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Brunetti M, Iasenza IA, Jenner AL, Raynal NJM, Eppert K, Craig M. Mathematical modelling of clonal reduction therapeutic strategies in acute myeloid leukemia. Leuk Res 2024; 140:107485. [PMID: 38579483 DOI: 10.1016/j.leukres.2024.107485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 02/21/2024] [Accepted: 03/12/2024] [Indexed: 04/07/2024]
Abstract
Over the years, the overall survival of older patients diagnosed with acute myeloid leukemia (AML) has not significantly increased. Although standard cytotoxic therapies that rapidly eliminate dividing myeloblasts are used to induce remission, relapse can occur due to surviving therapy-resistant leukemic stem cells (LSCs). Hence, anti-LSC strategies have become a key target to cure AML. We have recently shown that previously approved cardiac glycosides and glucocorticoids target LSC-enriched CD34+ cells in the primary human AML 8227 model with more efficacy than normal hematopoietic stem cells (HSCs). To translate these in vitro findings into humans, we developed a mathematical model of stem cell dynamics that describes the stochastic evolution of LSCs in AML post-standard-of-care. To this, we integrated population pharmacokinetic-pharmacodynamic (PKPD) models to investigate the clonal reduction potential of several promising candidate drugs in comparison to cytarabine, which is commonly used in high doses for consolidation therapy in AML patients. Our results suggest that cardiac glycosides (proscillaridin A, digoxin and ouabain) and glucocorticoids (budesonide and mometasone) reduce the expansion of LSCs through a decrease in their viability. While our model predicts that effective doses of cardiac glycosides are potentially too toxic to use in patients, simulations show the possibility of mometasone to prevent relapse through the glucocorticoid's ability to drastically reduce LSC population size. This work therefore highlights the prospect of these treatments for anti-LSC strategies and underlines the use of quantitative approaches to preclinical drug translation in AML.
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Affiliation(s)
- Mia Brunetti
- Département de Mathématiques et de Statistiques, Université de Montréal, 2900 Édouard Montpetit Blvd, Montréal, Québec H3T 1J4, Canada; Sainte-Justine University Hospital Azrieli Research Center, 3175 Chem. de la Côte-Sainte-Catherine, Montréal, Québec H3T 1C5, Canada
| | - Isabella A Iasenza
- Division of Experimental Medicine, Department of Medicine, McGill University, 845 Sherbrooke St W, Montréal, Québec H3A 0G4, Canada; Research Institute of the McGill University Health Centre, 1001 Décarie Blvd, Montréal, Québec H4A 3J1, Canada
| | - Adrianne L Jenner
- School of Mathematical Sciences, Queensland University of Technology, 2 George St, Brisbane, QLD 4000, Australia
| | - Noël J-M Raynal
- Sainte-Justine University Hospital Azrieli Research Center, 3175 Chem. de la Côte-Sainte-Catherine, Montréal, Québec H3T 1C5, Canada; Département de Pharmacologie et Physiologie, Université de Montréal, 2900 Édouard Montpetit Blvd, Montréal, Québec H3T 1J4, Canada
| | - Kolja Eppert
- Research Institute of the McGill University Health Centre, 1001 Décarie Blvd, Montréal, Québec H4A 3J1, Canada; Department of Pediatrics, McGill University, 845 Sherbrooke St W, Montréal, Québec H3A 0G4, Canada
| | - Morgan Craig
- Département de Mathématiques et de Statistiques, Université de Montréal, 2900 Édouard Montpetit Blvd, Montréal, Québec H3T 1J4, Canada; Sainte-Justine University Hospital Azrieli Research Center, 3175 Chem. de la Côte-Sainte-Catherine, Montréal, Québec H3T 1C5, Canada.
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Sheen J, Curtin L, Finley S, Konstorum A, McGee R, Craig M. Integrating Diversity, Equity, and Inclusion into Preclinical, Clinical, and Public Health Mathematical Models. Bull Math Biol 2024; 86:56. [PMID: 38625656 PMCID: PMC11021228 DOI: 10.1007/s11538-024-01282-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Accepted: 03/15/2024] [Indexed: 04/17/2024]
Abstract
Mathematical modelling applied to preclinical, clinical, and public health research is critical for our understanding of a multitude of biological principles. Biology is fundamentally heterogeneous, and mathematical modelling must meet the challenge of variability head on to ensure the principles of diversity, equity, and inclusion (DEI) are integrated into quantitative analyses. Here we provide a follow-up perspective on the DEI plenary session held at the 2023 Society for Mathematical Biology Annual Meeting to discuss key issues for the increased integration of DEI in mathematical modelling in biology.
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Affiliation(s)
- Justin Sheen
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, USA
| | - Lee Curtin
- Mathematical Neuro-Oncology Lab, Precision Neurotherapeutics Innovation Program, Mayo Clinic, Phoenix, AZ, USA
| | - Stacey Finley
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, USA.
- Alfred E. Mann Department of Biomedical Engineering, University of Southern California, Los Angeles, USA.
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, USA.
| | | | - Reginald McGee
- Department of Mathematics and Computer Science, College of the Holy Cross, Worcester, USA
| | - Morgan Craig
- Department of Mathematics and Statistics, Université de Montréal, Montréal, Canada.
- Sainte-Justine University Hospital Azrieli Research Centre, Montréal, Canada.
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3
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Shabman RS, Craig M, Laubenbacher R, Reeves D, Brown LL. NIAID/SMB Workshop on Multiscale Modeling of Infectious and Immune-Mediated Diseases. Bull Math Biol 2024; 86:44. [PMID: 38512541 PMCID: PMC10957590 DOI: 10.1007/s11538-024-01276-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Accepted: 02/22/2024] [Indexed: 03/23/2024]
Abstract
On July 19th, 2023, the National Institute of Allergy and Infectious Diseases co-organized a workshop with the Society of Mathematical Biology, with the authors of this paper as the organizing committee. The workshop, "Bridging multiscale modeling and practical clinical applications in infectious diseases" sought to create an environment for mathematical modelers, statisticians, and infectious disease researchers and clinicians to exchange ideas and perspectives.
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Affiliation(s)
- Reed S Shabman
- National Institute of Allergy and Infectious Diseases, Rockville, MD, 20852, USA.
| | - Morgan Craig
- Department of Mathematics and Statistics, Sainte-Justine University Hospital Research Centre, Université de Montréal, Montreal, Canada
| | | | - Daniel Reeves
- Department of Global Health, University of Washington, Seattle, WA, 98195, USA
| | - Liliana L Brown
- National Institute of Allergy and Infectious Diseases, Rockville, MD, 20852, USA.
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Le Sauteur-Robitaille J, Crosley P, Hitt M, Jenner AL, Craig M. Mathematical modeling predicts pathways to successful implementation of combination TRAIL-producing oncolytic virus and PAC-1 to treat granulosa cell tumors of the ovary. Cancer Biol Ther 2023; 24:2283926. [PMID: 38010777 PMCID: PMC10783843 DOI: 10.1080/15384047.2023.2283926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 11/10/2023] [Indexed: 11/29/2023] Open
Abstract
The development of new cancer therapies requires multiple rounds of validation from in vitro and in vivo experiments before they can be considered for clinical trials. Mathematical models assist in this preclinical phase by combining experimental data with human parameters to provide guidance about potential therapeutic regimens to bring forward into trials. However, granulosa cell tumors of the ovary lack a relevant mouse model, complexifying preclinical drug development for this rare tumor. To bridge this gap, we established a mathematical model as a framework to explore the potential of using a tumor necrosis factor-related apoptosis-inducing ligand (TRAIL)-producing oncolytic vaccinia virus in combination with the chemotherapeutic agent first procaspase activating compound (PAC-1). We have previously shown that TRAIL and PAC-1 act synergistically on granulosa tumor cells. In line with our previous results, our current model predicts that, although it is unable to stop the tumor from growing in its current form, combination oral PAC-1 with oncolytic virus (OV) provides the best result compared to monotherapies. Encouragingly, our results suggest that increases to the OV infection rate can lead to the success of this combination therapy within a year. The model developed here can continue to be improved as more data become available, allowing for regimen-tailoring via virtual clinical trials, ultimately shepherding effective regimens into trials.
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Affiliation(s)
- Justin Le Sauteur-Robitaille
- Department of Mathematics and Statistics, Université de Montréal, Quebec, Canada
- Sainte-Justine University Hospital Research Centre, Montréal, Québec, Canada
| | - Powel Crosley
- Department of Oncology, University of Alberta, Edmonton, Canada
| | - Mary Hitt
- Department of Oncology, University of Alberta, Edmonton, Canada
| | - Adrianne L Jenner
- School of Mathematics, Queensland University of Technology, Brisbane, Australia
| | - Morgan Craig
- Department of Mathematics and Statistics, Université de Montréal, Quebec, Canada
- Sainte-Justine University Hospital Research Centre, Montréal, Québec, Canada
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Deng X, Gantner P, Forestell J, Pagliuzza A, Brunet‐Ratnasingham E, Durand M, Kaufmann DE, Chomont N, Craig M. Plasma SARS-CoV-2 RNA elimination and RAGE kinetics distinguish COVID-19 severity. Clin Transl Immunology 2023; 12:e1468. [PMID: 38020729 PMCID: PMC10666810 DOI: 10.1002/cti2.1468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 09/01/2023] [Accepted: 09/08/2023] [Indexed: 12/01/2023] Open
Abstract
Objectives Identifying biomarkers causing differential SARS-CoV-2 infection kinetics associated with severe COVID-19 is fundamental for effective diagnostics and therapeutic planning. Methods In this work, we applied mathematical modelling to investigate the relationships between patient characteristics, plasma SARS-CoV-2 RNA dynamics and COVID-19 severity. Using a straightforward mathematical model of within-host viral kinetics, we estimated key model parameters from serial plasma viral RNA (vRNA) samples from 256 hospitalised COVID-19+ patients. Results Our model predicted that clearance rates distinguish key differences in plasma vRNA kinetics and severe COVID-19. Moreover, our analyses revealed a strong correlation between plasma vRNA kinetics and plasma receptor for advanced glycation end products (RAGE) concentrations (a plasma biomarker of lung damage), collected in parallel to plasma vRNA from patients in our cohort, suggesting that RAGE can substitute for viral plasma shedding dynamics to prospectively classify seriously ill patients. Conclusion Overall, our study identifies factors of COVID-19 severity, supports interventions to accelerate viral clearance and underlines the importance of mathematical modelling to better understand COVID-19.
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Affiliation(s)
- Xiaoyan Deng
- Research Centre of the Centre Hospitalier Universitaire Sainte‐JustineMontréalQCCanada
- Département de mathématiques et de statistiqueUniversité de MontréalMontréalQCCanada
| | - Pierre Gantner
- Research Centre of the Centre Hospitalier de l'Université de Montréal (CRCHUM)MontréalQCCanada
- Département de Microbiologie, Infectiologie et ImmunologieUniversité de MontréalMontréalQCCanada
| | - Julia Forestell
- Research Centre of the Centre Hospitalier Universitaire Sainte‐JustineMontréalQCCanada
| | - Amélie Pagliuzza
- Research Centre of the Centre Hospitalier de l'Université de Montréal (CRCHUM)MontréalQCCanada
- Département de Microbiologie, Infectiologie et ImmunologieUniversité de MontréalMontréalQCCanada
| | - Elsa Brunet‐Ratnasingham
- Research Centre of the Centre Hospitalier de l'Université de Montréal (CRCHUM)MontréalQCCanada
- Département de Microbiologie, Infectiologie et ImmunologieUniversité de MontréalMontréalQCCanada
| | - Madeleine Durand
- Research Centre of the Centre Hospitalier de l'Université de Montréal (CRCHUM)MontréalQCCanada
| | - Daniel E Kaufmann
- Research Centre of the Centre Hospitalier de l'Université de Montréal (CRCHUM)MontréalQCCanada
- Centre hospitalier de l'Université de Montréal (CHUM)MontréalQCCanada
- Département de MédecineUniversité de MontréalMontréalQCCanada
- Division of Infectious Diseases, Department of MedicineUniversity Hospital and University of LausanneLausanneSwitzerland
| | - Nicolas Chomont
- Research Centre of the Centre Hospitalier de l'Université de Montréal (CRCHUM)MontréalQCCanada
- Département de Microbiologie, Infectiologie et ImmunologieUniversité de MontréalMontréalQCCanada
| | - Morgan Craig
- Research Centre of the Centre Hospitalier Universitaire Sainte‐JustineMontréalQCCanada
- Département de mathématiques et de statistiqueUniversité de MontréalMontréalQCCanada
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Surendran A, Jenner AL, Karimi E, Fiset B, Quail DF, Walsh LA, Craig M. Agent-Based Modelling Reveals the Role of the Tumor Microenvironment on the Short-Term Success of Combination Temozolomide/Immune Checkpoint Blockade to Treat Glioblastoma. J Pharmacol Exp Ther 2023; 387:66-77. [PMID: 37442619 DOI: 10.1124/jpet.122.001571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 06/08/2023] [Accepted: 06/13/2023] [Indexed: 07/15/2023] Open
Abstract
Glioblastoma is the most common and deadly primary brain tumor in adults. All glioblastoma patients receiving standard-of-care surgery-radiotherapy-chemotherapy (i.e., temozolomide (TMZ)) recur, with an average survival time of only 15 months. New approaches to the treatment of glioblastoma, including immune checkpoint blockade and oncolytic viruses, offer the possibility of improving glioblastoma outcomes and have as such been under intense study. Unfortunately, these treatment modalities have thus far failed to achieve approval. Recently, in an attempt to bolster efficacy and improve patient outcomes, regimens combining chemotherapy and immune checkpoint inhibitors have been tested in trials. Unfortunately, these efforts have not resulted in significant increases to patient survival. To better understand the various factors impacting treatment outcomes of combined TMZ and immune checkpoint blockade, we developed a systems-level, computational model that describes the interplay between glioblastoma, immune, and stromal cells with this combination treatment. Initializing our model to spatial resection patient samples labeled using imaging mass cytometry, our model's predictions show how the localization of glioblastoma cells, influence therapeutic success. We further validated these predictions in samples of brain metastases from patients given they generally respond better to checkpoint blockade compared with primary glioblastoma. Ultimately, our model provides novel insights into the mechanisms of therapeutic success of immune checkpoint inhibitors in brain tumors and delineates strategies to translate combination immunotherapy regimens more effectively into the clinic. SIGNIFICANCE STATEMENT: Extending survival times for glioblastoma patients remains a critical challenge. Although immunotherapies in combination with chemotherapy hold promise, clinical trials have not shown much success. Here, systems models calibrated to and validated against patient samples can improve preclinical and clinical studies by shedding light on the factors distinguishing responses/failures. By initializing our model with imaging mass cytometry visualization of patient samples, we elucidate how factors such as localization of glioblastoma cells and CD8+ T cell infiltration impact treatment outcomes.
