1
|
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] [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.
Collapse
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
| |
Collapse
|
2
|
Shojaee P, Mornata F, Deutsch A, Locati M, Hatzikirou H. The impact of tumor associated macrophages on tumor biology under the lens of mathematical modelling: A review. Front Immunol 2022; 13:1050067. [PMID: 36439180 PMCID: PMC9685623 DOI: 10.3389/fimmu.2022.1050067] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 10/18/2022] [Indexed: 09/10/2023] Open
Abstract
In this article, we review the role of mathematical modelling to elucidate the impact of tumor-associated macrophages (TAMs) in tumor progression and therapy design. We first outline the biology of TAMs, and its current application in tumor therapies, and their experimental methods that provide insights into tumor cell-macrophage interactions. We then focus on the mechanistic mathematical models describing the role of macrophages as drug carriers, the impact of macrophage polarized activation on tumor growth, and the role of tumor microenvironment (TME) parameters on the tumor-macrophage interactions. This review aims to identify the synergies between biological and mathematical approaches that allow us to translate knowledge on fundamental TAMs biology in addressing current clinical challenges.
Collapse
Affiliation(s)
- Pejman Shojaee
- Centre for Information Services and High Performance Computing, Technische Universität (TU) Dresden, Dresden, Germany
| | - Federica Mornata
- Leukocyte Biology Lab, IRCCS Humanitas Research Hospital, Rozzano, Italy
| | - Andreas Deutsch
- Centre for Information Services and High Performance Computing, Technische Universität (TU) Dresden, Dresden, Germany
| | - Massimo Locati
- Leukocyte Biology Lab, IRCCS Humanitas Research Hospital, Rozzano, Italy
- Department of Medical Biotechnologies and Translational Medicine, Universitàdegli Studi di Milano, Milan, Italy
| | - Haralampos Hatzikirou
- Centre for Information Services and High Performance Computing, Technische Universität (TU) Dresden, Dresden, Germany
- Mathematics Department, Khalifa University, Abu Dhabi, United Arab Emirates
- Healthcare Engineering Innovation Centre (HEIC), Khalifa University, Abu Dhabi, United Arab Emirates
| |
Collapse
|
3
|
Jenner AL, Smalley M, Goldman D, Goins WF, Cobbs CS, Puchalski RB, Chiocca EA, Lawler S, Macklin P, Goldman A, Craig M. Agent-based computational modeling of glioblastoma predicts that stromal density is central to oncolytic virus efficacy. iScience 2022; 25:104395. [PMID: 35637733 PMCID: PMC9142563 DOI: 10.1016/j.isci.2022.104395] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 03/18/2022] [Accepted: 04/08/2022] [Indexed: 11/26/2022] Open
Abstract
Oncolytic viruses (OVs) are emerging cancer immunotherapy. Despite notable successes in the treatment of some tumors, OV therapy for central nervous system cancers has failed to show efficacy. We used an ex vivo tumor model developed from human glioblastoma tissue to evaluate the infiltration of herpes simplex OV rQNestin (oHSV-1) into glioblastoma tumors. We next leveraged our data to develop a computational, model of glioblastoma dynamics that accounts for cellular interactions within the tumor. Using our computational model, we found that low stromal density was highly predictive of oHSV-1 therapeutic success, suggesting that the efficacy of oHSV-1 in glioblastoma may be determined by stromal-to-tumor cell regional density. We validated these findings in heterogenous patient samples from brain metastatic adenocarcinoma. Our integrated modeling strategy can be applied to suggest mechanisms of therapeutic responses for central nervous system cancers and to facilitate the successful translation of OVs into the clinic.
Collapse
Affiliation(s)
- Adrianne L. Jenner
- Department of Mathematics and Statistics, Université de Montréal, Montréal, QC, Canada
- Sainte-Justine University Hospital Research Centre, Montréal, QC, Canada
| | - Munisha Smalley
- Division of Engineering in Medicine, Brigham and Women’s Hospital, Boston, MA, USA
| | | | - William F. Goins
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Charles S. Cobbs
- Ben and Catherine Ivy Center for Advanced Brain Tumor Treatment, Swedish Neuroscience Institute, Seattle, WA, USA
| | - Ralph B. Puchalski
- Ben and Catherine Ivy Center for Advanced Brain Tumor Treatment, Swedish Neuroscience Institute, Seattle, WA, USA
| | - E. Antonio Chiocca
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Sean Lawler
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Paul Macklin
- Department of Intelligent Systems Engineering, Indiana University, Bloomington, IN, USA
| | - Aaron Goldman
- Division of Engineering in Medicine, Brigham and Women’s Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Morgan Craig
- Department of Mathematics and Statistics, Université de Montréal, Montréal, QC, Canada
- Sainte-Justine University Hospital Research Centre, Montréal, QC, Canada
| |
Collapse
|
4
|
Prybutok AN, Cain JY, Leonard JN, Bagheri N. Fighting fire with fire: deploying complexity in computational modeling to effectively characterize complex biological systems. Curr Opin Biotechnol 2022; 75:102704. [DOI: 10.1016/j.copbio.2022.102704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Revised: 01/27/2022] [Accepted: 02/06/2022] [Indexed: 11/03/2022]
|
5
|
Rojas-Domínguez A, Arroyo-Duarte R, Rincón-Vieyra F, Alvarado-Mentado M. Modeling cancer immunoediting in tumor microenvironment with system characterization through the ising-model Hamiltonian. BMC Bioinformatics 2022; 23:200. [PMID: 35637445 PMCID: PMC9150349 DOI: 10.1186/s12859-022-04731-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Accepted: 05/11/2022] [Indexed: 12/02/2022] Open
Abstract
