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Pang JMB, Byrne DJ, Bergin ART, Caramia F, Loi S, Gorringe KL, Fox SB. Spatial transcriptomics and the anatomical pathologist: Molecular meets morphology. Histopathology 2024; 84:577-586. [PMID: 37991396 DOI: 10.1111/his.15093] [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: 06/18/2023] [Revised: 10/23/2023] [Accepted: 10/26/2023] [Indexed: 11/23/2023]
Abstract
In recent years anatomical pathology has been revolutionised by the incorporation of molecular findings into routine diagnostic practice, and in some diseases the presence of specific molecular alterations are now essential for diagnosis. Spatial transcriptomics describes a group of technologies that provide up to transcriptome-wide expression profiling while preserving the spatial origin of the data, with many of these technologies able to provide these data using a single tissue section. Spatial transcriptomics allows expression profiling of highly specific areas within a tissue section potentially to subcellular resolution, and allows correlation of expression data with morphology, tissue type and location relative to other structures. While largely still research laboratory-based, several spatial transcriptomics methods have now achieved compatibility with formalin-fixed paraffin-embedded tissue (FFPE), allowing their use in diagnostic tissue samples, and with further development potentially leading to their incorporation in routine anatomical pathology practice. This mini review provides an overview of spatial transcriptomics methods, with an emphasis on platforms compatible with FFPE tissue, approaches to assess the data and potential applications in anatomical pathology practice.
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Affiliation(s)
- Jia-Min B Pang
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - David J Byrne
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Alice R T Bergin
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - Franco Caramia
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - Sherene Loi
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - Kylie L Gorringe
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - Stephen B Fox
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
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2
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Jahangir CA, Page DB, Broeckx G, Gonzalez CA, Burke C, Murphy C, Reis-Filho JS, Ly A, Harms PW, Gupta RR, Vieth M, Hida AI, Kahila M, Kos Z, van Diest PJ, Verbandt S, Thagaard J, Khiroya R, Abduljabbar K, Acosta Haab G, Acs B, Adams S, Almeida JS, Alvarado-Cabrero I, Azmoudeh-Ardalan F, Badve S, Baharun NB, Bellolio ER, Bheemaraju V, Blenman KR, Botinelly Mendonça Fujimoto L, Burgues O, Chardas A, Cheang MCU, Ciompi F, Cooper LA, Coosemans A, Corredor G, Dantas Portela FL, Deman F, Demaria S, Dudgeon SN, Elghazawy M, Fernandez-Martín C, Fineberg S, Fox SB, Giltnane JM, Gnjatic S, Gonzalez-Ericsson PI, Grigoriadis A, Halama N, Hanna MG, Harbhajanka A, Hart SN, Hartman J, Hewitt S, Horlings HM, Husain Z, Irshad S, Janssen EA, Kataoka TR, Kawaguchi K, Khramtsov AI, Kiraz U, Kirtani P, Kodach LL, Korski K, Akturk G, Scott E, Kovács A, Laenkholm AV, Lang-Schwarz C, Larsimont D, Lennerz JK, Lerousseau M, Li X, Madabhushi A, Maley SK, Manur Narasimhamurthy V, Marks DK, McDonald ES, Mehrotra R, Michiels S, Kharidehal D, 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, Rajpoot NM, Rapoport BL, Rau TT, Ribeiro JM, Rimm D, Vincent-Salomon A, Saltz J, Sayed S, Hytopoulos E, Mahon 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, Verghese GE, Viale G, Wahab N, Walter T, Waumans Y, Wen HY, Yang W, Yuan Y, Bartlett J, Loibl S, Denkert C, Savas P, Loi S, Specht Stovgaard E, Salgado R, Gallagher WM, Rahman A. Image-based multiplex immune profiling of cancer tissues: translational implications. A report of the International Immuno-oncology Biomarker Working Group on Breast Cancer. J Pathol 2024; 262:271-288. [PMID: 38230434 DOI: 10.1002/path.6238] [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: 06/15/2023] [Accepted: 11/17/2023] [Indexed: 01/18/2024]
Abstract
Recent advances in the field of immuno-oncology have brought transformative changes in the management of cancer patients. The immune profile of tumours has been found to have key value in predicting disease prognosis and treatment response in various cancers. Multiplex immunohistochemistry and immunofluorescence have emerged as potent tools for the simultaneous detection of multiple protein biomarkers in a single tissue section, thereby expanding opportunities for molecular and immune profiling while preserving tissue samples. By establishing the phenotype of individual tumour cells when distributed within a mixed cell population, the identification of clinically relevant biomarkers with high-throughput multiplex immunophenotyping of tumour samples has great potential to guide appropriate treatment choices. Moreover, the emergence of novel multi-marker imaging approaches can now provide unprecedented insights into the tumour microenvironment, including the potential interplay between various cell types. However, there are significant challenges to widespread integration of these technologies in daily research and clinical practice. This review addresses the challenges and potential solutions within a structured framework of action from a regulatory and clinical trial perspective. New developments within the field of immunophenotyping using multiplexed tissue imaging platforms and associated digital pathology are also described, with a specific focus on translational implications across different subtypes of cancer. © 2024 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Chowdhury Arif Jahangir
- UCD School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin, Dublin, Ireland
| | - David B Page
- Earle A Chiles Research Institute, Providence Cancer Institute, Portland, OR, USA
| | - Glenn Broeckx
- Department of Pathology PA2, GZA-ZNA Hospitals, Antwerp, Belgium
- Centre for Oncological Research (CORE), MIPPRO, Faculty of Medicine, Antwerp University, Antwerp, Belgium
| | - Claudia A Gonzalez
- UCD School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin, Dublin, Ireland
| | - Caoimbhe Burke
- UCD School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin, Dublin, Ireland
| | - Clodagh Murphy
- UCD School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin, Dublin, Ireland
| | - Jorge S Reis-Filho
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Amy Ly
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Paul W Harms
- Departments of Pathology and Dermatology, University of Michigan, Ann Arbor, MI, USA
| | - Rajarsi R Gupta
- Department of Biomedical Informatics, Stony Brook University, Stony Brook, NY, USA
| | - Michael Vieth
- Institute of Pathology, Klinikum Bayreuth GmbH, Friedrich-Alexander-University Erlangen-Nuremberg, Bayreuth, Germany
| | - Akira I Hida
- Department of Pathology, Matsuyama Shimin Hospital, Matsuyama, Japan
| | - Mohamed Kahila
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Zuzana Kos
- Department of Pathology and Laboratory Medicine, University of British Columbia, BC Cancer, Vancouver, British Columbia, Canada
| | - Paul J van Diest
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
- Johns Hopkins Oncology Center, Baltimore, MD, USA
| | - Sara Verbandt
- Digestive Oncology, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Jeppe Thagaard
- Technical University of Denmark, Kgs. Lyngby, Denmark
- Visiopharm A/S, Hørsholm, Denmark
| | - Reena Khiroya
- Department of Cellular Pathology, University College Hospital, London, UK
| | - 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
- Department of Clinical Pathology and Cancer Diagnostics, Karolinska University Hospital, Stockholm, Sweden
| | - Sylvia Adams
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
- Department of Medicine, NYU Grossman School of Medicine, Manhattan, NY, USA
| | - Jonas S Almeida
- Division of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute (NCI), Rockville, MD, USA
| | | | | | - Sunil Badve
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Emory University Winship Cancer Institute, Atlanta, GA, USA
| | | | - Enrique R Bellolio
- Departamento de Anatomía Patológica, Facultad de Medicina, Universidad de La Frontera, Temuco, Chile
| | | | - Kim Rm Blenman
- Department of Internal Medicine Section of Medical Oncology and Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
- Department of Computer Science, Yale School of Engineering and Applied Science, New Haven, CT, USA
| | | | - Octavio Burgues
- Pathology Department, Hospital Cliníco Universitario de Valencia/Incliva, Valencia, Spain
| | - Alexandros Chardas
- Department of Pathobiology & Population Sciences, The Royal Veterinary College, London, UK
| | - Maggie Chon U Cheang
- Head of Integrative Genomics Analysis in Clinical Trials, ICR-CTSU, Division of Clinical Studies, The Institute of Cancer Research, London, UK
| | - Francesco Ciompi
- Department of Pathology, Radboud University Medical Center, 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 PA2, 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
- Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
| | - Mahmoud Elghazawy
- University of Surrey, Guildford, UK
- Ain Shams University, Cairo, Egypt
| | - Claudio Fernandez-Martín
- Instituto Universitario de Investigación en Tecnología Centrada en el Ser Humano, 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
- Pathology, Peter MacCallum Cancer Centre and Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | | | - Sacha Gnjatic
- Department of Oncological Sciences, Medicine Hem/Onc, and Pathology, Tisch Cancer Institute - Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Anita Grigoriadis
- Cancer Bioinformatics, Faculty of Life Sciences and Medicine, School of Cancer & Pharmaceutical Sciences, King's College London, London, UK
- The Breast Cancer Now Research Unit, Faculty of Life Sciences and Medicine, School of Cancer and Pharmaceutical Sciences, King's College London, London, UK
| | - Niels Halama
- Department of Translational Immunotherapy, German Cancer Research Center, Heidelberg, Germany
| | | | | | - Steven N Hart
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Johan Hartman
- Department of Clinical Pathology and Cancer Diagnostics, Karolinska University Hospital, Stockholm, Sweden
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Stephen Hewitt
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Hugo M Horlings
- Division of Pathology, Netherlands Cancer Institute (NKI), Amsterdam, The Netherlands
| | | | - Sheeba Irshad
- King's College London & Guys & 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
| | | | - Kosuke Kawaguchi
- Department of Breast Surgery, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Andrey I Khramtsov
- Department of 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
- 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
| | - Guray Akturk
- Translational Molecular Biomarkers, Merck & Co., Inc., Kenilworth, NJ, USA
| | - Ely Scott
- Translational Medicine, Bristol Myers Squibb, Princeton, NJ, USA
| | - Anikó Kovács
- Department of Clinical Pathology, Sahlgrenska University Hospital, Gothenburg, Sweden
- Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Anne-Vibeke Laenkholm
- Department of Surgical Pathology, Zealand University Hospital, Roskilde, Denmark
- Department of Surgical Pathology, University of Copenhagen, Copenhagen, Denmark
| | - Corinna Lang-Schwarz
- Institute of Pathology, Klinikum Bayreuth GmbH, Friedrich-Alexander-University Erlangen-Nuremberg, Bayreuth, Germany
| | - Denis Larsimont
- 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
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA, USA
| | - Anant Madabhushi
- Department of 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 Genomic Atlas, Pune, India
- Centre for Health, Innovation and Policy Foundation, Noida, India
| | - Stefan Michiels
- Office of Biostatistics and Epidemiology, Gustave Roussy, Oncostat U1018, Inserm, University Paris-Saclay, Ligue Contre le Cancer labeled Team, Villejuif, France
| | - Durga Kharidehal
- Department of Pathology, Narayana Medical College and Hospital, Nellore, India
| | - 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, Washington, USA
| | - David A Moore
- CRUK Lung Cancer Centre of Excellence, UCL and Cellular Pathology Department, 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
- Service de Pathologie et Biopathologie, Centre Jean PERRIN, INSERM U1240 Imagerie Moléculaire et Stratégies Théranostiques (IMoST), Université Clermont Auvergne, Clermont-Ferrand, France
| | - Rashindrie D Perera
- School of Electrical, Mechanical and Infrastructure Engineering, University of Melbourne, Melbourne, Victoria, Australia
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Christopher J Pinard
- Radiogenomics Laboratory, Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada
- Department of Clinical Studies, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
- Department of Oncology, Lakeshore Animal Health Partners, Mississauga, Ontario, Canada
- Centre for Advancing Responsible and Ethical Artificial Intelligence (CARE-AI), University of Guelph, Guelph, Ontario, 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
| | - Lajos Pusztai
- Yale Cancer Center, Yale University, New Haven, CT, USA
- Department of Medical Oncology, Yale School of Medicine, Yale University, New Haven, CT, USA
| | | | - Bernardo Leon Rapoport
- The Medical Oncology Centre of Rosebank, 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, Germany
| | | | - 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
| | - Joel Saltz
- Department of Biomedical Informatics, Stony Brook Medicine, New York, NY, USA
| | - Shahin Sayed
- Department of Pathology, Aga Khan University, Nairobi, Kenya
| | - Evangelos Hytopoulos
- Department of Pathology, Aga Khan University, Nairobi, Kenya
- iRhythm Technologies Inc., San Francisco, CA, USA
| | - Sarah Mahon
- Mater Misericordiae University Hospital, Dublin, Ireland
| | - 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 (H.U.B), Université Libre de Bruxelles (ULB), Brussels, Belgium
- Medical Oncology Department, Institut Jules Bordet, Hôpital Universitaire de Bruxelles (H.U.B), Université Libre de Bruxelles (ULB), 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 "Iuliu 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
- AI for Oncology Lab, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | | | - Trine Tramm
- Department of Pathology, 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, Canada
| | - Jeroen van der Laak
- Head of Integrative Genomics Analysis in Clinical Trials, ICR-CTSU, Division of Clinical Studies, The Institute of Cancer Research, London, UK
| | - Gregory E Verghese
- Cancer Bioinformatics, Faculty of Life Sciences and Medicine, School of Cancer & Pharmaceutical Sciences, King's College London, London, UK
- The Breast Cancer Now Research Unit, Faculty of Life Sciences and Medicine, School of Cancer and Pharmaceutical Sciences, King's College London, London, UK
| | - Giuseppe Viale
- Department of Pathology, European Institute of Oncology & University of Milan, Milan, Italy
| | - 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
- Department of Translational Molecular Pathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | - Sibylle Loibl
- Department of Medicine and Research, German Breast Group, Neu-Isenburg, 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, Victoria, Australia
- The Sir Peter MacCallum Department of Medical Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Sherene Loi
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia
| | | | - Roberto Salgado
- Department of Pathology PA2, GZA-ZNA Hospitals, Antwerp, Belgium
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - William M Gallagher
- UCD School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin, Dublin, Ireland
| | - Arman Rahman
- UCD School of Medicine, UCD Conway Institute, University College Dublin, Dublin, Ireland
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Andrew EC, Lewin J, Desai J, Orme L, Hamilton A, Bae S, Zhu W, Nicolson S, Varghese LN, Mitchell CB, Vissers JHA, Xu H, Grimmond SM, Fox SB, Luen SJ. Clinical Impact of Comprehensive Molecular Profiling in Adolescents and Young Adults with Sarcoma. J Pers Med 2024; 14:128. [PMID: 38392562 PMCID: PMC10890624 DOI: 10.3390/jpm14020128] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/13/2024] [Accepted: 01/18/2024] [Indexed: 02/24/2024] Open
Abstract
Sarcomas are a heterogenous group of tumours that commonly carry poor prognosis with limited therapeutic options. Adolescents and young adults (AYAs) with sarcoma are a unique and understudied patient population that have only achieved modest survival gains compared to other groups. We present our institutional experience of AYAs with sarcoma who underwent comprehensive molecular profiling (CMP) via either large-panel targeted DNA sequencing or whole genome and transcriptome sequencing and evaluated the feasibility and clinical impact of this approach. Genomic variants detected were determined to be clinically relevant and actionable following evaluation by the Molecular Tumour Board. Clinicians provided feedback regarding the utility of testing three months after reporting. Twenty-five patients who were recruited for CMP are included in this analysis. The median time from consent to final molecular report was 45 days (interquartile range: 37-57). Potentially actionable variants were detected for 14 patients (56%), and new treatment recommendations were identified for 12 patients (48%). Pathogenic germline variants were identified in three patients (12%), and one patient had a change in diagnosis. The implementation of CMP for AYAs with sarcoma is clinically valuable, feasible, and should be increasingly integrated into routine clinical practice as technologies and turnaround times continue to improve.
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Affiliation(s)
- Eden C Andrew
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Parkville, VIC 3000, Australia
- Children's Cancer Centre, Royal Children's Hospital, Parkville, VIC 3052, Australia
- Victorian Adolescent and Young Adult Cancer Service, Parkville, VIC 3000, Australia
| | - Jeremy Lewin
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Parkville, VIC 3000, Australia
- Victorian Adolescent and Young Adult Cancer Service, Parkville, VIC 3000, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Jayesh Desai
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Parkville, VIC 3000, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Lisa Orme
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Parkville, VIC 3000, Australia
- Children's Cancer Centre, Royal Children's Hospital, Parkville, VIC 3052, Australia
- Victorian Adolescent and Young Adult Cancer Service, Parkville, VIC 3000, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC 3010, Australia
- Department of Paediatrics, The University of Melbourne, Melbourne, VIC 3052, Australia
| | - Anne Hamilton
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Parkville, VIC 3000, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Susie Bae
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Parkville, VIC 3000, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Wenying Zhu
- Centre for Cancer Research and Department of Clinical Pathology, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Shannon Nicolson
- Centre for Cancer Research and Department of Clinical Pathology, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Leila N Varghese
- Centre for Cancer Research and Department of Clinical Pathology, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Camilla B Mitchell
- Centre for Cancer Research and Department of Clinical Pathology, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Joseph H A Vissers
- Centre for Cancer Research and Department of Clinical Pathology, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Huiling Xu
- Department of Pathology and Cancer Research Division, Peter MacCallum Cancer Centre, Parkville, VIC 3000, Australia
- Department of Clinical Pathology, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Sean M Grimmond
- Centre for Cancer Research and Department of Clinical Pathology, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Stephen B Fox
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC 3010, Australia
- Department of Pathology and Cancer Research Division, Peter MacCallum Cancer Centre, Parkville, VIC 3000, Australia
| | - Stephen J Luen
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Parkville, VIC 3000, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC 3010, Australia
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4
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Thagaard J, Broeckx G, Page DB, Jahangir CA, Verbandt S, Kos Z, Gupta R, Khiroya R, Abduljabbar K, Acosta Haab G, Acs B, Akturk G, Almeida JS, Alvarado‐Cabrero I, Amgad M, Azmoudeh‐Ardalan F, Badve S, Baharun NB, Balslev E, Bellolio ER, Bheemaraju V, Blenman KRM, Botinelly Mendonça Fujimoto L, Bouchmaa N, Burgues O, Chardas A, Chon U Cheang M, Ciompi F, Cooper LAD, Coosemans A, Corredor G, Dahl AB, Dantas Portela FL, Deman F, Demaria S, Doré Hansen J, Dudgeon SN, Ebstrup T, Elghazawy M, Fernandez‐Martín C, Fox SB, Gallagher WM, Giltnane JM, Gnjatic S, Gonzalez‐Ericsson PI, Grigoriadis A, Halama N, Hanna MG, Harbhajanka A, Hart SN, Hartman J, Hauberg S, 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 A, Lang‐Schwarz C, Larsimont D, Lennerz JK, Lerousseau M, Li X, Ly A, Madabhushi A, Maley SK, Manur Narasimhamurthy V, 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, Roslind A, Vincent‐Salomon A, Salto‐Tellez M, Saltz J, Sayed S, Scott E, Siziopikou KP, Sotiriou C, Stenzinger A, Sughayer MA, Sur D, Fineberg S, 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, Zin RM, Adams S, Bartlett J, Loibl S, Denkert C, Savas P, Loi S, Salgado R, Specht Stovgaard E. Pitfalls in machine learning-based assessment of tumor-infiltrating lymphocytes in breast cancer: A report of the International Immuno-Oncology Biomarker Working Group on Breast Cancer. J Pathol 2023; 260:498-513. [PMID: 37608772 PMCID: PMC10518802 DOI: 10.1002/path.6155] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [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: 04/21/2023] [Accepted: 06/07/2023] [Indexed: 08/24/2023]
Abstract
The clinical significance of the tumor-immune interaction in breast cancer is now established, and tumor-infiltrating lymphocytes (TILs) have emerged as predictive and prognostic biomarkers for patients with triple-negative (estrogen receptor, progesterone receptor, and HER2-negative) breast cancer and HER2-positive breast cancer. How computational assessments of TILs might complement manual TIL assessment in trial and daily practices is currently debated. Recent efforts to use machine learning (ML) to automatically evaluate TILs have shown promising results. We review state-of-the-art approaches and identify pitfalls and challenges of automated TIL evaluation by studying the root cause of ML discordances in comparison to manual TIL quantification. We categorize our findings into four main topics: (1) technical slide issues, (2) ML and image analysis aspects, (3) data challenges, and (4) validation issues. The main reason for discordant assessments is the inclusion of false-positive areas or cells identified by performance on certain tissue patterns or design choices in the computational implementation. To aid the adoption of ML for TIL assessment, we provide an in-depth discussion of ML and image analysis, including validation issues that need to be considered before reliable computational reporting of TILs can be incorporated into the trial and routine clinical management of patients with triple-negative breast cancer. © 2023 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Jeppe Thagaard
- Technical University of DenmarkKongens LyngbyDenmark
- Visiopharm A/SHørsholmDenmark
| | - Glenn Broeckx
- Department of PathologyGZA‐ZNA HospitalsAntwerpBelgium
- Centre for Oncological Research (CORE), MIPPRO, Faculty of MedicineAntwerp UniversityAntwerpBelgium
| | - David B Page
- Earle A Chiles Research InstituteProvidence Cancer InstitutePortlandORUSA
| | - Chowdhury Arif Jahangir
- UCD School of Biomolecular and Biomedical Science, UCD Conway InstituteUniversity College DublinDublinIreland
| | - Sara Verbandt
- Digestive Oncology, Department of OncologyKU LeuvenLeuvenBelgium
| | - Zuzana Kos
- Department of Pathology and Laboratory MedicineBC Cancer Vancouver Centre, University of British ColumbiaVancouverBritish ColumbiaCanada
| | - Rajarsi Gupta
- Department of Biomedical InformaticsStony Brook UniversityStony BrookNYUSA
| | - Reena Khiroya
- Department of Cellular PathologyUniversity College Hospital LondonLondonUK
| | | | | | - Balazs Acs
- Department of Oncology and PathologyKarolinska InstitutetStockholmSweden
- Department of Clinical Pathology and Cancer DiagnosticsKarolinska University HospitalStockholmSweden
| | - Guray Akturk
- Translational Molecular Biomarkers, Merck & Co IncRahwayNJUSA
| | - Jonas S Almeida
- Division of Cancer Epidemiology and Genetics (DCEG)National Cancer Institute (NCI)Rockville, MDUSA
| | | | - Mohamed Amgad
- Department of PathologyNorthwestern University Feinberg School of MedicineChicagoILUSA
| | | | - Sunil Badve
- Department of Pathology and Laboratory Medicine, Emory University School of MedicineEmory University Winship Cancer InstituteAtlantaGAUSA
| | | | - Eva Balslev
- Department of PathologyHerlev and Gentofte HospitalHerlevDenmark
| | - Enrique R Bellolio
- Departamento de Anatomía Patológica, Facultad de MedicinaUniversidad de La FronteraTemucoChile
| | | | - Kim RM Blenman
- Department of Internal Medicine Section of Medical Oncology and Yale Cancer CenterYale School of MedicineNew HavenCTUSA
- Department of Computer ScienceYale School of Engineering and Applied ScienceNew HavenCTUSA
| | | | - Najat Bouchmaa
- Institute of Biological Sciences, Faculty of Medical SciencesMohammed VI Polytechnic University (UM6P)Ben‐GuerirMorocco
| | - Octavio Burgues
- Pathology DepartmentHospital Cliníco Universitario de Valencia/InclivaValenciaSpain
| | - Alexandros Chardas
- Department of Pathobiology & Population SciencesThe Royal Veterinary CollegeLondonUK
| | - Maggie Chon U Cheang
- Head of Integrative Genomics Analysis in Clinical Trials, ICR‐CTSU, Division of Clinical StudiesThe Institute of Cancer ResearchLondonUK
| | - Francesco Ciompi
- Radboud University Medical CenterDepartment of PathologyNijmegenThe Netherlands
| | - Lee AD Cooper
- Department of PathologyNorthwestern Feinberg School of MedicineChicagoILUSA
| | - An Coosemans
- Department of Oncology, Laboratory of Tumor Immunology and ImmunotherapyKU LeuvenLeuvenBelgium
| | - Germán Corredor
- Biomedical Engineering DepartmentEmory UniversityAtlantaGAUSA
| | - Anders B Dahl
- Technical University of DenmarkKongens LyngbyDenmark
| | | | | | - Sandra Demaria
- Department of Radiation OncologyWeill Cornell MedicineNew YorkNYUSA
- Department of Pathology and Laboratory MedicineWeill Cornell MedicineNew YorkNYUSA
| | | | - Sarah N Dudgeon
- Conputational Biology and BioinformaticsYale UniversityNew HavenCTUSA
| | | | | | - Claudio Fernandez‐Martín
- Instituto Universitario de Investigación en Tecnología Centrada en el Ser Humano, HUMAN‐techUniversitat Politècnica de ValènciaValenciaSpain
| | - Stephen B Fox
- Pathology, Peter MacCallum Cancer Centre and Sir Peter MacCallum Department of OncologyUniversity of MelbourneMelbourneVictoriaAustralia
| | - William M Gallagher
- UCD School of Biomolecular and Biomedical Science, UCD Conway InstituteUniversity College DublinDublinIreland
| | | | - Sacha Gnjatic
- Department of Oncological Sciences, Medicine Hem/Onc, and Pathology, Tisch Cancer Institute – Precision Immunology InstituteIcahn School of Medicine at Mount SinaiNew YorkNYUSA
| | | | - Anita Grigoriadis
- Cancer Bioinformatics, School of Cancer & Pharmaceutical Sciences, Faculty of Life Sciences and MedicineKing's College LondonLondonUK
- The Breast Cancer Now Research Unit, School of Cancer and Pharmaceutical Sciences, Faculty of Life Sciences and MedicineKing's College LondonLondonUK
| | - Niels Halama
- Department of Translational ImmunotherapyGerman Cancer Research CenterHeidelbergGermany
| | - Matthew G Hanna
- Department of PathologyMemorial Sloan Kettering Cancer CenterNew YorkUSA
| | | | - Steven N Hart