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Affiliation(s)
- Anudeep Surendran
- Department of Mathematics and Statistics, Université de Montréal, Montréal, Canada (A.S., M.C.); Centre de recherches mathématiques, Montréal, Canada (A.S.); School of Mathematical Sciences, Queensland University of Technology, Brisbane, Australia (A.L.J.); Rosalind and Morris Goodman Cancer Institute, McGill University, Montréal, Canada (E.K., B.F., D.F.Q., L.A.W.); Department of Physiology, Faculty of Medicine, McGill University, Montréal, Canada (D.F.Q.); Department of Medicine, Division of Experimental Medicine, McGill University, Montréal, Canada (D.F.Q.); Department of Human Genetics, McGill University, Montréal, Canada (L.A.W.); and Sainte-Justine University Hospital Research Centre, Montréal, Canada (M.C.)
| | - Adrianne L Jenner
- Department of Mathematics and Statistics, Université de Montréal, Montréal, Canada (A.S., M.C.); Centre de recherches mathématiques, Montréal, Canada (A.S.); School of Mathematical Sciences, Queensland University of Technology, Brisbane, Australia (A.L.J.); Rosalind and Morris Goodman Cancer Institute, McGill University, Montréal, Canada (E.K., B.F., D.F.Q., L.A.W.); Department of Physiology, Faculty of Medicine, McGill University, Montréal, Canada (D.F.Q.); Department of Medicine, Division of Experimental Medicine, McGill University, Montréal, Canada (D.F.Q.); Department of Human Genetics, McGill University, Montréal, Canada (L.A.W.); and Sainte-Justine University Hospital Research Centre, Montréal, Canada (M.C.)
| | - Elham Karimi
- Department of Mathematics and Statistics, Université de Montréal, Montréal, Canada (A.S., M.C.); Centre de recherches mathématiques, Montréal, Canada (A.S.); School of Mathematical Sciences, Queensland University of Technology, Brisbane, Australia (A.L.J.); Rosalind and Morris Goodman Cancer Institute, McGill University, Montréal, Canada (E.K., B.F., D.F.Q., L.A.W.); Department of Physiology, Faculty of Medicine, McGill University, Montréal, Canada (D.F.Q.); Department of Medicine, Division of Experimental Medicine, McGill University, Montréal, Canada (D.F.Q.); Department of Human Genetics, McGill University, Montréal, Canada (L.A.W.); and Sainte-Justine University Hospital Research Centre, Montréal, Canada (M.C.)
| | - Benoit Fiset
- Department of Mathematics and Statistics, Université de Montréal, Montréal, Canada (A.S., M.C.); Centre de recherches mathématiques, Montréal, Canada (A.S.); School of Mathematical Sciences, Queensland University of Technology, Brisbane, Australia (A.L.J.); Rosalind and Morris Goodman Cancer Institute, McGill University, Montréal, Canada (E.K., B.F., D.F.Q., L.A.W.); Department of Physiology, Faculty of Medicine, McGill University, Montréal, Canada (D.F.Q.); Department of Medicine, Division of Experimental Medicine, McGill University, Montréal, Canada (D.F.Q.); Department of Human Genetics, McGill University, Montréal, Canada (L.A.W.); and Sainte-Justine University Hospital Research Centre, Montréal, Canada (M.C.)
| | - Daniela F Quail
- Department of Mathematics and Statistics, Université de Montréal, Montréal, Canada (A.S., M.C.); Centre de recherches mathématiques, Montréal, Canada (A.S.); School of Mathematical Sciences, Queensland University of Technology, Brisbane, Australia (A.L.J.); Rosalind and Morris Goodman Cancer Institute, McGill University, Montréal, Canada (E.K., B.F., D.F.Q., L.A.W.); Department of Physiology, Faculty of Medicine, McGill University, Montréal, Canada (D.F.Q.); Department of Medicine, Division of Experimental Medicine, McGill University, Montréal, Canada (D.F.Q.); Department of Human Genetics, McGill University, Montréal, Canada (L.A.W.); and Sainte-Justine University Hospital Research Centre, Montréal, Canada (M.C.)
| | - Logan A Walsh
- Department of Mathematics and Statistics, Université de Montréal, Montréal, Canada (A.S., M.C.); Centre de recherches mathématiques, Montréal, Canada (A.S.); School of Mathematical Sciences, Queensland University of Technology, Brisbane, Australia (A.L.J.); Rosalind and Morris Goodman Cancer Institute, McGill University, Montréal, Canada (E.K., B.F., D.F.Q., L.A.W.); Department of Physiology, Faculty of Medicine, McGill University, Montréal, Canada (D.F.Q.); Department of Medicine, Division of Experimental Medicine, McGill University, Montréal, Canada (D.F.Q.); Department of Human Genetics, McGill University, Montréal, Canada (L.A.W.); and Sainte-Justine University Hospital Research Centre, Montréal, Canada (M.C.)
| | - Morgan Craig
- Department of Mathematics and Statistics, Université de Montréal, Montréal, Canada (A.S., M.C.); Centre de recherches mathématiques, Montréal, Canada (A.S.); School of Mathematical Sciences, Queensland University of Technology, Brisbane, Australia (A.L.J.); Rosalind and Morris Goodman Cancer Institute, McGill University, Montréal, Canada (E.K., B.F., D.F.Q., L.A.W.); Department of Physiology, Faculty of Medicine, McGill University, Montréal, Canada (D.F.Q.); Department of Medicine, Division of Experimental Medicine, McGill University, Montréal, Canada (D.F.Q.); Department of Human Genetics, McGill University, Montréal, Canada (L.A.W.); and Sainte-Justine University Hospital Research Centre, Montréal, Canada (M.C.)
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Li R, Craig M, D'Argenio DZ, Betts A, Mager DE, Maurer TS. Editorial: Model-informed decision making in the preclinical stages of pharmaceutical research and development. Front Pharmacol 2023; 14:1184914. [PMID: 37124233 PMCID: PMC10131111 DOI: 10.3389/fphar.2023.1184914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Accepted: 03/27/2023] [Indexed: 05/02/2023] Open
Affiliation(s)
- Rui Li
- Translational Modeling and Simulation, Medicine Design, Pfizer Inc., Cambridge, MA, United States
| | - Morgan Craig
- Department of Mathematics and Statistics, Université de Montréal, Montréal, QC, Canada
- Sainte-Justine University Hospital Research Centre, Montréal, QC, Canada
| | - David Z. D'Argenio
- Department of Biomedical Engineering, University of Southern California, Los Angeles, CA, United States
| | - Alison Betts
- Applied BioMath, LLC, Concord, MA, United States
| | - Donald E. Mager
- Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, NY, United States
- Enhanced Pharmacodynamics, LLC, Buffalo, NY, United States
| | - Tristan S. Maurer
- Translational Modeling and Simulation, Medicine Design, Pfizer Inc., Cambridge, MA, United States
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8
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Ndiaye JF, Nekka F, Craig M. Understanding the Mechanisms and Treatment of Heart Failure: Quantitative Systems Pharmacology Models with a Focus on SGLT2 Inhibitors and Sex-Specific Differences. Pharmaceutics 2023; 15:pharmaceutics15031002. [PMID: 36986862 PMCID: PMC10052171 DOI: 10.3390/pharmaceutics15031002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/06/2023] [Accepted: 03/13/2023] [Indexed: 03/30/2023] Open
Abstract
Heart failure (HF), which is a major clinical and public health challenge, commonly develops when the myocardial muscle is unable to pump an adequate amount of blood at typical cardiac pressures to fulfill the body's metabolic needs, and compensatory mechanisms are compromised or fail to adjust. Treatments consist of targeting the maladaptive response of the neurohormonal system, thereby decreasing symptoms by relieving congestion. Sodium-glucose co-transporter 2 (SGLT2) inhibitors, which are a recent antihyperglycemic drug, have been found to significantly improve HF complications and mortality. They act through many pleiotropic effects, and show better improvements compared to others existing pharmacological therapies. Mathematical modeling is a tool used to describe the pathophysiological processes of the disease, quantify clinically relevant outcomes in response to therapies, and provide a predictive framework to improve therapeutic scheduling and strategies. In this review, we describe the pathophysiology of HF, its treatment, and how an integrated mathematical model of the cardiorenal system was built to capture body fluid and solute homeostasis. We also provide insights into sex-specific differences between males and females, thereby encouraging the development of more effective sex-based therapies in the case of heart failure.
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Affiliation(s)
- Jean François Ndiaye
- Department of Mathematics and Statistics, Université de Montréal, Montréal, QC H3C 3J7, Canada
- Sainte-Justine University Hospital Research Centre, Montréal, QC H3T 1C5, Canada
| | - Fahima Nekka
- Faculty of Pharmacy, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Morgan Craig
- Department of Mathematics and Statistics, Université de Montréal, Montréal, QC H3C 3J7, Canada
- Sainte-Justine University Hospital Research Centre, Montréal, QC H3T 1C5, Canada
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9
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Gazeau S, Deng X, Ooi HK, Mostefai F, Hussin J, Heffernan J, Jenner AL, Craig M. The race to understand immunopathology in COVID-19: Perspectives on the impact of quantitative approaches to understand within-host interactions. Immunoinformatics (Amst) 2023; 9:100021. [PMID: 36643886 PMCID: PMC9826539 DOI: 10.1016/j.immuno.2023.100021] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 11/16/2022] [Accepted: 01/03/2023] [Indexed: 01/09/2023]
Abstract
The COVID-19 pandemic has revealed the need for the increased integration of modelling and data analysis to public health, experimental, and clinical studies. Throughout the first two years of the pandemic, there has been a concerted effort to improve our understanding of the within-host immune response to the SARS-CoV-2 virus to provide better predictions of COVID-19 severity, treatment and vaccine development questions, and insights into viral evolution and the impacts of variants on immunopathology. Here we provide perspectives on what has been accomplished using quantitative methods, including predictive modelling, population genetics, machine learning, and dimensionality reduction techniques, in the first 26 months of the COVID-19 pandemic approaches, and where we go from here to improve our responses to this and future pandemics.
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Affiliation(s)
- Sonia Gazeau
- Department of Mathematics and Statistics, Université de Montréal, Montréal, Canada
- Sainte-Justine University Hospital Research Centre, Montréal, Canada
| | - Xiaoyan Deng
- Department of Mathematics and Statistics, Université de Montréal, Montréal, Canada
- Sainte-Justine University Hospital Research Centre, Montréal, Canada
| | - Hsu Kiang Ooi
- Digital Technologies Research Centre, National Research Council Canada, Toronto, Canada
| | - Fatima Mostefai
- Montréal Heart Institute Research Centre, Montréal, Canada
- Department of Medicine, Faculty of Medicine, Université de Montréal, Montréal, Canada
| | - Julie Hussin
- Montréal Heart Institute Research Centre, Montréal, Canada
- Department of Medicine, Faculty of Medicine, Université de Montréal, Montréal, Canada
| | - Jane Heffernan
- Modelling Infection and Immunity Lab, Mathematics Statistics, York University, Toronto, Canada
- Centre for Disease Modelling (CDM), Mathematics Statistics, York University, Toronto, Canada
| | - Adrianne L Jenner
- School of Mathematical Sciences, Queensland University of Technology, Brisbane Australia
| | - Morgan Craig
- Department of Mathematics and Statistics, Université de Montréal, Montréal, Canada
- Sainte-Justine University Hospital Research Centre, Montréal, Canada
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10
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Korosec CS, Farhang-Sardroodi S, Dick DW, Gholami S, Ghaemi MS, Moyles IR, Craig M, Ooi HK, Heffernan JM. Long-term durability of immune responses to the BNT162b2 and mRNA-1273 vaccines based on dosage, age and sex. Sci Rep 2022; 12:21232. [PMID: 36481777 PMCID: PMC9732004 DOI: 10.1038/s41598-022-25134-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Accepted: 11/25/2022] [Indexed: 12/13/2022] Open
Abstract
The lipid nanoparticle (LNP)-formulated mRNA vaccines BNT162b2 and mRNA-1273 are a widely adopted multi vaccination public health strategy to manage the COVID-19 pandemic. Clinical trial data has described the immunogenicity of the vaccine, albeit within a limited study time frame. Here, we use a within-host mathematical model for LNP-formulated mRNA vaccines, informed by available clinical trial data from 2020 to September 2021, to project a longer term understanding of immunity as a function of vaccine type, dosage amount, age, and sex. We estimate that two standard doses of either mRNA-1273 or BNT162b2, with dosage times separated by the company-mandated intervals, results in individuals losing more than 99% humoral immunity relative to peak immunity by 8 months following the second dose. We predict that within an 8 month period following dose two (corresponding to the original CDC time-frame for administration of a third dose), there exists a period of time longer than 1 month where an individual has lost more than 99% humoral immunity relative to peak immunity, regardless of which vaccine was administered. We further find that age has a strong influence in maintaining humoral immunity; by 8 months following dose two we predict that individuals aged 18-55 have a four-fold humoral advantage compared to aged 56-70 and 70+ individuals. We find that sex has little effect on the immune response and long-term IgG counts. Finally, we find that humoral immunity generated from two low doses of mRNA-1273 decays at a substantially slower rate relative to peak immunity gained compared to two standard doses of either mRNA-1273 or BNT162b2. Our predictions highlight the importance of the recommended third booster dose in order to maintain elevated levels of antibodies.
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Affiliation(s)
- Chapin S Korosec
- Modelling Infection and Immunity Lab, Mathematics and Statistics, York University, 4700 Keele St, Toronto, ON, M3J 1P3, Canada.