Background and objective Cancer Immunoediting (CI) describes the cellular-level interaction between tumor cells and the Immune System (IS) that takes place in the Tumor Micro-Environment (TME). CI is a highly dynamic and complex process comprising three distinct phases (Elimination, Equilibrium and Escape) wherein the IS can both protect against cancer development as well as, over time, promote the appearance of tumors with reduced immunogenicity. Herein we present an agent-based model for the simulation of CI in the TME, with the objective of promoting the understanding of this process. Methods Our model includes agents for tumor cells and for elements of the IS. The actions of these agents are governed by probabilistic rules, and agent recruitment (including cancer growth) is modeled via logistic functions. The system is formalized as an analogue of the Ising model from statistical mechanics to facilitate its analysis. The model was implemented in the Netlogo modeling environment and simulations were performed to verify, illustrate and characterize its operation. Results A main result from our simulations is the generation of emergent behavior in silico that is very difficult to observe directly in vivo or even in vitro. Our model is capable of generating the three phases of CI; it requires only a couple of control parameters and is robust to these. We demonstrate how our simulated system can be characterized through the Ising-model energy function, or Hamiltonian, which captures the “energy” involved in the interaction between agents and presents it in clear and distinct patterns for the different phases of CI. Conclusions The presented model is very flexible and robust, captures well the behaviors of the target system and can be easily extended to incorporate more variables such as those pertaining to different anti-cancer therapies. System characterization via the Ising-model Hamiltonian is a novel and powerful tool for a better understanding of CI and the development of more effective treatments. Since data of CI at the cellular level is very hard to procure, our hope is that tools such as this may be adopted to shed light on CI and related developing theories. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-022-04731-w.
Collapse
Affiliation(s)
- Alfonso Rojas-Domínguez
- Postgraduate Studies and Research Division, Tecnológico Nacional de México - IT de León, León, Mexico
| | | | - Fernando Rincón-Vieyra
- Depto. de Computación, CINVESTAV-IPN, Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, GAM, 07360, Mexico City, CDMX, Mexico
| | - Matías Alvarado-Mentado
- Depto. de Computación, CINVESTAV-IPN, Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, GAM, 07360, Mexico City, CDMX, Mexico.
| |
Collapse
|
6
|
Butner JD, Wang Z. Predicting immune checkpoint inhibitor response with mathematical modeling. Immunotherapy 2021; 13:1151-1155. [PMID: 34435504 DOI: 10.2217/imt-2021-0209] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Affiliation(s)
- Joseph D Butner
- Mathematics in Medicine Program, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Zhihui Wang
- Mathematics in Medicine Program, Houston Methodist Research Institute, Houston, TX 77030, USA.,Cancer Center, Houston Methodist Research Institute, Houston, TX 77030, USA.,Department of Physiology & Biophysics, Weill Cornell Medicine, New York, NY 10065, USA
| |
Collapse
|
7
|
The role of tumor heterogeneity in immune-tumor interactions. Cancer Metastasis Rev 2021; 40:377-389. [PMID: 33682030 DOI: 10.1007/s10555-021-09957-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 02/23/2021] [Indexed: 12/23/2022]
Abstract
The development of cancer stems from genetic instability and changes in genomic sequences, and hence, the heterogeneity exhibited by tumors is integral to the nature of cancer itself. Tumor heterogeneity can be further altered by factors that are not cancer cell intrinsic, i.e., by the microenvironment, including the patient's immune responses to tumors and administered therapies (immunotherapies, chemotherapies, and/or radiation therapies). The focus of this review is the impact of tumor heterogeneity on the interactions between immune cells and the tumor, taking into account that heterogeneity can exist at several levels. These levels include heterogeneity within an individual tumor, within an individual patient (particularly between the primary tumor and metastatic lesions), among the subtypes of a specific type of cancer, or within cancers that originate from different tissues. Because of the potential for immunity (either the natural immune system or via immunotherapeutics) to halt the progression of cancer, major clinical significance exists in understanding the impact of tumor heterogeneity on the associations between immune cells and tumor cells. Increased knowledge of why, whether, and how immune-tumor interactions occur provides the means to guide these interactions and improve outcomes for patients.
Collapse
|
8
|
Butner JD, Wang Z, Elganainy D, Al Feghali KA, Plodinec M, Calin GA, Dogra P, Nizzero S, Ruiz-Ramírez J, Martin GV, Tawbi HA, Chung C, Koay EJ, Welsh JW, Hong DS, Cristini V. A mathematical model for the quantification of a patient's sensitivity to checkpoint inhibitors and long-term tumour burden. Nat Biomed Eng 2021; 5:297-308. [PMID: 33398132 PMCID: PMC8669771 DOI: 10.1038/s41551-020-00662-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 11/14/2020] [Indexed: 02/06/2023]
Abstract
A large proportion of patients with cancer are unresponsive to treatment with immune checkpoint blockade and other immunotherapies. Here, we report a mathematical model of the time-course of tumour responses to immune-checkpoint inhibitors. The model takes into account intrinsic tumour-growth rates, the rates of immune activation and of tumour–immune-cell interactions, and the efficacy of immune-mediated tumour killing. For 124 patients, four cancer types and two immunotherapy agents, the model reliably described the immune responses and final tumour burden across all different cancers and drug combinations examined. In validation cohorts from four clinical trials of checkpoint inhibitors (with a total of 177 patients), the model accurately stratified the patients according to reduced or increased long-term tumour burden. We also provide model-derived quantitative measures of treatment sensitivity for specific drug–cancer combinations. The model can be used to predict responses to therapy and to quantify specific drug–cancer sensitivities in individual patients.
