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Bukkuri A, Pienta KJ, Hockett I, Austin RH, Hammarlund EU, Amend SR, Brown JS. Modeling cancer's ecological and evolutionary dynamics. Med Oncol 2023; 40:109. [PMID: 36853375 PMCID: PMC9974726 DOI: 10.1007/s12032-023-01968-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 02/05/2023] [Indexed: 03/01/2023]
Abstract
In this didactic paper, we present a theoretical modeling framework, called the G-function, that integrates both the ecology and evolution of cancer to understand oncogenesis. The G-function has been used in evolutionary ecology, but has not been widely applied to problems in cancer. Here, we build the G-function framework from fundamental Darwinian principles and discuss how cancer can be seen through the lens of ecology, evolution, and game theory. We begin with a simple model of cancer growth and add on components of cancer cell competition and drug resistance. To aid in exploration of eco-evolutionary modeling with this approach, we also present a user-friendly software tool. By the end of this paper, we hope that readers will be able to construct basic G function models and grasp the usefulness of the framework to understand the games cancer plays in a biologically mechanistic fashion.
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Affiliation(s)
- Anuraag Bukkuri
- Cancer Biology and Evolution Program and Department of Integrated Mathematical Oncology, Moffitt Cancer Center, Tampa, USA.
- Tissue Development and Evolution Research Group, Department of Laboratory Medicine, Lund University, Lund, Sweden.
| | - Kenneth J Pienta
- The Brady Urological Institute, Johns Hopkins School of Medicine, Baltimore, USA
| | - Ian Hockett
- The Brady Urological Institute, Johns Hopkins School of Medicine, Baltimore, USA
| | | | - Emma U Hammarlund
- Tissue Development and Evolution Research Group, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Sarah R Amend
- The Brady Urological Institute, Johns Hopkins School of Medicine, Baltimore, USA
| | - Joel S Brown
- Cancer Biology and Evolution Program and Department of Integrated Mathematical Oncology, Moffitt Cancer Center, Tampa, USA
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Farrokhian N, Maltas J, Dinh M, Durmaz A, Ellsworth P, Hitomi M, McClure E, Marusyk A, Kaznatcheev A, Scott JG. Measuring competitive exclusion in non-small cell lung cancer. SCIENCE ADVANCES 2022; 8:eabm7212. [PMID: 35776787 PMCID: PMC10883359 DOI: 10.1126/sciadv.abm7212] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
In this study, we experimentally measure the frequency-dependent interactions between a gefitinib-resistant non-small cell lung cancer population and its sensitive ancestor via the evolutionary game assay. We show that cost of resistance is insufficient to accurately predict competitive exclusion and that frequency-dependent growth rate measurements are required. Using frequency-dependent growth rate data, we then show that gefitinib treatment results in competitive exclusion of the ancestor, while the absence of treatment results in a likely, but not guaranteed, exclusion of the resistant strain. Then, using simulations, we demonstrate that incorporating ecological growth effects can influence the predicted extinction time. In addition, we show that higher drug concentrations may not lead to the optimal reduction in tumor burden. Together, these results highlight the potential importance of frequency-dependent growth rate data for understanding competing populations, both in the laboratory and as we translate adaptive therapy regimens to the clinic.
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Affiliation(s)
| | - Jeff Maltas
- Department of Translational Hematology and Oncology Research, Cleveland Clinic, Cleveland, OH, USA
| | - Mina Dinh
- Department of Translational Hematology and Oncology Research, Cleveland Clinic, Cleveland, OH, USA
| | | | | | - Masahiro Hitomi
- Department of Translational Hematology and Oncology Research, Cleveland Clinic, Cleveland, OH, USA
| | - Erin McClure
- Department of Translational Hematology and Oncology Research, Cleveland Clinic, Cleveland, OH, USA
| | - Andriy Marusyk
- Department of Cancer Physiology, Moffitt Cancer Center, Tampa, FL, USA
| | - Artem Kaznatcheev
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Jacob G Scott
- CWRU School of Medicine, Cleveland, OH, USA
- Department of Translational Hematology and Oncology Research, Cleveland Clinic, Cleveland, OH, USA
- Department of Radiation Oncology, Cleveland Clinic, Cleveland, OH, USA
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Ionescu F, Zhang J, Wang L. Clinical Applications of Liquid Biopsy in Prostate Cancer: From Screening to Predictive Biomarker. Cancers (Basel) 2022; 14:1728. [PMID: 35406500 PMCID: PMC8996910 DOI: 10.3390/cancers14071728] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 03/26/2022] [Accepted: 03/27/2022] [Indexed: 01/15/2023] Open
Abstract
Prostate cancer (PC) remains the most common malignancy and the second most common cause of cancer death in men. As a result of highly variable biological behavior and development of resistance to available agents under therapeutic pressure, optimal management is often unclear. Traditional surgical biopsies, even when augmented by genomic studies, may fail to provide adequate guidance for clinical decisions as these can only provide a snapshot of a dynamic process. Additionally, surgical biopsies are cumbersome to perform repeatedly and often involve risk. Liquid biopsies (LB) are defined as the analysis of either corpuscular (circulating tumor cells, extracellular vesicles) or molecular (circulating DNA or RNA) tumor-derived material. LB could more precisely identify clinically relevant alterations that characterize the metastatic potential of tumors, predict response to specific treatments or actively monitor for the emergence of resistance. These tests can potentially be repeated as often as deemed necessary and can detect real-time response to treatment with minimal inconvenience to the patient. In the current review, we consider common clinical scenarios to describe available LB assays in PC as a platform to explore existing evidence for their use in guiding decision making and to discuss current limitations to their adoption in the clinic.
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Affiliation(s)
- Filip Ionescu
- Department of Oncologic Sciences, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA;
| | - Jingsong Zhang
- Department of Genitourinary Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Liang Wang
- Department of Tumor Biology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
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Wölfl B, te Rietmole H, Salvioli M, Kaznatcheev A, Thuijsman F, Brown JS, Burgering B, Staňková K. The Contribution of Evolutionary Game Theory to Understanding and Treating Cancer. DYNAMIC GAMES AND APPLICATIONS 2021; 12:313-342. [PMID: 35601872 PMCID: PMC9117378 DOI: 10.1007/s13235-021-00397-w] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 07/05/2021] [Indexed: 05/05/2023]
Abstract
Evolutionary game theory mathematically conceptualizes and analyzes biological interactions where one's fitness not only depends on one's own traits, but also on the traits of others. Typically, the individuals are not overtly rational and do not select, but rather inherit their traits. Cancer can be framed as such an evolutionary game, as it is composed of cells of heterogeneous types undergoing frequency-dependent selection. In this article, we first summarize existing works where evolutionary game theory has been employed in modeling cancer and improving its treatment. Some of these game-theoretic models suggest how one could anticipate and steer cancer's eco-evolutionary dynamics into states more desirable for the patient via evolutionary therapies. Such therapies offer great promise for increasing patient survival and decreasing drug toxicity, as demonstrated by some recent studies and clinical trials. We discuss clinical relevance of the existing game-theoretic models of cancer and its treatment, and opportunities for future applications. Moreover, we discuss the developments in cancer biology that are needed to better utilize the full potential of game-theoretic models. Ultimately, we demonstrate that viewing tumors with evolutionary game theory has medically useful implications that can inform and create a lockstep between empirical findings and mathematical modeling. We suggest that cancer progression is an evolutionary competition between different cell types and therefore needs to be viewed as an evolutionary game.