- Centre for Disease Modelling, Mathematics and Statistics, York University, 4700 Keele St, Toronto, ON, M3J 1P3, Canada.
| | - Suzan Farhang-Sardroodi
- Centre for Disease Modelling, Mathematics and Statistics, York University, 4700 Keele St, Toronto, ON, M3J 1P3, Canada
- Department of Mathematics, University of Manitoba, 186 Dysart Road, Winnipeg, MB, R3T 2N2, Canada
| | - David W Dick
- Modelling Infection and Immunity Lab, Mathematics and Statistics, York University, 4700 Keele St, Toronto, ON, M3J 1P3, Canada
- Centre for Disease Modelling, Mathematics and Statistics, York University, 4700 Keele St, Toronto, ON, M3J 1P3, Canada
| | - Sameneh Gholami
- Modelling Infection and Immunity Lab, Mathematics and Statistics, York University, 4700 Keele St, Toronto, ON, M3J 1P3, Canada
- Centre for Disease Modelling, Mathematics and Statistics, York University, 4700 Keele St, Toronto, ON, M3J 1P3, Canada
| | - Mohammad Sajjad Ghaemi
- Digital Technologies Research Centre, National Research Council Canada, 222 College Street, Toronto, ON, M5T 3J1, Canada
| | - Iain R Moyles
- Modelling Infection and Immunity Lab, Mathematics and Statistics, York University, 4700 Keele St, Toronto, ON, M3J 1P3, Canada
- Centre for Disease Modelling, Mathematics and Statistics, York University, 4700 Keele St, Toronto, ON, M3J 1P3, Canada
| | - Morgan Craig
- Department of Mathematics and Statistics, Université de Montréal & Sainte-Justine University Hospital Research Centre, 3175, ch. Côte Sainte-Catherine, Montréal, QC, H3T 1C5, Canada
| | - Hsu Kiang Ooi
- Digital Technologies Research Centre, National Research Council Canada, 222 College Street, Toronto, ON, M5T 3J1, Canada
| | - Jane M Heffernan
- Modelling Infection and Immunity Lab, Mathematics and Statistics, York University, 4700 Keele St, Toronto, ON, M3J 1P3, Canada.
- Centre for Disease Modelling, Mathematics and Statistics, York University, 4700 Keele St, Toronto, ON, M3J 1P3, Canada.
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11
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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] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 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.
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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
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12
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Cardinal O, Burlot C, Fu Y, Crosley P, Hitt M, Craig M, Jenner AL. Establishing combination PAC‐1 and TRAIL regimens for treating ovarian cancer based on patient‐specific pharmacokinetic profiles using
in silico
clinical trials. Comp Sys Onco 2022. [DOI: 10.1002/cso2.1035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Affiliation(s)
- Olivia Cardinal
- Department of Mathematics and Statistics Université de Montréal Montréal Quebec Canada
| | - Chloé Burlot
- Department of Mathematics and Statistics Université de Montréal Montréal Quebec Canada
| | - Yangxin Fu
- Department of Oncology University of Alberta Edmonton Alberta Canada
| | - Powel Crosley
- Department of Oncology University of Alberta Edmonton Alberta Canada
| | - Mary Hitt
- Department of Oncology University of Alberta Edmonton Alberta Canada
| | - Morgan Craig
- Department of Mathematics and Statistics Université de Montréal Montréal Quebec Canada
- Research Centre Sainte‐Justine University Hospital Montréal Quebec Canada
| | - Adrianne L. Jenner
- Department of Mathematics and Statistics Université de Montréal Montréal Quebec Canada
- Research Centre Sainte‐Justine University Hospital Montréal Quebec Canada
- School of Mathematical Sciences Queensland University of Technology Brisbane Queensland
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13
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Farhang-Sardroodi S, Ghaemi MS, Craig M, Ooi HK, Heffernan JM. A machine learning approach to differentiate between COVID-19 and influenza infection using synthetic infection and immune response data. Math Biosci Eng 2022; 19:5813-5831. [PMID: 35603380 DOI: 10.3934/mbe.2022272] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Data analysis is widely used to generate new insights into human disease mechanisms and provide better treatment methods. In this work, we used the mechanistic models of viral infection to generate synthetic data of influenza and COVID-19 patients. We then developed and validated a supervised machine learning model that can distinguish between the two infections. Influenza and COVID-19 are contagious respiratory illnesses that are caused by different pathogenic viruses but appeared with similar initial presentations. While having the same primary signs COVID-19 can produce more severe symptoms, illnesses, and higher mortality. The predictive model performance was externally evaluated by the ROC AUC metric (area under the receiver operating characteristic curve) on 100 virtual patients from each cohort and was able to achieve at least AUC = 91% using our multiclass classifier. The current investigation highlighted the ability of machine learning models to accurately identify two different diseases based on major components of viral infection and immune response. The model predicted a dominant role for viral load and productively infected cells through the feature selection process.
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Affiliation(s)
- Suzan Farhang-Sardroodi
- Modelling Infection and Immunity Lab, Mathematics Statistics, York University, Toronto, Canada
- Centre for Disease Modelling (CDM), Mathematics Statistics, York University, Toronto, Canada
| | - Mohammad Sajjad Ghaemi
- Digital Technologies Research Centre, National Research Council Canada, Toronto, ON, Canada
| | - Morgan Craig
- Sainte-Justine University Hospital Research Centre and Department of Mathematics and Statistics, Université de Montréal, Montreal, Quebec, Canada
| | - Hsu Kiang Ooi
- Digital Technologies Research Centre, National Research Council Canada, Toronto, ON, Canada
| | - Jane M Heffernan
- Modelling Infection and Immunity Lab, Mathematics Statistics, York University, Toronto, Canada
- Centre for Disease Modelling (CDM), Mathematics Statistics, York University, Toronto, Canada
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14
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Mostefai F, Gamache I, N'Guessan A, Pelletier J, Huang J, Murall CL, Pesaranghader A, Gaonac'h-Lovejoy V, Hamelin DJ, Poujol R, Grenier JC, Smith M, Caron E, Craig M, Wolf G, Krishnaswamy S, Shapiro BJ, Hussin JG. Population Genomics Approaches for Genetic Characterization of SARS-CoV-2 Lineages. Front Med (Lausanne) 2022; 9:826746. [PMID: 35265640 PMCID: PMC8899026 DOI: 10.3389/fmed.2022.826746] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 01/17/2022] [Indexed: 11/13/2022] Open
Abstract
The genome of the Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2), the pathogen that causes coronavirus disease 2019 (COVID-19), has been sequenced at an unprecedented scale leading to a tremendous amount of viral genome sequencing data. To assist in tracing infection pathways and design preventive strategies, a deep understanding of the viral genetic diversity landscape is needed. We present here a set of genomic surveillance tools from population genetics which can be used to better understand the evolution of this virus in humans. To illustrate the utility of this toolbox, we detail an in depth analysis of the genetic diversity of SARS-CoV-2 in first year of the COVID-19 pandemic. We analyzed 329,854 high-quality consensus sequences published in the GISAID database during the pre-vaccination phase. We demonstrate that, compared to standard phylogenetic approaches, haplotype networks can be computed efficiently on much larger datasets. This approach enables real-time lineage identification, a clear description of the relationship between variants of concern, and efficient detection of recurrent mutations. Furthermore, time series change of Tajima's D by haplotype provides a powerful metric of lineage expansion. Finally, principal component analysis (PCA) highlights key steps in variant emergence and facilitates the visualization of genomic variation in the context of SARS-CoV-2 diversity. The computational framework presented here is simple to implement and insightful for real-time genomic surveillance of SARS-CoV-2 and could be applied to any pathogen that threatens the health of populations of humans and other organisms.
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Affiliation(s)
- Fatima Mostefai
- Research Centre, Montreal Heart Institute, Montreal, QC, Canada
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montreal, QC, Canada
| | - Isabel Gamache
- Research Centre, Montreal Heart Institute, Montreal, QC, Canada
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montreal, QC, Canada
| | - Arnaud N'Guessan
- Research Centre, Montreal Heart Institute, Montreal, QC, Canada
- Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
| | - Justin Pelletier
- Research Centre, Montreal Heart Institute, Montreal, QC, Canada
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montreal, QC, Canada
| | - Jessie Huang
- Department of Computer Science, Yale University, New Haven, CT, United States
| | - Carmen Lia Murall
- Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
| | | | - Vanda Gaonac'h-Lovejoy
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montreal, QC, Canada
- Research Centre, CHU Sainte-Justine, Montreal, QC, Canada
| | - David J. Hamelin
- Research Centre, Montreal Heart Institute, Montreal, QC, Canada
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montreal, QC, Canada
- Research Centre, CHU Sainte-Justine, Montreal, QC, Canada
| | - Raphaël Poujol
- Research Centre, Montreal Heart Institute, Montreal, QC, Canada
| | | | - Martin Smith
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montreal, QC, Canada
- Research Centre, CHU Sainte-Justine, Montreal, QC, Canada
| | - Etienne Caron
- Research Centre, CHU Sainte-Justine, Montreal, QC, Canada
- Département de Pathologie et Biologie Cellulaire, Université de Montréal, Montreal, QC, Canada
| | - Morgan Craig
- Research Centre, CHU Sainte-Justine, Montreal, QC, Canada
- Département de Mathématiques et Statistique, Université de Montréal, Montreal, QC, Canada
| | - Guy Wolf
- Mila – Quebec AI institute, Montreal, QC, Canada
- Département de Mathématiques et Statistique, Université de Montréal, Montreal, QC, Canada
| | - Smita Krishnaswamy
- Department of Computer Science, Yale University, New Haven, CT, United States
- Department of Genetics, Yale University, New Haven, CT, United States
| | - B. Jesse Shapiro
- Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
| | - Julie G. Hussin
- Research Centre, Montreal Heart Institute, Montreal, QC, Canada
- Département de Médecine, Université de Montréal, Montreal, QC, Canada
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15
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Getz M, Wang Y, An G, Asthana M, Becker A, Cockrell C, Collier N, Craig M, Davis CL, Faeder JR, Ford Versypt AN, Mapder T, Gianlupi JF, Glazier JA, Hamis S, Heiland R, Hillen T, Hou D, Islam MA, Jenner AL, Kurtoglu F, Larkin CI, Liu B, Macfarlane F, Maygrundter P, Morel PA, Narayanan A, Ozik J, Pienaar E, Rangamani P, Saglam AS, Shoemaker JE, Smith AM, Weaver JJA, Macklin P. Iterative community-driven development of a SARS-CoV-2 tissue simulator. bioRxiv 2021:2020.04.02.019075. [PMID: 32511322 PMCID: PMC7239052 DOI: 10.1101/2020.04.02.019075] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The 2019 novel coronavirus, SARS-CoV-2, is a pathogen of critical significance to international public health. Knowledge of the interplay between molecular-scale virus-receptor interactions, single-cell viral replication, intracellular-scale viral transport, and emergent tissue-scale viral propagation is limited. Moreover, little is known about immune system-virus-tissue interactions and how these can result in low-level (asymptomatic) infections in some cases and acute respiratory distress syndrome (ARDS) in others, particularly with respect to presentation in different age groups or pre-existing inflammatory risk factors. Given the nonlinear interactions within and among each of these processes, multiscale simulation models can shed light on the emergent dynamics that lead to divergent outcomes, identify actionable "choke points" for pharmacologic interventions, screen potential therapies, and identify potential biomarkers that differentiate patient outcomes. Given the complexity of the problem and the acute need for an actionable model to guide therapy discovery and optimization, we introduce and iteratively refine a prototype of a multiscale model of SARS-CoV-2 dynamics in lung tissue. The first prototype model was built and shared internationally as open source code and an online interactive model in under 12 hours, and community domain expertise is driving regular refinements. In a sustained community effort, this consortium is integrating data and expertise across virology, immunology, mathematical biology, quantitative systems physiology, cloud and high performance computing, and other domains to accelerate our response to this critical threat to international health. More broadly, this effort is creating a reusable, modular framework for studying viral replication and immune response in tissues, which can also potentially be adapted to related problems in immunology and immunotherapy.
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16
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Farhang-Sardroodi S, Korosec CS, Gholami S, Craig M, Moyles IR, Ghaemi MS, Ooi HK, Heffernan JM. Analysis of Host Immunological Response of Adenovirus-Based COVID-19 Vaccines. Vaccines (Basel) 2021; 9:861. [PMID: 34451985 PMCID: PMC8402548 DOI: 10.3390/vaccines9080861] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 07/22/2021] [Accepted: 07/27/2021] [Indexed: 12/18/2022] Open
Abstract
During the SARS-CoV-2 global pandemic, several vaccines, including mRNA and adenovirus vector approaches, have received emergency or full approval. However, supply chain logistics have hampered global vaccine delivery, which is impacting mass vaccination strategies. Recent studies have identified different strategies for vaccine dose administration so that supply constraints issues are diminished. These include increasing the time between consecutive doses in a two-dose vaccine regimen and reducing the dosage of the second dose. We consider both of these strategies in a mathematical modeling study of a non-replicating viral vector adenovirus vaccine in this work. We investigate the impact of different prime-boost strategies by quantifying their effects on immunological outcomes based on simple system of ordinary differential equations. The boost dose is administered either at a standard dose (SD) of 1000 or at a low dose (LD) of 500 or 250 vaccine particles. Results show dose-dependent immune response activity. Our model predictions show that by stretching the prime-boost interval to 18 or 20, in an SD/SD or SD/LD regimen, the minimum promoted antibody (Nab) response will be comparable with the neutralizing antibody level measured in COVID-19 recovered patients. Results also show that the minimum stimulated antibody in SD/SD regimen is identical with the high level observed in clinical trial data. We conclude that an SD/LD regimen may provide protective capacity, which will allow for conservation of vaccine doses.
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Affiliation(s)
- Suzan Farhang-Sardroodi
- Modelling Infection and Immunity Lab, Mathematics Statistics, York University, Toronto, ON M3J 1P3, Canada; (C.S.K.); (S.G.)
- Centre for Disease Modelling (CDM), Mathematics Statistics, York University, Toronto, ON M3J 1P3, Canada;
| | - Chapin S. Korosec
- Modelling Infection and Immunity Lab, Mathematics Statistics, York University, Toronto, ON M3J 1P3, Canada; (C.S.K.); (S.G.)
- Centre for Disease Modelling (CDM), Mathematics Statistics, York University, Toronto, ON M3J 1P3, Canada;
| | - Samaneh Gholami
- Modelling Infection and Immunity Lab, Mathematics Statistics, York University, Toronto, ON M3J 1P3, Canada; (C.S.K.); (S.G.)