- Department of Laboratory Medicine and PathologyMayo ClinicRochester, MNUSA
| | - Johan Hartman
- Department of Oncology and PathologyKarolinska InstitutetStockholmSweden
- Department of Clinical Pathology and Cancer DiagnosticsKarolinska University HospitalStockholmSweden
| | - Søren Hauberg
- Technical University of DenmarkKongens LyngbyDenmark
| | - Stephen Hewitt
- Laboratory of Pathology, Center for Cancer Research, National Cancer InstituteNational Institutes of HealthBethesdaMDUSA
| | - Akira I Hida
- Department of PathologyMatsuyama Shimin HospitalMatsuyamaJapan
| | - Hugo M Horlings
- Division of PathologyNetherlands Cancer Institute (NKI)AmsterdamThe Netherlands
| | | | | | - Sheeba Irshad
- King's College London & Guy's & St Thomas’ NHS TrustLondonUK
| | - Emiel AM Janssen
- Department of PathologyStavanger University HospitalStavangerNorway
- Department of Chemistry, Bioscience and Environmental TechnologyUniversity of StavangerStavangerNorway
| | | | | | - Kosuke Kawaguchi
- Department of Breast SurgeryKyoto University Graduate School of MedicineKyotoJapan
| | | | - Andrey I Khramtsov
- Department of Pathology and Laboratory MedicineAnn & Robert H. Lurie Children's Hospital of ChicagoChicagoILUSA
| | - Umay Kiraz
- Department of PathologyStavanger University HospitalStavangerNorway
- Department of Chemistry, Bioscience and Environmental TechnologyUniversity of StavangerStavangerNorway
| | - Pawan Kirtani
- Department of HistopathologyAakash Healthcare Super Speciality HospitalNew DelhiIndia
| | - Liudmila L Kodach
- Department of PathologyNetherlands Cancer Institute – Antoni van Leeuwenhoek HospitalAmsterdamThe Netherlands
| | - Konstanty Korski
- Data, Analytics and Imaging, Product DevelopmentF. Hoffmann‐La Roche AGBaselSwitzerland
| | - Anikó Kovács
- Department of Clinical PathologySahlgrenska University HospitalGothenburgSweden
- Institute of Biomedicine, Sahlgrenska AcademyUniversity of GothenburgGothenburgSweden
| | - Anne‐Vibeke Laenkholm
- Department of Surgical PathologyZealand University HospitalRoskildeDenmark
- Department of Surgical PathologyUniversity of CopenhagenCopenhagenDenmark
| | - Corinna Lang‐Schwarz
- Institute of Pathology, Klinikum Bayreuth GmbHFriedrich‐Alexander‐University Erlangen‐NurembergBayreuthGermany
| | - Denis Larsimont
- Institut Jules BordetUniversité Libre de BruxellesBrusselsBelgium
| | - Jochen K Lennerz
- Center for Integrated DiagnosticsMassachusetts General Hospital/Harvard Medical SchoolBostonMAUSA
| | - Marvin Lerousseau
- Centre for Computational Biology (CBIO)Mines Paris, PSL UniversityParisFrance
- Institut CuriePSL UniversityParisFrance
- INSERMParisFrance
| | - Xiaoxian Li
- Department of Pathology and Laboratory MedicineEmory UniversityAtlantaGAUSA
| | - Amy Ly
- Department of PathologyMassachusetts General HospitalBostonMAUSA
| | - Anant Madabhushi
- Department of Biomedical Engineering, Radiology and Imaging Sciences, Biomedical Informatics, PathologyGeorgia Institute of Technology and Emory UniversityAtlantaGAUSA
| | - Sai K Maley
- NRG Oncology/NSABP FoundationPittsburghPAUSA
| | | | | | - Elizabeth S McDonald
- Breast Cancer Translational Research GroupUniversity of PennsylvaniaPhiladelphiaPAUSA
| | - Ravi Mehrotra
- Indian Cancer Genomic AtlasPuneIndia
- Centre for Health, Innovation and Policy FoundationNoidaIndia
| | - Stefan Michiels
- Office of Biostatistics and Epidemiology, Gustave Roussy, Oncostat U1018, InsermUniversity Paris‐Saclay, Ligue Contre le Cancer labeled TeamVillejuifFrance
| | - Fayyaz ul Amir Afsar Minhas
- Tissue Image Analytics Centre, Warwick Cancer Research Centre, PathLAKE Consortium, Department of Computer ScienceUniversity of WarwickCoventryUK
| | - Shachi Mittal
- Department of Chemical Engineering, Department of Laboratory Medicine and PathologyUniversity of WashingtonSeattle, WAUSA
| | - David A Moore
- CRUK Lung Cancer Centre of Excellence, UCL and Cellular Pathology DepartmentUCLHLondonUK
| | - Shamim Mushtaq
- Department of BiochemistryZiauddin UniversityKarachiPakistan
| | - Hussain Nighat
- Pathology and Laboratory MedicineAll India Institute of Medical sciencesRaipurIndia
| | - Thomas Papathomas
- Institute of Metabolism and Systems ResearchUniversity of BirminghamBirminghamUK
- Department of Clinical PathologyDrammen Sykehus, Vestre Viken HFDrammenNorway
| | - Frederique Penault‐Llorca
- Centre Jean Perrin, Université Clermont Auvergne, INSERM, U1240 Imagerie Moléculaire et Stratégies ThéranostiquesClermont FerrandFrance
| | - Rashindrie D Perera
- School of Electrical, Mechanical and Infrastructure EngineeringUniversity of MelbourneMelbourneVictoriaAustralia
- Division of Cancer ResearchPeter MacCallum Cancer CentreMelbourneVictoriaAustralia
| | - Christopher J Pinard
- Radiogenomics LaboratorySunnybrook Health Sciences CentreTorontoOntarioCanada
- Department of Clinical Studies, Ontario Veterinary CollegeUniversity of GuelphGuelphOntarioCanada
- Department of OncologyLakeshore Animal Health PartnersMississaugaOntarioCanada
- Centre for Advancing Responsible and Ethical Artificial Intelligence (CARE‐AI)University of GuelphGuelphOntarioCanada
| | | | - Giancarlo Pruneri
- Department of Pathology and Laboratory MedicineFondazione IRCCS Istituto Nazionale dei TumoriMilanItaly
- Faculty of Medicine and SurgeryUniversity of MilanMilanItaly
| | - Lajos Pusztai
- Yale Cancer CenterYale UniversityNew HavenCTUSA
- Department of Medical Oncology, Yale School of MedicineYale UniversityNew HavenCTUSA
| | - Arman Rahman
- UCD School of Biomolecular and Biomedical Science, UCD Conway InstituteUniversity College DublinDublinIreland
| | | | - Bernardo Leon Rapoport
- The Medical Oncology Centre of RosebankJohannesburgSouth Africa
- Department of Immunology, Faculty of Health SciencesUniversity of PretoriaPretoriaSouth Africa
| | - Tilman T Rau
- Institute of PathologyUniversity Hospital Düsseldorf and Heinrich‐Heine‐University DüsseldorfDüsseldorfGermany
| | - Jorge S Reis‐Filho
- Department of Pathology and Laboratory MedicineMemorial Sloan Kettering Cancer CenterNew YorkNYUSA
| | - Joana M Ribeiro
- Département de Médecine OncologiqueGustave RoussyVillejuifFrance
| | - David Rimm
- Department of PathologyYale University School of MedicineNew HavenCTUSA
- Department of MedicineYale University School of MedicineNew HavenCTUSA
| | - Anne Roslind
- Department of PathologyHerlev and Gentofte HospitalHerlevDenmark
| | - Anne Vincent‐Salomon
- Department of Diagnostic and Theranostic Medicine, Institut CurieUniversity Paris‐Sciences et LettresParisFrance
| | - Manuel Salto‐Tellez
- Integrated Pathology UnitThe Institute of Cancer ResearchLondonUK
- Precision Medicine CentreQueen's University BelfastBelfastUK
| | - Joel Saltz
- Department of Biomedical InformaticsStony Brook UniversityStony BrookNYUSA
| | - Shahin Sayed
- Department of PathologyAga Khan UniversityNairobiKenya
| | - Ely Scott
- Translational PathologyTranslational Sciences and Diagnostics/Translational Medicine/R&D, Bristol Myers SquibbPrincetonNJUSA
| | - Kalliopi P Siziopikou
- Department of Pathology, Section of Breast PathologyNorthwestern University Feinberg School of MedicineChicagoILUSA
| | - Christos Sotiriou
- Breast Cancer Translational Research Laboratory J.‐C. Heuson, Institut Jules Bordet, Hôpital Universitaire de Bruxelles (HUB)Université Libre de Bruxelles (ULB)BrusselsBelgium
- Medical Oncology Department, Institut Jules Bordet, Hôpital Universitaire de Bruxelles (HUB)Université Libre de Bruxelles (ULB)BrusselsBelgium
| | - Albrecht Stenzinger
- Institute of PathologyUniversity Hospital HeidelbergHeidelbergGermany
- Centers for Personalized Medicine (ZPM)HeidelbergGermany
| | | | - Daniel Sur
- Department of Medical OncologyUniversity of Medicine and Pharmacy “Iuliu Hatieganu”Cluj‐NapocaRomania
| | - Susan Fineberg
- Montefiore Medical CenterBronxNYUSA
- Albert Einstein College of MedicineBronxNYUSA
| | - Fraser Symmans
- University of Texas MD Anderson Cancer CenterHoustonTXUSA
| | | | | | - Sabine Tejpar
- Digestive Oncology, Department of OncologyKU LeuvenLeuvenBelgium
| | - Jonas Teuwen
- AI for Oncology Lab, The Netherlands Cancer InstituteAmsterdamThe Netherlands
| | | | - Trine Tramm
- Department of PathologyAarhus University HospitalAarhusDenmark
- Institute of Clinical MedicineAarhus UniversityAarhusDenmark
| | - William T Tran
- Department of Radiation OncologyUniversity of Toronto and Sunnybrook Health Sciences CentreTorontoOntarioCanada
| | - Jeroen van der Laak
- Department of PathologyRadboud University Medical CenterNijmegenThe Netherlands
| | - Paul J van Diest
- Department of PathologyUniversity Medical Center UtrechtThe Netherlands
- Johns Hopkins Oncology CenterBaltimoreMDUSA
| | - Gregory E Verghese
- Cancer Bioinformatics, School of Cancer & Pharmaceutical Sciences, Faculty of Life Sciences and MedicineKing's College LondonLondonUK
- The Breast Cancer Now Research Unit, School of Cancer and Pharmaceutical Sciences, Faculty of Life Sciences and MedicineKing's College LondonLondonUK
| | - Giuseppe Viale
- Department of PathologyEuropean Institute of OncologyMilanItaly
- Department of PathologyUniversity of MilanMilanItaly
| | - Michael Vieth
- Institute of Pathology, Klinikum Bayreuth GmbHFriedrich‐Alexander‐University Erlangen‐NurembergBayreuthGermany
| | - Noorul Wahab
- Tissue Image Analytics Centre, Department of Computer ScienceUniversity of WarwickCoventryUK
| | - Thomas Walter
- Centre for Computational Biology (CBIO)Mines Paris, PSL UniversityParisFrance
- Institut CuriePSL UniversityParisFrance
- INSERMParisFrance
| | | | - Hannah Y Wen
- Department of PathologyMemorial Sloan Kettering Cancer CenterNew YorkUSA
| | - Wentao Yang
- Fudan Medical University Shanghai Cancer CenterShanghaiPR China
| | - Yinyin Yuan
- Department of Translational Molecular Pathology, Division of Pathology and Laboratory MedicineThe University of Texas MD Anderson Cancer CenterHoustonTXUSA
| | - Reena Md Zin
- Department of Pathology, Faculty of MedicineUniversiti Kebangsaan MalaysiaKuala LumpurMalaysia
| | - Sylvia Adams
- Perlmutter Cancer CenterNYU Langone HealthNew YorkNYUSA
- Department of MedicineNYU Grossman School of MedicineManhattanNYUSA
| | | | - Sibylle Loibl
- Department of Medicine and ResearchGerman Breast GroupNeu‐IsenburgGermany
| | - Carsten Denkert
- Institut für PathologiePhilipps‐Universität Marburg und Universitätsklinikum MarburgMarburgGermany
| | - Peter Savas
- Division of Cancer ResearchPeter MacCallum Cancer CentreMelbourneVictoriaAustralia
- The Sir Peter MacCallum Department of Medical OncologyUniversity of MelbourneMelbourneVictoriaAustralia
| | - Sherene Loi
- Division of Cancer ResearchPeter MacCallum Cancer CentreMelbourneVictoriaAustralia
- The Sir Peter MacCallum Department of Medical OncologyUniversity of MelbourneMelbourneVictoriaAustralia
| | - Roberto Salgado
- Department of PathologyGZA‐ZNA HospitalsAntwerpBelgium
- Division of Cancer ResearchPeter MacCallum Cancer CentreMelbourneVictoriaAustralia
| | - Elisabeth Specht Stovgaard
- Department of PathologyHerlev and Gentofte HospitalHerlevDenmark
- Department of Clinical MedicineUniversity of CopenhagenCopenhagenDenmark
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5
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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 KR, Botinelly Mendonça Fujimoto L, Bouchmaa N, Burgues O, Cheang MCU, Ciompi F, Cooper LA, Coosemans A, Corredor G, Dantas Portela FL, Deman F, Demaria S, Dudgeon SN, Elghazawy M, Ely S, Fernandez-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 EA, 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, Larsimont D, Lennerz JK, Lerousseau M, Li X, Ly A, Madabhushi A, Maley SK, Manur Narasimhamurthy V, 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 DOI: 10.1002/path.6165] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [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: 06/01/2023] [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, Hørsholm, 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 Anatomía 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/Incliva, 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 Fernandez-Martín
- Instituto Universitario de Investigación en Tecnología Centrada en el Ser Humano, 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/Onc, 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
- King's 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 Larsimont
- 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 U1018, 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
| | - Lajos 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 of Rosebank, 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 "Iuliu 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
- AI 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, Klinikum 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-Isenburg, 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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Takano EA, Younes MM, Meehan K, Spalding L, Yan M, Allan P, Fox SB, Redfern A, Clouston D, Giles GG, Christie EL, Anderson RL, Zethoven M, Phillips KA, Gorringe K, Britt KL. Estrogen receptor beta expression in triple negative breast cancers is not associated with recurrence or survival. BMC Cancer 2023; 23:459. [PMID: 37208678 DOI: 10.1186/s12885-023-10795-5] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 03/31/2023] [Indexed: 05/21/2023] Open
Abstract
BACKGROUND Triple negative BCa (TNBC) is defined by a lack of expression of estrogen (ERα), progesterone (PgR) receptors and human epidermal growth factor receptor 2 (HER2) as assessed by protein expression and/or gene amplification. It makes up ~ 15% of all BCa and often has a poor prognosis. TNBC is not treated with endocrine therapies as ERα and PR negative tumors in general do not show benefit. However, a small fraction of the true TNBC tumors do show tamoxifen sensitivity, with those expressing the most common isoform of ERβ1 having the most benefit. Recently, the antibodies commonly used to assess ERβ1 in TNBC have been found to lack specificity, which calls into question available data regarding the proportion of TNBC that express ERβ1 and any relationship to clinical outcome. METHODS To confirm the true frequency of ERβ1 in TNBC we performed robust ERβ1 immunohistochemistry using the specific antibody CWK-F12 ERβ1 on 156 primary TNBC cancers from patients with a median of 78 months (range 0.2-155 months) follow up. RESULTS We found that high expression of ERβ1 was not associated with increased recurrence or survival when assessed as percentage of ERβ1 positive tumor cells or as Allred > 5. In contrast, the non-specific PPG5-10 antibody did show an association with recurrence and survival. CONCLUSIONS Our data indicate that ERβ1 expression in TNBC tumours does not associate with prognosis.
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Affiliation(s)
- Elena A Takano
- Pathology, Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
| | - Melissa M Younes
- Breast Cancer Risk and Prevention Laboratory, Peter MacCallum Cancer Centre, Research Division 305 Grattan St, Melbourne, VIC, 3000, Australia
| | - Katie Meehan
- Department of Otorhinolaryngology, Head and Neck Surgery, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong
- The University of Western Australia (M504), 35 Stirling Highway, Perth, 6009, Australia
| | - Lisa Spalding
- The University of Western Australia (M504), 35 Stirling Highway, Perth, 6009, Australia
| | - Max Yan
- South Eastern Area Laboratory Services, Randwick, NSW, Australia
| | - Prue Allan
- Pathology, Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
| | - Stephen B Fox
- Pathology, Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
- School of Cancer Medicine, La Trobe University, Bundoora, VIC, 3086, Australia
| | - Andy Redfern
- The University of Western Australia (M504), 35 Stirling Highway, Perth, 6009, Australia
| | - David Clouston
- TissuPath, 32 Ricketts Rd, Mount Waverley, VIC, 3149, Australia
| | - Graham G Giles
- 7a Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VIC, 3004, Australia
- Centre for Epidemiology and Biostatistics, School of Population and Global Health, University of Melbourne, Parkville, VIC, 3012, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC, 3168, Australia
| | - Elizabeth L Christie
- School of Cancer Medicine, La Trobe University, Bundoora, VIC, 3086, Australia
- Peter MacCallum Cancer Centre Melbourne, Victoria, 3000, Australia
| | - Robin L Anderson
- School of Cancer Medicine, La Trobe University, Bundoora, VIC, 3086, Australia
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC, 3084, Australia
- The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, Australia
| | - Magnus Zethoven
- The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, Australia
- Peter Mac, Bioinformatics Core Facility, Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC, Australia
| | - Kelly-Anne Phillips
- The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, Australia
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Centre for Epidemiology and Biostatistics, School of Population and Global Health, The University of Melbourne, Parkville, VIC, Australia
| | - Kylie Gorringe
- The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, Australia
- Precision Cancer Medicine Laboratory, Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC, Australia
| | - Kara L Britt
- Breast Cancer Risk and Prevention Laboratory, Peter MacCallum Cancer Centre, Research Division 305 Grattan St, Melbourne, VIC, 3000, Australia.
- The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, Australia.
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7
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Dall G, Vandenberg CJ, Nesic K, Ratnayake G, Zhu W, Vissers JHA, Bedő J, Penington J, Wakefield MJ, Kee D, Carmagnac A, Lim R, Shield-Artin K, Milesi B, Lobley A, Kyran EL, O'Grady E, Tram J, Zhou W, Nugawela D, Stewart KP, Caldwell R, Papadopoulos L, Ng AP, Dobrovic A, Fox SB, McNally O, Power JD, Meniawy T, Tan TH, Collins IM, Klein O, Barnett S, Olesen I, Hamilton A, Hofmann O, Grimmond S, Papenfuss AT, Scott CL, Barker HE. Targeting homologous recombination deficiency in uterine leiomyosarcoma. J Exp Clin Cancer Res 2023; 42:112. [PMID: 37143137 PMCID: PMC10157936 DOI: 10.1186/s13046-023-02687-0] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 04/25/2023] [Indexed: 05/06/2023] Open
Abstract
BACKGROUND Uterine leiomyosarcoma (uLMS) is a rare and aggressive gynaecological malignancy, with individuals with advanced uLMS having a five-year survival of < 10%. Mutations in the homologous recombination (HR) DNA repair pathway have been observed in ~ 10% of uLMS cases, with reports of some individuals benefiting from poly (ADP-ribose) polymerase (PARP) inhibitor (PARPi) therapy, which targets this DNA repair defect. In this report, we screened individuals with uLMS, accrued nationally, for mutations in the HR repair pathway and explored new approaches to therapeutic targeting. METHODS A cohort of 58 individuals with uLMS were screened for HR Deficiency (HRD) using whole genome sequencing (WGS), whole exome sequencing (WES) or NGS panel testing. Individuals identified to have HRD uLMS were offered PARPi therapy and clinical outcome details collected. Patient-derived xenografts (PDX) were generated for therapeutic targeting. RESULTS All 13 uLMS samples analysed by WGS had a dominant COSMIC mutational signature 3; 11 of these had high genome-wide loss of heterozygosity (LOH) (> 0.2) but only two samples had a CHORD score > 50%, one of which had a homozygous pathogenic alteration in an HR gene (deletion in BRCA2). A further three samples harboured homozygous HRD alterations (all deletions in BRCA2), detected by WES or panel sequencing, with 5/58 (9%) individuals having HRD uLMS. All five individuals gained access to PARPi therapy. Two of three individuals with mature clinical follow up achieved a complete response or durable partial response (PR) with the subsequent addition of platinum to PARPi upon minor progression during initial PR on PARPi. Corresponding PDX responses were most rapid, complete and sustained with the PARP1-specific PARPi, AZD5305, compared with either olaparib alone or olaparib plus cisplatin, even in a paired sample of a BRCA2-deleted PDX, derived following PARPi therapy in the patient, which had developed PARPi-resistance mutations in PRKDC, encoding DNA-PKcs. CONCLUSIONS Our work demonstrates the value of identifying HRD for therapeutic targeting by PARPi and platinum in individuals with the aggressive rare malignancy, uLMS and suggests that individuals with HRD uLMS should be included in trials of PARP1-specific PARPi.
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Affiliation(s)
- Genevieve Dall
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Cassandra J Vandenberg
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia.
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia.
| | - Ksenija Nesic
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
| | | | - Wenying Zhu
- Centre for Cancer Research and Department of Clinical Pathology, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Joseph H A Vissers
- Centre for Cancer Research and Department of Clinical Pathology, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Justin Bedő
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- School of Computing and Information Systems, the University of Melbourne, Parkville, VIC, 3010, Australia
| | - Jocelyn Penington
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
| | - Matthew J Wakefield
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Damien Kee
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC, 3084, Australia
- Austin Health, Heidelberg, VIC, 3084, Australia
- Australian Rare Cancer Portal, BioGrid Australia, Melbourne Health, Parkville, VIC, 3052, Australia
- Peter MacCallum Cancer Centre and Sir Peter MacCallum Department of Oncology, The University of Melbourne, Victoria, 3010, Australia
| | - Amandine Carmagnac
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
| | - Ratana Lim
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
| | - Kristy Shield-Artin
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Briony Milesi
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- Royal Women's Hospital, Parkville, VIC, 3052, Australia
| | - Amanda Lobley
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- Royal Women's Hospital, Parkville, VIC, 3052, Australia
| | - Elizabeth L Kyran
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
| | - Emily O'Grady
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
| | - Joshua Tram
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
| | - Warren Zhou
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
| | - Devindee Nugawela
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
| | - Kym Pham Stewart
- Centre for Cancer Research and Department of Clinical Pathology, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Reece Caldwell
- Australian Rare Cancer Portal, BioGrid Australia, Melbourne Health, Parkville, VIC, 3052, Australia
| | - Lia Papadopoulos
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- Australian Rare Cancer Portal, BioGrid Australia, Melbourne Health, Parkville, VIC, 3052, Australia
| | - Ashley P Ng
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
- Peter MacCallum Cancer Centre and Sir Peter MacCallum Department of Oncology, The University of Melbourne, Victoria, 3010, Australia
- Royal Melbourne Hospital, Parkville, VIC, 3052, Australia
| | | | - Stephen B Fox
- Peter MacCallum Cancer Centre and Sir Peter MacCallum Department of Oncology, The University of Melbourne, Victoria, 3010, Australia
| | - Orla McNally
- Royal Women's Hospital, Parkville, VIC, 3052, Australia
- Peter MacCallum Cancer Centre and Sir Peter MacCallum Department of Oncology, The University of Melbourne, Victoria, 3010, Australia
- Department of Obstetrics and Gynaecology, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Jeremy D Power
- Launceston General Hospital, Launceston, TAS, 7250, Australia
| | - Tarek Meniawy
- University of Western Australia, Perth, WA, 6009, Australia
| | - Teng Han Tan
- Peter MacCallum Cancer Centre and Sir Peter MacCallum Department of Oncology, The University of Melbourne, Victoria, 3010, Australia
| | - Ian M Collins
- SouthWest Healthcare, Warrnambool, VIC, 3280, Australia
- Faculty of Health, School of Medicine, Deakin University, Warrnambool, VIC, 3280, Australia
| | - Oliver Klein
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC, 3084, Australia
- Austin Health, Heidelberg, VIC, 3084, Australia
| | - Stephen Barnett
- Royal Melbourne Hospital, Parkville, VIC, 3052, Australia
- Western Hospital, Footscray, VIC, 3011, Australia
| | - Inger Olesen
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- University Hospital Geelong, Geelong, VIC, 3220, Australia
| | - Anne Hamilton
- Royal Women's Hospital, Parkville, VIC, 3052, Australia
- Peter MacCallum Cancer Centre and Sir Peter MacCallum Department of Oncology, The University of Melbourne, Victoria, 3010, Australia
| | - Oliver Hofmann
- Centre for Cancer Research and Department of Clinical Pathology, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Sean Grimmond
- Centre for Cancer Research and Department of Clinical Pathology, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Anthony T Papenfuss
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
- Peter MacCallum Cancer Centre and Sir Peter MacCallum Department of Oncology, The University of Melbourne, Victoria, 3010, Australia
| | - Clare L Scott
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
- Royal Women's Hospital, Parkville, VIC, 3052, Australia
- Australian Rare Cancer Portal, BioGrid Australia, Melbourne Health, Parkville, VIC, 3052, Australia
- Peter MacCallum Cancer Centre and Sir Peter MacCallum Department of Oncology, The University of Melbourne, Victoria, 3010, Australia
- Royal Melbourne Hospital, Parkville, VIC, 3052, Australia
- Department of Obstetrics and Gynaecology, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Holly E Barker
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
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8
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Rickard JA, Rogers TM, Westerman DA, Carolan C, Fox SB. Identification errors in medical research: Privacy at all costs? Contemp Clin Trials 2023; 130:107206. [PMID: 37119991 DOI: 10.1016/j.cct.2023.107206] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 03/18/2023] [Accepted: 04/21/2023] [Indexed: 05/01/2023]
Abstract
In laboratory medicine, a misidentified patient sample can lead to an incorrect tissue diagnosis, a potentially fatal blood transfusion error or other serious adverse events. Although well characterised in routine patient care, the overall impacts of misidentification errors in the clinical research setting are less conspicuous but potentially greater, with downstream effects that may extend beyond care at an individual level. When data discrepancies or queries arise in a clinical trial data then a data clarification form (DCF) is issued to the researcher by the overseeing trial coordinator or sponsor. Higher rates of DCF's are sometimes used as a crude surrogate marker of poorer trial quality. However, data is scarce on misidentification rates in clinical trials. In five clinical trials involving 822 histology or blood specimens analysed by our pathology department, DCF's were issued for 21% (174) of specimens. Amongst these 67% (117 / 174) were related to sample identification. Although these errors were recognised before data was compromised or an adverse event occurred, they highlight an alarming lack of stringency of use of patient identifiers in the research setting. We therefore propose the use of an appropriate number of de-identified data points and a formalised specimen accession process as employed in routine care to mitigate misidentification errors and their impact in clinical research. Increased recognition in the research community of the likely effect of truncating or reducing the number of patient identifiers is needed to minimise misidentification errors in the research setting.
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Affiliation(s)
- James A Rickard
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia
| | - Toni-Maree Rogers
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia
| | - David A Westerman
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Cathy Carolan
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia
| | - Stephen B Fox
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria 3010, Australia.