Collapse
Affiliation(s)
- Joseph D Butner
- Mathematics in Medicine Program, Houston Methodist Research Institute, Houston, TX, USA
| | - Zhihui Wang
- Mathematics in Medicine Program, Houston Methodist Research Institute, Houston, TX, USA. .,Department of Imaging Physics, University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Dalia Elganainy
- Department of Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Karine A Al Feghali
- Department of Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Marija Plodinec
- Biozentrum and the Swiss Nanoscience Institute, University of Basel, Basel, Switzerland
| | - George A Calin
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Prashant Dogra
- Mathematics in Medicine Program, Houston Methodist Research Institute, Houston, TX, USA
| | - Sara Nizzero
- Mathematics in Medicine Program, Houston Methodist Research Institute, Houston, TX, USA
| | - Javier Ruiz-Ramírez
- Mathematics in Medicine Program, Houston Methodist Research Institute, Houston, TX, USA
| | - Geoffrey V Martin
- Department of Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Hussein A Tawbi
- Department of Melanoma Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Caroline Chung
- Department of Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Eugene J Koay
- Department of Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - James W Welsh
- Department of Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - David S Hong
- Department of Investigational Cancer Therapeutics, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Vittorio Cristini
- Mathematics in Medicine Program, Houston Methodist Research Institute, Houston, TX, USA. .,Department of Imaging Physics, University of Texas MD Anderson Cancer Center, Houston, TX, USA. .,Physiology, Biophysics, and Systems Biology Program, Graduate School of Medical Sciences, Weill Cornell Medicine, New York, NY, USA.
| |
Collapse
|
9
|
Abstract
The tumor microenvironment contains many cellular components influencing tumor behaviors, such as metastasis, angiogenesis and chemo-resistance. Tumor-associated macrophages (TAMs) are one of such components that can also manipulate the overall prognosis and patient survival. Analysis of tumor-macrophage crosstalk is crucial as tumor cells can polarize circulatory monocytes into TAMs. Such trans-polarization of macrophages support tumor mediated evasion and suppression of immune response. Additionally, such TAMs significantly influence tumor growth and proliferation, making them a potential candidate for precision therapeutics. However, the failure of macrophage-dependent therapies at clinical trials emphasizes the fault in current perception and research modality. This review discussed this field's progress regarding emerging model systems with a focused view on the in vitro platforms. The inadequacy of currently available models and their implications on existing studies also analyzed. The need for a conceptual and experimental leap toward a human-relevant in vitro custom-built platform for studying tumor-macrophage crosstalk is acknowledged.
Collapse
Affiliation(s)
- Tuli Dey
- Institute of Bioinformatics and Biotechnology, Savitribai Phule Pune University, Pune, India
| |
Collapse
|
10
|
Cess CG, Finley SD. Multi-scale modeling of macrophage-T cell interactions within the tumor microenvironment. PLoS Comput Biol 2020; 16:e1008519. [PMID: 33362239 PMCID: PMC7790427 DOI: 10.1371/journal.pcbi.1008519] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 01/07/2021] [Accepted: 11/11/2020] [Indexed: 02/06/2023] Open
Abstract
Within the tumor microenvironment, macrophages exist in an immunosuppressive state, preventing T cells from eliminating the tumor. Due to this, research is focusing on immunotherapies that specifically target macrophages in order to reduce their immunosuppressive capabilities and promote T cell function. In this study, we develop an agent-based model consisting of the interactions between macrophages, T cells, and tumor cells to determine how the immune response changes due to three macrophage-based immunotherapeutic strategies: macrophage depletion, recruitment inhibition, and macrophage reeducation. We find that reeducation, which converts the macrophages into an immune-promoting phenotype, is the most effective strategy and that the macrophage recruitment rate and tumor proliferation rate (tumor-specific properties) have large impacts on therapy efficacy. We also employ a novel method of using a neural network to reduce the computational complexity of an intracellular signaling mechanistic model.
Collapse
Affiliation(s)
- Colin G. Cess
- Department of Biomedical Engineering, University of Southern California, Los Angeles, California, United States of America
| | - Stacey D. Finley
- Department of Biomedical Engineering, University of Southern California, Los Angeles, California, United States of America
- Department of Quantitative and Biological Sciences, University of Southern California, Los Angeles, California, United States of America
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California, United States of America
| |
Collapse
|
11
|
Mi H, Gong C, Sulam J, Fertig EJ, Szalay AS, Jaffee EM, Stearns V, Emens LA, Cimino-Mathews AM, Popel AS. Digital Pathology Analysis Quantifies Spatial Heterogeneity of CD3, CD4, CD8, CD20, and FoxP3 Immune Markers in Triple-Negative Breast Cancer. Front Physiol 2020; 11:583333. [PMID: 33192595 PMCID: PMC7604437 DOI: 10.3389/fphys.2020.583333] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 09/24/2020] [Indexed: 12/17/2022] Open
Abstract
Overwhelming evidence has shown the significant role of the tumor microenvironment (TME) in governing the triple-negative breast cancer (TNBC) progression. Digital pathology can provide key information about the spatial heterogeneity within the TME using image analysis and spatial statistics. These analyses have been applied to CD8+ T cells, but quantitative analyses of other important markers and their correlations are limited. In this study, a digital pathology computational workflow is formulated for characterizing the spatial distributions of five immune markers (CD3, CD4, CD8, CD20, and FoxP3) and then the functionality is tested on whole slide images from patients with TNBC. The workflow is initiated by digital image processing to extract and colocalize immune marker-labeled cells and then convert this information to point patterns. Afterward invasive front (IF), central tumor (CT), and normal tissue (N) are characterized. For each region, we examine the intra-tumoral heterogeneity. The workflow is then repeated for all specimens to capture inter-tumoral heterogeneity. In this study, both intra- and inter-tumoral heterogeneities are observed for all five markers across all specimens. Among all regions, IF tends to have higher densities of immune cells and overall larger variations in spatial model fitting parameters and higher density in cell clusters and hotspots compared to CT and N. Results suggest a distinct role of IF in the tumor immuno-architecture. Though the sample size is limited in the study, the computational workflow could be readily reproduced and scaled due to its automatic nature. Importantly, the value of the workflow also lies in its potential to be linked to treatment outcomes and identification of predictive biomarkers for responders/non-responders, and its application to parameterization and validation of computational immuno-oncology models.