- Centre for Disease Modelling (CDM), Mathematics Statistics, York University, Toronto, ON M3J 1P3, Canada;
| | - Morgan Craig
- Sainte-Justine University Hospital Research Centre and Department of Mathematics and Statistics, Université de Montréal, Montreal, QC H3T 1J4, Canada;
| | - Iain R. Moyles
- Centre for Disease Modelling (CDM), Mathematics Statistics, York University, Toronto, ON M3J 1P3, Canada;
| | - Mohammad Sajjad Ghaemi
- Digital Technologies Research Centre, National Research Council Canada, Toronto, ON C1A 4P3, Canada; (M.S.G.); (H.K.O.)
| | - Hsu Kiang Ooi
- Digital Technologies Research Centre, National Research Council Canada, Toronto, ON C1A 4P3, Canada; (M.S.G.); (H.K.O.)
| | - Jane M. Heffernan
- Modelling Infection and Immunity Lab, Mathematics Statistics, York University, Toronto, ON M3J 1P3, Canada; (C.S.K.); (S.G.)
- Centre for Disease Modelling (CDM), Mathematics Statistics, York University, Toronto, ON M3J 1P3, Canada;
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17
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Paredes Bonilla RV, Nekka F, Craig M. A Quantitative Systems Pharmacology Framework for Optimal Doxorubicin Granulocyte Colony-Stimulating Factor Regimens in Triple-Negative Breast Cancer. Pharmacology 2021; 106:542-550. [PMID: 34350894 DOI: 10.1159/000518037] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 06/18/2021] [Indexed: 11/19/2022]
Abstract
INTRODUCTION To mitigate the risk of neutropenia during chemotherapy treatment of triple-negative breast cancer, prophylactic and supportive therapy with granulocyte colony-stimulating factor (G-CSF) is administered concomitant to chemotherapy. The proper timing of combined chemotherapy and G-CSF is crucial for treatment outcomes. METHODS Leveraging our established mathematical model of neutrophil production by G-CSF, we developed quantitative systems pharmacology (QSP) framework to investigate how modulating chemotherapy dose frequency and intensity can maximize antitumour effects. To establish schedules that best control tumour size while minimizing neutropenia, we combined Gompertzian tumour growth with pharmacokinetic/pharmacodynamic models of doxorubicin and G-CSF, and our QSP model of neutrophil production. RESULTS We optimized a range of chemotherapeutic cycle lengths and dose sizes to establish regimens that simultaneously reduced tumour burden while minimizing neutropenia. Our results suggest that cytotoxic chemotherapy with doxorubicin 45 mg/m2 every 14 days provides effective control of tumour growth while mitigating neutropenic risks. CONCLUSION This work suggests future avenues for optimal regimens of chemotherapy with prophylactic G-CSF support. Importantly, the algorithmic approach that we developed can aid in balancing the anticancer and the neutropenic effects of both drugs, and therefore contributes to rational considerations in clinical decision-making in triple-negative breast cancer.
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Affiliation(s)
| | - Fahima Nekka
- Faculty of Pharmacy, Université de Montréal, Montreal, Québec, Canada.,Centre de recherches mathématiques, Université de Montréal, Montreal, Québec, Canada
| | - Morgan Craig
- Centre de recherches mathématiques, Université de Montréal, Montreal, Québec, Canada.,Sainte-Justine University Hospital Research Centre, Montreal, Québec, Canada.,Department of Mathematics and Statistics, Université de Montréal, Montreal, Québec, Canada
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18
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Cassidy T, Nichol D, Robertson-Tessi M, Craig M, Anderson ARA. The role of memory in non-genetic inheritance and its impact on cancer treatment resistance. PLoS Comput Biol 2021; 17:e1009348. [PMID: 34460809 PMCID: PMC8432806 DOI: 10.1371/journal.pcbi.1009348] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 09/10/2021] [Accepted: 08/11/2021] [Indexed: 12/24/2022] Open
Abstract
Intra-tumour heterogeneity is a leading cause of treatment failure and disease progression in cancer. While genetic mutations have long been accepted as a primary mechanism of generating this heterogeneity, the role of phenotypic plasticity is becoming increasingly apparent as a driver of intra-tumour heterogeneity. Consequently, understanding the role of this plasticity in treatment resistance and failure is a key component of improving cancer therapy. We develop a mathematical model of stochastic phenotype switching that tracks the evolution of drug-sensitive and drug-tolerant subpopulations to clarify the role of phenotype switching on population growth rates and tumour persistence. By including cytotoxic therapy in the model, we show that, depending on the strategy of the drug-tolerant subpopulation, stochastic phenotype switching can lead to either transient or permanent drug resistance. We study the role of phenotypic heterogeneity in a drug-resistant, genetically homogeneous population of non-small cell lung cancer cells to derive a rational treatment schedule that drives population extinction and avoids competitive release of the drug-tolerant sub-population. This model-informed therapeutic schedule results in increased treatment efficacy when compared against periodic therapy, and, most importantly, sustained tumour decay without the development of resistance.
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Affiliation(s)
- Tyler Cassidy
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Daniel Nichol
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, United Kingdom
| | - Mark Robertson-Tessi
- Department of Integrated Mathematical Oncology, H. Lee Moffitt Cancer Center, Tampa, Florida, United States of America
| | - Morgan Craig
- Département de mathématiques et de statistique, Université de Montréal, Montreal, Canada
- CHU Sainte-Justine, Montreal, Canada
| | - Alexander R. A. Anderson
- Department of Integrated Mathematical Oncology, H. Lee Moffitt Cancer Center, Tampa, Florida, United States of America
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19
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Jenner AL, Aogo RA, Alfonso S, Crowe V, Deng X, Smith AP, Morel PA, Davis CL, Smith AM, Craig M. COVID-19 virtual patient cohort suggests immune mechanisms driving disease outcomes. PLoS Pathog 2021; 17:e1009753. [PMID: 34260666 PMCID: PMC8312984 DOI: 10.1371/journal.ppat.1009753] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 07/26/2021] [Accepted: 06/24/2021] [Indexed: 12/11/2022] Open
Abstract
To understand the diversity of immune responses to SARS-CoV-2 and distinguish features that predispose individuals to severe COVID-19, we developed a mechanistic, within-host mathematical model and virtual patient cohort. Our results suggest that virtual patients with low production rates of infected cell derived IFN subsequently experienced highly inflammatory disease phenotypes, compared to those with early and robust IFN responses. In these in silico patients, the maximum concentration of IL-6 was also a major predictor of CD8+ T cell depletion. Our analyses predicted that individuals with severe COVID-19 also have accelerated monocyte-to-macrophage differentiation mediated by increased IL-6 and reduced type I IFN signalling. Together, these findings suggest biomarkers driving the development of severe COVID-19 and support early interventions aimed at reducing inflammation.
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Affiliation(s)
- Adrianne L. Jenner
- Sainte-Justine University Hospital Research Centre, Montréal, Québec, Canada
- Department of Mathematics and Statistics, Université de Montréal, Montréal, Québec, Canada
| | - Rosemary A. Aogo
- Department of Pediatrics, University of Tennessee Health Science Center, Memphis, Tennessee, United States of America
| | - Sofia Alfonso
- Department of Physiology, McGill University, Montréal, Québec, Canada
| | - Vivienne Crowe
- Department of Mathematics and Statistics, Concordia University, Montréal, Québec, Canada
| | - Xiaoyan Deng
- Sainte-Justine University Hospital Research Centre, Montréal, Québec, Canada
- Department of Mathematics and Statistics, Université de Montréal, Montréal, Québec, Canada
| | - Amanda P. Smith
- Department of Pediatrics, University of Tennessee Health Science Center, Memphis, Tennessee, United States of America
| | - Penelope A. Morel
- Department of Immunology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Courtney L. Davis
- Natural Science Division, Pepperdine University, Malibu, California, United States of America
| | - Amber M. Smith
- Department of Pediatrics, University of Tennessee Health Science Center, Memphis, Tennessee, United States of America
| | - Morgan Craig
- Sainte-Justine University Hospital Research Centre, Montréal, Québec, Canada
- Department of Mathematics and Statistics, Université de Montréal, Montréal, Québec, Canada
- Department of Physiology, McGill University, Montréal, Québec, Canada
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20
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Jenner AL, Cassidy T, Belaid K, Bourgeois-Daigneault MC, Craig M. In silico trials predict that combination strategies for enhancing vesicular stomatitis oncolytic virus are determined by tumor aggressivity. J Immunother Cancer 2021; 9:jitc-2020-001387. [PMID: 33608375 PMCID: PMC7898884 DOI: 10.1136/jitc-2020-001387] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/22/2020] [Indexed: 12/19/2022] Open
Abstract
Background Immunotherapies, driven by immune-mediated antitumorigenicity, offer the potential for significant improvements to the treatment of multiple cancer types. Identifying therapeutic strategies that bolster antitumor immunity while limiting immune suppression is critical to selecting treatment combinations and schedules that offer durable therapeutic benefits. Combination oncolytic virus (OV) therapy, wherein complementary OVs are administered in succession, offer such promise, yet their translation from preclinical studies to clinical implementation is a major challenge. Overcoming this obstacle requires answering fundamental questions about how to effectively design and tailor schedules to provide the most benefit to patients. Methods We developed a computational biology model of combined oncolytic vaccinia (an enhancer virus) and vesicular stomatitis virus (VSV) calibrated to and validated against multiple data sources. We then optimized protocols in a cohort of heterogeneous virtual individuals by leveraging this model and our previously established in silico clinical trial platform. Results Enhancer multiplicity was shown to have little to no impact on the average response to therapy. However, the duration of the VSV injection lag was found to be determinant for survival outcomes. Importantly, through treatment individualization, we found that optimal combination schedules are closely linked to tumor aggressivity. We predicted that patients with aggressively growing tumors required a single enhancer followed by a VSV injection 1 day later, whereas a small subset of patients with the slowest growing tumors needed multiple enhancers followed by a longer VSV delay of 15 days, suggesting that intrinsic tumor growth rates could inform the segregation of patients into clinical trials and ultimately determine patient survival. These results were validated in entirely new cohorts of virtual individuals with aggressive or non-aggressive subtypes. Conclusions Based on our results, improved therapeutic schedules for combinations with enhancer OVs can be studied and implemented. Our results further underline the impact of interdisciplinary approaches to preclinical planning and the importance of computational approaches to drug discovery and development.
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Affiliation(s)
- Adrianne L Jenner
- Sainte-Justine University Hospital Research Centre, Montreal, Quebec, Canada.,Department of Mathematics and Statistics, Université de Montréal, Montreal, Quebec, Canada
| | - Tyler Cassidy
- Department of Mathematics and Statistics, McGill University, Montreal, Quebec, Canada.,Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, USA
| | - Katia Belaid
- Department of Mathematics and Statistics, Université de Montréal, Montreal, Quebec, Canada.,Statistique et Informatique Décisionnelle, Université Toulouse III Paul Sabatier, Toulouse, Occitanie, France
| | - Marie-Claude Bourgeois-Daigneault
- Institut du Cancer de Montréal, CHUM, Montreal, Quebec, Canada.,Department of Microbiology, Infectious diseases and Immunology, Université de Montréal, Montreal, Quebec, Canada
| | - Morgan Craig
- Sainte-Justine University Hospital Research Centre, Montreal, Quebec, Canada .,Department of Mathematics and Statistics, Université de Montréal, Montreal, Quebec, Canada
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21
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Aflaki M, Flannery A, Ferreira JP, Cheng MP, Kronfli N, Marelli A, Zannad F, Brophy J, Afillalo J, Huynh T, Giannetti N, Bessissow A, Ezekowitz JA, Lopes RD, Ambrosy AP, Craig M, Sharma A. Management of Renin-Angiotensin-Aldosterone System blockade in patients admitted to hospital with confirmed coronavirus disease (COVID-19) infection (The McGill RAAS-COVID- 19): A structured summary of a study protocol for a randomized controlled trial. Trials 2021; 22:115. [PMID: 33546734 PMCID: PMC7862851 DOI: 10.1186/s13063-021-05080-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 01/29/2021] [Indexed: 12/04/2022] Open
Abstract
Objectives The aim of the RAAS-COVID-19 randomized control trial is to evaluate whether an upfront strategy of temporary discontinuation of renin angiotensin aldosterone system (RAAS) inhibition versus continuation of RAAS inhibition among patients admitted with established COVID-19 infection has an impact on short term clinical and biomarker outcomes. We hypothesize that continuation of RAAS inhibition will be superior to temporary discontinuation with regards to the primary endpoint of a global rank sum score. The global rank sum score has been successfully used in previous cardiovascular clinical trials. Trial design This is an open label parallel two arm (1,1 ratio) randomized control superiority trial of approximately 40 COVID-19 patients who are on chronic RAAS inhibitor therapy. Participants Adults who are admitted to hospital within the McGill University Health Centre systems (MUHC) including Royal Victoria Hospital (RVH), Montreal General Hospital (MGH) and Jewish General Hospital (JGH) and who are within 96 hours of COVID-19 diagnosis (confirmed via PCR on any biological sample) will be considered for the trial. Of note, the initial protocol to screen and enrol within 48 hours of COVID-19 diagnosis was extended through an amendment, to 96 hours to increase feasibility. Participants have to be 18 years or older and would have to be on RAAS inhibitors for at least a month to be considered eligible for the study. Additionally, RAAS inhibitors should not have been held for more than 48 hours before randomization. A list of inclusion and exclusion criteria can be found in the full protocol document. In order to prevent heart failure exacerbation, patients with reduced ejection fraction were excluded from the trial. Once a patient is admitted on the ward with a diagnosis of COVID-19, we will confirm with the treating physician if the participant is suitable for the RAAS-COVID trial and meets all the inclusion and exclusion criteria. If the patient is eligible and informed consent has been obtained we will collect data on sex, age, ethnicity, past medical history and list of medications (e.g. other anti-hypertensives or anticoagulants), for further analysis. Intervention and comparator All the study participants will be randomized to a strategy of temporarily holding the RAAS inhibitor [intervention] versus continuing the RAAS inhibitor [continued standard of care]. Among participants who are randomized to the intervention arm, alternative guide-line directed anti-hypertensive medication will be provided to the treating physician team (detail in study protocol). In the intervention arm RAAS inhibitor will be withheld for a total of 7 days with the possibility of the withdrawn medication being initiated at any point after day 7 or on the day of discharge. The recommendation for re-initiating the withdrawn medication will be made to the treating physician. The re-initiation of these therapies are according to standard convention and follow-up as per Canadian guidelines. Additionally, the date of restarting the withdrawn medication or whether the medication was re-prescribed on discharge or not, will be collected. This will be used to conduct a sensitivity analysis. Furthermore, biomarkers such as troponin, c-reactive protein (CRP) and lymphocyte count will be assessed during the same time period. Samples will be collected on randomization, day 4 and day 7. Main outcomes Primary endpoint In this study the primary end point is a global rank score calculated for all participants, regardless of treatment assignment ( score from 0 to 7). Please refer to table 4 in the full protocol. In the context of the current trial, it is estimated that death is the most meaningful endpoint, and therefore has the highest score ( score of 7). This is followed by admission to ICU, the need for mechanical ventilation etc. The lowest scores ( score of 1) are assigned to biomarker changes (e.g. change in troponin, change in CRP). This strategy has been used successfully in cardiovascular disease trials and therefore is applicable to the current trial. The primary endpoint for the present trial is assessed from baseline to day 7 (or discharge). Participants are ranked across the clinical and biomarker domains. Lower values indicate better health (or stability). Participants who died during the 7th day of the study will be ranked based on all events occurring before their death and also including the fatal event in the score. Next, participants who did not die but were transferred to ICU for invasive ventilation will be ranked based on all the events occurring before the ICU entry and also including the ICU admission in the score. Those participants who did not die were not transferred to ICU for invasive ventilation, will be ranked based on the subsequent outcomes. The mean rank score will then be compared between groups. In this scheme, a lower mean rank score indicates greater overall stability for participants. Secondary endpoints : The key secondary endpoints are the individual components of the primary components and include the following: death, transfer to ICU primarily for invasive ventilation, transfer to ICU for other indication, non-fatal MACE ( any of following, MI, stroke, acute HF, new onset Afib), length of stay > 4 days, development of acute kidney injury ( > 40% decline in eGFR or doubling of serum creatinine), urgent intravenous treatment for high blood pressure, 30% increase in baseline high sensitivity troponin, 30% increase in baseline BNP, increase in CRP to > 30% in 48 hours and lymphocyte count drop> 30%. We will also look at the World Health Organization (WHO) ordinal scale for clinical improvement (in COVID-19) in our data. In this scale death will be assigned the highest score of 8. Patients with no limitation of activity will be assigned a score of 1 which indicates overall more stability (3). Additionally, we will evaluate the potential effects of discontinuing RAAS inhibition on alternative schedules (longer/shorter than 7 days, intermittent discontinuation) using a mechanistic mathematical model of COVID-19 immunopathology calibrated to data collected from our patient cohort. In particular, we will assess the impact of alternative schedules on primary and secondary endpoints including increases to baseline CRP and lymphocyte counts. Randomization Participants will be randomized in a 1:1 ratio. Randomization will be performed within an electronic database system at the time of enrolment using a random number generator, an approach that has been successfully used in other clinical trials. Neither participant, study team, or treating team will be blinded to the intervention arm. Blinding This is an open label study with no blinding. Numbers to be randomised (sample size) The approximate number of participants required for this trial is 40 patients (randomized 1:1 to continuation versus discontinuation of RAAS inhibitors). This number was calculated based on previous rates of outcomes for COVID-19 in the literature (e.g. death, ICU transfer) and statistical power calculations. Trial Status Protocol number: MP-37-2021-6641, Version 4: 01-10-2020. Trial start date September 1st 2020 and currently enrolling participants. Estimated end date for recruitment of participants : July 2021. Estimated end date for study completion: September 1st 2021. Trial registration Trial registration: ClincalTrials.gov: NCT04508985, date of registration: August 11th , 2020 Full protocol The full protocol is attached as an additional file, accessible from the Trials website (Additional file 1). In the interest in expediting dissemination of this material, the familiar formatting has been eliminated; this Letter serves as a summary of the key elements of the full protocol. Supplementary Information The online version contains supplementary material available at 10.1186/s13063-021-05080-4.