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Markham JF, Fellowes AP, Green T, Leal JL, Legaie R, Cullerne D, Morris T, John T, Solomon B, Fox SB. Predicting response to immune checkpoint blockade in NSCLC with tumour-only RNA-seq. Br J Cancer 2023; 128:1148-1154. [PMID: 36572732 PMCID: PMC10006283 DOI: 10.1038/s41416-022-02105-w] [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: 07/07/2022] [Revised: 12/04/2022] [Accepted: 12/06/2022] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Targeted RNA sequencing (RNA-seq) from FFPE specimens is used clinically in cancer for its ability to estimate gene expression and to detect fusions. Using a cohort of NSCLC patients, we sought to determine whether targeted RNA-seq could be used to measure tumour mutational burden (TMB) and the expression of immune-cell-restricted genes from FFPE specimens and whether these could predict response to immune checkpoint blockade. METHODS Using The Cancer Genome Atlas LUAD dataset, we developed a method for determining TMB from tumour-only RNA-seq and showed a correlation with DNA sequencing derived TMB calculated from tumour/normal sample pairs (Spearman correlation = 0.79, 95% CI [0.73, 0.83]. We applied this method to targeted sequencing data from our patient cohort and validated these results against TMB estimates obtained using an orthogonal assay (Spearman correlation = 0.49, 95% CI [0.24, 0.68]). RESULTS We observed that the RNA measure of TMB was significantly higher in responders to immune blockade treatment (P = 0.028) and that it was predictive of response (AUC = 0.640 with 95% CI [0.493, 0.786]). By contrast, the expression of immune-cell-restricted genes was uncorrelated with patient outcome. CONCLUSION TMB calculated from targeted RNA sequencing has a similar diagnostic ability to TMB generated from targeted DNA sequencing.
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Affiliation(s)
- John F Markham
- Peter MacCallum Cancer Centre, 305 Grattan Street, Parkville, VIC, 3000, Australia
- Department of Pathology, Peter MacCallum Cancer Centre, Parkville, VIC, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - Andrew P Fellowes
- Peter MacCallum Cancer Centre, 305 Grattan Street, Parkville, VIC, 3000, Australia.
- Department of Pathology, Peter MacCallum Cancer Centre, Parkville, VIC, Australia.
| | - Thomas Green
- Peter MacCallum Cancer Centre, 305 Grattan Street, Parkville, VIC, 3000, Australia
- Department of Pathology, Peter MacCallum Cancer Centre, Parkville, VIC, Australia
| | - Jose Luis Leal
- Peter MacCallum Cancer Centre, 305 Grattan Street, Parkville, VIC, 3000, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - Roxane Legaie
- Peter MacCallum Cancer Centre, 305 Grattan Street, Parkville, VIC, 3000, Australia
- Department of Pathology, Peter MacCallum Cancer Centre, Parkville, VIC, Australia
| | - Darren Cullerne
- Murdoch Children's Research Institute, Flemington Road, Parkville, VIC, 3052, Australia
| | - Tessa Morris
- Southern Blood and Cancer Service, Te Whatu Ora Southern, Dunedin, New Zealand
- Mercy Cancer Care, Mercy Hospital, Dunedin, New Zealand
| | - Tom John
- Peter MacCallum Cancer Centre, 305 Grattan Street, Parkville, VIC, 3000, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - Ben Solomon
- Peter MacCallum Cancer Centre, 305 Grattan Street, Parkville, VIC, 3000, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - Stephen B Fox
- Peter MacCallum Cancer Centre, 305 Grattan Street, Parkville, VIC, 3000, Australia
- Department of Pathology, Peter MacCallum Cancer Centre, Parkville, VIC, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
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10
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Md Nasir ND, Koh VCY, Cree IA, Ruiz BII, Del Águila J, Armon S, Fox SB, Lakhani SR, Tan PH. Phyllodes tumour evidence gaps mapped from the 5th edition of the WHO classification of tumours of the breast. Histopathology 2023; 82:704-712. [PMID: 36579383 DOI: 10.1111/his.14856] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [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: 08/04/2022] [Revised: 12/21/2022] [Accepted: 12/24/2022] [Indexed: 12/30/2022]
Abstract
AIMS Breast phyllodes tumours (PTs) are a rare subset of fibroepithelial neoplasms categorised into benign, borderline, and malignant grades according to the World Health Organization (WHO) Classification of Tumours (WCTs). In this report, we developed an evidence gap map (EGM) based on the literature cited in the PT chapter of the 5th edition of the breast WCT in order to identify knowledge and research gaps in PT. METHODS A framework was first established where the dimensions of the EGM were defined as categories of tumour descriptors, tumour types, and evidence levels. Citations were collected into a Microsoft Excel form and imported into EPPI-reviewer to produce the EGM. RESULTS The EGM showed that the "Histopathology" and "Pathogenesis" sections contained the most citations, the majority being of low-level evidence. The highest number of citations considered of moderate-level evidence were found in the "Histopathology" section. There was no high-level evidence cited in this chapter. The "Localisation", "Aetiology", and "Staging" sections had the fewest citations. CONCLUSION This EGM provides a visual representation of the cited literature in the PT chapter of the breast WCT, revealing the lack of high-level evidence citations. There is an uneven distribution of references, probably due to citation practices. Pockets of low-level evidence are highlighted, possibly related to referencing habits, lack of relevant research, or the belief that the information presented is standard accepted fact, without the need for specific citations. Future work needs to bridge evidence gaps and broaden citations beyond those in the latest WCT.
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Affiliation(s)
- Nur Diyana Md Nasir
- Department of Anatomical Pathology, Singapore General Hospital, Singapore, Singapore
| | - Valerie C Y Koh
- Department of Anatomical Pathology, Singapore General Hospital, Singapore, Singapore
| | - Ian A Cree
- WHO/IARC Classification of Tumours, International Agency for Research on Cancer (IARC), Lyon, France
| | - Blanca I I Ruiz
- WHO/IARC Classification of Tumours, International Agency for Research on Cancer (IARC), Lyon, France
| | - Javier Del Águila
- WHO/IARC Classification of Tumours, International Agency for Research on Cancer (IARC), Lyon, France
| | - Subasri Armon
- WHO/IARC Classification of Tumours, International Agency for Research on Cancer (IARC), Lyon, France
| | - Stephen B Fox
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Sunil R Lakhani
- University of Queensland Centre for Clinical Research and Pathology, Brisbane, QLD, Australia
| | - Puay Hoon Tan
- Luma Medical Centre, Singapore, Singapore
- Department of Anatomy, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- KK Women's and Children's Hospital, Singapore, Singapore
- Department of Pathology, University of Western Sydney, Sydney, Australia
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11
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Stark Z, Boughtwood T, Haas M, Braithwaite J, Gaff CL, Goranitis I, Spurdle AB, Hansen DP, Hofmann O, Laing N, Metcalfe S, Newson AJ, Scott HS, Thorne N, Ward RL, Dinger ME, Best S, Long JC, Grimmond SM, Pearson J, Waddell N, Barnett CP, Cook M, Field M, Fielding D, Fox SB, Gecz J, Jaffe A, Leventer RJ, Lockhart PJ, Lunke S, Mallett AJ, McGaughran J, Mileshkin L, Nones K, Roscioli T, Scheffer IE, Semsarian C, Simons C, Thomas DM, Thorburn DR, Tothill R, White D, Dunwoodie S, Simpson PT, Phillips P, Brion MJ, Finlay K, Quinn MC, Mattiske T, Tudini E, Boggs K, Murray S, Wells K, Cannings J, Sinclair AH, Christodoulou J, North KN. Australian Genomics: Outcomes of a 5-year national program to accelerate the integration of genomics in healthcare. Am J Hum Genet 2023; 110:419-426. [PMID: 36868206 PMCID: PMC10027474 DOI: 10.1016/j.ajhg.2023.01.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Accepted: 01/27/2023] [Indexed: 03/05/2023] Open
Abstract
Australian Genomics is a national collaborative partnership of more than 100 organizations piloting a whole-of-system approach to integrating genomics into healthcare, based on federation principles. In the first five years of operation, Australian Genomics has evaluated the outcomes of genomic testing in more than 5,200 individuals across 19 rare disease and cancer flagship studies. Comprehensive analyses of the health economic, policy, ethical, legal, implementation and workforce implications of incorporating genomics in the Australian context have informed evidence-based change in policy and practice, resulting in national government funding and equity of access for a range of genomic tests. Simultaneously, Australian Genomics has built national skills, infrastructure, policy, and data resources to enable effective data sharing to drive discovery research and support improvements in clinical genomic delivery.
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Affiliation(s)
- Zornitza Stark
- Australian Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia; Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia; University of Melbourne, Melbourne, VIC, Australia.
| | - Tiffany Boughtwood
- Australian Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia; Murdoch Children's Research Institute, Melbourne, VIC, Australia; Childhood Dementia Initiative, Sydney, NSW, Australia
| | - Matilda Haas
- Australian Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia; Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Jeffrey Braithwaite
- Centre for Healthcare Resilience and Implementation Science, Australian Institute of Health Innovation, Macquarie University, Sydney, NSW, Australia; International Society for Quality in Health Care, Dublin, Ireland
| | - Clara L Gaff
- Australian Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia; University of Melbourne, Melbourne, VIC, Australia; Murdoch Children's Research Institute, Melbourne, VIC, Australia; Melbourne Genomics Health Alliance, Melbourne, VIC, Australia; Walter and Eliza Hall Institute, Melbourne, VIC, Australia
| | - Ilias Goranitis
- Australian Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia; Murdoch Children's Research Institute, Melbourne, VIC, Australia; Health Economics Unit, Centre for Health Policy, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, VIC, Australia
| | - Amanda B Spurdle
- Population Health Program, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - David P Hansen
- Australian e-Health Research Centre, CSIRO Health and Biosecurity, Royal Brisbane and Women's Hospital, Brisbane, QLD, Australia
| | - Oliver Hofmann
- University of Melbourne Centre for Cancer Research, Melbourne, VIC, Australia
| | - Nigel Laing
- Centre for Medical Research, University of Western Australia, Harry Perkins Institute of Medical Research, Perth, WA, Australia
| | - Sylvia Metcalfe
- Australian Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia; Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Ainsley J Newson
- Australian Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia; The University of Sydney, Faculty of Medicine and Health, Sydney School of Public Health, Sydney Health Ethics, Sydney, NSW, Australia
| | - Hamish S Scott
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, SA, Australia; Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, Australia; Clinical and Health Sciences, University of South Australia, Adelaide, SA, Australia; Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia
| | - Natalie Thorne
- Australian Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia; University of Melbourne, Melbourne, VIC, Australia; Murdoch Children's Research Institute, Melbourne, VIC, Australia; Melbourne Genomics Health Alliance, Melbourne, VIC, Australia; Walter and Eliza Hall Institute, Melbourne, VIC, Australia
| | - Robyn L Ward
- Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
| | - Marcel E Dinger
- School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney, NSW, Australia
| | - Stephanie Best
- Australian Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia; Centre for Healthcare Resilience and Implementation Science, Australian Institute of Health Innovation, Macquarie University, Sydney, NSW, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia; Department of Health Services Research, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia; Victorian Comprehensive Cancer Centre, Melbourne, VIC, Australia
| | - Janet C Long
- Centre for Healthcare Resilience and Implementation Science, Australian Institute of Health Innovation, Macquarie University, Sydney, NSW, Australia
| | - Sean M Grimmond
- University of Melbourne Centre for Cancer Research, Melbourne, VIC, Australia
| | - John Pearson
- Genome Informatics Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Nicola Waddell
- Medical Genomics Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Christopher P Barnett
- Paediatric and Reproductive Genetics Unit, Women's and Children's Hospital, North Adelaide, SA, Australia
| | - Matthew Cook
- Centre for Personalised Immunology, Australian National University, Canberra, ACT, Australia; Department of Medicine, University of Cambridge, Puddicombe Way, Cambridge, UK
| | - Michael Field
- Genetics of Learning Disability Service, Hunter Genetics, Newcastle, NSW, Australia
| | - David Fielding
- Department of Thoracic Medicine, The Royal Brisbane and Women's Hospital, Brisbane, QLD, Australia; Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - Stephen B Fox
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia; Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Jozef Gecz
- Adelaide Medical School and Robinson Research Institute, University of Adelaide, Adelaide, SA, Australia
| | - Adam Jaffe
- School of Clinical Medicine, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW, Australia; Sydney Children's Hospital Network, Randwick, Sydney, NSW, Australia
| | - Richard J Leventer
- University of Melbourne, Melbourne, VIC, Australia; Murdoch Children's Research Institute, Melbourne, VIC, Australia; Department of Neurology, Royal Children's Hospital, Melbourne, VIC, Australia
| | - Paul J Lockhart
- University of Melbourne, Melbourne, VIC, Australia; Bruce Lefroy Centre, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Sebastian Lunke
- Australian Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia; Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia; University of Melbourne, Melbourne, VIC, Australia
| | - Andrew J Mallett
- KidGen Collaborative, Australian Genomics, Melbourne, VIC, Australia; Department of Renal Medicine, Townsville University Hospital, Townsville, QLD, Australia; College of Medicine and Dentistry, James Cook University, Townsville, QLD, Australia; Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Julie McGaughran
- Genetic Health Queensland, Royal Brisbane & Women's Hospital, Brisbane, QLD, Australia; School of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - Linda Mileshkin
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Katia Nones
- Medical Genomics Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Tony Roscioli
- Centre for Clinical Genetics, Sydney Children's Hospital, Sydney, NSW, Australia; Randwick Genomics Laboratory, NSW Health Pathology, Prince of Wales Hospital, Sydney, NSW, Australia; Neuroscience Research Australia (NeuRA) and Prince of Wales Clinical School, UNSW, Sydney, NSW, Australia
| | - Ingrid E Scheffer
- University of Melbourne, Melbourne, VIC, Australia; Murdoch Children's Research Institute, Melbourne, VIC, Australia; Department of Neurology, Royal Children's Hospital, Melbourne, VIC, Australia; Department of Medicine, University of Melbourne, Austin Health, Melbourne, VIC, Australia; Florey Institute of Neuroscience and Mental Health, Melbourne, VIC, Australia
| | - Christopher Semsarian
- Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia; Agnes Ginges Centre for Molecular Cardiology at Centenary Institute, The University of Sydney, Sydney, NSW, Australia; Department of Cardiology, Royal Prince Alfred Hospital, Sydney, NSW, Australia
| | - Cas Simons
- Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia; Centre for Population Genomics, Garvan Institute of Medical Research, and University of New South Wales, Sydney, NSW, Australia
| | - David M Thomas
- Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - David R Thorburn
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia; University of Melbourne, Melbourne, VIC, Australia; Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Richard Tothill
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia; Department of Clinical Pathology and Centre for Cancer Research, University of Melbourne, Melbourne, VIC, Australia
| | - Deborah White
- Blood Cancer Program, Precision Cancer Medicine Theme, The South Australian Medical Research Institute, Adelaide, SA, Australia; Faculty of Health and Medical Science, The University of Adelaide, Adelaide, SA, Australia
| | - Sally Dunwoodie
- School of Clinical Medicine, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW, Australia; Victor Chang Cardiac Research Institute, Sydney, NSW, Australia
| | - Peter T Simpson
- Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - Peta Phillips
- Australian Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Marie-Jo Brion
- Australian Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Keri Finlay
- Australian Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Michael Cj Quinn
- Australian Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia; College of Medicine and Dentistry, James Cook University, Townsville, QLD, Australia
| | - Tessa Mattiske
- Australian Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Emma Tudini
- Australian Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia; Health Economics Unit, Centre for Health Policy, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, VIC, Australia
| | - Kirsten Boggs
- Australian Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia; Sydney Children's Hospital Network, Randwick, Sydney, NSW, Australia; Sydney Children's Hospital Network, Westmead, NSW, Australia
| | - Sean Murray
- Australian Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia; Mito Foundation, Sydney, NSW, Australia
| | - Kathy Wells
- Australian Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia; Breast Cancer Network Australia, Melbourne, VIC, Australia
| | - John Cannings
- Australian Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia; Thoracic Oncology Group of Australasia, Melbourne, VIC, Australia; ProCan, Children's Medical Research Institute, The University of Sydney, Sydney, NSW, Australia
| | - Andrew H Sinclair
- Australian Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia; University of Melbourne, Melbourne, VIC, Australia; Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - John Christodoulou
- Australian Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia; University of Melbourne, Melbourne, VIC, Australia; Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Kathryn N North
- Australian Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia; University of Melbourne, Melbourne, VIC, Australia; Murdoch Children's Research Institute, Melbourne, VIC, Australia.
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12
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Doig KD, Fellowes AP, Fox SB. Homologous Recombination Repair Deficiency: An Overview for Pathologists. Mod Pathol 2023; 36:100049. [PMID: 36788098 DOI: 10.1016/j.modpat.2022.100049] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 10/11/2022] [Accepted: 11/09/2022] [Indexed: 01/11/2023]
Abstract
The repair of DNA double-stranded breaks relies on the homologous recombination repair pathway and is critical to cell function. However, this pathway can be lost in some cancers such as breast, ovarian, endometrial, pancreatic, and prostate cancers. Cancer cells with homologous recombination deficiency (HRD) are sensitive to targeted inhibition of poly-ADP ribose polymerase (PARP), a key component of alternative backup DNA repair pathways. Identifying patients with cancer with HRD biomarkers allows the identification of patients likely to benefit from PARP inhibitor therapies. In this study, we describe the causes of HRD, the underlying molecular changes resulting from HRD that form the basis of different molecular HRD assays, and discuss the issues around their clinical use. This overview is directed toward practicing pathologists wishing to be informed of this new predictive biomarker, as PARP inhibitors are increasingly used in standard care settings.
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Affiliation(s)
- Kenneth D Doig
- Department of Pathology, Peter MacCallum Cancer Centre, Parkville, Victoria, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia.
| | - Andrew P Fellowes
- Department of Pathology, Peter MacCallum Cancer Centre, Parkville, Victoria, Australia
| | - Stephen B Fox
- Department of Pathology, Peter MacCallum Cancer Centre, Parkville, Victoria, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
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13
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Deb S, Chakrabarti A, Fox SB. Prognostic and Predictive Biomarkers in Familial Breast Cancer. Cancers (Basel) 2023; 15:cancers15041346. [PMID: 36831687 PMCID: PMC9953970 DOI: 10.3390/cancers15041346] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 02/06/2023] [Accepted: 02/15/2023] [Indexed: 02/23/2023] Open
Abstract
Large numbers of breast cancers arise within a familial context, either with known inherited germline mutations largely within DNA repair genes, or with a strong family history of breast and/or ovarian cancer, with unknown genetic underlying mechanisms. These cancers appear to be different to sporadic cases, with earlier age of onset, increased multifocality and with association with specific breast cancer histological and phenotypic subtypes. Furthermore, tumours showing homologous recombination deficiency, due to loss of BRCA1, BRCA2, PALB2 and CHEK2 function, have been shown to be especially sensitive to platinum-based chemotherapeutics and PARP inhibition. While there is extensive research and data accrued on risk stratification and genetic predisposition, there are few data pertaining to relevant prognostic and predictive biomarkers within this breast cancer subgroup. The following is a review of such biomarkers in male and female familial breast cancer, although the data for the former are particularly sparse.
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Affiliation(s)
- Siddhartha Deb
- Anatpath, Gardenvale, VIC 3185, Australia
- Monash Health Pathology, Clayton, VIC 3168, Australia
- Correspondence:
| | | | - Stephen B. Fox
- Sir Peter MacCallum Department of Oncology, Peter MacCallum Cancer Centre, University of Mebourne, Melbourne, VIC 3101, Australia
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14
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Yu SL, Hsiao YJ, Cooper WA, Choi YL, Avilés-Salas A, Chou TY, Coudry R, Raskin GA, Fox SB, Huang CC, Jeon YK, Ko YH, Ku WH, Kwon GY, Leslie C, Lin MC, Lou PJ, Scapulatempo-Neto C, Mendoza Ramírez S, Savelov N, Shim HS, Lara Torres CO, Cunha IW, Zavalishina L, Chen YM. The Ring Study: an international comparison of PD-L1 diagnostic assays and their interpretation in non-small cell lung cancer, head and neck squamous cell cancer and urothelial cancer. Pathology 2023; 55:19-30. [PMID: 36319485 DOI: 10.1016/j.pathol.2022.07.016] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 07/11/2022] [Accepted: 07/21/2022] [Indexed: 01/11/2023]
Abstract
PD-L1 immunohistochemistry has been approved as a diagnostic assay for immunotherapy. However, an international comparison across multiple cancers is lacking. This study aimed to assess the performance of PD-L1 diagnostic assays in non-small cell lung cancer (NSCLC), head and neck squamous cell cancer (HNSCC) and urothelial cancer (UC). The excisional specimens of NSCLC, HNSCC and UC were assayed by Ventana SP263 and scored at three sites in each country, including Australia, Brazil, Korea, Mexico, Russia and Taiwan. All slides were rotated to two other sites for interobserver scoring. The same cohort of NSCLC was assessed with Dako 22C3 pharmDx PD-L1 for comparison. The PD-L1 immunopositivity was scored according to the approved PD-L1 scoring algorithms which were the percentage of PD-L1-expressing tumour cell (TC) and tumour proportion score (TPS) by Ventana SP263 and Dako 22C3 staining, respectively. In NSCLC, the comparison demonstrated the comparability of the SP263 and 22C3 assays (cut-off of 1%, κ=0.71; 25%, κ=0.75; 50%, κ=0.81). The interobserver comparisons showed moderate to almost perfect agreement for SP263 in TC staining at 25% cut-off (NSCLC, κ=0.72 to 0.86; HNSCC, κ=0.60 to 0.82; UC, κ=0.68 to 0.91) and at 50% cut-off for NSCLC (κ=0.64 to 0.90). Regarding the immune cell (IC) scoring in UC, there was a lower correlation (concordance correlation coefficient=0.10 to 0.68) and poor to substantial agreements at the 1%, 5%, 10% and 25% cut-offs (κ= -0.04 to 0.76). The interchangeability of SP263 and 22C3 in NSCLC might be acceptable, especially at the 50% cut-off. In HNSCC, the performance of SP263 is comparable across five countries. In UC, there was low concordance of IC staining, which may affect treatment decisions. Overall, the study showed the reliability and reproducibility of SP263 in NSCLC, HNSCC and UC.
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Affiliation(s)
- Sung-Liang Yu
- Department of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan University, Taipei, Taiwan; Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan.
| | - Yi-Jing Hsiao
- Department of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan University, Taipei, Taiwan.
| | - Wendy A Cooper
- Tissue Pathology and Diagnostic Oncology, NSW Health Pathology, Royal Prince Alfred Hospital, Sydney, NSW, Australia; Sydney Medical School, University of Sydney, Sydney, NSW, Australia; School of Medicine, Western Sydney University, Sydney, NSW, Australia.
| | - Yoon-La Choi
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea.
| | | | - Teh-Ying Chou
- Department of Pathology and Laboratory Medicine, Taipei Veterans General Hospital, Taipei, Taiwan.
| | - Renata Coudry
- Department of Pathology, Sirio Libanes Hospital and United Health Group Brazil, Sao Paulo, Brazil.
| | - Grigory A Raskin
- A.M. Granov Russian Scientific Center of Radiological and Surgical Technologies, St Petersburg, Russia.
| | - Stephen B Fox
- Molecular Pathology Laboratory, Peter MacCallum Cancer Centre and University of Melbourne, Melbourne, Vic, Australia
| | - Chao-Cheng Huang
- Biobank and Tissue Bank and Department of Pathology, Kaohsiung Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Yoon Kyung Jeon
- Department of Pathology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, South Korea; Cancer Research Institute, Seoul National University, Seoul, South Korea
| | - Young-Hyeh Ko
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Wen-Hui Ku
- Taipei Institute of Pathology, Taipei, Taiwan
| | - Ghee-Young Kwon
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | | | - Mei-Chun Lin
- National Taiwan University Cancer Center, Taipei, Taiwan; Department of Otolaryngology, National Taiwan University Hospital and College of Medicine, Taipei, Taiwan
| | - Pei-Jen Lou
- Department of Otolaryngology, National Taiwan University Hospital and College of Medicine, Taipei, Taiwan
| | - Cristovam Scapulatempo-Neto
- Pathology and Molecular Diagnostics, Diagnósticos da América, DASA, São Paulo, Brazil; Molecular Oncology Research Center, Hospital de Amor de Barretos, Barretos, Brazil
| | | | | | - Hyo-Sup Shim
- Department of Pathology, Severance Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea
| | | | - Isabela Werneck Cunha
- Institute of Anatomical Pathology, Rede D'Or São Luiz Hospitals Network, Rio de Janeiro and São Paulo, Brazil; D'Or Institute for Research and Education, Rio de Janeiro and São Paulo, Brazil
| | - Larisa Zavalishina
- Pathology Department of the Russian Medical Academy of Continuous Professional Education, Moscow, Russia
| | - Yan-Ming Chen
- Department of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan University, Taipei, Taiwan
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15
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Posner A, Sivakumaran T, Pattison A, Etemadmoghadam D, Thio N, Wood C, Fisher K, Webb S, DeFazio A, Wilcken N, Gao B, Karapetis CS, Singh M, Collins IM, Richardson G, Steer C, Warren M, Karanth N, Fellowes A, Fox SB, Hicks RJ, Schofield P, Bowtell D, Prall OWJ, Tothill RW, Mileshkin L. Immune and genomic biomarkers of immunotherapy response in cancer of unknown primary. J Immunother Cancer 2023; 11:jitc-2022-005809. [PMID: 36720497 PMCID: PMC10098268 DOI: 10.1136/jitc-2022-005809] [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] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/02/2023] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND Cancer of unknown primary (CUP) is a heterogeneous group of metastatic cancers where a primary tissue of origin (TOO) is uncertain. Most patients with CUP have limited treatment options and poor survival outcomes. Immune checkpoint inhibitors (ICIs) can be efficacious in some patients with CUP, but the optimal predictive biomarkers are unknown. We therefore assessed immune and genomic biomarkers as well as predicted TOO in patients with CUP, including a subset treated with ICIs. METHODS Patients with CUP were subject to gene-expression profiling (GEP) and DNA panel sequencing. Immune and stromal-related gene expression was explored by NanoString, including genes associated with immunotherapy response (IR) in other solid malignancies. ICI responsive cancer types were assigned based on Food and Drug Administration-approved indications, and either detection of a latent primary tumor or the TOO was suspected based on genomics informed pathology review. Tumor mutation burden (TMB) and gene mutations were also assessed. RESULTS A total of 219 patients with CUP were included, 215 assessed for TOO in a previous study, with the majority (163) receiving both RNA and DNA tests. Of GEP profiled cases, 33% (59/175) had a high IR gene-expression score. Of the DNA sequenced cases, 16% (32/203) had high TMB (>10 mutations/Mb), including two with mismatch repair deficiency. Low correlation was observed between TMB and an IR score (R=0.26, p<0.001). Among 110 CUPs with a latent primary or suspected TOO, 47% (52/110) belonged to ICI-responsive cancer types. More than half of the CUPs had at least one feature that may predict ICI response (high IR score, high TMB, ICI-responsive cancer type). Among patients with CUP treated with ICIs, 8/28 (29%) responded (2 complete responses and 6 partial responses). Among non-responders, 9 had stable and 11 had progressive disease. All responders had a high IR score (7/8) and/or high TMB (3/8), while most (5/8) belonged to ICI-responsive cancer types. These features were detected at a lower frequency in non-responders and mostly in patients with stable disease. CONCLUSIONS A significant fraction of CUP tumors had genomic features previously associated with ICI response. High IR score was the most sensitive predictive feature of ICI response, warranting evaluation in a larger patient series.
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Affiliation(s)
- Atara Posner
- Department of Clinical Pathology and Centre for Cancer Research, The University of Melbourne, Melbourne, Victoria, Australia
| | - Tharani Sivakumaran
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Andrew Pattison
- Department of Clinical Pathology and Centre for Cancer Research, The University of Melbourne, Melbourne, Victoria, Australia
| | | | - Niko Thio
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Colin Wood
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Krista Fisher
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Samantha Webb
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Anna DeFazio
- Department of Gynaecological Oncology, and Westmead Institute for Medical Research, Westmead Hospital, Westmead, New South Wales, Australia.,The Daffodil Centre, The University of Sydney, a joint venture with Cancer Council NSW, Sydney, New South Wales, Australia
| | - Nicholas Wilcken
- Department of Medical Oncology, Westmead Hospital The Crown Princess Mary Cancer Centre, Sydney, New South Wales, Australia
| | - Bo Gao
- Department of Medical Oncology, Westmead Hospital The Crown Princess Mary Cancer Centre, Sydney, New South Wales, Australia
| | - Christos S Karapetis
- Department of Medical Oncology and Flinders Medical Centre, Flinders University, Adelaide, South Australia, Australia
| | - Madhu Singh
- Department of Medical Oncology, Barwon Health Cancer Services, Geelong, Victoria, Australia
| | - Ian M Collins
- Department of Medical Oncology and SouthWest HealthCare, Deakin University - Warrnambool Campus, Warrnambool, Victoria, Australia
| | - Gary Richardson
- Medical Oncology, Cabrini Health, Malvern, Victoria, Australia
| | - Christopher Steer
- Border Medical Oncology, Albury Wodonga Regional Cancer Centre, Albury, Victoria, Australia
| | - Mark Warren
- Medical Oncology, Bendigo Health, Bendigo, Victoria, Australia
| | - Narayan Karanth
- Division of Medicine, Top End Health and Hospital Services, Alan Walker Cancer Centre, Darwin, Northern Territory, Australia
| | - Andrew Fellowes
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Stephen B Fox
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia.,Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Rodney J Hicks
- St Vincent's Hospital Department of Medicine, University of Melbourne, Melbourne, Victoria, Australia
| | - Penelope Schofield
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia.,Behavioural Sciences Unit, Health Services Research and Implementation Sciences, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - David Bowtell
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia.,Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Owen W J Prall
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Richard William Tothill
- Department of Clinical Pathology and Centre for Cancer Research, The University of Melbourne, Melbourne, Victoria, Australia .,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Linda Mileshkin
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia .,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia
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16
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Udayasiri RI, Luo T, Gorringe KL, Fox SB. Identifying recurrences and metastasis after ductal carcinoma in situ (DCIS) of the breast. Histopathology 2023; 82:106-118. [PMID: 36482277 PMCID: PMC10953414 DOI: 10.1111/his.14804] [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: 08/17/2022] [Revised: 09/06/2022] [Accepted: 09/11/2022] [Indexed: 12/13/2022]
Abstract
Ductal carcinoma in situ (DCIS) of the breast is a non-invasive tumour that has the potential to progress to invasive ductal carcinoma (IDC). Thus, it represents a treatment dilemma: alone it does not present a risk to life, however, left untreated it may progress to a life-threatening condition. Current clinico-pathological features cannot accurately predict which patients with DCIS have invasive potential, and therefore clinicians are unable to quantify the risk of progression for an individual patient. This leads to many women being over-treated, while others may not receive sufficient treatment to prevent invasive recurrence. A better understanding of the molecular features of DCIS, both tumour-intrinsic and the microenvironment, could offer the ability to better predict which women need aggressive treatment, and which can avoid therapies carrying significant side-effects and such as radiotherapy. In this review, we summarise the current knowledge of DCIS, and consider future research directions.
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Affiliation(s)
- Ruwangi I Udayasiri
- Peter MacCallum Cancer Centre and the Sir Peter MacCallum Department of OncologyThe University of MelbourneMelbourneVICAustralia
| | - Tongtong Luo
- Peter MacCallum Cancer Centre and the Sir Peter MacCallum Department of OncologyThe University of MelbourneMelbourneVICAustralia
| | - Kylie L Gorringe
- Peter MacCallum Cancer Centre and the Sir Peter MacCallum Department of OncologyThe University of MelbourneMelbourneVICAustralia
| | - Stephen B Fox
- Peter MacCallum Cancer Centre and the Sir Peter MacCallum Department of OncologyThe University of MelbourneMelbourneVICAustralia
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17
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Posner A, Prall OW, Sivakumaran T, Etemadamoghadam D, Thio N, Pattison A, Balachander S, Fisher K, Webb S, Wood C, DeFazio A, Wilcken N, Gao B, Karapetis CS, Singh M, Collins IM, Richardson G, Steer C, Warren M, Karanth N, Wright G, Williams S, George J, Hicks RJ, Boussioutas A, Gill AJ, Solomon BJ, Xu H, Fellowes A, Fox SB, Schofield P, Bowtell D, Mileshkin L, Tothill RW. A comparison of DNA sequencing and gene expression profiling to assist tissue of origin diagnosis in cancer of unknown primary. J Pathol 2023; 259:81-92. [PMID: 36287571 PMCID: PMC10099529 DOI: 10.1002/path.6022] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 10/02/2022] [Accepted: 10/24/2022] [Indexed: 11/11/2022]
Abstract
Cancer of unknown primary (CUP) is a syndrome defined by clinical absence of a primary cancer after standardised investigations. Gene expression profiling (GEP) and DNA sequencing have been used to predict primary tissue of origin (TOO) in CUP and find molecularly guided treatments; however, a detailed comparison of the diagnostic yield from these two tests has not been described. Here, we compared the diagnostic utility of RNA and DNA tests in 215 CUP patients (82% received both tests) in a prospective Australian study. Based on retrospective assessment of clinicopathological data, 77% (166/215) of CUPs had insufficient evidence to support TOO diagnosis (clinicopathology unresolved). The remainder had either a latent primary diagnosis (10%) or clinicopathological evidence to support a likely TOO diagnosis (13%) (clinicopathology resolved). We applied a microarray (CUPGuide) or custom NanoString 18-class GEP test to 191 CUPs with an accuracy of 91.5% in known metastatic cancers for high-medium confidence predictions. Classification performance was similar in clinicopathology-resolved CUPs - 80% had high-medium predictions and 94% were concordant with pathology. Notably, only 56% of the clinicopathology-unresolved CUPs had high-medium confidence GEP predictions. Diagnostic DNA features were interrogated in 201 CUP tumours guided by the cancer type specificity of mutations observed across 22 cancer types from the AACR Project GENIE database (77,058 tumours) as well as mutational signatures (e.g. smoking). Among the clinicopathology-unresolved CUPs, mutations and mutational signatures provided additional diagnostic evidence in 31% of cases. GEP classification was useful in only 13% of cases and oncoviral detection in 4%. Among CUPs where genomics informed TOO, lung and biliary cancers were the most frequently identified types, while kidney tumours were another identifiable subset. In conclusion, DNA and RNA profiling supported an unconfirmed TOO diagnosis in one-third of CUPs otherwise unresolved by clinicopathology assessment alone. DNA mutation profiling was the more diagnostically informative assay. © 2022 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Atara Posner
- Department of Clinical Pathology and Centre for Cancer Research, University of Melbourne, Melbourne, VIC, Australia
| | - Owen Wj Prall
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Tharani Sivakumaran
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | | | - Niko Thio
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Andrew Pattison
- Department of Clinical Pathology and Centre for Cancer Research, University of Melbourne, Melbourne, VIC, Australia
| | - Shiva Balachander
- Department of Clinical Pathology and Centre for Cancer Research, University of Melbourne, Melbourne, VIC, Australia
| | - Krista Fisher
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Samantha Webb
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Colin Wood
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Anna DeFazio
- The Westmead Institute for Medical Research, Sydney, NSW, Australia.,Department of Gynaecological Oncology, Westmead Hospital, Sydney, NSW, Australia.,The Daffodil Centre, The University of Sydney, a joint venture with Cancer Council NSW, Sydney, NSW, Australia
| | - Nicholas Wilcken
- Department of Medical Oncology, Crown Princess Mary Cancer Centre, Westmead Hospital, Sydney, NSW, Australia
| | - Bo Gao
- Department of Medical Oncology, Crown Princess Mary Cancer Centre, Westmead Hospital, Sydney, NSW, Australia
| | - Christos S Karapetis
- Department of Medical Oncology, Flinders University and Flinders Medical Centre, Adelaide, SA, Australia
| | - Madhu Singh
- Department of Medical Oncology, Barwon Health Cancer Services, Geelong, VIC, Australia
| | - Ian M Collins
- Department of Medical Oncology, SouthWest HealthCare, Warrnambool and Deakin University, Geelong, VIC, Australia
| | - Gary Richardson
- Department of Medical Oncology, Cabrini Health, Melbourne, VIC, Australia
| | - Christopher Steer
- Border Medical Oncology, Albury Wodonga Regional Cancer Centre, Albury, NSW, Australia
| | - Mark Warren
- Department of Medical Oncology, Bendigo Health, Bendigo, VIC, Australia
| | - Narayan Karanth
- Division of Medicine, Alan Walker Cancer Centre, Darwin, NT, Australia
| | - Gavin Wright
- Department of Cardiothoracic Surgery, St Vincent's Hospital, Melbourne, VIC, Australia
| | - Scott Williams
- Department of Radiation Oncology, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Joshy George
- Department of Computational Sciences, The Jackson Laboratory, Farmington, Connecticut, USA
| | - Rodney J Hicks
- The St Vincent's Hospital Department of Medicine, University of Melbourne, Melbourne, VIC, Australia
| | - Alex Boussioutas
- Department of Medicine, Royal Melbourne Hospital, University of Melbourne, Melbourne, VIC, Australia
| | - Anthony J Gill
- Cancer Diagnosis and Pathology Group, Kolling Institute of Medical, Research and Sydney Medical School, University of Sydney, Sydney, NSW, Australia
| | - Benjamin J Solomon
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Huiling Xu
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Andrew Fellowes
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Stephen B Fox
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - Penelope Schofield
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia.,Department of Psychology, and Iverson Health Innovation Research Institute, Swinburne University, Melbourne, VIC, Australia.,Behavioural Sciences Unit, Health Services Research and Implementation Sciences, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - David Bowtell
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia.,Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Linda Mileshkin
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - Richard W Tothill
- Department of Clinical Pathology and Centre for Cancer Research, University of Melbourne, Melbourne, VIC, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
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18
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Tan BY, Fox SB, Lakhani SR, Tan PH. Survey of recurrent diagnostic challenges in breast phyllodes tumours. Histopathology 2023; 82:95-105. [PMID: 36468287 DOI: 10.1111/his.14730] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 07/15/2022] [Indexed: 12/07/2022]
Abstract
BACKGROUND Breast phyllodes tumours (PTs) are graded as benign, borderline, or malignant by analysis of multiple histological features. PT grading is often inconsistent, likely due to variation in the weighting of grading criteria by pathologists. DESIGN The hierarchy of use of diagnostic criteria was identified using a 20-question survey. RESULTS In all, 213 pathologists from 29 countries responded. 54% reported 10-50 PT cases per year. Criteria considered key to PT diagnosis were: increased stromal cellularity (84.3%), stromal overgrowth (76.6%), increased stromal mitoses (67.8%), stromal atypia (61.5%), stromal fronding (59.0%), periductal stromal condensation (58.0%), irregular tumour borders (46.3%), and/or lesional heterogeneity (33.7%). The importance of grading parameters were: mitotic activity (55.5%), stromal overgrowth (54.0%), stromal atypia (51.9%), increased stromal cellularity (41.7%), and nature of the tumour border (38.9%). 49% would diagnose malignant PT without a full array of adverse features. 89% used the term "cellular fibroepithelial lesion (FEL)" for difficult cases; 45% would diagnose an FEL with stromal fronding (but lacking other PT features) as fibroadenoma (FA), 35% FEL, and 17% PT. 59% deemed clinico-radiological findings diagnostically significant; 68% considered age (≥40 years) important in determining if an FEL was a FA or PT. In FELs from young patients, increased stromal cellularity (83%), fronding (52%), and mitoses (41%) were more common. 34% regarded differentiating cellular FA from PT as a specific challenge; 54% had issues assigning a borderline PT grade. CONCLUSION Criteria for grading PT lie on a spectrum, leading to interpretive variability. The survey highlights the criteria most used by pathologists, which do not completely align with WHO recommendations.
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Affiliation(s)
| | - Stephen B Fox
- Peter MacCallum Cancer Centre and University of Melbourne, Australia
| | - Sunil R Lakhani
- The University of Queensland and Pathology Queensland, Australia
| | - Puay Hoon Tan
- Division of Pathology, Singapore General Hospital, Singapore
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19
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Mejía-Hernández JO, Keam SP, Saleh R, Muntz F, Fox SB, Byrne D, Kogan A, Pang L, Huynh J, Litchfield C, Caramia F, Lozano G, He H, You JM, Sandhu S, Williams SG, Haupt Y, Haupt S. Modelling aggressive prostate cancers of young men in immune-competent mice, driven by isogenic Trp53 alterations and Pten loss. Cell Death Dis 2022; 13:777. [PMID: 36075907 PMCID: PMC9465983 DOI: 10.1038/s41419-022-05211-y] [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: 05/26/2022] [Revised: 08/18/2022] [Accepted: 08/23/2022] [Indexed: 01/21/2023]
Abstract
Understanding prostate cancer onset and progression in order to rationally treat this disease has been critically limited by a dire lack of relevant pre-clinical animal models. We have generated a set of genetically engineered mice that mimic human prostate cancer, initiated from the gland epithelia. We chose driver gene mutations that are specifically relevant to cancers of young men, where aggressive disease poses accentuated survival risks. An outstanding advantage of our models are their intact repertoires of immune cells. These mice provide invaluable insight into the importance of immune responses in prostate cancer and offer scope for studying treatments, including immunotherapies. Our prostate cancer models strongly support the role of tumour suppressor p53 in functioning to critically restrain the emergence of cancer pathways that drive cell cycle progression; alter metabolism and vasculature to fuel tumour growth; and mediate epithelial to mesenchymal-transition, as vital to invasion. Importantly, we also discovered that the type of p53 alteration dictates the specific immune cell profiles most significantly disrupted, in a temporal manner, with ramifications for disease progression. These new orthotopic mouse models demonstrate that each of the isogenic hotspot p53 amino acid mutations studied (R172H and R245W, the mouse equivalents of human R175H and R248W respectively), drive unique cellular changes affecting pathways of proliferation and immunity. Our findings support the hypothesis that individual p53 mutations confer their own particular oncogenic gain of function in prostate cancer.
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Affiliation(s)
- Javier Octavio Mejía-Hernández
- grid.1055.10000000403978434Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC 3000 Australia ,grid.1008.90000 0001 2179 088XSir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3010 Australia ,grid.1055.10000000403978434Tumour Suppression and Cancer Sex Disparity Laboratory, Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC 3000 Australia ,Present Address: Telix Pharmaceuticals Ltd, Melbourne, VIC 3051 Australia
| | - Simon P. Keam
- grid.1055.10000000403978434Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC 3000 Australia ,grid.1008.90000 0001 2179 088XSir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3010 Australia ,grid.1055.10000000403978434Tumour Suppression and Cancer Sex Disparity Laboratory, Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC 3000 Australia ,grid.1135.60000 0001 1512 2287Present Address: CSL Innovation, CSL Ltd, Melbourne, VIC 3052 Australia
| | - Reem Saleh
- grid.1055.10000000403978434Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC 3000 Australia ,grid.1008.90000 0001 2179 088XSir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3010 Australia ,grid.1055.10000000403978434Tumour Suppression and Cancer Sex Disparity Laboratory, Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC 3000 Australia
| | - Fenella Muntz
- grid.1055.10000000403978434Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC 3000 Australia
| | - Stephen B. Fox
- grid.1055.10000000403978434Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC 3000 Australia ,grid.1008.90000 0001 2179 088XSir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3010 Australia ,grid.1055.10000000403978434Pathology Department, Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC 3000 Australia
| | - David Byrne
- grid.1055.10000000403978434Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC 3000 Australia ,grid.1055.10000000403978434Pathology Department, Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC 3000 Australia
| | - Arielle Kogan
- grid.1055.10000000403978434Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC 3000 Australia ,grid.1008.90000 0001 2179 088XSir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3010 Australia ,grid.1055.10000000403978434Tumour Suppression and Cancer Sex Disparity Laboratory, Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC 3000 Australia
| | - Lokman Pang
- grid.1018.80000 0001 2342 0938Olivia Newton-John Cancer Research Institute, School of Cancer Medicine, La Trobe University, Heidelberg, VIC 3084 Australia
| | - Jennifer Huynh
- grid.1018.80000 0001 2342 0938Olivia Newton-John Cancer Research Institute, School of Cancer Medicine, La Trobe University, Heidelberg, VIC 3084 Australia
| | - Cassandra Litchfield
- grid.1055.10000000403978434Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC 3000 Australia ,grid.1008.90000 0001 2179 088XSir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3010 Australia ,grid.1055.10000000403978434Tumour Suppression and Cancer Sex Disparity Laboratory, Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC 3000 Australia
| | - Franco Caramia
- grid.1055.10000000403978434Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC 3000 Australia ,grid.1008.90000 0001 2179 088XSir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3010 Australia ,grid.1055.10000000403978434Tumour Suppression and Cancer Sex Disparity Laboratory, Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC 3000 Australia
| | - Guillermina Lozano
- grid.240145.60000 0001 2291 4776Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX USA ,grid.267308.80000 0000 9206 2401University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, University of Texas, Houston, TX USA
| | - Hua He
- grid.240145.60000 0001 2291 4776Department of Hematopathology, UT MD Anderson Cancer Center, Houston, TX USA
| | - James M. You
- grid.267308.80000 0000 9206 2401University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, University of Texas, Houston, TX USA ,grid.240145.60000 0001 2291 4776Department of Hematopathology, UT MD Anderson Cancer Center, Houston, TX USA
| | - Shahneen Sandhu
- grid.1055.10000000403978434Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC 3000 Australia ,grid.1008.90000 0001 2179 088XSir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3010 Australia ,grid.1055.10000000403978434Department of Medical Oncology, Peter MacCallum Cancer Centre, Parkville, VIC 3000 Australia
| | - Scott G. Williams
- grid.1055.10000000403978434Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC 3000 Australia ,grid.1008.90000 0001 2179 088XSir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3010 Australia ,grid.1055.10000000403978434Division of Radiation Oncology, Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC 3000 Australia
| | - Ygal Haupt
- grid.1055.10000000403978434Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC 3000 Australia ,grid.1008.90000 0001 2179 088XSir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3010 Australia ,grid.1055.10000000403978434Tumour Suppression and Cancer Sex Disparity Laboratory, Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC 3000 Australia ,Present Address: Vittail Ltd, Melbourne, VIC 3146 Australia
| | - Sue Haupt
- grid.1055.10000000403978434Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC 3000 Australia ,grid.1008.90000 0001 2179 088XSir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3010 Australia ,grid.1055.10000000403978434Tumour Suppression and Cancer Sex Disparity Laboratory, Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC 3000 Australia
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20
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Winship AL, Alesi LR, Sant S, Stringer JM, Cantavenera A, Hegarty T, Requesens CL, Liew SH, Sarma U, Griffiths MJ, Zerafa N, Fox SB, Brown E, Caramia F, Zareie P, La Gruta NL, Phillips KA, Strasser A, Loi S, Hutt KJ. Checkpoint inhibitor immunotherapy diminishes oocyte number and quality in mice. Nat Cancer 2022; 3:1-13. [PMID: 36008687 DOI: 10.1038/s43018-022-00413-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 06/23/2022] [Indexed: 06/15/2023]
Abstract
Loss of fertility is a major concern for female reproductive-age cancer survivors, since a common side-effect of conventional cytotoxic cancer therapies is permanent damage to the ovary. While immunotherapies are increasingly becoming a standard of care for many cancers-including in the curative setting-their impacts on ovarian function and fertility are unknown. We evaluated the effect of immune checkpoint inhibitors blocking programmed cell death protein ligand 1 and cytotoxic T lymphocyte-associated antigen 4 on the ovary using tumor-bearing and tumor-free mouse models. We find that immune checkpoint inhibition increases immune cell infiltration and tumor necrosis factor-α expression within the ovary, diminishes the ovarian follicular reserve and impairs the ability of oocytes to mature and ovulate. These data demonstrate that immune checkpoint inhibitors have the potential to impair both immediate and future fertility, and studies in women should be prioritized. Additionally, fertility preservation should be strongly considered for women receiving these immunotherapies, and preventative strategies should be investigated in future studies.
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Affiliation(s)
- Amy L Winship
- Development and Stem Cell Program and Department of Anatomy and Developmental Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Lauren R Alesi
- Development and Stem Cell Program and Department of Anatomy and Developmental Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Sneha Sant
- Division of Research, Peter MacCallum Cancer Centre, University of Melbourne, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Jessica M Stringer
- Development and Stem Cell Program and Department of Anatomy and Developmental Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Aldana Cantavenera
- Development and Stem Cell Program and Department of Anatomy and Developmental Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Teharn Hegarty
- Development and Stem Cell Program and Department of Anatomy and Developmental Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Carolina Lliberos Requesens
- Development and Stem Cell Program and Department of Anatomy and Developmental Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Seng H Liew
- Development and Stem Cell Program and Department of Anatomy and Developmental Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Urooza Sarma
- Development and Stem Cell Program and Department of Anatomy and Developmental Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Meaghan J Griffiths
- Development and Stem Cell Program and Department of Anatomy and Developmental Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Nadeen Zerafa
- Development and Stem Cell Program and Department of Anatomy and Developmental Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Stephen B Fox
- Division of Research, Peter MacCallum Cancer Centre, University of Melbourne, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Emmaline Brown
- Division of Research, Peter MacCallum Cancer Centre, University of Melbourne, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Franco Caramia
- Division of Research, Peter MacCallum Cancer Centre, University of Melbourne, Melbourne, Victoria, Australia
| | - Pirooz Zareie
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Nicole L La Gruta
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Kelly-Anne Phillips
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Andreas Strasser
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Sherene Loi
- Division of Research, Peter MacCallum Cancer Centre, University of Melbourne, Melbourne, Victoria, Australia.
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia.
| | - Karla J Hutt
- Development and Stem Cell Program and Department of Anatomy and Developmental Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.
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Fox SB, Webster F, Chen CJ, Chua B, Collins LC, Foschini MP, Mann GB, Millar EKA, Pinder SE, Rakha E, Shaaban AM, Tan BY, Tse GM, Watson PH, Tan PH. Dataset for pathology reporting of ductal carcinoma in situ, variants of lobular carcinoma in situ and low grade lesions: recommendations from the International Collaboration on Cancer Reporting (ICCR). Histopathology 2022; 81:467-476. [DOI: 10.1111/his.14725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 07/05/2022] [Accepted: 07/05/2022] [Indexed: 11/28/2022]
Affiliation(s)
- SB Fox
- Department of Pathology, Peter MacCallum Cancer Centre, Level 4 Victorian Comprehensive Cancer Centre Melbourne VIC 3000 Australia
| | - F Webster
- International Collaboration on Cancer Reporting, Albion St, Surry Hills NSW 2010 Australia
| | - CJ Chen
- Department of Pathology and Laboratory Medicine, Taichung Veterans General Hospital, 1650 Taiwan Boulevard Sect. 4 Taichung 40705 Taiwan
| | - B Chua
- Prince of Wales Clinical School, UNSW Sydney The University of New South Wales Randwick NSW 2031 Australia
| | - LC Collins
- Department of Pathology, Beth Israel Deaconess Medical Center, 330 Brookline Ave and Harvard Medical School Boston MA 02215 USA
| | - MP Foschini
- Department Anatomic Pathology University of Bologna Department of Biomedical and Neuromotor Sciences Unit of Anatomic Pathology at Bellaria Hospital, Via Altura 3 40139 Bologna Italy
| | - GB Mann
- The Breast Service, The Royal Melbourne Hospital, Grattan St Parkville VIC 3050 Australia
| | - EKA Millar
- Department of Anatomical Pathology Heath Pathology St George Hospital, Kogarah NSW 2217 & St George & Sutherland Clinical School, UNSW NSW Sydney Australia
| | - SE Pinder
- School of Cancer & Pharmaceutical Sciences King's College London, 9th Floor, Innovation Hub, Comprehensive Cancer Centre at Guy's Hospital, Great Maze Pond. London SE1 9RT United Kingdom
| | - E Rakha
- Department of Histopathology The University of Nottingham Nottingham City Hospital, Hucknall Road Nottingham NG5 1PB United Kingdom
| | - AM Shaaban
- Department of Cellular Pathology, Queen Elizabeth Hospital Birmingham and Cancer and Genomic Sciences University of Birmingham, Mindelsohn Way Birmingham B15 2GW United Kingdom
| | - BY Tan
- Department of Anatomical Pathology, Singapore General Hospital College Rd Singapore 169856
| | - GM Tse
- Department of Anatomical and Cellular Pathology, Prince of Wales Hospital The Chinese University of Hong Kong, Ngan Shing Street Shatin Hong Kong
| | - PH Watson
- Department of Pathology, Biobanking and Biospecimen Research Services, Deeley Research Centre, BC Cancer Agency, 2410 Lee Ave Victoria BC V8R 6V5 Canada Victoria British Columbia Canada
| | - PH Tan
- Division of Pathology Singapore General Hospital Singapore
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22
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van Geelen CT, Savas P, Teo ZL, Luen SJ, Weng CF, Ko YA, Kuykhoven KS, Caramia F, Salgado R, Francis PA, Dawson SJ, Fox SB, Fellowes A, Loi S. Correction to: Clinical implications of prospective genomic profiling of metastatic breast cancer patients. Breast Cancer Res 2022; 24:50. [PMID: 35841108 PMCID: PMC9284837 DOI: 10.1186/s13058-022-01539-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
| | - Peter Savas
- Division of Research, Peter MacCallum Cancer Centre, Melbourne, Australia.,Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Zhi Ling Teo
- Division of Research, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Stephen J Luen
- Division of Research, Peter MacCallum Cancer Centre, Melbourne, Australia.,Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Chen-Fang Weng
- Division of Research, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Yi-An Ko
- Division of Research, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Keilly S Kuykhoven
- Australian Centre for Disease Preparedness, Commonwealth Scientific and Industrial Research Organisation (CSIRO) Health and Biosecurity, Geelong, Australia
| | - Franco Caramia
- Division of Research, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Roberto Salgado
- Division of Research, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Prudence A Francis
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, 305 Grattan St, Melbourne, VIC, 3000, Australia
| | - Sarah-Jane Dawson
- Division of Research, Peter MacCallum Cancer Centre, Melbourne, Australia.,Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, 305 Grattan St, Melbourne, VIC, 3000, Australia
| | - Stephen B Fox
- Division of Research, Peter MacCallum Cancer Centre, Melbourne, Australia.,Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, 305 Grattan St, Melbourne, VIC, 3000, Australia
| | - Andrew Fellowes
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Sherene Loi
- Division of Research, Peter MacCallum Cancer Centre, Melbourne, Australia. .,Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, Australia. .,Sir Peter MacCallum Department of Oncology, University of Melbourne, 305 Grattan St, Melbourne, VIC, 3000, Australia.
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23
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Lin FPY, Thavaneswaran S, Grady JP, Napier CE, Kansara M, Sebastian L, Kee D, Oakes SR, Blackburn J, Scott HS, Glover A, Fox SB, Goldstein D, Leo P, Amanuel B, Desai J, Lee CK, Ballinger ML, Simes J, Thomas DM. Molecular therapy selection in treatment-refractory advanced cancers: A retrospective cohort study determining the utility of TOPOGRAPH knowledge base. J Clin Oncol 2022. [DOI: 10.1200/jco.2022.40.16_suppl.3073] [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: 11/20/2022] Open
Abstract
3073 Background: Comprehensive genomic profiling (CGP) is increasingly used to guide therapy selection in advanced cancer patients who have exhausted standard therapy options. Here we assess the utility of Therapy Oriented Precision Oncology Guidelines for Recommending Anticancer Pharmaceuticals (TOPOGRAPH) to guide matching of drug treatments based on CGP in this setting. Methods: This study was conducted in an Australia-wide precision oncology program, the Molecular Screening and Therapeutics Study (MoST, ANZCTR registration ACTRN12616000908437). All patients with advanced cancer after exhausting standard treatments underwent CGP in 2016-2021 were stratified into cohort A (no further therapy received) and B (received ≥1 therapy after CGP). The primary outcome was overall survival (OS) estimated by the Kaplan-Meier method, using the log rank test to assess between-group differences. TOPOGRAPH matched the treatment history to the CGP results, stratified into clinically active (Tiers 1-3, T1-3), investigational (T3B/4), inactive (R2) or unmatched groups. Results: Over a median follow-up of 21.7 months (mo) for 2852 patients (75% with rare cancers, n = 2150), the median OS (mOS) from the date of CGP result was 7.0 mo (95% CI 6.4-7.6) for cohort A (n = 1562) and 15.8 mo (95% CI 14.5-16.9) for cohort B (n = 1290). In both cohorts, patients with CGP results matching any TOPOGRAPH tier (T1-4) had shorter OS compared to patients without a matching tier (A: 6.4 v 20.5 mo, hazard ratio for death [HR] 2.15, p<0.001; B: 14.7 v 23.6 mo, HR 1.43, p<0.001). Patients in cohort B receiving matched therapy (n=342, 27%) had a longer mOS than 948 patients who received only unmatched therapy (16.9 v 10.4 mo, HR 0.70, p<0.001). For CGP results matched to T1-3, 122 patients who received a T1-3 therapy had a significantly longer mOS than those who received unmatched therapy (22.1 v 9.8 mo, HR 0.51, p<0.001). For CGP results matched only to T3B/4, a trend toward longer mOS was observed in patients receiving matched therapy in T3B/4 (n = 138, 14.5 v unmatched 10.0 mo, HR 0.81, P = 0.07). In tier-matched analysis, the mOS were not significantly different between patients who received genomics matched v unmatched therapy in T3B (matching outside cognate histotypes, n = 48 v 508, 11.9 v 9.7 mo, HR 0.84, p = 0.36) and T4 (n = 32 v 134; therapy with preclinical/early clinical evidence, 17.1 v 12.2 mo, HR 0.69, p = 0.17). Conclusions: TOPOGRAPH is prognostic and likely predictive of treatment effect based on CGP, supporting its utility in guiding molecular therapy selection in patients who have exhausted standard treatment options. [Table: see text]
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Affiliation(s)
- Frank Po-Yen Lin
- NHMRC Clinical Trials Centre, University of Sydney, Sydney, NSW, Australia
| | | | - John P. Grady
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | | | - Maya Kansara
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Lucille Sebastian
- NHMRC Clinical Trials Centre, University of Sydney, Sydney, Australia
| | - Damien Kee
- Rare Cancer Laboratory, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | | | - James Blackburn
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Hamish S. Scott
- Centre for Cancer Biology, An SA Pathology & UniSA Alliance, Adelaide, SA, Australia
| | | | | | - David Goldstein
- Prince of Wales Hospital, University of New South Wales, Cancer Survivors Centre, Randwick, Australia
| | - Paul Leo
- Center for Genomics and Personalized Health, Queensland University of Technology, Brisbane, QLD, Australia
| | - Benhur Amanuel
- Department of Anatomical Pathology, PathWest Laboratory Medicine, Western Australia, Australia
| | - Jayesh Desai
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | | | | | - John Simes
- NHMRC Clinical Trials Centre, University of Sydney, Sydney, NSW, Australia
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24
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Loi S, Francis PA, Zdenkowski N, Gebski V, Fox SB, White M, Kiely BE, Woodward NE, Hui R, Redfern AD, Calvert R, Rennie L, Boyle FM. Neoadjuvant ipilimumab and nivolumab in combination with paclitaxel following anthracycline-based chemotherapy in patients with treatment resistant early-stage triple-negative breast cancer (TNBC): A single-arm phase 2 trial. J Clin Oncol 2022. [DOI: 10.1200/jco.2022.40.16_suppl.602] [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: 11/20/2022] Open
Abstract
602 Background: We examined the efficacy and safety of neoadjuvant ipilimumab and nivolumab combined with paclitaxel following suboptimal response to anthracycline-based chemotherapy in patients with early-stage TNBC. Methods: This single arm multicentre phase 2 study enrolled 34 patients in 8 sites. Patients were aged ≥18 years with previously untreated stage 3 TNBC and were required to have ≥15mm of tumor remaining or 10mm of tumor with one positive lymph node after 4 cycles of anthracycline-based therapy. A suboptimal response subset at baseline was defined as < 50% reduction in tumor volume after initial anthracycline-based chemotherapy. Patients received neoadjuvant ipilimumab 1mg/kg IV 6 weekly for 2 doses and nivolumab 240mg every 2 weeks for 6 doses, with weekly paclitaxel at 80mg/m2 for 12 weeks, followed by surgery. Nivolumab (480mg 4-weekly) continued post operatively for further 9 months. Primary endpoint was pathological complete response (pCR) in breast and axilla, with secondary endpoints pCR in the suboptimal responders, pCR in PD-L1 positive patients (≥1% by SP142 assay), clinical response in the breast (ORR by RECIST), event-free (EFS) and overall survival (OS). Results: Between December 2018 and April 2020, 34 patients were enrolled, 33 were evaluable for the primary endpoint. Median age was 46.6yrs. At diagnosis, all patients were clinical stage III (AJCC v8), 16/34 (47%) were node positive, 8/31 (26%) were PD-L1 positive. At study entry (following anthracycline-based chemo), the median tumor size by ultrasound was 28mm (12-62). 16/33 (48%) were considered suboptimal responders. The pCR rate (ypT0ypN0) was 24.2% (95% CI, 11.09-42.26) in all evaluable, 37.5% [3/11] in PD-L1+ and 23% [5/22] in PD-L1- patients. In patients with suboptimal anthracycline response (< 50% tumor reduction), the pCR rate was 18.8% (95% CI, 8.52-75.51) (3/16). ORR in the breast was 57.6% (19/33) in all evaluable patients and 43.7% (8/20) in the suboptimal responders. The number of patients with residual cancer burden (RCB) class 0,1,2,3 was 8 (24%), 1 (3%), 19 (57.5%) and 5 (15%) respectively. With 14 months median follow up, 12-months EFS was estimated at 85% and OS 94%. For patients with pCR vs non-pCR, the hazard ratio (HR) for EFS was 0.62, 12 mo EFS was 100% vs 75%. In the neoadjuvant phase, 15/33 (45%) patients experienced at least one grade 3-4 adverse event. Most common immune-related event was grade 1 or 2 pneumonitis 9/33 (27%), which generally occurred with fever after the first dose of ipilimumab, and resolved. There was one case of grade 3 colitis. Conclusions: In these high risk patients, the addition of ipilimumab and nivolumab to neoadjuvant paclitaxel resulted in promising ORR and pCR rates, regardless of PD-L1 status. Rates of low grade pneumonitis were high. Follow up continues. Clinical trial information: ACTRN12617000651381.
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Affiliation(s)
- Sherene Loi
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Prudence A. Francis
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | | | - Val Gebski
- NHMRC Clinical Trials Centre, University of Sydney, Sydney, Australia
| | | | | | | | | | - Rina Hui
- Westmead Breast Cancer Institute, Westmead Hospital and the University of Sydney, Sydney, NSW, Australia
| | | | - Raewyn Calvert
- Breast Cancer Trials - Australia and New Zealand, Newcastle, NSW, Australia
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25
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White C, Scott RJ, Paul C, Ziolkowski A, Mossman D, Fox SB, Michael M, Ackland S. Dihydropyrimidine Dehydrogenase Deficiency and Implementation of Upfront DPYD Genotyping. Clin Pharmacol Ther 2022; 112:791-802. [PMID: 35607723 DOI: 10.1002/cpt.2667] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 05/13/2022] [Indexed: 12/27/2022]
Abstract
Fluoropyrimidines (FP; 5-fluorouracil, capecitabine, and tegafur) are a commonly prescribed class of antimetabolite chemotherapies, used for various solid organ malignancies in over 2 million patients globally per annum. Dihydropyrimidine dehydrogenase (DPD), encoded by the DPYD gene, is the critical enzyme implicated in FP metabolism. DPYD variant genotypes can result in decreased DPD production, leading to the development of severe toxicities resulting in hospitalization, intensive care admission, and even death. Management of toxicity incurs financial burden on both patients and healthcare systems alike. Upfront DPYD genotyping to identify variant carriers allows an opportunity to identify patients who are at high risk to suffer from serious toxicities and allow prospective dose adjustment of FP treatment. This approach has been shown to reduce patient morbidity, as well as improve the cost-effectiveness of managing FP treatment. Upfront DPYD genotyping has been recently endorsed by several countries in Europe and the United Kingdom. This review summarizes current knowledge about DPD deficiency and upfront DPYD genotyping, including clinical and cost-effectiveness outcomes, with the intent of supporting implementation of an upfront DPYD genotyping service with individualized dose-personalization.
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Affiliation(s)
- Cassandra White
- School of Medicine and Public Health, University of Newcastle, College of Health, Medicine and Wellbeing, Callaghan, New South Wales, Australia.,Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia
| | - Rodney J Scott
- Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia.,School of Biomedical Science and Pharmacy, University of Newcastle, College of Health, Medicine and Wellbeing, Callaghan, New South Wales, Australia.,Department of Molecular Genetics, Pathology North John Hunter Hospital, New Lambton Heights, New South Wales, Australia
| | - Christine Paul
- School of Medicine and Public Health, University of Newcastle, College of Health, Medicine and Wellbeing, Callaghan, New South Wales, Australia.,Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia
| | - Andrew Ziolkowski
- Department of Molecular Genetics, Pathology North John Hunter Hospital, New Lambton Heights, New South Wales, Australia
| | - David Mossman
- Department of Molecular Genetics, Pathology North John Hunter Hospital, New Lambton Heights, New South Wales, Australia
| | - Stephen B Fox
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Michael Michael
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Stephen Ackland
- School of Medicine and Public Health, University of Newcastle, College of Health, Medicine and Wellbeing, Callaghan, New South Wales, Australia.,Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia.,Hunter Cancer Centre, Lake Macquarie Private Hospital, Gateshead, New South Wales, Australia
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26
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Arnolda R, Howlett K, Chan T, Raleigh J, Hatzimihalis A, Bell A, Fellowes A, Sandhu S, McArthur GA, Fox SB, Dawson SJ, Hewitt C, Jones K, Wong SQ. Clinical validation and implementation of droplet digital PCR for the detection of BRAF mutations from cell-free DNA. Pathology 2022; 54:772-778. [DOI: 10.1016/j.pathol.2022.02.010] [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] [Received: 09/13/2021] [Revised: 02/03/2022] [Accepted: 02/17/2022] [Indexed: 10/18/2022]
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27
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Doig KD, Love CG, Conway T, Seleznev A, Ma D, Fellowes A, Blombery P, Fox SB. Findings from precision oncology in the clinic: rare, novel variants are a significant contributor to scaling molecular diagnostics. BMC Med Genomics 2022; 15:70. [PMID: 35346197 PMCID: PMC8962530 DOI: 10.1186/s12920-022-01214-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 03/15/2022] [Indexed: 11/24/2022] Open
Abstract
Background Next generation sequencing for oncology patient management is now routine in clinical pathology laboratories. Although wet lab, sequencing and pipeline tasks are largely automated, the analysis of variants for clinical reporting remains largely a manual task. The increasing volume of sequencing data and the limited availability of genetic experts to analyse and report on variants in the data is a key scalability limit for molecular diagnostics. Method To determine the impact and size of the issue, we examined the longitudinally compiled genetic variants from 48,036 cancer patients over a six year period in a large cancer hospital from ten targeted cancer panel tests in germline, solid tumour and haematology contexts using hybridization capture and amplicon assays. This testing generated 24,168,398 sequenced variants of which 23,255 (8214 unique) were clinically reported. Results Of the reported variants, 17,240 (74.1%) were identified in more than one assay which allowed curated variant data to be reused in later reports. The remainder, 6015 (25.9%) were not subsequently seen in later assays and did not provide any reuse benefit. The number of new variants requiring curation has significantly increased over time from 1.72 to 3.73 variants per sample (292 curated variants per month). Analysis of the 23,255 variants reported, showed 28.6% (n = 2356) were not present in common public variant resources and therefore required de novo curation. These in-house only variants were enriched for indels, tumour suppressor genes and from solid tumour assays. Conclusion This analysis highlights the significant percentage of variants not present within common public variant resources and the level of non-recurrent variants that consequently require greater curation effort. Many of these variants are unique to a single patient and unlikely to appear in other patients reflecting the personalised nature of cancer genomics. This study depicts the real-world situation for pathology laboratories faced with curating increasing numbers of low-recurrence variants while needing to expedite the process of manual variant curation. In the absence of suitably accurate automated methods, new approaches are needed to scale oncology diagnostics for future genetic testing volumes. Supplementary Information The online version contains supplementary material available at 10.1186/s12920-022-01214-y.
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28
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Delahunty R, Nguyen L, Craig S, Creighton B, Ariyaratne D, Garsed DW, Christie E, Fereday S, Andrews L, Lewis A, Limb S, Pandey A, Hendley J, Traficante N, Carvajal N, Spurdle AB, Thompson B, Parsons MT, Beshay V, Volcheck M, Semple T, Lupat R, Doig K, Yu J, Chen XQ, Marsh A, Love C, Bilic S, Beilin M, Nichols CB, Greer C, Lee YC, Gerty S, Gill L, Newton E, Howard J, Williams R, Norris C, Stephens AN, Tutty E, Smyth C, O'Connell S, Jobling T, Stewart CJR, Tan A, Fox SB, Pachter N, Li J, Ellul J, Mir Arnau G, Young MA, Gordon L, Forrest L, Harris M, Livingstone K, Hill J, Chenevix-Trench G, Cohen PA, Webb PM, Friedlander M, James P, Bowtell D, Alsop K. TRACEBACK: Testing of Historical Tubo-Ovarian Cancer Patients for Hereditary Risk Genes as a Cancer Prevention Strategy in Family Members. J Clin Oncol 2022; 40:2036-2047. [PMID: 35263119 PMCID: PMC9197360 DOI: 10.1200/jco.21.02108] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
PURPOSE Tubo-ovarian cancer (TOC) is a sentinel cancer for BRCA1 and BRCA2 pathogenic variants (PVs). Identification of a PV in the first member of a family at increased genetic risk (the proband) provides opportunities for cancer prevention in other at-risk family members. Although Australian testing rates are now high, PVs in patients with TOC whose diagnosis predated revised testing guidelines might have been missed. We assessed the feasibility of detecting PVs in this population to enable genetic risk reduction in relatives. PATIENTS AND METHODS In this pilot study, deceased probands were ascertained from research cohort studies, identification by a relative, and gynecologic oncology clinics. DNA was extracted from archival tissue or stored blood for panel sequencing of 10 risk-associated genes. Testing of deceased probands ascertained through clinic records was performed with a consent waiver. RESULTS We identified 85 PVs in 84 of 787 (11%) probands. Familial contacts of 39 of 60 (65%) deceased probands with an identified recipient (60 of 84; 71%) have received a written notification of results, with follow-up verbal contact made in 85% (33 of 39). A minority of families (n = 4) were already aware of the PV. For many (29 of 33; 88%), the genetic result provided new information and referral to a genetic service was accepted in most cases (66%; 19 of 29). Those who declined referral (4 of 29) were all male next of kin whose family member had died more than 10 years before. CONCLUSION We overcame ethical and logistic challenges to demonstrate that retrospective genetic testing to identify PVs in previously untested deceased probands with TOC is feasible. Understanding reasons for a family member's decision to accept or decline a referral will be important for guiding future TRACEBACK projects. Genetic testing of deceased patients allows identification of at-risk families for cancer prevention![]()
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Affiliation(s)
- Rachel Delahunty
- Peter MacCallum Cancer Centre, Parkville, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Victoria, Australia
| | - Linh Nguyen
- Peter MacCallum Cancer Centre, Parkville, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Victoria, Australia
| | - Stuart Craig
- Peter MacCallum Cancer Centre, Parkville, Victoria, Australia
| | | | | | - Dale W Garsed
- Peter MacCallum Cancer Centre, Parkville, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Victoria, Australia
| | - Elizabeth Christie
- Peter MacCallum Cancer Centre, Parkville, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Victoria, Australia
| | - Sian Fereday
- Peter MacCallum Cancer Centre, Parkville, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Victoria, Australia
| | - Lesley Andrews
- Prince of Wales Hospital, Randwick, New South Wales, Australia.,Royal Hospital for Women, Randwick, New South Wales Australia
| | - Alexandra Lewis
- Parkville Familial Cancer Centre, Peter MacCallum Cancer Centre and Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Sharne Limb
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Victoria, Australia.,Parkville Familial Cancer Centre, Peter MacCallum Cancer Centre and Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Ahwan Pandey
- Peter MacCallum Cancer Centre, Parkville, Victoria, Australia
| | - Joy Hendley
- Peter MacCallum Cancer Centre, Parkville, Victoria, Australia
| | - Nadia Traficante
- Peter MacCallum Cancer Centre, Parkville, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Victoria, Australia
| | | | - Amanda B Spurdle
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Bryony Thompson
- Department of Pathology, Royal Melbourne Hospital, Parkville, Victoria, Australia.,Department of Clinical Pathology, University of Melbourne, Parkville, Victoria, Australia
| | - Michael T Parsons
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Victoria Beshay
- Peter MacCallum Cancer Centre, Parkville, Victoria, Australia
| | - Mila Volcheck
- Peter MacCallum Cancer Centre, Parkville, Victoria, Australia.,The Royal Women's Hospital, Melbourne Victoria, Australia.,The Royal Children's Hospital, Melbourne Victoria, Australia
| | - Timothy Semple
- Peter MacCallum Cancer Centre, Parkville, Victoria, Australia
| | - Richard Lupat
- Peter MacCallum Cancer Centre, Parkville, Victoria, Australia
| | - Kenneth Doig
- Peter MacCallum Cancer Centre, Parkville, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Victoria, Australia
| | - Jiaan Yu
- Peter MacCallum Cancer Centre, Parkville, Victoria, Australia
| | - Xiao Qing Chen
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Anna Marsh
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | | | - Sanela Bilic
- Department of Gynecological Oncology, St John of God Hospital, Subiaco, Western Australia, Australia
| | - Maria Beilin
- Department of Gynecological Oncology, St John of God Hospital, Subiaco, Western Australia, Australia
| | | | - Christina Greer
- Genetic Services of Western Australia, Perth, Western Australia, Australia
| | - Yeh Chen Lee
- Prince of Wales Hospital, Randwick, New South Wales, Australia.,Royal Hospital for Women, Randwick, New South Wales Australia.,Prince of Wales Clinical School, Faculty of Medicine, University of New South Wales, Sydney, Australia
| | - Susan Gerty
- Prince of Wales Hospital, Randwick, New South Wales, Australia
| | - Lynette Gill
- Prince of Wales Hospital, Randwick, New South Wales, Australia
| | - Emma Newton
- Prince of Wales Hospital, Randwick, New South Wales, Australia
| | - Julie Howard
- Prince of Wales Hospital, Randwick, New South Wales, Australia
| | - Rachel Williams
- Prince of Wales Clinical School, Faculty of Medicine, University of New South Wales, Sydney, Australia.,Prince of Wales Hereditary Cancer Centre, Prince of Wales Hospital Randwick, New South Wales, Australia
| | - Christie Norris
- Prince of Wales Hospital, Randwick, New South Wales, Australia
| | - Andrew N Stephens
- Hudson Institute of Medical Research, Clayton, Victoria, Australia.,Department of Molecular and Translational Sciences, Monash University, Clayton, Victoria, Australia.,School of Health and Biomedical Sciences, RMIT University, Melbourne, Australia
| | - Erin Tutty
- Parkville Familial Cancer Centre, Peter MacCallum Cancer Centre and Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Courtney Smyth
- Monash Health Familial Cancer Centre, Clayton, Victoria, Australia
| | - Shona O'Connell
- Monash Health Familial Cancer Centre, Clayton, Victoria, Australia
| | | | - Colin J R Stewart
- PathWest, King Edward Memorial Hospital, Subiaco, Western Australia, Australia
| | - Adeline Tan
- Clinipath Pathology, Osborne Park, Western Australia, Australia
| | - Stephen B Fox
- Peter MacCallum Cancer Centre, Parkville, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Victoria, Australia
| | - Nicholas Pachter
- Genetic Services of Western Australia, Perth, Western Australia, Australia.,King Edward Memorial Hospital, Perth, Western Australia, Australia.,Faculty of Health and Medical Sciences, University of Western Australia, Perth Australia
| | - Jason Li
- Peter MacCallum Cancer Centre, Parkville, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Victoria, Australia
| | - Jason Ellul
- Peter MacCallum Cancer Centre, Parkville, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Victoria, Australia
| | - Gisela Mir Arnau
- Peter MacCallum Cancer Centre, Parkville, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Victoria, Australia
| | - Mary-Anne Young
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research Darlinghurst, New South Wales, Australia
| | - Louisa Gordon
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia.,School of Nursing, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Laura Forrest
- Peter MacCallum Cancer Centre, Parkville, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Victoria, Australia
| | | | | | - Jane Hill
- Ovarian Cancer Australia, Melbourne, Victoria, Australia
| | | | - Paul A Cohen
- Department of Gynecological Oncology, St John of God Hospital, Subiaco, Western Australia, Australia.,Division of Obstetrics and Gynaecology, Faculty of Health and Medical Sciences, University of Western Australia, Perth, Australia
| | - Penelope M Webb
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Michael Friedlander
- Prince of Wales Hospital, Randwick, New South Wales, Australia.,Royal Hospital for Women, Randwick, New South Wales Australia.,Genetic Services of Western Australia, Perth, Western Australia, Australia
| | - Paul James
- Peter MacCallum Cancer Centre, Parkville, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Victoria, Australia
| | - David Bowtell
- Peter MacCallum Cancer Centre, Parkville, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Victoria, Australia
| | - Kathryn Alsop
- Peter MacCallum Cancer Centre, Parkville, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Victoria, Australia
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Mweempwa A, Xu H, Vissers JHA, Tothill RW, Pattison AD, Fellowes AP, Thomas DM, Richardson G, Hicks RJ, Grimmond SM, Fox SB, Luen SJ, Desai J, Solomon BJ. Novel RET Fusion RET-SEPTIN9 Predicts Response to Selective RET Inhibition With Selpercatinib in Malignant Pheochromocytoma. JCO Precis Oncol 2022; 5:1160-1165. [PMID: 34994633 DOI: 10.1200/po.21.00127] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Affiliation(s)
- Angela Mweempwa
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Huiling Xu
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Department of Clinical Pathology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Australia
| | - Joseph H A Vissers
- Centre for Cancer Research and Department of Clinical Pathology, The University of Melbourne, Parkville, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
| | - Richard W Tothill
- Centre for Cancer Research and Department of Clinical Pathology, The University of Melbourne, Parkville, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
| | - Andrew D Pattison
- Centre for Cancer Research and Department of Clinical Pathology, The University of Melbourne, Parkville, Victoria, Australia
| | - Andrew P Fellowes
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - David M Thomas
- The Kinghorn Cancer Centre and Cancer Division, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Gary Richardson
- Cabrini Health, Department of Medical Oncology, Malvern, Victoria, Australia
| | - Rodney J Hicks
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia.,Molecular Imaging and Therapeutic Nuclear Medicine, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Sean M Grimmond
- Centre for Cancer Research and Department of Clinical Pathology, The University of Melbourne, Parkville, Victoria, Australia
| | - Stephen B Fox
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Department of Clinical Pathology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
| | - Stephen J Luen
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Jayesh Desai
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
| | - Benjamin J Solomon
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
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30
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Lau LMS, Mayoh C, Xie J, Barahona P, MacKenzie KL, Wong M, Kamili A, Tsoli M, Failes TW, Kumar A, Mould EVA, Gifford A, Chow SO, Pinese M, Fletcher JI, Arndt GM, Khuong-Quang DA, Wadham C, Eden G, Trebilcock P, Joshi S, Alfred S, Gopalakrishnan A, Khan A, Grebert Wade D, Strong PA, Manouvrier E, Morgan LT, Cadiz R, Ung C, Thomas DM, Tucker KM, Warby M, McCowage GB, Dalla-Pozza L, Byrne JA, Saletta F, Fellowes A, Fox SB, Norris MD, Tyrrell V, Trahair TN, Lock RB, Cowley MJ, Ekert PG, Haber M, Ziegler DS, Marshall GM. In vitro and in vivo drug screens of tumor cells identify novel therapies for high-risk child cancer. EMBO Mol Med 2021; 14:e14608. [PMID: 34927798 PMCID: PMC8988207 DOI: 10.15252/emmm.202114608] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [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: 05/28/2021] [Revised: 11/25/2021] [Accepted: 12/01/2021] [Indexed: 01/08/2023] Open
Abstract
Biomarkers which better match anticancer drugs with cancer driver genes hold the promise of improved clinical responses and cure rates. We developed a precision medicine platform of rapid high-throughput drug screening (HTS) and patient-derived xenografting (PDX) of primary tumor tissue, and evaluated its potential for treatment identification among 56 consecutively enrolled high-risk pediatric cancer patients, compared with conventional molecular genomics and transcriptomics. Drug hits were seen in the majority of HTS and PDX screens, which identified therapeutic options for 10 patients for whom no targetable molecular lesions could be found. Screens also provided orthogonal proof of drug efficacy suggested by molecular analyses and negative results for some molecular findings. We identified treatment options across the whole testing platform for 70% of patients. Only molecular therapeutic recommendations were provided to treating oncologists and led to a change in therapy in 53% of patients, of whom 29% had clinical benefit. These data indicate that in vitro and in vivo drug screening of tumor cells could increase therapeutic options and improve clinical outcomes for high-risk pediatric cancer patients.
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Affiliation(s)
- Loretta M S Lau
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia.,School of Women's and Children's Health, UNSW Sydney, Kensington, NSW, Australia.,Kids Cancer Centre, Sydney Children's Hospital, Randwick, NSW, Australia
| | - Chelsea Mayoh
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia.,School of Women's and Children's Health, UNSW Sydney, Kensington, NSW, Australia
| | - Jinhan Xie
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia
| | - Paulette Barahona
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia
| | - Karen L MacKenzie
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia
| | - Marie Wong
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia.,School of Women's and Children's Health, UNSW Sydney, Kensington, NSW, Australia
| | - Alvin Kamili
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia.,School of Women's and Children's Health, UNSW Sydney, Kensington, NSW, Australia
| | - Maria Tsoli
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia
| | - Tim W Failes
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia.,ACRF Drug Discovery Centre for Childhood Cancer, Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia
| | - Amit Kumar
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia.,Children's Cancer Centre, Royal Children's Hospital, Parkville, Vic., Australia
| | - Emily V A Mould
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia
| | - Andrew Gifford
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia.,School of Women's and Children's Health, UNSW Sydney, Kensington, NSW, Australia
| | - Shu-Oi Chow
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia.,ACRF Drug Discovery Centre for Childhood Cancer, Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia
| | - Mark Pinese
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia.,School of Women's and Children's Health, UNSW Sydney, Kensington, NSW, Australia
| | - Jamie I Fletcher
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia.,School of Women's and Children's Health, UNSW Sydney, Kensington, NSW, Australia
| | - Greg M Arndt
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia.,ACRF Drug Discovery Centre for Childhood Cancer, Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia
| | - Dong-Anh Khuong-Quang
- Children's Cancer Centre, Royal Children's Hospital, Parkville, Vic., Australia.,Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Vic., Australia
| | - Carol Wadham
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia
| | - Georgina Eden
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia
| | - Peter Trebilcock
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia
| | - Swapna Joshi
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia
| | - Stephanie Alfred
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia
| | - Anjana Gopalakrishnan
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia
| | - Aaminah Khan
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia
| | - Dylan Grebert Wade
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia
| | - Patrick A Strong
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia
| | - Elodie Manouvrier
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia
| | - Lisa T Morgan
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia
| | - Roxanne Cadiz
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia
| | - Caitlin Ung
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia
| | - David M Thomas
- Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.,Faculty of Medicine, St Vincent's Clinical School, UNSW Sydney, Kensington, NSW, Australia
| | - Katherine M Tucker
- Hereditary Cancer Centre, Prince of Wales Hospital, Randwick, NSW, Australia.,Prince of Wales Hospital Clinical School, UNSW Sydney, Randwick, NSW, Australia
| | - Meera Warby
- Hereditary Cancer Centre, Prince of Wales Hospital, Randwick, NSW, Australia
| | - Geoffrey B McCowage
- Cancer Centre for Children, The Children's Hospital at Westmead, Westmead, NSW, Australia
| | - Luciano Dalla-Pozza
- Cancer Centre for Children, The Children's Hospital at Westmead, Westmead, NSW, Australia
| | - Jennifer A Byrne
- Children's Cancer Research Unit, Kids Research, Westmead, NSW, Australia.,Faculty of Medicine and Health, The University of Sydney, NSW, Australia
| | - Federica Saletta
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia
| | | | - Stephen B Fox
- Peter MacCallum Cancer Centre, Melbourne, Vic., Australia.,Department of Medical Oncology, University of Melbourne, Melbourne, Vic., Australia
| | - Murray D Norris
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia.,School of Women's and Children's Health, UNSW Sydney, Kensington, NSW, Australia.,University of New South Wales Centre for Childhood Cancer Research, UNSW Sydney, Kensington, Vic., Australia
| | - Vanessa Tyrrell
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia
| | - Toby N Trahair
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia.,School of Women's and Children's Health, UNSW Sydney, Kensington, NSW, Australia.,Kids Cancer Centre, Sydney Children's Hospital, Randwick, NSW, Australia
| | - Richard B Lock
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia.,School of Women's and Children's Health, UNSW Sydney, Kensington, NSW, Australia
| | - Mark J Cowley
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia.,School of Women's and Children's Health, UNSW Sydney, Kensington, NSW, Australia.,Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Paul G Ekert
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia.,School of Women's and Children's Health, UNSW Sydney, Kensington, NSW, Australia.,Peter MacCallum Cancer Centre, Melbourne, Vic., Australia
| | - Michelle Haber
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia.,School of Women's and Children's Health, UNSW Sydney, Kensington, NSW, Australia
| | - David S Ziegler
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia.,School of Women's and Children's Health, UNSW Sydney, Kensington, NSW, Australia.,Kids Cancer Centre, Sydney Children's Hospital, Randwick, NSW, Australia
| | - Glenn M Marshall
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia.,School of Women's and Children's Health, UNSW Sydney, Kensington, NSW, Australia.,Kids Cancer Centre, Sydney Children's Hospital, Randwick, NSW, Australia
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31
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Dinh P, Graham JD, Elder EN, Kabir M, Doan TB, French J, Meybodi F, Hui R, Wilcken NR, Harnett PR, Hsu J, Stuart KE, Wang T, Ahern V, Brennan M, Fox SB, Dear RF, Lim E, White M, Mann GB, Pathmanathan N. Impact of the EndoPredict genomic assay on treatment decisions for oestrogen receptor-positive early breast cancer patients: benefits of physician selective testing. Breast Cancer Res Treat 2021; 191:501-511. [PMID: 34853987 DOI: 10.1007/s10549-021-06456-5] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 11/14/2021] [Indexed: 01/26/2023]
Abstract
PURPOSE Genomic tests improve accuracy of risk prediction for early breast cancers but these are expensive. This study evaluated the clinical utility of EndoPredict®, in terms of impact on adjuvant therapy recommendations and identification of parameters to guide selective application. METHODS Patients with ER-positive, HER2-negative, and early-stage invasive breast cancer were tested with EndoPredict®. Two cohorts were recruited: one consecutively and another at clinical team discretion. Systemic treatment recommendations were recorded before and after EndoPredict® results were revealed to the multidisciplinary team. RESULTS 233 patients were recruited across five sites: 123 consecutive and 110 at clinical team discretion. In the consecutive cohort 50.6% (62/123) cases were classified high risk of recurrence by EndoPredict®, compared with 62.7% (69/110) in the selective cohort. A change in treatment recommendation was significantly more likely (p < 0.0001) in the selective cohort (43/110, 39.1%) compared to the consecutive group (11/123, 8.9%). The strongest driver of selective recruitment was intermediate grade histology, whilst logistic regression modelling demonstrated that nodal status (p < 0.001), proliferative rate (p = 0.001), and progesterone receptor positivity (p < 0.001) were the strongest discriminators of risk. CONCLUSION Whilst molecular risk can be predicted by traditional variables in a high proportion of cases, EndoPredict® had a greater impact on treatment decisions in those cases selected for testing at team discretion. This is indicative of the robust ability of the clinical team to identify cases most likely to benefit from testing, underscoring the value of genomic tests in the oncologists' tool kit.
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Affiliation(s)
- Phuong Dinh
- Westmead Breast Cancer Institute, Westmead, NSW, 2145, Australia.,Crown Princess Mary Cancer Centre, Western Sydney Local Health District, Westmead, NSW, 2145, Australia.,Westmead Clinical School, University of Sydney, Westmead, NSW, 2145, Australia
| | - J Dinny Graham
- Westmead Breast Cancer Institute, Westmead, NSW, 2145, Australia.,The Westmead Institute for Medical Research, The University of Sydney, Westmead, NSW, 2145, Australia.,Westmead Clinical School, University of Sydney, Westmead, NSW, 2145, Australia
| | - Elisabeth N Elder
- Westmead Breast Cancer Institute, Westmead, NSW, 2145, Australia.,Westmead Clinical School, University of Sydney, Westmead, NSW, 2145, Australia
| | - Masrura Kabir
- Westmead Breast Cancer Institute, Westmead, NSW, 2145, Australia
| | - Tram B Doan
- The Westmead Institute for Medical Research, The University of Sydney, Westmead, NSW, 2145, Australia
| | - James French
- Westmead Breast Cancer Institute, Westmead, NSW, 2145, Australia.,Westmead Clinical School, University of Sydney, Westmead, NSW, 2145, Australia
| | - Farid Meybodi
- Westmead Breast Cancer Institute, Westmead, NSW, 2145, Australia.,Westmead Clinical School, University of Sydney, Westmead, NSW, 2145, Australia
| | - Rina Hui
- Westmead Breast Cancer Institute, Westmead, NSW, 2145, Australia.,Crown Princess Mary Cancer Centre, Western Sydney Local Health District, Westmead, NSW, 2145, Australia.,Westmead Clinical School, University of Sydney, Westmead, NSW, 2145, Australia
| | - Nicholas R Wilcken
- Crown Princess Mary Cancer Centre, Western Sydney Local Health District, Westmead, NSW, 2145, Australia.,Westmead Clinical School, University of Sydney, Westmead, NSW, 2145, Australia
| | - Paul R Harnett
- Crown Princess Mary Cancer Centre, Western Sydney Local Health District, Westmead, NSW, 2145, Australia.,Westmead Clinical School, University of Sydney, Westmead, NSW, 2145, Australia
| | - Jeremy Hsu
- Westmead Breast Cancer Institute, Westmead, NSW, 2145, Australia.,Westmead Clinical School, University of Sydney, Westmead, NSW, 2145, Australia
| | - Kirsty E Stuart
- Westmead Breast Cancer Institute, Westmead, NSW, 2145, Australia.,Crown Princess Mary Cancer Centre, Western Sydney Local Health District, Westmead, NSW, 2145, Australia.,Westmead Clinical School, University of Sydney, Westmead, NSW, 2145, Australia
| | - Tim Wang
- Westmead Breast Cancer Institute, Westmead, NSW, 2145, Australia.,Crown Princess Mary Cancer Centre, Western Sydney Local Health District, Westmead, NSW, 2145, Australia.,Westmead Clinical School, University of Sydney, Westmead, NSW, 2145, Australia
| | - Verity Ahern
- Crown Princess Mary Cancer Centre, Western Sydney Local Health District, Westmead, NSW, 2145, Australia.,Westmead Clinical School, University of Sydney, Westmead, NSW, 2145, Australia
| | - Meagan Brennan
- Crown Princess Mary Cancer Centre, Western Sydney Local Health District, Westmead, NSW, 2145, Australia.,Westmead Clinical School, University of Sydney, Westmead, NSW, 2145, Australia
| | - Stephen B Fox
- Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
| | - Rachel F Dear
- St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Darlinghurst, NSW, 2010, Australia
| | - Elgene Lim
- St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Darlinghurst, NSW, 2010, Australia.,Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia
| | | | - G Bruce Mann
- Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia.,Royal Melbourne Hospital, Parkville, VIC, 3050, Australia
| | - Nirmala Pathmanathan
- Westmead Breast Cancer Institute, Westmead, NSW, 2145, Australia. .,Westmead Clinical School, University of Sydney, Westmead, NSW, 2145, Australia. .,Douglass Hanly Moir Pathology, Macquarie Park, NSW, 2113, Australia.
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32
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Scolyer RA, Atkinson V, Gyorki DE, Lambie D, O'Toole S, Saw RP, Amanuel B, Angel CM, Button-Sloan AE, Carlino MS, Ch'ng S, Colebatch AJ, Daneshvar D, Pires da Silva I, Dawson T, Ferguson PM, Foster-Smith E, Fox SB, Gill AJ, Gupta R, Henderson MA, Hong AM, Howle JR, Jackett LA, James C, Lee CS, Lochhead A, Loh D, McArthur GA, McLean CA, Menzies AM, Nieweg OE, O'Brien BH, Pennington TE, Potter AJ, Prakash S, Rawson RV, Read RL, Rtshiladze MA, Shannon KF, Smithers BM, Spillane AJ, Stretch JR, Thompson JF, Tucker P, Varey AH, Vilain RE, Wood BA, Long GV. BRAF mutation testing for patients diagnosed with stage III or stage IV melanoma: practical guidance for the Australian setting. Pathology 2021; 54:6-19. [DOI: 10.1016/j.pathol.2021.11.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 11/21/2021] [Indexed: 01/19/2023]
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33
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Bouchè V, Aldegheri G, Donofrio CA, Fioravanti A, Roberts-Thomson S, Fox SB, Schettini F, Generali D. BRAF Signaling Inhibition in Glioblastoma: Which Clinical Perspectives? Front Oncol 2021; 11:772052. [PMID: 34804975 PMCID: PMC8595319 DOI: 10.3389/fonc.2021.772052] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [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: 09/07/2021] [Accepted: 10/20/2021] [Indexed: 12/26/2022] Open
Abstract
IDH-wild type (wt) glioblastoma (GB) accounts for approximately 90% of all GB and has a poor outcome. Surgery and adjuvant therapy with temozolomide and radiotherapy is the main therapeutic approach. Unfortunately, after relapse and progression, which occurs in most cases, there are very limited therapeutic options available. BRAF which plays a role in the oncogenesis of several malignant tumors, is also involved in a small proportion of IDH-wt GB. Previous successes with anti-B-Raf targeted therapy in tumors with V600E BRAF mutation like melanoma, combined with the poor prognosis and paucity of therapeutic options for GB patients is leading to a growing interest in the potential efficacy of this approach. This review is thus focused on dissecting the state of the art and future perspectives on BRAF pathway inhibition in IDH-wt GB. Overall, clinical efficacy is mostly described within case reports and umbrella trials, with promising but still insufficient results to draw more definitive conclusions. Further studies are needed to better define the molecular and phenotypic features that predict for a favorable response to treatment. In addition, limitations of B-Raf-inhibitors, in monotherapy or in combination with other therapeutic partners, to penetrate the blood-brain barrier and the development of acquired resistance mechanisms responsible for tumor progression need to be addressed.
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Affiliation(s)
- Victoria Bouchè
- Department of Medicine, Surgery and Health Sciences, Cattinara Hospital, University of Trieste, Trieste, Italy
| | - Giovanni Aldegheri
- Department of Medicine, Surgery and Health Sciences, Cattinara Hospital, University of Trieste, Trieste, Italy
| | - Carmine Antonio Donofrio
- Department of Neurosurgery, Manchester Centre for Clinical Neurosciences, Salford Royal National Health System (NHS) Foundation Trust, Manchester Academic Health Sciences Centre, University of Manchester, Manchester, United Kingdom
| | - Antonio Fioravanti
- Medical Oncology and Translational Research Unit, Azienda Socio-Sanitaria Territoriale (ASST) of Cremona, Cremona Hospital, Cremona, Italy
| | | | - Stephen B. Fox
- Department of Pathology, Peter MacCallum Cancer Centre, The University of Melbourne, Melbourne, VIC, Australia
| | - Francesco Schettini
- Translational Genomics and Targeted Therapies in Solid Tumors Group, August Pi I Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain
- Department of Medical Oncology, Hospital Clinic of Barcelona, Barcelona, Spain
| | - Daniele Generali
- Department of Medicine, Surgery and Health Sciences, Cattinara Hospital, University of Trieste, Trieste, Italy
- Unit of Neurosurgery, Azienda Socio-Sanitaria Territoriale (ASST) of Cremona, Cremona Hospital, Cremona, Italy
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34
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Prall OWJ, Browning J, Nastevski V, Caporarello S, Bates B, Hewitt CA, Arenas A, Lamb G, Howlett K, Arnolda R, Adeloju R, Stuart S, Xu H, Fellowes A, Fox SB. ROS1 rearrangements in non-small cell lung cancer: screening by immunohistochemistry using proportion of cells staining without intensity and excluding cases with MAPK pathway drivers improves test performance. Pathology 2021; 54:279-285. [PMID: 34635319 DOI: 10.1016/j.pathol.2021.07.006] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 07/02/2021] [Accepted: 07/08/2021] [Indexed: 11/16/2022]
Abstract
Therapeutically actionable ROS1 rearrangements have been described in 1-3% of non-small cell lung cancer (NSCLC). Screening for ROS1 rearrangements is recommended to be by immunohistochemistry (IHC), followed by confirmation with fluorescence in situ hybridisation (FISH) or sequencing. However, in practise ROS1 IHC presents difficulties due to conflicting scoring systems, multiple clones and expression in tumours that are wild-type for ROS1. We assessed ROS1 IHC in 285 consecutive cases of NSCLC with non-squamous histology over a nearly 2-year period. IHC was scored with ROS1 clone D4D6 (n=270), clone SP384 (n=275) or both clones (n=260). Results were correlated with ROS1 break-apart FISH (n=67), ALK status (n=194), and sequence data of EGFR (n=178) and other drivers, where possible. ROS1 expression was detected in 161/285 cases (56.5%), including 13/14 ROS1 FISH-positive cases. There was no ROS1 expression in one ROS1 FISH-positive case in which sequencing detected an ALK-EML4 fusion, but not a ROS1 fusion. The other 13 ROS1 FISH-positive cases showed moderate to strong staining with both IHC clones. However, one case with a TPM3-ROS1 fusion would have been scored as negative with SP384 and D4D6 clones by some previous criteria. ROS1 expression was also detected in 58/285 cases (20.4%) that had driver mutations in genes other than ROS1. A sensitivity of 100% for detecting a ROS1 rearrangement by FISH was achieved by omitting intensity from the IHC scoring criteria and expression in >0% cells with D4D6 or in ≥50% cells with SP384. Excluding cases with driver events in any MAPK pathway gene (e.g., in ALK, EGFR, KRAS, BRAF, ERBB2 and MET) substantially reduced the number of cases proceeding to ROS1 FISH. Only 15.9% of MAPK-negative NSCLC would proceed to FISH for an IHC threshold of >0% cells with D4D6, with a specificity of 42.4%. For a threshold of ≥50% cells with SP384, only 18.5% of MAPK-negative cases would proceed to FISH, with a specificity of 31.4%. Based on our data we suggest an algorithm for screening for ROS1 rearrangements in NSCLC in which ROS1 FISH is only performed in cases that have been demonstrated to lack activating mutations in any MAPK pathway gene by comprehensive sequencing and ALK IHC, and show staining at any intensity in ≥50% of cells with clone SP384, or >0% cells with D4D6.
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Affiliation(s)
- Owen W J Prall
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Vic, Australia.
| | - Judy Browning
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Vic, Australia
| | - Violeta Nastevski
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Vic, Australia
| | - Shana Caporarello
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Vic, Australia
| | - Bindi Bates
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Vic, Australia
| | - Chelsee A Hewitt
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Vic, Australia
| | - Andrea Arenas
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Vic, Australia
| | - Gareth Lamb
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Vic, Australia
| | - Kerryn Howlett
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Vic, Australia
| | - Rainier Arnolda
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Vic, Australia
| | - Roshana Adeloju
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Vic, Australia
| | - Shani Stuart
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Vic, Australia
| | - Huiling Xu
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Vic, Australia; Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Vic, Australia; Department of Clinical Pathology, Faculty of Medicine and Dental Science, The University of Melbourne, Parkville, Vic, Australia
| | - Andrew Fellowes
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Vic, Australia
| | - Stephen B Fox
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Vic, Australia
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Zelli V, Silvestri V, Valentini V, Bucalo A, Rizzolo P, Zanna I, Bianchi S, Coppa A, Giannini G, Cortesi L, Calistri D, Tibiletti MG, Fox SB, Palli D, Ottini L. Transcriptome of Male Breast Cancer Matched with Germline Profiling Reveals Novel Molecular Subtypes with Possible Clinical Relevance. Cancers (Basel) 2021; 13:cancers13184515. [PMID: 34572741 PMCID: PMC8469418 DOI: 10.3390/cancers13184515] [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: 07/30/2021] [Revised: 08/30/2021] [Accepted: 09/01/2021] [Indexed: 11/16/2022] Open
Abstract
Simple Summary Breast cancer in men is a rare disease; however, morbidity and mortality in male breast cancer (MBC) patients is a serious concern. The identification of specific molecular features in MBC is essential for developing more appropriate and targeted therapeutic strategies for MBC patients. In this study, by transcriptome analysis of 63 MBCs characterized for germline mutations in the most relevant BC susceptibility genes, mainly BRCA1/2, we highlighted possible differences in the molecular pathways underlying MBC pathogenesis in relation to germline mutation status. Furthermore, we identified two distinct subgroups of MBCs of clinical relevance, which are characterized by different biological features and prognosis. Overall, our results showed that transcriptome profiling by RNA sequencing is a valuable approach to dissect the molecular heterogeneity of MBC and suggest that the transcriptome matched with germline profiling may lead to the identification of MBC subtypes with possible relevance in the clinical setting, which is a primary step to improve the clinical management of MBC patients. Abstract Male breast cancer (MBC) is a rare and understudied disease compared with female BC. About 15% of MBCs are associated with germline mutation in BC susceptibility genes, mainly BRCA1/2 and PALB2. Hereditary MBCs are likely to represent a subgroup of tumors with a peculiar phenotype. Here, we performed a whole transcriptome analysis of MBCs characterized for germline mutations in the most relevant BC susceptibility genes in order to identify molecular subtypes with clinical relevance. A series of 63 MBCs, including 16 BRCA2, 6 BRCA1, 2 PALB2, 1 RAD50, and 1 RAD51D germline-mutated cases, was analyzed by RNA-sequencing. Differential expression and hierarchical clustering analyses were performed. Module signatures associated with central biological processes involved in breast cancer pathogenesis were also examined. Different transcriptome profiles for genes mainly involved in the cell cycle, DNA damage, and DNA repair pathways emerged between MBCs with and without germline mutations. Unsupervised clustering analysis revealed two distinct subgroups, one of which was characterized by a higher expression of immune response genes, high scores of gene-expression signatures suggestive of aggressive behavior, and worse overall survival. Our results suggest that transcriptome matched with germline profiling may be a valuable approach for the identification and characterization of MBC subtypes with possible relevance in the clinical setting.
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Affiliation(s)
- Veronica Zelli
- Department of Molecular Medicine, Sapienza University of Rome, 00161 Rome, Italy; (V.Z.); (V.S.); (V.V.); (A.B.); (P.R.); (G.G.)
| | - Valentina Silvestri
- Department of Molecular Medicine, Sapienza University of Rome, 00161 Rome, Italy; (V.Z.); (V.S.); (V.V.); (A.B.); (P.R.); (G.G.)
| | - Virginia Valentini
- Department of Molecular Medicine, Sapienza University of Rome, 00161 Rome, Italy; (V.Z.); (V.S.); (V.V.); (A.B.); (P.R.); (G.G.)
| | - Agostino Bucalo
- Department of Molecular Medicine, Sapienza University of Rome, 00161 Rome, Italy; (V.Z.); (V.S.); (V.V.); (A.B.); (P.R.); (G.G.)
| | - Piera Rizzolo
- Department of Molecular Medicine, Sapienza University of Rome, 00161 Rome, Italy; (V.Z.); (V.S.); (V.V.); (A.B.); (P.R.); (G.G.)
| | - Ines Zanna
- Cancer Risk Factors and Lifestyle Epidemiology Unit, Institute for Cancer Research, Prevention and Clinical Network (ISPRO), 08518 Florence, Italy; (I.Z.); (D.P.)
| | - Simonetta Bianchi
- Division of Pathological Anatomy, Department of Health Sciences, University of Florence, 08518 Florence, Italy;
| | - Anna Coppa
- Department of Experimental Medicine, Sapienza University of Rome, 00161 Rome, Italy;
| | - Giuseppe Giannini
- Department of Molecular Medicine, Sapienza University of Rome, 00161 Rome, Italy; (V.Z.); (V.S.); (V.V.); (A.B.); (P.R.); (G.G.)
| | - Laura Cortesi
- Department of Oncology and Haematology, University of Modena and Reggio Emilia, 41124 Modena, Italy;
| | - Daniele Calistri
- IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy;
| | - Maria Grazia Tibiletti
- Department of Pathology, ASST Settelaghi and Centro di Ricerca per lo Studio dei Tumori Eredo-Familiari, Università dell’Insubria, 21100 Varese, Italy;
| | - Stephen B. Fox
- Department of Pathology, Peter MacCallum Cancer Centre, The University of Melbourne, Melbourne, VIC 3000, Australia;
| | - kConFab
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC 3000, Australia;
- Kathleen Cuningham Foundation Consortium for Research into Familial Breast Cancer (kConFab), Research Department, PeterMacCallum Cancer Centre, Melbourne, VIC 3000, Australia
| | - Domenico Palli
- Cancer Risk Factors and Lifestyle Epidemiology Unit, Institute for Cancer Research, Prevention and Clinical Network (ISPRO), 08518 Florence, Italy; (I.Z.); (D.P.)
| | - Laura Ottini
- Department of Molecular Medicine, Sapienza University of Rome, 00161 Rome, Italy; (V.Z.); (V.S.); (V.V.); (A.B.); (P.R.); (G.G.)
- Correspondence: ; Tel.: +39-06-49918268
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36
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Pang JMB, Castles B, Byrne DJ, Button P, Hendry S, Lakhani SR, Sivasubramaniam V, Cooper WA, Armes J, Millar EK, Raymond W, Roberts-Thomson S, Kumar B, Burr M, Selinger C, Harvey K, Chan C, Beith J, Clouston D, O’Toole SA, Fox SB. SP142 PD-L1 Scoring Shows High Interobserver and Intraobserver Agreement in Triple-negative Breast Carcinoma But Overall Low Percentage Agreement With Other PD-L1 Clones SP263 and 22C3. Am J Surg Pathol 2021; 45:1108-1117. [PMID: 34232604 PMCID: PMC8277187 DOI: 10.1097/pas.0000000000001701] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
SP142 programmed cell death ligand 1 (PD-L1) status predicts response to atezolizumab in triple-negative breast carcinoma (TNBC). Prevalence of VENTANA PD-L1 (SP142) Assay positivity, concordance with the VENTANA PD-L1 (SP263) Assay and Dako PD-L1 IHC 22C3 pharmDx assay, and association with clinicopathologic features were assessed in 447 TNBCs. SP142 PD-L1 intraobserver and interobserver agreement was investigated in a subset of 60 TNBCs, with scores enriched around the 1% cutoff. The effect of a 1-hour training video on pretraining and posttraining scores was ascertained. At a 1% cutoff, 34.2% of tumors were SP142 PD-L1 positive. SP142 PD-L1 positivity was significantly associated with tumor-infiltrating lymphocytes (P <0.01), and node negativity (P=0.02), but not with tumor grade (P=0.35), tumor size (P=0.58), or BRCA mutation (P=0.53). Overall percentage agreement (OPA) for intraobserver and interobserver agreement was 95.0% and 93.7%, respectively, among 5 pathologists trained in TNBC SP142 PD-L1 scoring. In 5 TNBC SP142 PD-L1-naive pathologists, significantly higher OPA to the reference score was achieved after video training (posttraining OPA 85.7%, pretraining OPA 81.5%, P<0.05). PD-L1 status at a 1% cutoff was assessed by SP142 and SP263 in 420 cases, and by SP142 and 22C3 in 423 cases, with OPA of 88.1% and 85.8%, respectively. The VENTANA PD-L1 (SP142) Assay is reproducible for classifying TNBC PD-L1 status by trained observers; however, it is not analytically equivalent to the VENTANA PD-L1 (SP263) Assay and Dako PD-L1 IHC 22C3 pharmDx assay.
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Affiliation(s)
| | | | | | | | | | - Sunil R. Lakhani
- University of Queensland Centre for Clinical Research
- Pathology Queensland, Brisbane
| | | | - Wendy A. Cooper
- Sydney Medical School, The University of Sydney
- Department of Tissue Pathology, Royal Prince Alfred Hospital, NSW Health Pathology
- Western Sydney University, Campbelltown
| | - Jane Armes
- Pathology Queensland, Sunshine Coast, QLD
| | - Ewan K.A. Millar
- NSW Health Pathology, St George Hospital
- St. George and Sutherland Clinical School, University of New South Wales, Kogarah
| | - Wendy Raymond
- Flinders Medical Centre, Flinders University of South Australia
- Clinpath Laboratories, Adelaide, SA, Australia
| | | | | | - Marian Burr
- Royal Melbourne Hospital
- Sir Peter MacCallum Department of Oncology, University of Melbourne
- Department of Medicine, Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), University of Cambridge, Cambridge, UK
| | | | - Kate Harvey
- The Garvan Institute of Medical Research, Darlinghurst
| | - Charles Chan
- Concord Clinical School, The University of Sydney, Sydney
- Concord Repatriation General Hospital, Concord, NSW
| | - Jane Beith
- Sydney Medical School, The University of Sydney
- Chris O’Brien Lifehouse, Camperdown
| | | | - Sandra A. O’Toole
- Sydney Medical School, The University of Sydney
- The Garvan Institute of Medical Research, Darlinghurst
- Department of Tissue Pathology, Royal Prince Alfred Hospital, NSW Health Pathology
- Western Sydney University, Campbelltown
| | - Stephen B. Fox
- Peter MacCallum Cancer Centre
- Sir Peter MacCallum Department of Oncology, University of Melbourne
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37
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O Haire S, Degeling K, Franchini F, Tran B, Luen SJ, Smith KM, Fox SB, Desai J, IJzerman MJ. Comparing survival outcomes for advanced cancer patients who access comprehensive genomic sequencing using a registry-based synthetic control arm. J Clin Oncol 2021. [DOI: 10.1200/jco.2021.39.15_suppl.e18851] [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: 11/20/2022] Open
Abstract
e18851 Background: Studies evaluating the clinical benefit from Comprehensive Genomic Sequencing (CGS) in cancer patients (pts) have been limited by heterogeneous populations in cancer types and treatment history, outcomes analysis focused on pts who received treatment, and single arm designs. This study evaluated the clinical utility of CGS in a unique real-world advanced cancer patient cohort by comparing a series of pts who received CGS to inform investigational treatment compared to those who did not. Methods: Two cohorts of advanced and refractory pts with diverse cancer types seen for early phase trial consideration were identified from the Peter MacCallum Cancer Centre (PMCC) phase 1 trials clinic. The CGS group (N = 142) accessed an in-house assay on FFPE tissue and matched blood (PMCC Comprehensive Cancer Panel - 391 genes) through a research study between 2017-2018. A second cohort was defined as clinic pts in the following 12 months when profiling was unavailable (NoCGS, N = 133). Difference in overall survival (OS) from initial appointment between the two cohorts was analysed through Kaplan-Meier curves and Cox proportional hazard models. Potential confounding was analysed and adjusted for using stabilised weights based on propensity scores. Results: Within the CGS group, 25 (17.6%) pts received targeted treatment informed by CGS results via trials recruiting at that time (n = 16) or off label drug access (n = 9). This subgroup had improved survival compared with CGS pts in whom results did not alter treatment plan (unadjusted HR = 0.48, (0.27-0.88), p = 0.02). Comparing the CGS and NoCGS cohorts, there were proportional differences in clinical factors including ECOG, cancer types and previous lines of therapy, with standardised differences ranging from 0.23-0.63. Rates of trial participation were similar (CGS: n = 31 [22%], NoCGS: n = 34 [26%]) and CGS had improved unadjusted median OS of 14.5 mos (12.3-19.0) compared to 9.9 (8.6-13.4) for NoCGS (unadjusted HR = 0.71, (0.53-0.96), p = 0.03). In the adjusted analysis, weights ranged from 0.54-2.89 ensuring no individual pts had excessive influence on analysis and resulted in well-balanced populations (range of standardised differences: 0.0-0.09). Adjusted median OS for CGS was 13.5 mos (9.9-17.8) compared to 11.0 (9.2-17.4) for NoCGS (adjusted HR = 0.88, 0.63-1.23, p = 0.50). Conclusions: We utilised real world data in a novel approach to comparative analysis of the clinical benefit of CGS in a heterogenous cancer cohort. Although the subset of CGS pts who went on to receive targeted treatments had improved outcomes, this was insufficient to drive an overall survival gain when considering the overall CGS vs NoCGS cohort. Therefore, translation into clinics requires strategies to ensure a greater proportion of tested pts obtain benefit to deliver on the value proposition of CGS in an advanced cancer population.
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Affiliation(s)
- Sophie O Haire
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Koen Degeling
- Cancer Health Services Research Unit, University of Melbourne, Melbourne, Australia
| | | | - Ben Tran
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | | | | | | | - Jayesh Desai
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
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38
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McEvoy CR, Holliday H, Thio N, Mitchell C, Choong DY, Yellapu B, Leong HS, Xu H, Lade S, Browning J, Takano EA, Byrne DJ, Gill AJ, Duong CP, Li J, Fellowes AP, Fox SB, Swarbrick A, Prall OWJ. A MXI1-NUTM1 fusion protein with MYC-like activity suggests a novel oncogenic mechanism in a subset of NUTM1-rearranged tumors. J Transl Med 2021; 101:26-37. [PMID: 32873880 DOI: 10.1038/s41374-020-00484-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 08/10/2020] [Accepted: 08/17/2020] [Indexed: 12/21/2022] Open
Abstract
Most NUTM1-rearranged neoplasms (NRNs) have fusions between NUTM1 and BRD (bromodomain-containing) family members and are termed NUT carcinomas (NCs) because they show some squamous differentiation. However, some NRNs are associated with fusions between NUTM1 and members of the MAD (MAX dimerization) gene family of MYC antagonists. Here we describe a small round cell malignancy from the gastro-esophageal junction with a previously unreported fusion between NUTM1 and the MAD family member MXI1. In contrast to NCs, the MXI1-NUTM1 tumor did not show squamous differentiation and did not express MYC, TP63 or SOX2, genes known to be targets of BRD-NUTM1 proteins and critical for NC oncogenesis. Transcriptome analysis showed paradoxical enrichment of MYC target genes in the MXI1-NUTM1 tumor despite the lack of MYC expression. When expressed in vitro MXI1-NUTM1 partially phenocopied MYC, enhancing cell proliferation and cooperating with oncogenic HRAS to produce anchorage-independent cell growth. These data provide evidence that MAD family members, which are normally repressors of MYC activity, can be converted into MYC-like mimics by fusion to NUTM1. The pathological features and novel oncogenic mechanism of the MXI1-NUTM1 tumor show that identification of NUTM1 fusion partners can be important for accurate diagnostic classification of some NRN subtypes, and potentially may guide therapeutic options.
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Affiliation(s)
- Christopher R McEvoy
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
| | - Holly Holliday
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia
- Faculty of Medicine, St Vincent's Clinical School, UNSW Sydney, Sydney, NSW, 2010, Australia
| | - Niko Thio
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
| | - Catherine Mitchell
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
| | - David Y Choong
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
| | - Bhargavi Yellapu
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
- Epworth Healthcare, Melbourne, VIC, Australia
| | - Hui San Leong
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
| | - Huiling Xu
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
| | - Stephen Lade
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
| | - Judy Browning
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
| | - Elena A Takano
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
| | - David J Byrne
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
| | - Anthony J Gill
- Cancer Diagnosis and Pathology Group, Kolling Institute of Medical Research, Royal North Shore Hospital, St Leonards, NSW, 2065, Australia
- NSW Health Pathology, Department of Anatomical Pathology, Royal North Shore Hospital, Sydney, NSW, 2065, Australia
- University of Sydney, Sydney, NSW, 2065, Australia
| | - Cuong P Duong
- Division of Cancer Surgery, Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
| | - Jason Li
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
| | - Andrew P Fellowes
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
| | - Stephen B Fox
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
- University of Melbourne, Parkville, VIC, 3010, Australia
| | - Alexander Swarbrick
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia
- Faculty of Medicine, St Vincent's Clinical School, UNSW Sydney, Sydney, NSW, 2010, Australia
| | - Owen W J Prall
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia.
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39
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Khuong-Quang DA, Brown LM, Wong M, Mayoh C, Sexton-Oates A, Kumar A, Pinese M, Nagabushan S, Lau L, Ludlow LE, Gifford AJ, Rodriguez M, Desai J, Fox SB, Haber M, Ziegler DS, Hansford JR, Marshall GM, Cowley MJ, Ekert PG. Recurrent SPECC1L-NTRK fusions in pediatric sarcoma and brain tumors. Cold Spring Harb Mol Case Stud 2020; 6:mcs.a005710. [PMID: 33144287 PMCID: PMC7784491 DOI: 10.1101/mcs.a005710] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 10/22/2020] [Indexed: 12/02/2022] Open
Abstract
The identification of rearrangements driving expression of neurotrophic receptor tyrosine kinase (NTRK) family kinases in tumors has become critically important because of the availability of effective, specific inhibitor drugs. Whole-genome sequencing (WGS) combined with RNA sequencing (RNA-seq) can identify novel and recurrent expressed fusions. Here we describe three SPECC1L–NTRK fusions identified in two pediatric central nervous system cancers and an extracranial solid tumor using WGS and RNA-seq. These fusions arose either through a simple balanced rearrangement or in the context of a complex chromoplexy event. We cloned the SPECC1L–NTRK2 fusion directly from a patient sample and showed that enforced expression of this fusion is sufficient to promote cytokine-independent survival and proliferation. Cells transformed by SPECC1L–NTRK2 expression are sensitive to a TRK inhibitor drug. We report here that SPECC1L–NTRK fusions can arise in a range of pediatric cancers. Although WGS and RNA-seq are not required to detect NTRK fusions, these techniques may be of benefit when NTRK fusions are not suspected on clinical grounds or not identified by other methods.
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Affiliation(s)
- Dong-Anh Khuong-Quang
- Children's Cancer Institute, University of New South Wales, Randwick, 2031, Australia.,Children's Cancer Centre, Royal Children's Hospital, Parkville, 3052, Australia.,Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, 3052, Australia
| | - Lauren M Brown
- Children's Cancer Institute, University of New South Wales, Randwick, 2031, Australia.,Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, 3052, Australia.,Department of Pediatrics, University of Melbourne, Parkville, 3052, Australia
| | - Marie Wong
- Children's Cancer Institute, University of New South Wales, Randwick, 2031, Australia.,School of Women's and Children's Health, UNSW Medicine, UNSW Sydney, Randwick, 2031, Australia
| | - Chelsea Mayoh
- Children's Cancer Institute, University of New South Wales, Randwick, 2031, Australia
| | - Alexandra Sexton-Oates
- Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, 3052, Australia
| | - Amit Kumar
- Children's Cancer Institute, University of New South Wales, Randwick, 2031, Australia.,Peter MacCallum Cancer Centre, Melbourne, 3000, Australia
| | - Mark Pinese
- Children's Cancer Institute, University of New South Wales, Randwick, 2031, Australia
| | - Sumanth Nagabushan
- Kids Cancer Centre, Sydney Children's Hospital, Randwick, 2031, Australia
| | - Loretta Lau
- Children's Cancer Institute, University of New South Wales, Randwick, 2031, Australia.,Kids Cancer Centre, Sydney Children's Hospital, Randwick, 2031, Australia
| | - Louise E Ludlow
- Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, 3052, Australia
| | - Andrew J Gifford
- Children's Cancer Institute, University of New South Wales, Randwick, 2031, Australia.,Department of Anatomical Pathology, Prince of Wales Hospital, Randwick, 2031, Australia
| | - Michael Rodriguez
- Department of Anatomical Pathology, Prince of Wales Hospital, Randwick, 2031, Australia
| | - Jayesh Desai
- Peter MacCallum Cancer Centre, Melbourne, 3000, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, 3000, Australia
| | - Stephen B Fox
- Sir Peter MacCallum Department of Oncology, University of Melbourne, 3000, Australia.,Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, 3000, Australia
| | - Michelle Haber
- Children's Cancer Institute, University of New South Wales, Randwick, 2031, Australia
| | - David S Ziegler
- Children's Cancer Institute, University of New South Wales, Randwick, 2031, Australia.,Kids Cancer Centre, Sydney Children's Hospital, Randwick, 2031, Australia
| | - Jordan R Hansford
- Children's Cancer Centre, Royal Children's Hospital, Parkville, 3052, Australia.,Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, 3052, Australia.,Department of Pediatrics, University of Melbourne, Parkville, 3052, Australia
| | - Glenn M Marshall
- Children's Cancer Institute, University of New South Wales, Randwick, 2031, Australia.,Kids Cancer Centre, Sydney Children's Hospital, Randwick, 2031, Australia
| | - Mark J Cowley
- Children's Cancer Institute, University of New South Wales, Randwick, 2031, Australia.,School of Women's and Children's Health, UNSW Medicine, UNSW Sydney, Randwick, 2031, Australia
| | - Paul G Ekert
- Children's Cancer Institute, University of New South Wales, Randwick, 2031, Australia.,Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, 3052, Australia.,School of Women's and Children's Health, UNSW Medicine, UNSW Sydney, Randwick, 2031, Australia.,Peter MacCallum Cancer Centre, Melbourne, 3000, Australia
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40
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Rakha EA, Quinn CM, Foschini MP, Muñoz Martin M, Dabbs DJ, Lakhani S, Varga Z, Pinder SE, Schmitt FC, Reis-Filho JS, Fox SB, Ellis IO, Tan PH, Mihai R. Metaplastic carcinomas of the breast without evidence of epithelial differentiation: a diagnostic approach for management. Histopathology 2020; 78:759-771. [PMID: 33113154 DOI: 10.1111/his.14290] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [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: 08/23/2020] [Revised: 10/11/2020] [Accepted: 10/26/2020] [Indexed: 12/16/2022]
Abstract
AIMS Although rare, malignant sarcomatoid breast tumours without evidence of epithelial differentiation comprise a diagnostic challenge with management implications. Earlier studies have generally considered these to be primary breast sarcomas; however, supporting evidence is lacking and management remains variable. This study aimed to provide an evidence-based approach to improve the consistency of diagnosis and management for such cases. METHODS AND RESULTS A large series (n = 140) of metaplastic breast carcinoma (MBC) diagnosed in Nottingham over 18 years was analysed. Only cases with available data on immunohistochemical expression of cytokeratins (CKs) were included. The prevalence and pattern of expression for various CKs were assessed and details of tumours negative for CKs were collected. A diagnostic approach based on our experience is provided. Forty-seven cases (34%) showed foci of conventional type invasive breast carcinoma or ductal carcinoma in situ (DCIS), while 93 cases (66%) were diagnosed as MBC based on morphology and/or CK expression. Ninety-seven cases (69%) were negative for one or more CKs, with 18 cases (13%) negative for five or more CKs. Eight cases (6%) lacked expression of all CKs tested. Further examination showed evidence of carcinomatous nature in five cases, and three were diagnosed as MBC following extensive diagnostic work-up and based on our experience. CONCLUSION This study suggests that MBC represents a spectrum of neoplasms, with some lacking CK expression. Sarcomatoid neoplasms of the breast lacking evidence of carcinomatous morphology and CK expression may represent an extreme end of differentiation that can be considered as carcinomas rather than sarcomas for management purposes (following extensive work-up).
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Affiliation(s)
- Emad A Rakha
- Department of Histopathology, The University of Nottingham and the Nottingham University Hospitals NHS Trust, Nottingham City Hospital, Nottingham, UK
| | - Cecily M Quinn
- Department of Histopathology, St Vincent's University Hospital, University College, Dublin, Ireland
| | - Maria Pia Foschini
- Department of Biomedical and Neuromotor Sciences, Section of Anatomic Pathology at Bellaria Hospital, University of Bologna, Bologna, Italy
| | - Monica Muñoz Martin
- Department of Histopathology, The University of Nottingham and the Nottingham University Hospitals NHS Trust, Nottingham City Hospital, Nottingham, UK
| | - David J Dabbs
- John A. Burns University of Hawaii Cancer Center, Honolulu, HI, USA.,Department of Pathology, Magee-Women's Hospital of UPMC, Pittsburgh, PA, USA
| | - Sunil Lakhani
- Faculty of Medicine and Pathology Queensland, University of Queensland Centre for Clinical Research, Brisbane, Australia
| | - Zsuzsanna Varga
- Institute of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Sarah E Pinder
- Division of Cancer Studies, King's College London, Guy's Hospital, London, UK
| | - Fernando C Schmitt
- Institute of Molecular Pathology and Immunology (IPATIMUP) and Medical Faculty, University of Porto, Porto, Portugal
| | - Jorge S Reis-Filho
- Department of Pathology, Memorial Sloan Kettering Cancer Centre, New York, NY, USA
| | - Stephen B Fox
- Pathology Department, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Ian O Ellis
- Department of Histopathology, The University of Nottingham and the Nottingham University Hospitals NHS Trust, Nottingham City Hospital, Nottingham, UK
| | - Puay-Hoon Tan
- Department of Pathology, Singapore General Hospital, Singapore, Singapore
| | - Raluca Mihai
- Department of Histopathology, The University of Nottingham and the Nottingham University Hospitals NHS Trust, Nottingham City Hospital, Nottingham, UK
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41
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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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42
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Williams SG, Aw Yeang HX, Mitchell C, Caramia F, Byrne DJ, Fox SB, Haupt S, Schittenhelm RB, Neeson PJ, Haupt Y, Keam SP. Immune molecular profiling of a multiresistant primary prostate cancer with a neuroendocrine-like phenotype: a case report. BMC Urol 2020; 20:171. [PMID: 33115461 PMCID: PMC7592533 DOI: 10.1186/s12894-020-00738-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 10/06/2020] [Indexed: 02/06/2023] Open
Abstract
Background Understanding the drivers of recurrence in aggressive prostate cancer requires detailed molecular and genomic understanding in order to aid therapeutic interventions.
We provide here a case report of histological, transcriptional, proteomic, immunological, and genomic features in a longitudinal study of multiple biopsies from diagnosis, through treatment, and subsequent recurrence.
Case presentation Here we present a case study of a male in 70 s with high-grade clinically-localised acinar adenocarcinoma treated with definitive hormone therapy and radiotherapy. The patient progressed rapidly with rising PSA and succumbed without metastasis 52 months after diagnosis.
We identified the expression of canonical histological markers of neuroendocrine PC (NEPC) including synaptophysin, neuron-specific enolase and thyroid transcription factor 1, as well as intact AR expression, in the recurrent disease only.
The resistant disease was also marked by an extremely low immune infiltrate, extensive genomic chromosomal aberrations, and overactivity in molecular hallmarks of NEPC disease including Aurora kinase and E2F, as well as novel alterations in the cMYB pathway. We also observed that responses to both primary treatments (high dose-rate brachytherapy and androgen deprivation therapies) were consistent with known optimal responses—ruling out treatment inefficacy as a factor in relapse.
Conclusions These data provide novel insights into a case of locally recurrent aggressive prostate cancer harbouring NEPC pathology, in the absence of detected metastasis.
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Affiliation(s)
- Scott G Williams
- Division of Radiation Oncology and Cancer Imaging, Peter MacCallum Cancer Centre, Melbourne, Australia.,Tumor Suppression Laboratory, Peter MacCallum Cancer Centre, Melbourne, Australia.,Pathology Department, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Han Xian Aw Yeang
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Australia
| | - Catherine Mitchell
- Pathology Department, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Franco Caramia
- Tumor Suppression Laboratory, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - David J Byrne
- Pathology Department, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Stephen B Fox
- Pathology Department, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Sue Haupt
- Tumor Suppression Laboratory, Peter MacCallum Cancer Centre, Melbourne, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Australia
| | - Ralf B Schittenhelm
- Monash Proteomics & Metabolomics Facility, Monash University, Melbourne, Australia.,Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Australia
| | - Paul J Neeson
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Australia
| | - Ygal Haupt
- Tumor Suppression Laboratory, Peter MacCallum Cancer Centre, Melbourne, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Australia.,Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Australia
| | - Simon P Keam
- Tumor Suppression Laboratory, Peter MacCallum Cancer Centre, Melbourne, Australia. .,Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, Australia. .,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Australia.
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43
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van Geelen CT, Savas P, Teo ZL, Luen SJ, Weng CF, Ko YA, Kuykhoven KS, Caramia F, Salgado R, Francis PA, Dawson SJ, Fox SB, Fellowes A, Loi S. Clinical implications of prospective genomic profiling of metastatic breast cancer patients. Breast Cancer Res 2020; 22:91. [PMID: 32811538 PMCID: PMC7436992 DOI: 10.1186/s13058-020-01328-0] [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] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 08/10/2020] [Indexed: 12/19/2022] Open
Abstract
Background Metastatic breast cancer remains incurable. Next-generation sequencing (NGS) offers the ability to identify actionable genomic alterations in tumours which may then be matched with targeted therapies, but the implementation and utility of this approach is not well defined for patients with metastatic breast cancer. Methods We recruited patients with advanced breast cancer of any subtype for prospective targeted NGS of their most recent tumour samples, using a panel of 108 breast cancer-specific genes. Genes were classified as actionable or non-actionable using the European Society of Medical Oncology Scale for Clinical Actionability of Molecular Targets (ESCAT) guidelines. Results Between February 2014 and May 2019, 322 patients were enrolled onto the study, with 72% (n = 234) of patients successfully sequenced (n = 357 samples). The majority (74%, n = 171) of sequenced patients were found to carry a potentially actionable alteration, the most common being a PIK3CA mutation. Forty-three percent (n = 74) of patients with actionable alterations were referred for a clinical trial or referred for confirmatory germline testing or had a change in therapy outside of clinical trials. We found alterations in AKT1, BRCA2, CHEK2, ESR1, FGFR1, KMT2C, NCOR1, PIK3CA and TSC2 to be significantly enriched in our metastatic population compared with primary breast cancers. Concordance between primary and metastatic samples for key driver genes (TP53, ERBB2 amplification) was > 75%. Additionally, we found that patients with a higher number of mutations had a significantly worse overall survival. Conclusion Genomic profiling of patients with metastatic breast cancer can have clinical implications and should be considered in all suitable patients.
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Affiliation(s)
| | - Peter Savas
- Division of Research, Peter MacCallum Cancer Centre, Melbourne, Australia.,Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Zhi Ling Teo
- Division of Research, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Stephen J Luen
- Division of Research, Peter MacCallum Cancer Centre, Melbourne, Australia.,Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Chen-Fang Weng
- Division of Research, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Yi-An Ko
- Division of Research, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Keilly S Kuykhoven
- Australian Centre for Disease Preparedness, Commonwealth Scientific and Industrial Research Organisation (CSIRO) Health and Biosecurity, Geelong, Australia
| | - Franco Caramia
- Division of Research, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Roberto Salgado
- Division of Research, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Prudence A Francis
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, 305 Grattan St, Melbourne, VIC, 3000, Australia
| | - Sarah-Jane Dawson
- Division of Research, Peter MacCallum Cancer Centre, Melbourne, Australia.,Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, 305 Grattan St, Melbourne, VIC, 3000, Australia
| | - Stephen B Fox
- Division of Research, Peter MacCallum Cancer Centre, Melbourne, Australia.,Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, 305 Grattan St, Melbourne, VIC, 3000, Australia
| | - Andrew Fellowes
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Sherene Loi
- Division of Research, Peter MacCallum Cancer Centre, Melbourne, Australia. .,Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, Australia. .,Sir Peter MacCallum Department of Oncology, University of Melbourne, 305 Grattan St, Melbourne, VIC, 3000, Australia.
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44
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Schettini F, Sobhani N, Ianza A, Triulzi T, Molteni A, Lazzari MC, Strina C, Milani M, Corona SP, Sirico M, Bernocchi O, Giudici F, Cappelletti MR, Ciruelos E, Jerusalem G, Loi S, Fox SB, Generali D. Immune system and angiogenesis-related potential surrogate biomarkers of response to everolimus-based treatment in hormone receptor-positive breast cancer: an exploratory study. Breast Cancer Res Treat 2020; 184:421-431. [PMID: 32770287 PMCID: PMC7599144 DOI: 10.1007/s10549-020-05856-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 07/31/2020] [Indexed: 01/08/2023]
Abstract
Purpose mTOR inhibitor everolimus is used for hormone receptor-positive (HR+)/HER2-negative metastatic breast cancer (mBC). No reliable predictive biomarker of response is available. Following evidences from other solid tumors, we aimed to assess the association between treatment-associated immune system features and everolimus activity. Methods We retrospectively explored a correlation with the therapeutic activity of everolimus and tumor-associated immune pathways with ingenuity pathway analysis (IPA), neutrophil-to-lymphocyte ratio (NLR), circulating lymphocytes, and endothelial cells (CECs) in 3 different HR+ mBC studies, including the BALLET phase IIIb study. Results The circulating levels of CD3+/CD8+, CD3+/CD4+, and overall T lymphocytes were higher in responders versus non-responders at baseline (p = 0.017, p < 0.001, p = 0.034) and after treatment (p = 0.01, p = 0.003, p = 0.023). Reduced CECs, a tumor neoangiogenesis marker, were observed in responders after treatment (p < 0.001). Patients with low NLR (≤ 4.4) showed a better progression-free survival compared to patients with high NLR (> 4.4) (p = 0.01). IPA showed that the majority of immunity-related genes were found upregulated in responders compared to non-responders before treatment, but not after. Conclusions Lymphocytes subpopulations, CECs and NLR could be interesting biomarkers predictive of response to everolimus-based regimens, potentially useful in daily clinical practice to select/monitor everolimus-based treatment in mBC. Further studies to confirm such hypotheses are warranted.
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Affiliation(s)
- Francesco Schettini
- Department of Clinical Medicine and Surgery, University of Naples Federico II, Naples, Italy.,Translational Genomics and Targeted Therapeutics in Solid Tumors, August Pi I Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain.,SOLTI Breast Cancer Research Group, Barcelona, Spain
| | - Navid Sobhani
- Department of Medical, Surgery & Health Sciences, University of Trieste, Piazza Ospitale 1, 34129, Trieste, Italy
| | - Anna Ianza
- Department of Medical, Surgery & Health Sciences, University of Trieste, Piazza Ospitale 1, 34129, Trieste, Italy
| | - Tiziana Triulzi
- Molecular Targeting Unit, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Alfredo Molteni
- UO Ematologia e CTMO, ASST di Cremona, Viale Concordia 1, 26100, Cremona, Italy
| | | | - Carla Strina
- UO Multidisciplinare di Patologia Mammaria e Ricerca Traslazionale, ASST di Cremona, Viale Concordia 1, 26100, Cremona, Italy
| | - Manuela Milani
- UO Multidisciplinare di Patologia Mammaria e Ricerca Traslazionale, ASST di Cremona, Viale Concordia 1, 26100, Cremona, Italy
| | - Silvia Paola Corona
- Department of Medical, Surgery & Health Sciences, University of Trieste, Piazza Ospitale 1, 34129, Trieste, Italy
| | - Marianna Sirico
- UO Multidisciplinare di Patologia Mammaria e Ricerca Traslazionale, ASST di Cremona, Viale Concordia 1, 26100, Cremona, Italy
| | - Ottavia Bernocchi
- Department of Medical, Surgery & Health Sciences, University of Trieste, Piazza Ospitale 1, 34129, Trieste, Italy.,UO Multidisciplinare di Patologia Mammaria e Ricerca Traslazionale, ASST di Cremona, Viale Concordia 1, 26100, Cremona, Italy
| | - Fabiola Giudici
- Department of Medical, Surgery & Health Sciences, University of Trieste, Piazza Ospitale 1, 34129, Trieste, Italy
| | - Maria Rosaria Cappelletti
- UO Multidisciplinare di Patologia Mammaria e Ricerca Traslazionale, ASST di Cremona, Viale Concordia 1, 26100, Cremona, Italy
| | - Eva Ciruelos
- SOLTI Breast Cancer Research Group, Barcelona, Spain.,Department of Medical Oncology, Breast Cancer Unit, University Hospital, 12 de Octubre, Avda de Córdoba s/n, Madrid, Spain
| | - Guy Jerusalem
- Department of Medical Oncology, Centre Hospitalier Universitaire de Liège and Liège University, Avenue de L'Hòpital 1, 4000, Liège, Belgium
| | - Sherine Loi
- Peter MacCallum Cancer Center, 305 Grattan Street, Melbourne, VIC, Australia.,University of Melbourne, Melbourne, VIC, Australia
| | - Stephen B Fox
- Peter MacCallum Cancer Center, 305 Grattan Street, Melbourne, VIC, Australia.,University of Melbourne, Melbourne, VIC, Australia
| | - Daniele Generali
- Department of Medical, Surgery & Health Sciences, University of Trieste, Piazza Ospitale 1, 34129, Trieste, Italy. .,UO Multidisciplinare di Patologia Mammaria e Ricerca Traslazionale, ASST di Cremona, Viale Concordia 1, 26100, Cremona, Italy.
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45
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Cheasley D, Devereux L, Hughes S, Nickson C, Procopio P, Lee G, Li N, Pridmore V, Elder K, Bruce Mann G, Kader T, Rowley SM, Fox SB, Byrne D, Saunders H, Fujihara KM, Lim B, Gorringe KL, Campbell IG. The TP53 mutation rate differs in breast cancers that arise in women with high or low mammographic density. NPJ Breast Cancer 2020; 6:34. [PMID: 32802943 PMCID: PMC7414106 DOI: 10.1038/s41523-020-00176-7] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Accepted: 07/13/2020] [Indexed: 01/01/2023] Open
Abstract
Mammographic density (MD) influences breast cancer risk, but how this is mediated is unknown. Molecular differences between breast cancers arising in the context of the lowest and highest quintiles of mammographic density may identify the mechanism through which MD drives breast cancer development. Women diagnosed with invasive or in situ breast cancer where MD measurement was also available (n = 842) were identified from the Lifepool cohort of >54,000 women participating in population-based mammographic screening. This group included 142 carcinomas in the lowest quintile of MD and 119 carcinomas in the highest quintile. Clinico-pathological and family history information were recorded. Tumor DNA was collected where available (n = 56) and sequenced for breast cancer predisposition and driver gene mutations, including copy number alterations. Compared to carcinomas from low-MD breasts, those from high-MD breasts were significantly associated with a younger age at diagnosis and features associated with poor prognosis. Low- and high-MD carcinomas matched for grade, histological subtype, and hormone receptor status were compared for somatic genetic features. Low-MD carcinomas had a significantly increased frequency of TP53 mutations, higher homologous recombination deficiency, higher fraction of the genome altered, and more copy number gains on chromosome 1q and losses on 17p. While high-MD carcinomas showed enrichment of tumor-infiltrating lymphocytes in the stroma. The data demonstrate that when tumors were matched for confounding clinico-pathological features, a proportion in the lowest quintile of MD appear biologically distinct, reflective of microenvironment differences between the lowest and highest quintiles of MD.
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Affiliation(s)
- Dane Cheasley
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC Australia
| | - Lisa Devereux
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC Australia
- Lifepool, Peter MacCallum Cancer Centre, Melbourne, VIC Australia
| | - Siobhan Hughes
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC Australia
| | - Carolyn Nickson
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, VIC Australia
- Cancer Research Division, Cancer Council NSW, Sydney, NSW Australia
- Sydney School of Public Health, University of Sydney, Sydney, NSW Australia
| | - Pietro Procopio
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, VIC Australia
- Cancer Research Division, Cancer Council NSW, Sydney, NSW Australia
- Sydney School of Public Health, University of Sydney, Sydney, NSW Australia
| | - Grant Lee
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, VIC Australia
| | - Na Li
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC Australia
| | | | - Kenneth Elder
- Department of Surgery, University of Melbourne, Melbourne, VIC Australia
- The Royal Melbourne and Royal Women’s Hospitals, Parkville, VIC Australia
- The Edinburgh Breast Unit, Western General Hospital, Edinburgh, UK
| | - G. Bruce Mann
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC Australia
- Department of Surgery, University of Melbourne, Melbourne, VIC Australia
- The Royal Melbourne and Royal Women’s Hospitals, Parkville, VIC Australia
| | - Tanjina Kader
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC Australia
| | - Simone M. Rowley
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC Australia
| | - Stephen B. Fox
- Department of Pathology, Peter MacCallum Cancer Centre, and University of Melbourne, Melbourne, VIC Australia
| | - David Byrne
- Department of Pathology, Peter MacCallum Cancer Centre, and University of Melbourne, Melbourne, VIC Australia
| | - Hugo Saunders
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC Australia
| | - Kenji M. Fujihara
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC Australia
| | - Belle Lim
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC Australia
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, Australia
| | - Kylie L. Gorringe
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC Australia
- Cancer Genetics and Genomics Program, Peter MacCallum Cancer Centre, Melbourne, VIC Australia
| | - Ian G. Campbell
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC Australia
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Tan PH, Ellis I, Allison K, Brogi E, Fox SB, Lakhani S, Lazar AJ, Morris EA, Sahin A, Salgado R, Sapino A, Sasano H, Schnitt S, Sotiriou C, van Diest P, White VA, Lokuhetty D, Cree IA. The 2019 World Health Organization classification of tumours of the breast. Histopathology 2020; 77:181-185. [PMID: 32056259 DOI: 10.1111/his.14091] [Citation(s) in RCA: 308] [Impact Index Per Article: 77.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 01/29/2020] [Accepted: 02/10/2020] [Indexed: 12/13/2022]
Affiliation(s)
| | - Ian Ellis
- University of Nottingham and Nottingham University Hospitals, Nottingham, UK
| | | | - Edi Brogi
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Stephen B Fox
- Peter MacCallum Cancer Centre and University of Melbourne, Melbourne, Australia
| | - Sunil Lakhani
- University of Queensland and Pathology Queensland, Royal Brisbane and Women's Hospital, Herston, Australia
| | | | | | - Aysegul Sahin
- University of Texas MD Anderson Cancer, Houston, TX, USA
| | | | - Anna Sapino
- Department of Medical Sciences, University of Torino, Torino, Italy
- Candiolo Cancer Institute-FPO, IRCCS, Candiolo, Italy
| | | | - Stuart Schnitt
- Brigham and Women's Hospital/Dana-Farber Cancer Institute, Boston, MA, USA
| | - Christos Sotiriou
- Institut Jules Bordet (Université Libre de Bruxelles), Brussels, Belgium
| | - Paul van Diest
- University Medical Centre Utrecht, Utrecht, The Netherlands
| | | | | | - Ian A Cree
- International Agency for Research on Cancer, Lyon, France
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47
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Itchins M, Lau B, Hudson AL, Westman H, Xia CY, Hayes SA, Howell VM, Rodriguez M, Cooper WA, Wei H, Buckland M, Li BT, Li M, Rathi V, Fox SB, Gill AJ, Clarke SJ, Boyer MJ, Pavlakis N. ALK-Rearranged Non-Small Cell Lung Cancer in 2020: Real-World Triumphs in an Era of Multigeneration ALK-Inhibitor Sequencing Informed by Drug Resistance Profiling. Oncologist 2020; 25:641-649. [PMID: 32558067 PMCID: PMC7418351 DOI: 10.1634/theoncologist.2020-0075] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Accepted: 05/13/2020] [Indexed: 12/13/2022] Open
Abstract
Since its discovery in 2007, we have seen the lives of patients diagnosed with advanced anaplastic lymphoma kinase (ALK)-rearranged non-small cell lung cancers (NSCLC) transform with the advent of molecular therapies with first-, second-, and third-generation ALK inhibitors now available in the clinic. Despite great gains in patient survival now measured in years and preserved quality of life with targeted therapies, drug resistance is unfortunately inevitably encountered in this rare and unique molecular subset of lung cancer, and patients will eventually succumb to the disease. As these patients are often young, fit, and never smokers, the clinical and scientific communities have aligned to expedite drug development and access. Drug resistance profiling and further strategies are being explored through clinical trials, including the evaluation of specific drug sequencing and combinations to overcome such resistance and promote patient longevity. The cases of this report focus on precision medicine and aim to portray the pertinent aspects to consider when treating ALK-rearranged NSCLC in 2020, an ever-shifting space. By way of case examples, this report offers valuable information to the treating clinician, including the evolution of systemic treatments and the management of oligo-progression and multisite drug resistance. With the maturation of real-world data, we are fortunate to be experiencing quality and length of life for patients with this disease surpassing prior expectations in advanced lung cancer. KEY POINTS: This report focuses on the importance of genetic analysis of serial biopsies to capture the dynamic therapeutic vulnerabilities of a patient's tumor, providing a perspective on the complexity of ALK tyrosine kinase inhibitor (ALKi) treatment sequencing. These case examples contribute to the literature on ALK-rearranged and oncogene addicted non-small cell lung cancer (NSCLC), providing a framework for care in the clinic. In oligo-progressive disease, local ablative therapy and continuation of ALKi postprogression should be considered with potential for sustained disease control. ALK G1202R kinase domain mutations (KDM), highly prevalent at resistance to second-generation ALKi resistances, may emerge in non-EML4-ALK variant 3 cases and is sensitive to third-generation lorlatinib. When in compound with one or more ALK KDMs, resistance to lorlatinib is expected. In the case of rampantly progressive disease, rebiopsy and redefining biology in a timely manner may be informative.
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Affiliation(s)
- Malinda Itchins
- Department of Medical Oncology, Royal North Shore HospitalSt LeonardsNew South WalesAustralia
- Bill Walsh Translational Research Laboratory, Kolling InstituteSt LeonardsNew South WalesAustralia
- Northern Clinical School, Faculty of Medicine and Health, University of SydneySt LeonardsNew South WalesAustralia
| | - Brandon Lau
- Chris O'Brien LifehouseCamperdownNew South WalesAustralia
| | - Amanda L. Hudson
- Bill Walsh Translational Research Laboratory, Kolling InstituteSt LeonardsNew South WalesAustralia
- Northern Clinical School, Faculty of Medicine and Health, University of SydneySt LeonardsNew South WalesAustralia
| | - Helen Westman
- Department of Medical Oncology, Royal North Shore HospitalSt LeonardsNew South WalesAustralia
| | - Cathy Yi Xia
- Department of Medical Oncology, Royal North Shore HospitalSt LeonardsNew South WalesAustralia
| | - Sarah A. Hayes
- Bill Walsh Translational Research Laboratory, Kolling InstituteSt LeonardsNew South WalesAustralia
- Northern Clinical School, Faculty of Medicine and Health, University of SydneySt LeonardsNew South WalesAustralia
| | - Viive M. Howell
- Bill Walsh Translational Research Laboratory, Kolling InstituteSt LeonardsNew South WalesAustralia
- Northern Clinical School, Faculty of Medicine and Health, University of SydneySt LeonardsNew South WalesAustralia
| | - Michael Rodriguez
- Bill Walsh Translational Research Laboratory, Kolling InstituteSt LeonardsNew South WalesAustralia
- Northern Clinical School, Faculty of Medicine and Health, University of SydneySt LeonardsNew South WalesAustralia
- Department of Anatomical Pathology, Douglas Hanly MoirMacquarie ParkNew South WalesAustralia
| | - Wendy A. Cooper
- Central Clinical School, School of Medicine, University of SydneySt LeonardsNew South WalesAustralia
- Department of Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred HospitalSydneyNew South WalesAustralia
- School of Medicine, Western Sydney UniversitySydneyNew South WalesAustralia
| | - Heng Wei
- Brain and Mind Centre, University of SydneySt LeonardsNew South WalesAustralia
| | - Michael Buckland
- Brain and Mind Centre, University of SydneySt LeonardsNew South WalesAustralia
- Department of Neuropathology, Royal Prince Alfred HospitalSydneyNew South WalesAustralia
| | - Bob T. Li
- Northern Clinical School, Faculty of Medicine and Health, University of SydneySt LeonardsNew South WalesAustralia
- Memorial Sloan Kettering Cancer Center, and Weill Cornell Medical CollegeNew YorkNew YorkUSA
| | - Mark Li
- Resolution BioscienceRedmondWashingtonUSA
| | - Vivek Rathi
- Department of Anatomical Pathology, St Vincent's, Victoria ParadeFitzroyVictoriaAustralia
| | - Stephen B. Fox
- Department of Pathology, Peter MacCallum Cancer Centre, and University of MelbourneVictoriaAustralia
| | - Anthony J. Gill
- Department of Anatomical Pathology, Royal North Shore HospitalSt LeonardsNew South WalesAustralia
- Northern Clinical School, Faculty of Medicine and Health, University of SydneySt LeonardsNew South WalesAustralia
| | - Stephen J. Clarke
- Department of Medical Oncology, Royal North Shore HospitalSt LeonardsNew South WalesAustralia
- Bill Walsh Translational Research Laboratory, Kolling InstituteSt LeonardsNew South WalesAustralia
- Northern Clinical School, Faculty of Medicine and Health, University of SydneySt LeonardsNew South WalesAustralia
| | - Michael J. Boyer
- Chris O'Brien LifehouseCamperdownNew South WalesAustralia
- Department of Pathology, Peter MacCallum Cancer Centre, and University of MelbourneVictoriaAustralia
| | - Nick Pavlakis
- Department of Medical Oncology, Royal North Shore HospitalSt LeonardsNew South WalesAustralia
- Bill Walsh Translational Research Laboratory, Kolling InstituteSt LeonardsNew South WalesAustralia
- Northern Clinical School, Faculty of Medicine and Health, University of SydneySt LeonardsNew South WalesAustralia
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48
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Li N, McInerny S, Zethoven M, Cheasley D, Lim BWX, Rowley SM, Devereux L, Grewal N, Ahmadloo S, Byrne D, Lee JEA, Li J, Fox SB, John T, Antill Y, Gorringe KL, James PA, Campbell IG. Combined Tumor Sequencing and Case-Control Analyses of RAD51C in Breast Cancer. J Natl Cancer Inst 2020; 111:1332-1338. [PMID: 30949688 DOI: 10.1093/jnci/djz045] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 02/07/2019] [Accepted: 04/03/2019] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Loss-of-function variants in RAD51C are associated with familial ovarian cancer, but its role in hereditary breast cancer remains unclear. The aim of this study was to couple breast tumor sequencing with case-control data to clarify the contribution of RAD51C to hereditary breast cancer. METHODS RAD51C was sequenced in 3080 breast cancer index cases that were negative in BRCA1/2 clinical tests and 4840 population-matched cancer-free controls. Pedigree and pathology data were analyzed. Nine breast cancers and one ovarian cancer from RAD51C variant carriers were sequenced to identify biallelic inactivation of RAD51C, copy number variation, mutational signatures, and the spectrum of somatic mutations in breast cancer driver genes. The promoter of RAD51C was analyzed for DNA methylation. RESULTS A statistically significant excess of loss-of-function variants was identified in 3080 cases (0.4%) compared with 2 among 4840 controls (0.04%; odds ratio = 8.67, 95% confidence interval = 1.89 to 80.52, P< .001), with more than half of the carriers having no personal or family history of ovarian cancer. In addition, the association was highly statistically significant among cases with estrogen-negative (P <. 001) or triple-negative cancer (P < .001), but not in estrogen-positive cases. Tumor sequencing from carriers confirmed bi-allelic inactivation in all the triple-negative cases and was associated with high homologous recombination deficiency scores and mutational signature 3 indicating homologous recombination repair deficiency. CONCLUSIONS This study provides evidence that germline loss-of-function variants of RAD51C are associated with hereditary breast cancer, particularly triple-negative type. RAD51C-null breast cancers possess similar genomic and clinical features to BRCA1-null cancers and may also be vulnerable to DNA double-strand break inducing chemotherapies and poly ADP-ribose polymerase inhibitors.
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Smith KM, O Haire S, Khuong-Quang DA, Markman B, Gan HK, Ekert PG, O'Byrne KJ, Millward M, Solomon BJ, Tran B, Scott CL, Kee D, McArthur GA, Fellowes A, Weerasuriya R, Lynch E, Martyn M, Gaff C, Fox SB, Desai J. Evaluating barriers to uptake of comprehensive genomic profiling (CGP) in advanced cancer patients (pts). J Clin Oncol 2020. [DOI: 10.1200/jco.2020.38.15_suppl.2033] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
2033 Background: Despite increasing evidence of benefit supporting CGP in personalizing cancer therapy, its widespread uptake remains limited. Barriers include low patient understanding, unmet patient expectations related to low utility, clinician concerns over cost-effectiveness, perceived value, and discomfort in management of complex genomic results. Methods: This prospective cross-institutional demonstration study was designed to evaluate implementation of CGP in the care of adult and paediatric advanced cancer pts, incorporating pt reported outcomes (PROMs), discrete choice experiment (DCE), ongoing process optimization and clinician evaluations. DNA sequencing of FFPE tumor and matched blood was completed with CGP (PMCC Comprehensive Cancer Panel; 391 genes) via central laboratory. A tumor board reported results weekly with emphasis on therapeutic relevance. Oncologists performed consent and results delivery. Pts completed pre-and post-test surveys, including validated and study-specific questions, DCE and if eligible, semi-structured interviews. Qualitative interviews were undertaken with study clinicians and laboratory staff to evaluate processes. Results: 86% (315) of 365 enrolled pts had successful CGP; of these 63% (199) had relevant therapeutic, diagnostic or germline results. 50 (16%) had treatment change at 6m, 49 (16%) had germline mutations. 293 (88% of adult pts) completed PROMs. 17 of 19 clinicians/laboratory staff approached consented to an interview. At consent pts cited multifaceted value in testing, showed good understanding of basic concepts, but most (69%) overestimated the likelihood of result-led change. Post-test pts remained consistently satisfied with accessing CGP; valuing research contribution, taking opportunities and information for family. 21% struggled with understanding results but there were low levels of decisional regret following participation (89% had nil/mild regret). Pt-elicited preferences (via DCE) indicated priority for high rates of clinical utility and timeliness. Clinicians sited collaboration and communication as critical to delivery of CGP. Conclusions: Pts undergoing CGP are generally satisfied, and derive value on its use beyond potential therapeutic benefit. Our results suggest that to improve test utility and delivery of CGP with value to pts and investing institution, focus must be placed on addressing the additional barriers to its wider implications including efforts to improve process efficiencies, clinician genomic literacy and decision-making support.
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Affiliation(s)
| | | | | | - Ben Markman
- Monash Health and Monash University, Melbourne, Australia
| | - Hui Kong Gan
- Olivia Newton-John Cancer Research Institute, Victoria, NSW, Australia
| | - Paul G Ekert
- Royal Children's Hospital, Parkville, VIC, Australia
| | | | | | | | - Ben Tran
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Clare L. Scott
- Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
| | - Damien Kee
- Peter MacCallum Cancer Centre, Melbourne, Australia
| | | | | | | | - Elly Lynch
- Melbourne Genomics Health Alliance, Melbourne, VIC, Australia
| | - Melissa Martyn
- Melbourne Genomics Health Alliance, Melbourne, VIC, Australia
| | - Clara Gaff
- Melbourne Genomics Health Alliance, Melbourne, VIC, Australia
| | | | - Jayesh Desai
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
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50
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Kee D, Kondrashova O, Ananda S, Brown MP, Cohen PA, Dean A, Desai J, Fellowes A, Fox SB, Hadley A, Lindsay D, Mileshkin LR, O'Byrne KJ, Prall OW, Scott H, Thomas DM, Vines R, Waddell N, Papenfuss A, Scott CL. NOMINATOR: Feasibility of genomic testing of rare cancers to match cancer to treatment. J Clin Oncol 2020. [DOI: 10.1200/jco.2020.38.15_suppl.103] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
103 Background: Rare cancers (RCs) often lack proven treatments and consequently have poorer outcomes. Identification of molecular biomarkers can facilitate treatment selection and trials access for RC patients (pts) where histology-based trials are not feasible. We assessed the potential for next-generation sequencing (NGS) to impact RC care. Methods: Pts with a rare histology, poor-prognosis solid-tumor and no standard of care therapy underwent NGS genomic profiling of paired FFPE tumor and blood (PMCC comprehensive cancer panel; 391 genes). A virtual molecular tumour board (MTB) reviewed curated results regarding diagnosis, actionability (OncoKB) and treatment recommendations. Results: Between July 2017 and Nov 2019, 121 pt were prospectively enrolled across 4 Australian sites. 109 (91%) pts had a tumour with an incidence of < 1/100,000 person/years with 83 diverse RC histologies represented. 100 (83%) cases were successfully sequenced. The most commonly aberrant genes ( > 10%) were: TP53 (45%), CDKN2A/B, RB1, PTEN and NF1. 51 (51%) had at least one potentially actionable finding, with 27 matched to a clinically validated drug (OncoKB level 3 or better) [Table]. In 6 cases NGS resulted in a revised diagnosis (includes 4 with FDA approved therapy). Actionable germline mutations were detected in 3 individuals of which 2 were previously known. The majority of pts remain in follow-up, however, 8 died prior to or within 28 days of NGS result availability. Drug access remains a limitation with only 12 receiving therapy based on NGS/MTB guidance. Clinical trial information: ACTRN12616001000493 . Conclusions: NGS in RCs is feasible with potential impact in half of cases. Earlier testing and improved off-label/trial drug access is necessary to increase the likelihood that RC patients may benefit from molecularly guided therapy. [Table: see text]
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Affiliation(s)
- Damien Kee
- Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Olga Kondrashova
- QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | | | | | | | - Andrew Dean
- St. John of God Hospital, Subiaco, Australia
| | - Jayesh Desai
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | | | - Stephen B. Fox
- University of Newcastle/Australian New Zealand Breast Cancer Trials Group, Newcastle, Australia
| | - Alison Hadley
- Royal Brisbane & Women's Hospital, Brisbane, QLD, Australia
| | - Dianne Lindsay
- Walter Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
| | | | | | | | - Hamish Scott
- Centre for Cancer Biology, An SA Pathology & UniSA Alliance, Adelaide, SA, Australia
| | | | | | - Nic Waddell
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Anthony Papenfuss
- Walter Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
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