Collapse
Affiliation(s)
- Haoyang Mi
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Chang Gong
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Jeremias Sulam
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, United States.,Johns Hopkins Mathematical Institute for Data Science, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD, United States
| | - Elana J Fertig
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, United States.,Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, United States
| | - Alexander S Szalay
- Henry A. Rowland Department of Physics and Astronomy, Krieger School of Arts and Sciences, Johns Hopkins University, Baltimore, MD, United States.,Department of Computer Science, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD, United States
| | - Elizabeth M Jaffee
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, United States.,The Bloomberg∼Kimmel Institute for Cancer Immunotherapy, Johns Hopkins School of Medicine, Baltimore, MD, United States
| | - Vered Stearns
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, United States
| | - Leisha A Emens
- Department of Medicine/Hematology-Oncology, Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, PA, United States
| | - Ashley M Cimino-Mathews
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, United States.,Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Aleksander S Popel
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, United States.,Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, United States
| |
Collapse
|
12
|
Li B, Yang Q, Li Z, Xu Z, Sun S, Wu Q, Sun S. Expression of Monocarboxylate Transporter 1 in Immunosuppressive Macrophages Is Associated With the Poor Prognosis in Breast Cancer. Front Oncol 2020; 10:574787. [PMID: 33178603 PMCID: PMC7596686 DOI: 10.3389/fonc.2020.574787] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 09/07/2020] [Indexed: 01/06/2023] Open
Abstract
Monocarboxylate transporter 1 (MCT1) participates in the transport of lactate to facilitate metabolic reprogramming during tumor progression. Tumor-associated macrophages (TAMs) are also involved in the inflammatory adaptation of the tumor microenvironment (TME). This study aimed to determine the correlation between metabolite changes and the polarization of macrophages in the TME. We demonstrated that the expression of CD163 on macrophages was significantly higher in breast cancer tissues than in normal tissues, especially in the HER2 subtype, although it was not statistically associated with recurrence-free survival (RFS). The presence of MCT1+ and CD163+ macrophages in the invasive margin was significantly correlated with decreased RFS. A significant correlation existed between MCT1 and CD163 expression in the margin, and high infiltration of MCT1+CD163+ macrophages into the margin predicted rapid progression and poor survival outcomes for breast cancer patients. These data suggested that MCT1 at least partially promoted the alternative polarization of macrophages to inhibit antitumor immunity, and blocking this interaction may be a promising method for breast cancer therapy.
Collapse
Affiliation(s)
- Bei Li
- Department of Pathology, Renmin Hospital of Wuhan University, Wuhan, China.,Department of Breast and Thyroid Surgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Qian Yang
- Department of Breast and Thyroid Surgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Zhiyu Li
- Department of Breast and Thyroid Surgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Zhiliang Xu
- Department of Breast and Thyroid Surgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Si Sun
- Department of Clinical Laboratory, Renmin Hospital of Wuhan University, Wuhan, China
| | - Qi Wu
- Department of Breast and Thyroid Surgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Shengrong Sun
- Department of Breast and Thyroid Surgery, Renmin Hospital of Wuhan University, Wuhan, China
| |
Collapse
|
13
|
Abstract
Tumor immunology is undergoing a renaissance due to the recent profound clinical successes of tumor immunotherapy. These advances have coincided with an exponential growth in the development of -omics technologies. Armed with these technologies and their associated computational and modeling toolsets, systems biologists have turned their attention to tumor immunology in an effort to understand the precise nature and consequences of interactions between tumors and the immune system. Such interactions are inherently multivariate, spanning multiple time and size scales, cell types, and organ systems, rendering systems biology approaches particularly amenable to their interrogation. While in its infancy, the field of 'Cancer Systems Immunology' has already influenced our understanding of tumor immunology and immunotherapy. As the field matures, studies will move beyond descriptive characterizations toward functional investigations of the emergent behavior that govern tumor-immune responses. Thus, Cancer Systems Immunology holds incredible promise to advance our ability to fight this disease.
Collapse
Affiliation(s)
| | - Edgar G Engleman
- Department of Pathology, Stanford University School of MedicineStanfordUnited States
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University School of MedicineStanfordUnited States
- Stanford Cancer Institute, Stanford UniversityStanfordUnited States
| |
Collapse
|
14
|
Aguilar B, Gibbs DL, Reiss DJ, McConnell M, Danziger SA, Dervan A, Trotter M, Bassett D, Hershberg R, Ratushny AV, Shmulevich I. A generalizable data-driven multicellular model of pancreatic ductal adenocarcinoma. Gigascience 2020; 9:giaa075. [PMID: 32696951 PMCID: PMC7374045 DOI: 10.1093/gigascience/giaa075] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 02/14/2020] [Accepted: 06/21/2020] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Mechanistic models, when combined with pertinent data, can improve our knowledge regarding important molecular and cellular mechanisms found in cancer. These models make the prediction of tissue-level response to drug treatment possible, which can lead to new therapies and improved patient outcomes. Here we present a data-driven multiscale modeling framework to study molecular interactions between cancer, stromal, and immune cells found in the tumor microenvironment. We also develop methods to use molecular data available in The Cancer Genome Atlas to generate sample-specific models of cancer. RESULTS By combining published models of different cells relevant to pancreatic ductal adenocarcinoma (PDAC), we built an agent-based model of the multicellular pancreatic tumor microenvironment, formally describing cell type-specific molecular interactions and cytokine-mediated cell-cell communications. We used an ensemble-based modeling approach to systematically explore how variations in the tumor microenvironment affect the viability of cancer cells. The results suggest that the autocrine loop involving EGF signaling is a key interaction modulator between pancreatic cancer and stellate cells. EGF is also found to be associated with previously described subtypes of PDAC. Moreover, the model allows a systematic exploration of the effect of possible therapeutic perturbations; our simulations suggest that reducing bFGF secretion by stellate cells will have, on average, a positive impact on cancer apoptosis. CONCLUSIONS The developed framework allows model-driven hypotheses to be generated regarding therapeutically relevant PDAC states with potential molecular and cellular drivers indicating specific intervention strategies.
Collapse
Affiliation(s)
- Boris Aguilar
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA 98109, USA
| | - David L Gibbs
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA 98109, USA
| | - David J Reiss
- Bristol-Myers Squibb, 400 Dexter Avenue North, Suite 1200, Seattle, WA 98109, USA
| | - Mark McConnell
- Bristol-Myers Squibb, 400 Dexter Avenue North, Suite 1200, Seattle, WA 98109, USA
| | - Samuel A Danziger
- Bristol-Myers Squibb, 400 Dexter Avenue North, Suite 1200, Seattle, WA 98109, USA
| | - Andrew Dervan
- Bristol-Myers Squibb, 400 Dexter Avenue North, Suite 1200, Seattle, WA 98109, USA
| | - Matthew Trotter
- BMS Center for Innovation and Translational Research Europe (CITRE), Pabellon de Italia, Calle Isaac Newton 4, Sevilla 41092, Spain
| | - Douglas Bassett
- Bristol-Myers Squibb, 400 Dexter Avenue North, Suite 1200, Seattle, WA 98109, USA
| | - Robert Hershberg
- Formerly Celgene Corporation, 400 Dexter Avenue North, Suite 1200, Seattle, WA 98109, USA
| | - Alexander V Ratushny
- Bristol-Myers Squibb, 400 Dexter Avenue North, Suite 1200, Seattle, WA 98109, USA
| | - Ilya Shmulevich
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA 98109, USA
| |
Collapse
|
15
|
Liu T, Yao R, Pang Y, Sun W. Review on biofabrication and applications of heterogeneous tumor models. J Tissue Eng Regen Med 2019; 13:2101-2120. [PMID: 31359625 DOI: 10.1002/term.2949] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 07/08/2019] [Accepted: 07/19/2019] [Indexed: 11/12/2022]
Abstract
Resolving the origin and development of tumor heterogeneity has proven to be a crucial challenge in cancer research. In vitro tumor models have been widely used for both scientific and clinical research. Currently, tumor models based on 2D cell culture, animal models, and 3D cell-laden constructs are widely used. Heterogeneous tumor models, which consist of more than one cell type and mimic cell-cell as well as cell-matrix interactions, are attracting increasing attention. Heterogeneous tumor models can serve as pathological models to study the microenvironment and tumor development such as tumorigenesis, invasiveness, and malignancy. They also provide disease models for drug screening and personalized therapy. In this review, the current techniques, models, and oncological applications regarding 3D heterogeneous tumor models are summarized and discussed.
Collapse
Affiliation(s)
- Tiankun Liu
- Tsinghua University, Biomanufacturing and Rapid Forming Technology Key Laboratory of Beijing, Beijing, People's Republic of China.,Biomanufacturing Center, Department of Mechanical Engineering, Tsinghua University, Beijing, People's Republic of China.,Tsinghua University, 111 "Biomanufacturing and Engineering Living Systems" Innovation International Talents Base, Beijing, People's Republic of China.,Key Laboratory of Advanced Forming and Manufacturing, Ministry of Education, Department of Mechanical Engineering, Tsinghua University, Beijing, People's Republic of China
| | - Rui Yao
- Tsinghua University, Biomanufacturing and Rapid Forming Technology Key Laboratory of Beijing, Beijing, People's Republic of China.,Biomanufacturing Center, Department of Mechanical Engineering, Tsinghua University, Beijing, People's Republic of China.,Tsinghua University, 111 "Biomanufacturing and Engineering Living Systems" Innovation International Talents Base, Beijing, People's Republic of China.,Key Laboratory of Advanced Forming and Manufacturing, Ministry of Education, Department of Mechanical Engineering, Tsinghua University, Beijing, People's Republic of China
| | - Yuan Pang
- Tsinghua University, Biomanufacturing and Rapid Forming Technology Key Laboratory of Beijing, Beijing, People's Republic of China.,Biomanufacturing Center, Department of Mechanical Engineering, Tsinghua University, Beijing, People's Republic of China.,Tsinghua University, 111 "Biomanufacturing and Engineering Living Systems" Innovation International Talents Base, Beijing, People's Republic of China.,Key Laboratory of Advanced Forming and Manufacturing, Ministry of Education, Department of Mechanical Engineering, Tsinghua University, Beijing, People's Republic of China
| | - Wei Sun
- Tsinghua University, Biomanufacturing and Rapid Forming Technology Key Laboratory of Beijing, Beijing, People's Republic of China.,Biomanufacturing Center, Department of Mechanical Engineering, Tsinghua University, Beijing, People's Republic of China.,Tsinghua University, 111 "Biomanufacturing and Engineering Living Systems" Innovation International Talents Base, Beijing, People's Republic of China.,Key Laboratory of Advanced Forming and Manufacturing, Ministry of Education, Department of Mechanical Engineering, Tsinghua University, Beijing, People's Republic of China.,Department of Mechanical Engineering, Drexel University, Philadelphia, PA
| |
Collapse
|
16
|
Norton KA, Gong C, Jamalian S, Popel AS. Multiscale Agent-Based and Hybrid Modeling of the Tumor Immune Microenvironment. Processes (Basel) 2019; 7:37. [PMID: 30701168 PMCID: PMC6349239 DOI: 10.3390/pr7010037] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Multiscale systems biology and systems pharmacology are powerful methodologies that are playing increasingly important roles in understanding the fundamental mechanisms of biological phenomena and in clinical applications. In this review, we summarize the state of the art in the applications of agent-based models (ABM) and hybrid modeling to the tumor immune microenvironment and cancer immune response, including immunotherapy. Heterogeneity is a hallmark of cancer; tumor heterogeneity at the molecular, cellular, and tissue scales is a major determinant of metastasis, drug resistance, and low response rate to molecular targeted therapies and immunotherapies. Agent-based modeling is an effective methodology to obtain and understand quantitative characteristics of these processes and to propose clinical solutions aimed at overcoming the current obstacles in cancer treatment. We review models focusing on intra-tumor heterogeneity, particularly on interactions between cancer cells and stromal cells, including immune cells, the role of tumor-associated vasculature in the immune response, immune-related tumor mechanobiology, and cancer immunotherapy. We discuss the role of digital pathology in parameterizing and validating spatial computational models and potential applications to therapeutics.
Collapse
Affiliation(s)
- Kerri-Ann Norton
- Department of Biomedical Engineering, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
- Computer Science Program, Department of Science, Mathematics, and Computing, Bard College, Annandale-on-Hudson, NY 12504, USA
| | - Chang Gong
- Department of Biomedical Engineering, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Samira Jamalian
- Department of Biomedical Engineering, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Aleksander S. Popel
- Department of Biomedical Engineering, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
- Department of Oncology and the Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| |
Collapse
|
17
|
Sinha VC, Piwnica-Worms H. Intratumoral Heterogeneity in Ductal Carcinoma In Situ: Chaos and Consequence. J Mammary Gland Biol Neoplasia 2018; 23:191-205. [PMID: 30194658 PMCID: PMC6934090 DOI: 10.1007/s10911-018-9410-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 08/30/2018] [Indexed: 02/06/2023] Open
Abstract
Ductal carcinoma in situ (DCIS) is a non-invasive proliferative growth in the breast that serves as a non-obligate precursor to invasive ductal carcinoma. The widespread adoption of screening mammography has led to a steep increase in the detection of DCIS, which now comprises approximately 20% of new breast cancer diagnoses in the United States. Interestingly, the intratumoral heterogeneity (ITH) that has been observed in invasive breast cancers may have been established early in tumorigenesis, given the vast and varied ITH that has been detected in DCIS. This review will discuss the intratumoral heterogeneity of DCIS, focusing on the phenotypic and genomic heterogeneity of tumor cells, as well as the compositional heterogeneity of the tumor microenvironment. In addition, we will assess the spatial heterogeneity that is now being appreciated in these lesions, and summarize new approaches to evaluate heterogeneity of tumor and stromal cells in the context of their spatial organization. Importantly, we will discuss how a growing understanding of ITH has led to a more holistic appreciation of the complex biology of DCIS, specifically its evolution and natural history. Finally, we will consider ways in which our knowledge of DCIS ITH might be translated in the future to guide clinical care for DCIS patients.
Collapse
Affiliation(s)
- Vidya C Sinha
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, 6565 MD Anderson Blvd, Houston, TX, 77030, USA
| | - Helen Piwnica-Worms
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, 6565 MD Anderson Blvd, Houston, TX, 77030, USA.
| |
Collapse
|
18
|
Norton KA, Jin K, Popel AS. Modeling triple-negative breast cancer heterogeneity: Effects of stromal macrophages, fibroblasts and tumor vasculature. J Theor Biol 2018; 452:56-68. [PMID: 29750999 DOI: 10.1016/j.jtbi.2018.05.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 04/13/2018] [Accepted: 05/03/2018] [Indexed: 12/20/2022]
Abstract
A hallmark of breast tumors is its spatial heterogeneity that includes its distribution of cancer stem cells and progenitor cells, but also heterogeneity in the tumor microenvironment. In this study we focus on the contributions of stromal cells, specifically macrophages, fibroblasts, and endothelial cells on tumor progression. We develop a computational model of triple-negative breast cancer based on our previous work and expand it to include macrophage infiltration, fibroblasts, and angiogenesis. In vitro studies have shown that the secretomes of tumor-educated macrophages and fibroblasts increase both the migration and proliferation rates of triple-negative breast cancer cells. In vivo studies also demonstrated that blocking signaling of selected secreted factors inhibits tumor growth and metastasis in mouse xenograft models. We investigate the influences of increased migration and proliferation rates on tumor growth, the effect of the presence on fibroblasts or macrophages on growth and morphology, and the contributions of macrophage infiltration on tumor growth. We find that while the presence of macrophages increases overall tumor growth, the increase in macrophage infiltration does not substantially increase tumor growth and can even stifle tumor growth at excessive rates.
Collapse
Affiliation(s)
| | - Kideok Jin
- Department of Biomedical Engineering; Department of Pharmaceutical Science, Albany College of Pharmacy and Health Science, USA
| | - Aleksander S Popel
- Department of Biomedical Engineering; Department of Oncology and the Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, USA
| |
Collapse
|
19
|
Konstorum A, Vella AT, Adler AJ, Laubenbacher RC. Addressing current challenges in cancer immunotherapy with mathematical and computational modelling. J R Soc Interface 2018; 14:rsif.2017.0150. [PMID: 28659410 DOI: 10.1098/rsif.2017.0150] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 05/31/2017] [Indexed: 02/06/2023] Open
Abstract
The goal of cancer immunotherapy is to boost a patient's immune response to a tumour. Yet, the design of an effective immunotherapy is complicated by various factors, including a potentially immunosuppressive tumour microenvironment, immune-modulating effects of conventional treatments and therapy-related toxicities. These complexities can be incorporated into mathematical and computational models of cancer immunotherapy that can then be used to aid in rational therapy design. In this review, we survey modelling approaches under the umbrella of the major challenges facing immunotherapy development, which encompass tumour classification, optimal treatment scheduling and combination therapy design. Although overlapping, each challenge has presented unique opportunities for modellers to make contributions using analytical and numerical analysis of model outcomes, as well as optimization algorithms. We discuss several examples of models that have grown in complexity as more biological information has become available, showcasing how model development is a dynamic process interlinked with the rapid advances in tumour-immune biology. We conclude the review with recommendations for modellers both with respect to methodology and biological direction that might help keep modellers at the forefront of cancer immunotherapy development.
Collapse
Affiliation(s)
- Anna Konstorum
- Center for Quantitative Medicine, UConn Health, Farmington, CT, USA
| | | | - Adam J Adler
- Department of Immunology, UConn Health, Farmington, CT, USA
| | - Reinhard C Laubenbacher
- Center for Quantitative Medicine, UConn Health, Farmington, CT, USA .,Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| |
Collapse
|
20
|
Nilendu P, Kumar A, Kumar A, Pal JK, Sharma NK. Breast cancer stem cells as last soldiers eluding therapeutic burn: A hard nut to crack. Int J Cancer 2017; 142:7-17. [PMID: 28722143 DOI: 10.1002/ijc.30898] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 07/13/2017] [Indexed: 12/26/2022]
Abstract
Cancer stem cells (CSCs) are found in many cancer types, including breast carcinoma. Breast cancer stem cells (BCSCs) are considered as seed of cancer formation and they are associated with metastasis and genotoxic drug resistance. Several studies highlighted the presence of BCSCs in tumor microenvironment and they are accentuated with several carcinoma events including metastasis and resistance to genotoxic drugs and they also rebound after genotoxic burn. Stemness properties of a small population of cells in carcinoma have provided clues regarding the role of tumor microenvironment in tumor pathophysiology. Hence, insights in cancer stem cell biology with respect to molecular signaling, genetics and epigenetic behavior of CSCs have been used to modulate tumor drug resistance due to genotoxic drugs and signaling protein inhibitors. This review summarizes major scientific breakthroughs in understanding the contribution of BCSCs towards tumor's capability to endure destruction inflicted by molecular as well as genotoxic drugs.
Collapse
Affiliation(s)
- Pritish Nilendu
- Cancer and Translational Research Lab, Dr. D.Y. Patil Biotechnology & Bioinformatics Institute, Dr. D. Y. Patil Vidyapeeth, Pune, Maharashtra, 411033, India
| | - Ajay Kumar
- Cancer and Translational Research Lab, Dr. D.Y. Patil Biotechnology & Bioinformatics Institute, Dr. D. Y. Patil Vidyapeeth, Pune, Maharashtra, 411033, India
| | - Azad Kumar
- Cancer and Translational Research Lab, Dr. D.Y. Patil Biotechnology & Bioinformatics Institute, Dr. D. Y. Patil Vidyapeeth, Pune, Maharashtra, 411033, India
| | - Jayanta K Pal
- Cancer and Translational Research Lab, Dr. D.Y. Patil Biotechnology & Bioinformatics Institute, Dr. D. Y. Patil Vidyapeeth, Pune, Maharashtra, 411033, India
| | - Nilesh Kumar Sharma
- Cancer and Translational Research Lab, Dr. D.Y. Patil Biotechnology & Bioinformatics Institute, Dr. D. Y. Patil Vidyapeeth, Pune, Maharashtra, 411033, India
| |
Collapse
|
21
|
Gough A, Stern AM, Maier J, Lezon T, Shun TY, Chennubhotla C, Schurdak ME, Haney SA, Taylor DL. Biologically Relevant Heterogeneity: Metrics and Practical Insights. SLAS DISCOVERY 2017; 22:213-237. [PMID: 28231035 DOI: 10.1177/2472555216682725] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Heterogeneity is a fundamental property of biological systems at all scales that must be addressed in a wide range of biomedical applications, including basic biomedical research, drug discovery, diagnostics, and the implementation of precision medicine. There are a number of published approaches to characterizing heterogeneity in cells in vitro and in tissue sections. However, there are no generally accepted approaches for the detection and quantitation of heterogeneity that can be applied in a relatively high-throughput workflow. This review and perspective emphasizes the experimental methods that capture multiplexed cell-level data, as well as the need for standard metrics of the spatial, temporal, and population components of heterogeneity. A recommendation is made for the adoption of a set of three heterogeneity indices that can be implemented in any high-throughput workflow to optimize the decision-making process. In addition, a pairwise mutual information method is suggested as an approach to characterizing the spatial features of heterogeneity, especially in tissue-based imaging. Furthermore, metrics for temporal heterogeneity are in the early stages of development. Example studies indicate that the analysis of functional phenotypic heterogeneity can be exploited to guide decisions in the interpretation of biomedical experiments, drug discovery, diagnostics, and the design of optimal therapeutic strategies for individual patients.
Collapse
Affiliation(s)
- Albert Gough
- 1 Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA.,2 University of Pittsburgh Drug Discovery Institute, Pittsburgh, PA, USA
| | - Andrew M Stern
- 1 Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA.,2 University of Pittsburgh Drug Discovery Institute, Pittsburgh, PA, USA
| | - John Maier
- 3 Department of Family Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Timothy Lezon
- 1 Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA.,2 University of Pittsburgh Drug Discovery Institute, Pittsburgh, PA, USA
| | - Tong-Ying Shun
- 2 University of Pittsburgh Drug Discovery Institute, Pittsburgh, PA, USA
| | - Chakra Chennubhotla
- 1 Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA.,2 University of Pittsburgh Drug Discovery Institute, Pittsburgh, PA, USA
| | - Mark E Schurdak
- 1 Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA.,2 University of Pittsburgh Drug Discovery Institute, Pittsburgh, PA, USA.,4 University of Pittsburgh Cancer Institute, Pittsburgh, PA, USA
| | - Steven A Haney
- 5 Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN, USA
| | - D Lansing Taylor
- 1 Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA.,2 University of Pittsburgh Drug Discovery Institute, Pittsburgh, PA, USA.,4 University of Pittsburgh Cancer Institute, Pittsburgh, PA, USA
| |
Collapse
|
22
|
Synergistic Communication between CD4+ T Cells and Monocytes Impacts the Cytokine Environment. Sci Rep 2016; 6:34942. [PMID: 27721433 PMCID: PMC5056362 DOI: 10.1038/srep34942] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 09/20/2016] [Indexed: 12/24/2022] Open
Abstract
Physiological cytokine environments arise from factors produced by diverse cell types in coordinated concert. Understanding the contributions of each cell type in the context of cell-cell communication is important for effectively designing disease modifying interventions. Here, we present multi-plexed measurement of 48 cytokines from a coculture system of primary human CD4+ T cells and monocytes across a spectrum of stimuli and for a range of relative T cell/monocyte compositions, coupled with corresponding measurements from PBMCs and plasma from the same donors. Computational analysis of the resulting data-sets elucidated communication-independent and communication-dependent contributions, including both positive and negative synergies. We find that cytokines in cell supernatants were uncorrelated to those found in plasma. Additionally, as an example of positive synergy, production levels of CXCR3 cytokines IP-10 and MIG, depend non-linearly on both IFNγ and TNFα levels in cross-talk between T cells and monocytes. Overall, this work demonstrates that communication between cell types can significantly impact the consequent cytokine environment, emphasizing the value of mixed cell population studies.
Collapse
|
23
|
Yu JS, Bagheri N. Multi-class and multi-scale models of complex biological phenomena. Curr Opin Biotechnol 2016; 39:167-173. [PMID: 27115496 DOI: 10.1016/j.copbio.2016.04.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 03/28/2016] [Accepted: 04/01/2016] [Indexed: 02/06/2023]
Abstract
Computational modeling has significantly impacted our ability to analyze vast (and exponentially increasing) quantities of experimental data for a variety of applications, such as drug discovery and disease forecasting. Single-scale, single-class models persist as the most common group of models, but biological complexity often demands more sophisticated approaches. This review surveys modeling approaches that are multi-class (incorporating multiple model types) and/or multi-scale (accounting for multiple spatial or temporal scales) and describes how these models, and combinations thereof, should be used within the context of the problem statement. We end by highlighting agent-based models as an intuitive, modular, and flexible framework within which multi-scale and multi-class models can be implemented.
Collapse
Affiliation(s)
- Jessica S Yu
- Chemical & Biological Engineering, Northwestern University, Evanston, IL, United States
| | - Neda Bagheri
- Chemical & Biological Engineering, Northwestern University, Evanston, IL, United States.
| |
Collapse
|
24
|
Nawaz S, Yuan Y. Computational pathology: Exploring the spatial dimension of tumor ecology. Cancer Lett 2015; 380:296-303. [PMID: 26592351 DOI: 10.1016/j.canlet.2015.11.018] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Revised: 11/09/2015] [Accepted: 11/10/2015] [Indexed: 02/06/2023]
Abstract
Tumors are evolving ecosystems where cancer subclones and the microenvironment interact. This is analogous to interaction dynamics between species in their natural habitats, which is a prime area of study in ecology. Spatial statistics are frequently used in ecological studies to infer complex relations including predator-prey, resource dependency and co-evolution. Recently, the emerging field of computational pathology has enabled high-throughput spatial analysis by using image processing to identify different cell types and their locations within histological tumor samples. We discuss how these data may be analyzed with spatial statistics used in ecology to reveal patterns and advance our understanding of ecological interactions occurring among cancer cells and their microenvironment.
Collapse
Affiliation(s)
- Sidra Nawaz
- Centre for Molecular Pathology, Institute of Cancer Research, London SM2 5NG, UK; Centre for Evolution and Cancer, Institute of Cancer Research, London SM2 5NG, UK; Division of Molecular Pathology, The Institute of Cancer Research, London SM2 5NG, UK
| | - Yinyin Yuan
- Centre for Molecular Pathology, Institute of Cancer Research, London SM2 5NG, UK; Centre for Evolution and Cancer, Institute of Cancer Research, London SM2 5NG, UK; Division of Molecular Pathology, The Institute of Cancer Research, London SM2 5NG, UK.
| |
Collapse
|