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Affiliation(s)
- Mona Aflaki
- Division of Internal Medicine, McGill University Health Centre, McGill University, Montreal, Quebec, Canada
| | - Alexandria Flannery
- Division of Cardiology, McGill University Health Centre, McGill University, 1001 Decarie Blvd, Montreal, Quebec, H4A 3J1, Canada.,DREAM-CV Lab, McGill University Health Centre Research Institute, McGill University, Montreal, Quebec, Canada
| | - João Pedro Ferreira
- Centre D'Investigation Clinique- Plurithématique Inserm CIC-P 1433, Inserm U1116, CHRU Nancy Hôpitaux de Brabois, F-CRIN INI-CRCT (Cardiovascular and Renal Clinical Trialists), Université de Lorraine, Nancy, France
| | - Matthew Pellan Cheng
- Division of Infectious Disease, McGill University Health Centre, McGill University, Montreal, Quebec, Canada
| | - Nadine Kronfli
- Division of Infectious Disease, McGill University Health Centre, McGill University, Montreal, Quebec, Canada
| | - Ariane Marelli
- Division of Cardiology, McGill University Health Centre, McGill University, 1001 Decarie Blvd, Montreal, Quebec, H4A 3J1, Canada
| | - Faiez Zannad
- Centre D'Investigation Clinique- Plurithématique Inserm CIC-P 1433, Inserm U1116, CHRU Nancy Hôpitaux de Brabois, F-CRIN INI-CRCT (Cardiovascular and Renal Clinical Trialists), Université de Lorraine, Nancy, France
| | - James Brophy
- Division of Cardiology, McGill University Health Centre, McGill University, 1001 Decarie Blvd, Montreal, Quebec, H4A 3J1, Canada
| | - Jon Afillalo
- Division of Cardiology, Jewish General Hospital, McGill University, Montreal, Quebec, Canada
| | - Thao Huynh
- Division of Cardiology, McGill University Health Centre, McGill University, 1001 Decarie Blvd, Montreal, Quebec, H4A 3J1, Canada
| | - Nadia Giannetti
- Division of Cardiology, McGill University Health Centre, McGill University, 1001 Decarie Blvd, Montreal, Quebec, H4A 3J1, Canada
| | - Amal Bessissow
- Division of Internal Medicine, McGill University Health Centre, McGill University, Montreal, Quebec, Canada
| | - Justin A Ezekowitz
- Canadian VIGOUR Centre, University of Alberta, Edmonton, Alberta, Canada
| | - Renato D Lopes
- Duke Clinical Research Institute, Duke University, Durham, North Carolina, USA
| | - Andrew P Ambrosy
- Department of Cardiology, Kaiser Permanente San Francisco Medical Center, San Francisco, California, USA.,Division of Research, Kaiser Permanente Northern California, Oakland, California, USA
| | - Morgan Craig
- Sainte-Justine University Hospital Research Centre and Department of Mathematics and Statistics, Université de Montréal, Montreal, Quebec, Canada
| | - Abhinav Sharma
- Division of Cardiology, McGill University Health Centre, McGill University, 1001 Decarie Blvd, Montreal, Quebec, H4A 3J1, Canada. .,DREAM-CV Lab, McGill University Health Centre Research Institute, McGill University, Montreal, Quebec, Canada.
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22
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Jenner AL, Aogo RA, Alfonso S, Crowe V, Smith AP, Morel PA, Davis CL, Smith AM, Craig M. COVID-19 virtual patient cohort reveals immune mechanisms driving disease outcomes. bioRxiv 2021:2021.01.05.425420. [PMID: 33442689 PMCID: PMC7805446 DOI: 10.1101/2021.01.05.425420] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
To understand the diversity of immune responses to SARS-CoV-2 and distinguish features that predispose individuals to severe COVID-19, we developed a mechanistic, within-host mathematical model and virtual patient cohort. Our results indicate that virtual patients with low production rates of infected cell derived IFN subsequently experienced highly inflammatory disease phenotypes, compared to those with early and robust IFN responses. In these in silico patients, the maximum concentration of IL-6 was also a major predictor of CD8 + T cell depletion. Our analyses predicted that individuals with severe COVID-19 also have accelerated monocyte-to-macrophage differentiation that was mediated by increased IL-6 and reduced type I IFN signalling. Together, these findings identify biomarkers driving the development of severe COVID-19 and support early interventions aimed at reducing inflammation. AUTHOR SUMMARY Understanding of how the immune system responds to SARS-CoV-2 infections is critical for improving diagnostic and treatment approaches. Identifying which immune mechanisms lead to divergent outcomes can be clinically difficult, and experimental models and longitudinal data are only beginning to emerge. In response, we developed a mechanistic, mathematical and computational model of the immunopathology of COVID-19 calibrated to and validated against a broad set of experimental and clinical immunological data. To study the drivers of severe COVID-19, we used our model to expand a cohort of virtual patients, each with realistic disease dynamics. Our results identify key processes that regulate the immune response to SARS-CoV-2 infection in virtual patients and suggest viable therapeutic targets, underlining the importance of a rational approach to studying novel pathogens using intra-host models.
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Affiliation(s)
- Adrianne L. Jenner
- CHU Sainte-Justine Research Centre, Montréal, Québec, Canada
- Department of Mathematics and Statistics, Université de Montréal, Montréal, Québec, Canada
| | - Rosemary A. Aogo
- Department of Pediatrics, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Sofia Alfonso
- Department of Physiology, McGill University, Montréal, Québec, Canada
| | - Vivienne Crowe
- Department of Mathematics and Statistics, Concordia University, Montréal, Québec, Canada
| | - Amanda P. Smith
- Department of Pediatrics, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Penelope A. Morel
- Department of Immunology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Courtney L. Davis
- Natural Science Division, Pepperdine University, Malibu, California, USA
| | - Amber M. Smith
- Department of Pediatrics, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Morgan Craig
- CHU Sainte-Justine Research Centre, Montréal, Québec, Canada
- Department of Mathematics and Statistics, Université de Montréal, Montréal, Québec, Canada
- Department of Physiology, McGill University, Montréal, Québec, Canada
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23
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Krieger MS, Moreau JM, Zhang H, Chien M, Zehnder JL, Craig M. A Blueprint for Identifying Phenotypes and Drug Targets in Complex Disorders with Empirical Dynamics. Patterns (N Y) 2020; 1:100138. [PMID: 33336196 PMCID: PMC7733879 DOI: 10.1016/j.patter.2020.100138] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 09/25/2020] [Accepted: 10/12/2020] [Indexed: 02/06/2023]
Abstract
A central challenge in medicine is translating from observational understanding to mechanistic understanding, where some observations are recognized as causes for the others. This can lead not only to new treatments and understanding, but also to recognition of novel phenotypes. Here, we apply a collection of mathematical techniques (empirical dynamics), which infer mechanistic networks in a model-free manner from longitudinal data, to hematopoiesis. Our study consists of three subjects with markers for cyclic thrombocytopenia, in which multiple cells and proteins undergo abnormal oscillations. One subject has atypical markers and may represent a rare phenotype. Our analyses support this contention, and also lend new evidence to a theory for the cause of this disorder. Simulations of an intervention yield encouraging results, even when applied to patient data outside our three subjects. These successes suggest that this blueprint has broader applicability in understanding and treating complex disorders.
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Affiliation(s)
- Madison S. Krieger
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Joshua M. Moreau
- Department of Dermatology, University of California, San Francisco, CA, USA
| | - Haiyu Zhang
- Department of Pathology, Stanford School of Medicine, Stanford, CA, USA
| | - May Chien
- Department of Medicine (Hematology), Stanford, CA, USA
| | - James L. Zehnder
- Department of Pathology, Stanford School of Medicine, Stanford, CA, USA
- Department of Medicine (Hematology), Stanford, CA, USA
| | - Morgan Craig
- Département de Mathématiques et de Statistique, Université de Montréal, Montréal, QC, Canada
- CHU Sainte-Justine Research Centre, 3175 Chemin de la Côte-Sainte-Catherine, Montréal, QC H3T 1C5, Canada
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24
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Alfonso S, Jenner AL, Craig M. Translational approaches to treating dynamical diseases through in silico clinical trials. Chaos 2020; 30:123128. [PMID: 33380031 DOI: 10.1063/5.0019556] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 11/20/2020] [Indexed: 06/12/2023]
Abstract
The primary goal of drug developers is to establish efficient and effective therapeutic protocols. Multifactorial pathologies, including dynamical diseases and complex disorders, can be difficult to treat, given the high degree of inter- and intra-patient variability and nonlinear physiological relationships. Quantitative approaches combining mechanistic disease modeling and computational strategies are increasingly leveraged to rationalize pre-clinical and clinical studies and to establish effective treatment strategies. The development of clinical trials has led to new computational methods that allow for large clinical data sets to be combined with pharmacokinetic and pharmacodynamic models of diseases. Here, we discuss recent progress using in silico clinical trials to explore treatments for a variety of complex diseases, ultimately demonstrating the immense utility of quantitative methods in drug development and medicine.
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Affiliation(s)
- Sofia Alfonso
- Department of Physiology, McGill University, Montreal, Quebec H3A 0G4, Canada
| | - Adrianne L Jenner
- Department of Mathematics and Statistics, Université de Montréal, Montreal, Quebec H3C 3J7, Canada
| | - Morgan Craig
- Department of Physiology, McGill University, Montreal, Quebec H3A 0G4, Canada
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25
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Craig M, Jenner AL, Namgung B, Lee LP, Goldman A. Engineering in Medicine To Address the Challenge of Cancer Drug Resistance: From Micro- and Nanotechnologies to Computational and Mathematical Modeling. Chem Rev 2020; 121:3352-3389. [PMID: 33152247 DOI: 10.1021/acs.chemrev.0c00356] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Drug resistance has profoundly limited the success of cancer treatment, driving relapse, metastasis, and mortality. Nearly all anticancer drugs and even novel immunotherapies, which recalibrate the immune system for tumor recognition and destruction, have succumbed to resistance development. Engineers have emerged across mechanical, physical, chemical, mathematical, and biological disciplines to address the challenge of drug resistance using a combination of interdisciplinary tools and skill sets. This review explores the developing, complex, and under-recognized role of engineering in medicine to address the multitude of challenges in cancer drug resistance. Looking through the "lens" of intrinsic, extrinsic, and drug-induced resistance (also referred to as "tolerance"), we will discuss three specific areas where active innovation is driving novel treatment paradigms: (1) nanotechnology, which has revolutionized drug delivery in desmoplastic tissues, harnessing physiochemical characteristics to destroy tumors through photothermal therapy and rationally designed nanostructures to circumvent cancer immunotherapy failures, (2) bioengineered tumor models, which have benefitted from microfluidics and mechanical engineering, creating a paradigm shift in physiologically relevant environments to predict clinical refractoriness and enabling platforms for screening drug combinations to thwart resistance at the individual patient level, and (3) computational and mathematical modeling, which blends in silico simulations with molecular and evolutionary principles to map mutational patterns and model interactions between cells that promote resistance. On the basis that engineering in medicine has resulted in discoveries in resistance biology and successfully translated to clinical strategies that improve outcomes, we suggest the proliferation of multidisciplinary science that embraces engineering.
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Affiliation(s)
- Morgan Craig
- Department of Mathematics and Statistics, University of Montreal, Montreal, Quebec H3C 3J7, Canada.,Sainte-Justine University Hospital Research Centre, Montreal, Quebec H3S 2G4, Canada
| | - Adrianne L Jenner
- Department of Mathematics and Statistics, University of Montreal, Montreal, Quebec H3C 3J7, Canada.,Sainte-Justine University Hospital Research Centre, Montreal, Quebec H3S 2G4, Canada
| | - Bumseok Namgung
- Division of Engineering in Medicine, Brigham and Women's Hospital, Boston, Massachusetts 02115, United States.,Department of Medicine, Harvard Medical School, Boston, Massachusetts 02139, United States
| | - Luke P Lee
- Division of Engineering in Medicine, Brigham and Women's Hospital, Boston, Massachusetts 02115, United States.,Department of Medicine, Harvard Medical School, Boston, Massachusetts 02139, United States
| | - Aaron Goldman
- Division of Engineering in Medicine, Brigham and Women's Hospital, Boston, Massachusetts 02115, United States.,Department of Medicine, Harvard Medical School, Boston, Massachusetts 02139, United States
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26
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Cassidy T, Humphries AR, Craig M, Mackey MC. Characterizing Chemotherapy-Induced Neutropenia and Monocytopenia Through Mathematical Modelling. Bull Math Biol 2020; 82:104. [PMID: 32737602 DOI: 10.1007/s11538-020-00777-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 07/11/2020] [Indexed: 12/18/2022]
Abstract
In spite of the recent focus on the development of novel targeted drugs to treat cancer, cytotoxic chemotherapy remains the standard treatment for the vast majority of patients. Unfortunately, chemotherapy is associated with high hematopoietic toxicity that may limit its efficacy. We have previously established potential strategies to mitigate chemotherapy-induced neutropenia (a lack of circulating neutrophils) using a mechanistic model of granulopoiesis to predict the interactions defining the neutrophil response to chemotherapy and to define optimal strategies for concurrent chemotherapy/prophylactic granulocyte colony-stimulating factor (G-CSF). Here, we extend our analyses to include monocyte production by constructing and parameterizing a model of monocytopoiesis. Using data for neutrophil and monocyte concentrations during chemotherapy in a large cohort of childhood acute lymphoblastic leukemia patients, we leveraged our model to determine the relationship between the monocyte and neutrophil nadirs during cyclic chemotherapy. We show that monocytopenia precedes neutropenia by 3 days, and rationalize the use of G-CSF during chemotherapy by establishing that the onset of monocytopenia can be used as a clinical marker for G-CSF dosing post-chemotherapy. This work therefore has important clinical applications as a comprehensive approach to understanding the relationship between monocyte and neutrophils after cyclic chemotherapy with or without G-CSF support.
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Affiliation(s)
- Tyler Cassidy
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
| | - Antony R Humphries
- Department of Mathematics and Statistics, McGill University, Montréal, QC, H3A 0B9, Canada.,Department of Physiology, McGill University, Montréal, QC, H3A 0B9, Canada
| | - Morgan Craig
- Department of Mathematics and Statistics, Université de Montréal, Montréal, Canada. .,CHU Sainte-Justine Research Centre, University of Montreal, Montréal, Canada.
| | - Michael C Mackey
- Department of Physiology, McGill University, 3655 Drummond, Montréal, QC, H3G 1Y6, Canada.,Department of Mathematics and Statistics, McGill University, 3655 Drummond, Montréal, QC, H3G 1Y6, Canada.,Department of Physics, McGill University, 3655 Drummond, Montréal, QC, H3G 1Y6, Canada
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27
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Mackey MC, Glisovic S, Leclerc JM, Pastore Y, Krajinovic M, Craig M. The timing of cyclic cytotoxic chemotherapy can worsen neutropenia and neutrophilia. Br J Clin Pharmacol 2020; 87:687-693. [PMID: 32533708 DOI: 10.1111/bcp.14424] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 05/17/2020] [Accepted: 05/28/2020] [Indexed: 01/16/2023] Open
Abstract
Despite recent advances in immunotherapies, cytotoxic chemotherapy continues to be a first-line treatment option for the majority of cancers. Unfortunately, a common side effect in patients undergoing chemotherapy treatment is neutropenia. To mitigate the risk of neutropenia and febrile neutropenia, prophylactic treatment with granulocyte-colony stimulating factor (G-CSF) is administered. Extensive pharmacokinetic/pharmacodynamic modelling of myelosuppression during chemotherapy has suggested avenues for therapy optimization to mitigate this neutropenia. However, the issue of resonance, whereby neutrophil oscillations are induced by the periodic administration of cytotoxic chemotherapy and the coadministration of G-CSF, potentially aggravating a patient's neutropenic/neutrophilic status, is not well-characterized in the clinical literature. Here, through analysis of neutrophil data from young acute lymphoblastic leukaemia patients, we find that resonance is occurring during cyclic chemotherapy treatment in 26% of these patients. Motivated by these data and our previous modelling studies on adult lymphoma patients, we examined resonance during treatment with or without G-CSF. Using our quantitative systems pharmacology model of granulopoiesis, we show that the timing of cyclic chemotherapy can worsen neutropenia or neutrophilia, and suggest clinically-actionable schedules to reduce the resonant effect. We emphasize that delaying supportive G-CSF therapy to 6-7 days after chemotherapy can mitigate myelosuppressive effects. This study therefore highlights the importance of quantitative systems pharmacology for the clinical practice for developing rational therapeutic strategies.
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Affiliation(s)
| | | | - Jean-Marie Leclerc
- CHU Sainte-Justine Research Centre, Montreal, Canada.,Department of Pediatrics, University of Montreal, Montreal, Canada
| | - Yves Pastore
- CHU Sainte-Justine Research Centre, Montreal, Canada.,Department of Pediatrics, University of Montreal, Montreal, Canada
| | - Maja Krajinovic
- CHU Sainte-Justine Research Centre, Montreal, Canada.,Department of Pharmacology and Physiology, University of Montreal, Montreal, Canada
| | - Morgan Craig
- Department of Physiology, McGill University, Montreal, Canada.,CHU Sainte-Justine Research Centre, Montreal, Canada.,Department of Mathematics and Statistics, University of Montreal, Montreal, Canada
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28
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Msayib Y, Craig M, Simard MA, Larkin JR, Shin DD, Liu TT, Sibson NR, Okell TW, Chappell MA. Robust estimation of quantitative perfusion from multi-phase pseudo-continuous arterial spin labeling. Magn Reson Med 2020; 83:815-829. [PMID: 31429999 PMCID: PMC6899553 DOI: 10.1002/mrm.27965] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 07/31/2019] [Accepted: 08/02/2019] [Indexed: 11/25/2022]
Abstract
PURPOSE Multi-phase PCASL has been proposed as a means to achieve accurate perfusion quantification that is robust to imperfect shim in the labeling plane. However, there exists a bias in the estimation process that is a function of noise in the data. In this work, this bias is characterized and then addressed in animal and human data. METHODS The proposed algorithm to overcome bias uses the initial biased voxel-wise estimate of phase tracking error to cluster regions with different off-resonance phase shifts, from which a high-SNR estimate of regional phase offset is derived. Simulations were used to predict the bias expected at typical SNR. Multi-phase PCASL in 3 rat strains (n = 21) at 9.4 T was considered, along with 20 human subjects previously imaged using ASL at 3 T. The algorithm was extended to include estimation of arterial blood flow velocity. RESULTS Based on simulations, a perfusion estimation bias of 6-8% was expected using 8-phase data at typical SNR. This bias was eliminated when a high-precision estimate of phase error was available. In the preclinical data, the bias-corrected measure of perfusion (107 ± 14 mL/100g/min) was lower than the standard analysis (116 ± 14 mL/100g/min), corresponding to a mean observed bias across strains of 8.0%. In the human data, bias correction resulted in a 15% decrease in the estimate of perfusion. CONCLUSIONS Using a retrospective algorithmic approach, it was possible to exploit common information found in multiple voxels within a whole region of the brain, offering superior SNR and thus overcoming the bias in perfusion quantification from multi-phase PCASL.
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Affiliation(s)
- Y. Msayib
- Department of Engineering ScienceInstitute of Biomedical EngineeringUniversity of OxfordOxfordUnited Kingdom
| | - M. Craig
- Department of Engineering ScienceInstitute of Biomedical EngineeringUniversity of OxfordOxfordUnited Kingdom
| | - M. A. Simard
- Department of OncologyCancer Research UK and Medical Research Council (CRUK/MRC) Oxford Institute for Radiation OncologyUniversity of OxfordOxfordUnited Kingdom
| | - J. R. Larkin
- Department of OncologyCancer Research UK and Medical Research Council (CRUK/MRC) Oxford Institute for Radiation OncologyUniversity of OxfordOxfordUnited Kingdom
| | | | - T. T. Liu
- Center for Functional MRIUniversity of CaliforniaSan DiegoCalifornia
| | - N. R. Sibson
- Department of OncologyCancer Research UK and Medical Research Council (CRUK/MRC) Oxford Institute for Radiation OncologyUniversity of OxfordOxfordUnited Kingdom
- Wellcome Centre for Integrative NeuroimagingFMRIBNuffield Department of Clinical NeurosciencesUniversity of OxfordOxfordUnited Kingdom
| | - T. W. Okell
- Wellcome Centre for Integrative NeuroimagingFMRIBNuffield Department of Clinical NeurosciencesUniversity of OxfordOxfordUnited Kingdom
| | - M. A. Chappell
- Department of Engineering ScienceInstitute of Biomedical EngineeringUniversity of OxfordOxfordUnited Kingdom
- Wellcome Centre for Integrative NeuroimagingFMRIBNuffield Department of Clinical NeurosciencesUniversity of OxfordOxfordUnited Kingdom
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Cassidy T, Craig M. Determinants of combination GM-CSF immunotherapy and oncolytic virotherapy success identified through in silico treatment personalization. PLoS Comput Biol 2019; 15:e1007495. [PMID: 31774808 PMCID: PMC6880985 DOI: 10.1371/journal.pcbi.1007495] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 10/20/2019] [Indexed: 12/15/2022] Open
Abstract
Oncolytic virotherapies, including the modified herpes simplex virus talimogene laherparepvec (T-VEC), have shown great promise as potent instigators of anti-tumour immune effects. The OPTiM trial, in particular, demonstrated the superior anti-cancer effects of T-VEC as compared to systemic immunotherapy treatment using exogenous administration of granulocyte-macrophage colony-stimulating factor (GM-CSF). Theoretically, a combined approach leveraging exogenous cytokine immunotherapy and oncolytic virotherapy would elicit an even greater immune response and improve patient outcomes. However, regimen scheduling of combination immunostimulation and T-VEC therapy has yet to be established. Here, we calibrate a computational biology model of sensitive and resistant tumour cells and immune interactions for implementation into an in silico clinical trial to test and individualize combination immuno- and virotherapy. By personalizing and optimizing combination oncolytic virotherapy and immunostimulatory therapy, we show improved simulated patient outcomes for individuals with late-stage melanoma. More crucially, through evaluation of individualized regimens, we identified determinants of combination GM-CSF and T-VEC therapy that can be translated into clinically-actionable dosing strategies without further personalization. Our results serve as a proof-of-concept for interdisciplinary approaches to determining combination therapy, and suggest promising avenues of investigation towards tailored combination immunotherapy/oncolytic virotherapy. The advent of biological therapies for anti-cancer treatment has had a significant impact on patient outcomes. Targeted xenobiotics, including oncolytic viruses, in combination with existing, more general, immunotherapies like exogenous cytokines show great promise for continuing to improve cancer care. However, determining optimal combination regimens can be difficult, given that testing proposed schedules would require large cohorts of patients enrolled in clinical trials. Fortunately, computational biology can help to address treatment scheduling while simultaneously helping to unravel the mechanisms driving therapeutic responses. In this work, we integrate a mathematical model of GM-CSF and talimogene laherparepvec (T-VEC) oncolytic virotherapy into a virtual clinical trial to optimize their administration in combination. Using this platform, we inferred a clinically-actionable combination schedule for patients with late-stage melanoma that significantly improved virtual patient outcome when compared to GM-CSF and T-VEC monotherapies, and a standard combination strategy. Our results outline a rational approach to therapy optimization with meaningful consequences for how we effectively design and implement clinical trials to maximize their success, and how we treat melanoma with combined immuno- and virotherapy.
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Affiliation(s)
- Tyler Cassidy
- Department of Mathematics and Statistics, McGill University, Montreal, Quebec, Canada
| | - Morgan Craig
- Département de mathématiques et de statistique, Université de Montréal, Montreal, Quebec, Canada.,Department of Physiology, McGill University, Montreal, Quebec, Canada
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Mullane KM, Morrison VA, Camacho LH, Arvin A, McNeil SA, Durrand J, Campbell B, Su SC, Chan ISF, Parrino J, Kaplan SS, Popmihajlov Z, Annunziato PW, Cerana S, Dictar MO, Bonvehi P, Tregnaghi JP, Fein L, Ashley D, Singh M, Hayes T, Playford G, Morrissey O, Thaler J, Kuehr T, Greil R, Pecherstorfer M, Duck L, Van Eygen K, Aoun M, De Prijck B, Franke FA, Barrios CHE, Mendes AVA, Serrano SV, Garcia RF, Moore F, Camargo JFC, Pires LA, Alves RS, Radinov A, Oreshkov K, Minchev V, Hubenova AI, Koynova T, Ivanov I, Rabotilova B, Minchev V, Petrov PA, Chilingirov P, Karanikolov S, Raynov J, Grimard D, McNeil S, Kumar D, Larratt LM, Weiss K, Delage R, Diaz-Mitoma FJ, Cano PO, Couture F, Carvajal P, Yepes A, Torres Ulloa R, Fardella P, Caglevic C, Rojas C, Orellana E, Gonzalez P, Acevedo A, Galvez KM, Gonzalez ME, Franco S, Restrepo JG, Rojas CA, Bonilla C, Florez LE, Ospina AV, Manneh R, Zorica R, Vrdoljak DV, Samarzija M, Petruzelka L, Vydra J, Mayer J, Cibula D, Prausova J, Paulson G, Ontaneda M, Palk K, Vahlberg A, Rooneem R, Galtier F, Postil D, Lucht F, Laine F, Launay O, Laurichesse H, Duval X, Cornely OA, Camerer B, Panse J, Zaiss M, Derigs HG, Menzel H, Verbeek M, Georgoulias V, Mavroudis D, Anagnostopoulos A, Terpos E, Cortes D, Umanzor J, Bejarano S, Galeano RW, Wong RSM, Hui P, Pedrazzoli P, Ruggeri L, Aversa F, Bosi A, Gentile G, Rambaldi A, Contu A, Marei L, Abbadi A, Hayajneh W, Kattan J, Farhat F, Chahine G, Rutkauskiene J, Marfil Rivera LJ, Lopez Chuken YA, Franco Villarreal H, Lopez Hernandez J, Blacklock H, Lopez RI, Alvarez R, Gomez AM, Quintana TS, Moreno Larrea MDC, Zorrilla SJ, Alarcon E, Samanez FCA, Caguioa PB, Tiangco BJ, Mora EM, Betancourt-Garcia RD, Hallman-Navarro D, Feliciano-Lopez LJ, Velez-Cortes HA, Cabanillas F, Ganea DE, Ciuleanu TE, Ghizdavescu DG, Miron L, Cebotaru CL, Cainap CI, Anghel R, Dvorkin MV, Gladkov OA, Fadeeva NV, Kuzmin AA, Lipatov ON, Zbarskaya II, Akhmetzyanov FS, Litvinov IV, Afanasyev BV, Cherenkova M, Lioznov D, Lisukov IA, Smirnova YA, Kolomietz S, Halawani H, Goh YT, Drgona L, Chudej J, Matejkova M, Reckova M, Rapoport BL, Szpak WM, Malan DR, Jonas N, Jung CW, Lee DG, Yoon SS, Lopez Jimenez J, Duran Martinez I, Rodriguez Moreno JF, Solano Vercet C, de la Camara R, Batlle Massana M, Yeh SP, Chen CY, Chou HH, Tsai CM, Chiu CH, Siritanaratkul N, Norasetthada L, Sriuranpong V, Seetalarom K, Akan H, Dane F, Ozcan MA, Ozsan GH, Kalayoglu Besisik SF, Cagatay A, Yalcin S, Peniket A, Mullan SR, Dakhil KM, Sivarajan K, Suh JJG, Sehgal A, Marquez F, Gomez EG, Mullane MR, Skinner WL, Behrens RJ, Trevarthe DR, Mazurczak MA, Lambiase EA, Vidal CA, Anac SY, Rodrigues GA, Baltz B, Boccia R, Wertheim MS, Holladay CS, Zenk D, Fusselman W, Wade III JL, Jaslowsk AJ, Keegan J, Robinson MO, Go RS, Farnen J, Amin B, Jurgens D, Risi GF, Beatty PG, Naqvi T, Parshad S, Hansen VL, Ahmed M, Steen PD, Badarinath S, Dekker A, Scouros MA, Young DE, Graydon Harker W, Kendall SD, Citron ML, Chedid S, Posada JG, Gupta MK, Rafiyath S, Buechler-Price J, Sreenivasappa S, Chay CH, Burke JM, Young SE, Mahmood A, Kugler JW, Gerstner G, Fuloria J, Belman ND, Geller R, Nieva J, Whittenberger BP, Wong BMY, Cescon TP, Abesada-Terk G, Guarino MJ, Zweibach A, Ibrahim EN, Takahashi G, Garrison MA, Mowat RB, Choi BS, Oliff IA, Singh J, Guter KA, Ayrons K, Rowland KM, Noga SJ, Rao SB, Columbie A, Nualart MT, Cecchi GR, Campos LT, Mohebtash M, Flores MR, Rothstein-Rubin R, O'Connor BM, Soori G, Knapp M, Miranda FG, Goodgame BW, Kassem M, Belani R, Sharma S, Ortiz T, Sonneborn HL, Markowitz AB, Wilbur D, Meiri E, Koo VS, Jhangiani HS, Wong L, Sanani S, Lawrence SJ, Jones CM, Murray C, Papageorgiou C, Gurtler JS, Ascensao JL, Seetalarom K, Venigalla ML, D'Andrea M, De Las Casas C, Haile DJ, Qazi FU, Santander JL, Thomas MR, Rao VP, Craig M, Garg RJ, Robles R, Lyons RM, Stegemoller RK, Goel S, Garg S, Lowry P, Lynch C, Lash B, Repka T, Baker J, Goueli BS, Campbell TC, Van Echo DA, Lee YJ, Reyes EA, Senecal FM, Donnelly G, Byeff P, Weiss R, Reid T, Roeland E, Goel A, Prow DM, Brandt DS, Kaplan HG, Payne JE, Boeckh MG, Rosen PJ, Mena RR, Khan R, Betts RF, Sharp SA, Morrison VA, Fitz-Patrick D, Congdon J, Erickson N, Abbasi R, Henderson S, Mehdi A, Wos EJ, Rehmus E, Beltzer L, Tamayo RA, Mahmood T, Reboli AC, Moore A, Brown JM, Cruz J, Quick DP, Potz JL, Kotz KW, Hutchins M, Chowhan NM, Devabhaktuni YD, Braly P, Berenguer RA, Shambaugh SC, O'Rourke TJ, Conkright WA, Winkler CF, Addo FEK, Duic JP, High KP, Kutner ME, Collins R, Carrizosa DR, Perry DJ, Kailath E, Rosen N, Sotolongo R, Shoham S, Chen T. Safety and efficacy of inactivated varicella zoster virus vaccine in immunocompromised patients with malignancies: a two-arm, randomised, double-blind, phase 3 trial. The Lancet Infectious Diseases 2019; 19:1001-1012. [DOI: 10.1016/s1473-3099(19)30310-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 05/02/2019] [Accepted: 05/03/2019] [Indexed: 12/25/2022]
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Cassidy T, Craig M, Humphries AR. Equivalences between age structured models and state dependent distributed delay differential equations. Math Biosci Eng 2019; 16:5419-5450. [PMID: 31499719 DOI: 10.3934/mbe.2019270] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
We use the McKendrick equation with variable ageing rate and randomly distributed mat-uration time to derive a state dependent distributed delay differential equation. We show that the resulting delay differential equation preserves non-negativity of initial conditions and we characterise local stability of equilibria. By specifying the distribution of maturation age, we recover state depen-dent discrete, uniform and gamma distributed delay differential equations. We show how to reduce the uniform case to a system of state dependent discrete delay equations and the gamma distributed case to a system of ordinary differential equations. To illustrate the benefits of these reductions, we convert previously published transit compartment models into equivalent distributed delay differential equations.
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Affiliation(s)
- Tyler Cassidy
- Department of Mathematics and Statistics, McGill University, 805 Sherbrooke Street West, Montréal, H3A 0B9, Canada
| | - Morgan Craig
- Département de mathématiques et de statistique, Université de Montréal, 2920 chemin de la Tour, Montréal, H3T 1J4, Canada
- Department of Physiology, McGill University, 3655 Promenade Sir-William-Osler, Montréal, H3G 1Y6, Canada
| | - Antony R Humphries
- Department of Mathematics and Statistics, McGill University, 805 Sherbrooke Street West, Montréal, H3A 0B9, Canada
- Department of Physiology, McGill University, 3655 Promenade Sir-William-Osler, Montréal, H3G 1Y6, Canada
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Pillai N, Craig M, Dokoumetzidis A, Schwartz SL, Bies R, Freedman I. Chaos synchronization and Nelder-Mead search for parameter estimation in nonlinear pharmacological systems: Estimating tumor antigenicity in a model of immunotherapy. Prog Biophys Mol Biol 2018; 139:23-30. [PMID: 29928905 DOI: 10.1016/j.pbiomolbio.2018.06.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 06/11/2018] [Accepted: 06/13/2018] [Indexed: 11/29/2022]
Abstract
In mathematical pharmacology, models are constructed to confer a robust method for optimizing treatment. The predictive capability of pharmacological models depends heavily on the ability to track the system and to accurately determine parameters with reference to the sensitivity in projected outcomes. To closely track chaotic systems, one may choose to apply chaos synchronization. An advantageous byproduct of this methodology is the ability to quantify model parameters. In this paper, we illustrate the use of chaos synchronization combined with Nelder-Mead search to estimate parameters of the well-known Kirschner-Panetta model of IL-2 immunotherapy from noisy data. Chaos synchronization with Nelder-Mead search is shown to provide more accurate and reliable estimates than Nelder-Mead search based on an extended least squares (ELS) objective function. Our results underline the strength of this approach to parameter estimation and provide a broader framework of parameter identification for nonlinear models in pharmacology.
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Affiliation(s)
- Nikhil Pillai
- University at Buffalo, State University of New York, USA.
| | | | | | | | - Robert Bies
- University at Buffalo, State University of New York, USA.
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Yourshaw J, Armstrong C, Mishra P, Steinberg D, Ramu B, Craig M, Van Bakel A, Tedford R, Houston B. Effects of Percutaneous LVAD Support on Right Ventricular Load and Adaptation Acutely and Over Time. J Heart Lung Transplant 2018. [DOI: 10.1016/j.healun.2018.01.096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Craig M. Towards Quantitative Systems Pharmacology Models of Chemotherapy-Induced Neutropenia. CPT Pharmacometrics Syst Pharmacol 2017; 6:293-304. [PMID: 28418603 PMCID: PMC5445232 DOI: 10.1002/psp4.12191] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Revised: 02/21/2017] [Accepted: 02/21/2017] [Indexed: 12/22/2022] Open
Abstract
Neutropenia is a serious toxic complication of chemotherapeutic treatment. For years, mathematical models have been developed to better predict hematological outcomes during chemotherapy in both the traditional pharmaceutical sciences and mathematical biology disciplines. An increasing number of quantitative systems pharmacology (QSP) models that combine systems approaches, physiology, and pharmacokinetics/pharmacodynamics have been successfully developed. Here, I detail the shift towards QSP efforts, emphasizing the importance of incorporating systems-level physiological considerations in pharmacometrics.
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Affiliation(s)
- M Craig
- Program for Evolutionary Dynamics, Harvard UniversityCambridgeMassachusettsUSA
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Affiliation(s)
- M Craig
- Dalhousie Medicine New Brunswick, Saint John, New Brunswick E2L 4L5, Canada
| | - W Hill
- Institute of Biomedical Engineering, University of New Brunswick, Fredericton, New Brunswick E3B5A3, Canada
| | - K Englehart
- Institute of Biomedical Engineering, University of New Brunswick, Fredericton, New Brunswick E3B5A3, Canada
| | - A Adisesh
- Dalhousie Medicine New Brunswick, Saint John, New Brunswick E2L 4L5, Canada
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Affiliation(s)
- Morgan Craig
- Program for Evolutionary Dynamics, Harvard University, Cambridge, MA; Centre for Applied Mathematics in Bioscience and Medicine, Montreal, QC, Canada
| | - Antony R Humphries
- Centre for Applied Mathematics in Bioscience and Medicine, Montreal, QC, Canada; Department of Mathematics and Statistics, McGill University, Montreal, QC, Canada; and
| | - Michael C Mackey
- Centre for Applied Mathematics in Bioscience and Medicine, Montreal, QC, Canada; Department of Physiology, McGill University, Montreal, QC, Canada
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Craig M, Humphries AR, Mackey MC. A Mathematical Model of Granulopoiesis Incorporating the Negative Feedback Dynamics and Kinetics of G-CSF/Neutrophil Binding and Internalization. Bull Math Biol 2016; 78:2304-2357. [PMID: 27324993 DOI: 10.1007/s11538-016-0179-8] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 05/19/2016] [Indexed: 11/24/2022]
Abstract
We develop a physiological model of granulopoiesis which includes explicit modelling of the kinetics of the cytokine granulocyte colony-stimulating factor (G-CSF) incorporating both the freely circulating concentration and the concentration of the cytokine bound to mature neutrophils. G-CSF concentrations are used to directly regulate neutrophil production, with the rate of differentiation of stem cells to neutrophil precursors, the effective proliferation rate in mitosis, the maturation time, and the release rate from the mature marrow reservoir into circulation all dependent on the level of G-CSF in the system. The dependence of the maturation time on the cytokine concentration introduces a state-dependent delay into our differential equation model, and we show how this is derived from an age-structured partial differential equation model of the mitosis and maturation and also detail the derivation of the rest of our model. The model and its estimated parameters are shown to successfully predict the neutrophil and G-CSF responses to a variety of treatment scenarios, including the combined administration of chemotherapy and exogenous G-CSF. This concomitant treatment was reproduced without any additional fitting to characterize drug-drug interactions.
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Affiliation(s)
- M Craig
- Faculté de Pharmacie, Université de Montréal, Montréal, QC, H3T 1J4, Canada.
- Program for Evolutionary Dynamics, Harvard University, Cambridge, MA, 02138, USA.
| | - A R Humphries
- Department of Mathematics and Statistics, McGill University, Montréal, QC, H3A 0B9, Canada
| | - M C Mackey
- Departments of Mathematics, Physics and Physiology, McGill University, Montréal, QC, H3G 1Y6, Canada
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Veasey T, Strout S, Rieger K, Floroff C, Brisco M, Cook J, Toole J, Craig M, VanBakel A, Heyward D, Uber W, Meadows H. Evaluation of Anticoagulation and Non-Surgical Major Bleeding in Recipients of Continuous-Flow Left Ventricular Assist Devices. J Heart Lung Transplant 2016. [DOI: 10.1016/j.healun.2016.01.336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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Craig M, González-Sales M, Li J, Nekka F. Approaching Pharmacometrics as a Paleontologist Would: Recovering the Links Between Drugs and the Body Through Reconstruction. CPT Pharmacometrics Syst Pharmacol 2016; 5:158-60. [PMID: 27069779 PMCID: PMC4809624 DOI: 10.1002/psp4.12069] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Revised: 01/08/2016] [Accepted: 02/16/2016] [Indexed: 11/08/2022]
Abstract
Our knowledge of dinosaurs comes primarily from the fossil record. Notwithstanding the condition of these vestiges, paleontologists reconstruct early reptilian life by comparison to previously discovered specimens. When relics are missing, reasonable deductions are used to fill in the gaps.
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Affiliation(s)
- M Craig
- Faculté de Pharmacie Université de Montréal Montréal QC Canada; Centre for Applied Mathematics in Bioscience and Medicine (CAMBAM) McGill University Montreal Quebec Canada
| | - M González-Sales
- Faculté de Pharmacie Université de Montréal Montréal QC Canada; inVentiv Health Clinical Montréal Quebec Canada
| | - J Li
- Faculté de Pharmacie Université de Montréal Montréal QC Canada; Centre for Applied Mathematics in Bioscience and Medicine (CAMBAM) McGill University Montreal Quebec Canada
| | - F Nekka
- Faculté de Pharmacie Université de Montréal Montréal QC Canada; Centre for Applied Mathematics in Bioscience and Medicine (CAMBAM) McGill University Montreal Quebec Canada
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Craig M, González-Sales M, Li J, Nekka F. Impact of Pharmacokinetic Variability on a Mechanistic Physiological Pharmacokinetic/Pharmacodynamic Model: A Case Study of Neutrophil Development, PM00104, and Filgrastim. Springer Proceedings in Mathematics & Statistics 2016. [DOI: 10.1007/978-3-319-31323-8_6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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Craig M, Humphries AR, Nekka F, Bélair J, Li J, Mackey MC. Neutrophil dynamics during concurrent chemotherapy and G-CSF administration: Mathematical modelling guides dose optimisation to minimise neutropenia. J Theor Biol 2015; 385:77-89. [PMID: 26343861 DOI: 10.1016/j.jtbi.2015.08.015] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Revised: 06/10/2015] [Accepted: 08/20/2015] [Indexed: 11/18/2022]
Abstract
The choice of chemotherapy regimens is often constrained by the patient's tolerance to the side effects of chemotherapeutic agents. This dose-limiting issue is a major concern in dose regimen design, which is typically focused on maximising drug benefits. Chemotherapy-induced neutropenia is one of the most prevalent toxic effects patients experience and frequently threatens the efficient use of chemotherapy. In response, granulocyte colony-stimulating factor (G-CSF) is co-administered during chemotherapy to stimulate neutrophil production, increase neutrophil counts, and hopefully avoid neutropenia. Its clinical use is, however, largely dictated by trial and error processes. Based on up-to-date knowledge and rational considerations, we develop a physiologically realistic model to mathematically characterise the neutrophil production in the bone marrow which we then integrate with pharmacokinetic and pharmacodynamic (PKPD) models of a chemotherapeutic agent and an exogenous form of G-CSF (recombinant human G-CSF, or rhG-CSF). In this work, model parameters represent the average values for a general patient and are extracted from the literature or estimated from available data. The dose effect predicted by the model is confirmed through previously published data. Using our model, we were able to determine clinically relevant dosing regimens that advantageously reduce the number of rhG-CSF administrations compared to original studies while significantly improving the neutropenia status. More particularly, we determine that it could be beneficial to delay the first administration of rhG-CSF to day seven post-chemotherapy and reduce the number of administrations from ten to three or four for a patient undergoing 14-day periodic chemotherapy.
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Affiliation(s)
- Morgan Craig
- Faculté de Pharmacie, Université de Montréal, Montréal, QC, Canada H3C 3J7; Centre for Applied Mathematics in Bioscience and Medicine (CAMBAM), McGill University, Montreal, QC, Canada H3G 1Y6.
| | - Antony R Humphries
- Department of Mathematics and Statistics, McGill University, Montreal, QC, Canada H3A 0B9; Centre for Applied Mathematics in Bioscience and Medicine (CAMBAM), McGill University, Montreal, QC, Canada H3G 1Y6; Centre de recherches mathématiques, Université de Montréal, Montréal, QC, Canada H3C 3J7.
| | - Fahima Nekka
- Centre for Applied Mathematics in Bioscience and Medicine (CAMBAM), McGill University, Montreal, QC, Canada H3G 1Y6; Centre de recherches mathématiques, Université de Montréal, Montréal, QC, Canada H3C 3J7.
| | - Jacques Bélair
- Département de mathématiques et de statistique, Université de Montréal, Montréal, QC, Canada H3C 3J7; Centre for Applied Mathematics in Bioscience and Medicine (CAMBAM), McGill University, Montreal, QC, Canada H3G 1Y6; Centre de recherches mathématiques, Université de Montréal, Montréal, QC, Canada H3C 3J7.
| | - Jun Li
- Faculté de Pharmacie, Université de Montréal, Montréal, QC, Canada H3C 3J7; Centre for Applied Mathematics in Bioscience and Medicine (CAMBAM), McGill University, Montreal, QC, Canada H3G 1Y6; Centre de recherches mathématiques, Université de Montréal, Montréal, QC, Canada H3C 3J7.
| | - Michael C Mackey
- Department of Mathematics and Statistics, McGill University, Montreal, QC, Canada H3A 0B9; Centre for Applied Mathematics in Bioscience and Medicine (CAMBAM), McGill University, Montreal, QC, Canada H3G 1Y6; Departments of Physiology and Physics, McGill University, Montreal, QC, Canada H3G 1Y6.
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Affiliation(s)
- Marta Di Forti
- Department of Social Genetic and Developmental Psychiatry, Institute of Psychiatry, Kings College London.
| | - Evangelos Vassos
- Department of Social Genetic and Developmental Psychiatry, Institute of Psychiatry, Kings College London
| | - Michael Lynskey
- Department of Addiction, Institute of Psychiatry, Kings College London
| | - Morgan Craig
- Department of Health Services and Public Health, Institute of Psychiatry, Kings College London
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Grant EN, Tao W, Craig M, McIntire D, Leveno K. Neuraxial analgesia effects on labour progression: facts, fallacies, uncertainties and the future. BJOG 2014; 122:288-93. [PMID: 25088476 DOI: 10.1111/1471-0528.12966] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/12/2014] [Indexed: 01/31/2023]
Abstract
Approximately 60% of women who labour in the USA receive some form of neuraxial analgesia, but concerns have been raised regarding whether it negatively impacts the labour and delivery process. In this review, we attempt to clarify what has been established as truths, falsities and uncertainties regarding the effects of this form of pain relief on labour progression, negative and/or positive. Additionally, although the term 'epidural' has become synonymous with neuraxial analgesia, we discuss two other techniques, combined spinal-epidural and continuous spinal analgesia, that are gaining popularity, as well as their effects on labour progression.
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Affiliation(s)
- E N Grant
- Department of Anesthesiology and Pain Management, University of Texas Southwestern Medical Center, Dallas, TX, USA
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Tedd KM, Coxon CE, Misstear BDR, Daly D, Craig M, Mannix A, Williams NHH. An integrated pressure and pathway approach to the spatial analysis of groundwater nitrate: a case study from the southeast of Ireland. Sci Total Environ 2014; 476-477:460-476. [PMID: 24486501 DOI: 10.1016/j.scitotenv.2013.12.085] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Revised: 12/18/2013] [Accepted: 12/18/2013] [Indexed: 06/03/2023]
Abstract
Excess nitrogen in soil, aquatic and atmospheric environments is an escalating global problem. Eutrophication is the principal threat to surface water quality in the Republic of Ireland. European Union Water Framework Directive (2000/60/EC) water quality status assessments found that 16% of Irish groundwater bodies were 'at risk' of poor status due to the potential deterioration of associated estuarine and coastal water quality by nitrate from groundwater. This paper presents a methodology for evaluating pressure and pathway parameters affecting the spatial distribution of groundwater nitrate, investigated at a regional scale using existing national spatial datasets. The potential for nitrate transfer to groundwater was rated based on the introduced concepts of Pressure Loading and Pathway Connectivity Rating, each based on a combination of selected pressure and pathway parameters respectively. In the region studied, the South Eastern River Basin District of Ireland, this methodology identified that pathway parameters were more important than pressure parameters in understanding the spatial distribution of groundwater nitrate. Statistical analyses supported these findings and further demonstrated that the proportion of poorly drained soils, arable land, karstic flow regimes, regionally important bedrock aquifers and high vulnerability groundwater within the zones of contribution of the monitoring points are statistically significantly related to groundwater nitrate concentrations. Soil type was found to be the most important parameter. Analysis of variance showed that a number of the pressure and pathway parameters are interrelated. The parameters identified by the presented methodology may provide useful insights into the best way to manage and mitigate the influence of nitrate contamination of groundwater in this region. It is suggested that the identification of critical source areas based on the identified parameters would be an appropriate management tool, enabling planning and enforcement resources to be focussed on areas which will yield most benefit.
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Affiliation(s)
- K M Tedd
- Department of Geology, School of Natural Sciences, Trinity College Dublin, Dublin 2, Ireland; Hydrometric & Groundwater Section, Environmental Protection Agency, Richview, Dublin 14, Ireland
| | - C E Coxon
- Department of Geology, School of Natural Sciences, Trinity College Dublin, Dublin 2, Ireland
| | - B D R Misstear
- Department of Civil, Structural and Environmental Engineering, Trinity College Dublin, Dublin 2, Ireland
| | - D Daly
- Hydrometric & Groundwater Section, Environmental Protection Agency, Richview, Dublin 14, Ireland
| | - M Craig
- Hydrometric & Groundwater Section, Environmental Protection Agency, Richview, Dublin 14, Ireland
| | - A Mannix
- Hydrometric & Groundwater Section, Environmental Protection Agency, Richview, Dublin 14, Ireland
| | - N H Hunter Williams
- Groundwater Section, Geological Survey of Ireland, Haddington Road, Dublin 4, Ireland
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Cumpston A, Craig M, Hamadani M, Abraham J, Hobbs GR, Sarwari AR. Extended follow-up of an antibiotic cycling program for the management of febrile neutropenia in a hematologic malignancy and hematopoietic cell transplantation unit. Transpl Infect Dis 2012; 15:142-9. [PMID: 23279656 DOI: 10.1111/tid.12035] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2012] [Revised: 06/08/2012] [Accepted: 08/09/2012] [Indexed: 11/30/2022]
Abstract
BACKGROUND Febrile neutropenia is a common complication during treatment of hematological malignancies and hematopoietic cell transplantation. Empiric antibiotic therapy in this setting, while standard of care, commonly leads to microbial resistance. We have previously shown that cycling antibiotics in this patient population is feasible. This report provides long-term follow-up of cycling antibiotics in this patient population. METHODS In a prospective cohort of hematological malignancy patients with neutropenic fever, we sought to evaluate the role of empiric antibiotic cycling in preventing antibiotic resistance. Antibiotic cycling was initiated in March 2002 and, until June 2005, antibiotics were cycled every 8 months (Cycling Period A). From July 2005 to December 2009, antibiotics were cycled every 3 months (Cycling Period B). The rates of bacteremia, resistance, and complications were compared to a retrospective cohort (Pre-cycling Period). RESULTS The rate of gram-negative bacteremia decreased when compared to Cycling Periods A and B (5.3 vs. 2.1 and 3.3 episodes/1000 patient-days, respectively, P < 0.0001), most likely owing to implementation of quinolone prophylaxis. The resistance profile of the gram-negative organisms isolated remained stable over the 3 time periods, with the exception of an increase in quinolone resistance during the cycling periods. Gram-positive bacteremia rates remained stable, but vancomycin-resistant Enterococcus (VRE) increased significantly (0.1 vs. 1.0 and 1.6 episodes/1000 patient-days, respectively, P = 0.005) during cycling periods. Mortality rates were comparable. CONCLUSIONS Antibiotic cycling for neutropenic fever was effectively implemented and followed over an extended time period. Gram-negative resistance remained stable, but there is some concern for selection of resistant gram-positive bacteria, specifically VRE. Although antibiotic cycling did not seem to cause resistance in our study, further study is necessary to clarify the effect of cycling on antibiotic resistance, patient outcomes, and hospital cost.
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Affiliation(s)
- A Cumpston
- Pharmacy Department, West Virginia University Healthcare, Morgantown, West Virginia 26506, USA.
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Srinivasan A, Craig M, Cardo D. The Power of Policy Change, Federal Collaboration, and State Coordination in Healthcare-Associated Infection Prevention. Clin Infect Dis 2012; 55:426-31. [DOI: 10.1093/cid/cis407] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
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Rogers JE, Cumpston A, Newton M, Craig M. Onset and complications of varicella zoster reactivation in the autologous hematopoietic cell transplant population. Transpl Infect Dis 2011; 13:480-4. [PMID: 21615848 DOI: 10.1111/j.1399-3062.2011.00655.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
BACKGROUND Varicella zoster virus (VZV) infections are a common complication in patients receiving autologous or allogeneic hematopoietic cell transplant (HCT). Recent guideline revisions suggest extending VZV prophylaxis to 1 year after autologous HCT. We retrospectively evaluated reactivation at our center, before implementation of extended acyclovir prophylaxis, to determine onset and outcome in the autologous HCT population. METHODS Inclusion criteria consisted of adult patients who received an autologous HCT with documentation for at least 1 year post transplant. Those excluded from review were patients who received acyclovir prophylaxis for >30 days post transplant or subsequently received an allogeneic transplant within 1 year. For patients in whom reactivation occurred, the severity of infection, the timing of onset, treatment of the reactivation, and any complications were recorded. RESULTS In the final analysis, 56 patients were assessed. Reactivation of zoster occurred in 16% of recipients with a median onset of 4.5 months post transplant. Complications that were observed include postherpetic neuralgia, severe pain, scarring, and motor weakness. Two patients required hospitalization for treatment, with 1 patient requiring 6 months of rehabilitation for motor weakness following the infection. CONCLUSIONS Our study revealed a 16% incidence of VZV reactivation in our autologous HCT population. The onset of these occurrences ranged from 2 to 10 months post transplant, with significant VZV-associated complications. We consider VZV reactivation a serious concern in the autologous transplant setting, requiring extended prophylaxis.
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Affiliation(s)
- J E Rogers
- Department of Pharmacy, MD Anderson Cancer Center, University of Texas, Houston, Texas, USA
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Faderl S, Wetzler M, Rizzieri D, Schiller GJ, