity histomorphometric-based image classifier (OHbIC). The classifier was then validated for its ability to risk stratify patients for disease-specific outcomes on the test set. On the test set, the classifier yielded an area under the receiver operating characteristic curve of 0.72 in distinguishing disease-specific outcomes. In univariate survival analysis, high-risk patients predicted by the classifier had significantly poorer disease-specific survival (P=0.0335). In multivariate analysis controlling for T/N-stage, resection margins, and smoking status, positive classifier results were independently predictive of poorer disease-specific survival: hazard ratio (95% confidence interval)=11.023 (2.62-46.38) and P=0.001. Our results suggest that quantitative histomorphometric features of local nuclear architecture derived from digitized H&E slides of oral cavity squamous cell carcinomas are independently predictive of patient survival.
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Affiliation(s)
- Cheng Lu
- College of Computer Science, Shaanxi Normal University, Xian, China
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, OH, USA
| | - James S Lewis
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Otolaryngology, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Pathology and Immunology, Washington University in St Louis, St Louis, MO, USA
- Department of Otolaryngology Head and Neck Surgery, Washington University in St Louis, St Louis, MO, USA
| | - William D Dupont
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - W Dale Plummer
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Andrew Janowczyk
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, OH, USA
| | - Anant Madabhushi
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, OH, USA
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Biomarkers in diagnosis and therapy of oral squamous cell carcinoma: A review of the literature. J Craniomaxillofac Surg 2017; 45:722-730. [DOI: 10.1016/j.jcms.2017.01.033] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 12/22/2016] [Accepted: 01/30/2017] [Indexed: 12/26/2022] Open
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17
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Abstract
Recent developments in studies of tumor heterogeneity have provoked new thoughts on cancer management. There is a desperate need to understand influence of the tumor microenvironment on cancer development and evolution. Applying principles and quantitative methods from ecology can suggest novel solutions to fulfil this need. We discuss spatial heterogeneity as a fundamental biological feature of the microenvironment, which has been largely ignored. Histological samples can provide spatial context of diverse cell types coexisting within the microenvironment. Advanced computer-vision techniques have been developed for spatial mapping of cells in histological samples. This has enabled the applications of experimental and analytical tools from ecology to cancer research, generating system-level knowledge of microenvironmental spatial heterogeneity. We focus on studies of immune infiltrate and tumor resource distribution, and highlight statistical approaches for addressing the emerging challenges based on these new approaches.
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Affiliation(s)
- Yinyin Yuan
- Centre for Evolution and Cancer and Division of Molecular Pathology, The Institute of Cancer Research, London; and Centre for Molecular Pathology, Royal Marsden Hospital, London
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