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Affiliation(s)
- Benjamin Wölfl
- Department of Mathematics, University of Vienna, Vienna, Austria
- Vienna Graduate School of Population Genetics, Vienna, Austria
| | - Hedy te Rietmole
- Department of Molecular Cancer Research, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Monica Salvioli
- Department of Mathematics, University of Trento, Trento, Italy
- Department of Data Science and Knowledge Engineering, Maastricht University, Maastricht, The Netherlands
| | - Artem Kaznatcheev
- Department of Biology, University of Pennsylvania, Philadelphia, USA
- Department of Computer Science, University of Oxford, Oxford, UK
| | - Frank Thuijsman
- Department of Data Science and Knowledge Engineering, Maastricht University, Maastricht, The Netherlands
| | - Joel S. Brown
- Department of Integrated Mathematical Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL USA
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL USA
| | - Boudewijn Burgering
- Department of Molecular Cancer Research, University Medical Center Utrecht, Utrecht, The Netherlands
- The Oncode Institute, Utrecht, The Netherlands
| | - Kateřina Staňková
- Department of Data Science and Knowledge Engineering, Maastricht University, Maastricht, The Netherlands
- Department of Engineering Systems and Services, Faculty of Technology, Policy and Management, Delft University of Technology, Delft, The Netherlands
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West J, Ma Y, Kaznatcheev A, Anderson ARA. IsoMaTrix: a framework to visualize the isoclines of matrix games and quantify uncertainty in structured populations. Bioinformatics 2020; 36:5542-5544. [PMID: 33325501 PMCID: PMC8016459 DOI: 10.1093/bioinformatics/btaa1025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 11/24/2020] [Accepted: 11/30/2020] [Indexed: 11/13/2022] Open
Abstract
Evolutionary game theory describes frequency-dependent selection for fixed, heritable strategies in a population of competing individuals using a payoff matrix. We present a software package to aid in the construction, analysis, and visualization of three-strategy matrix games. The IsoMaTrix package computes the isoclines (lines of zero growth) of matrix games, and facilitates direct comparison of well-mixed dynamics to structured populations on a lattice grid. IsoMaTrix computes fixed points, phase flow, trajectories, (sub)velocities, and uncertainty quantification for stochastic effects in spatial matrix games. We describe a result obtained via IsoMaTrix's spatial games functionality, which shows that the timing of competitive release in a cancer model (under continuous treatment) critically depends on the initial spatial configuration of the tumor. AVAILABILITY The code is available at: https://github.com/mathonco/isomatrix. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Jeffrey West
- Integrated Mathematical Oncology Department, H. Lee Moffitt Cancer Center & Research Institute, Tampa, 33612, Florida
| | - Yongqian Ma
- Department of Physics & Astronomy, University of Southern California, Los Angeles, CA, 90089-1191
| | - Artem Kaznatcheev
- Department of Translational Hematology & Oncology Research, Cleveland Clinic, Cleveland, OH, USA
| | - Alexander R A Anderson
- Integrated Mathematical Oncology Department, H. Lee Moffitt Cancer Center & Research Institute, Tampa, 33612, Florida
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Enderling H, Altrock PM, Andor N, Basanta D, Brown JS, Gatenby RA, Marusyk A, Rejniak KA, Silva A, Anderson ARA. High School Internship Program in Integrated Mathematical Oncology (HIP IMO): Five-Year Experience at Moffitt Cancer Center. Bull Math Biol 2020; 82:91. [PMID: 32648152 DOI: 10.1007/s11538-020-00768-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 06/22/2020] [Indexed: 01/02/2023]
Abstract
Modern cancer research, and the wealth of data across multiple spatial and temporal scales, has created the need for researchers that are well versed in the life sciences (cancer biology, developmental biology, immunology), medical sciences (oncology) and natural sciences (mathematics, physics, engineering, computer sciences). College undergraduate education traditionally occurs in disciplinary silos, which creates a steep learning curve at the graduate and postdoctoral levels that increasingly bridge multiple disciplines. Numerous colleges have begun to embrace interdisciplinary curricula, but students who double major in mathematics (or other quantitative sciences) and biology (or medicine) remain scarce. We identified the need to educate junior and senior high school students about integrating mathematical and biological skills, through the lens of mathematical oncology, to better prepare students for future careers at the interdisciplinary interface. The High school Internship Program in Integrated Mathematical Oncology (HIP IMO) at Moffitt Cancer Center has so far trained 59 students between 2015 and 2019. We report here on the program structure, training deliverables, curriculum and outcomes. We hope to promote interdisciplinary educational activities early in a student's career.
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Affiliation(s)
- Heiko Enderling
- Department of Integrated Mathematical Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA.
| | - Philipp M Altrock
- Department of Integrated Mathematical Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Noemi Andor
- Department of Integrated Mathematical Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - David Basanta
- Department of Integrated Mathematical Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Joel S Brown
- Department of Integrated Mathematical Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Robert A Gatenby
- Department of Radiology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Andriy Marusyk
- Department of Cancer Physiology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Katarzyna A Rejniak
- Department of Integrated Mathematical Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
- Department of Oncologic Sciences, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Ariosto Silva
- Department of Cancer Physiology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Alexander R A Anderson
- Department of Integrated Mathematical Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
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Camacho A, Jerez S. Bone metastasis treatment modeling via optimal control. J Math Biol 2018; 78:497-526. [DOI: 10.1007/s00285-018-1281-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 07/29/2018] [Indexed: 12/14/2022]
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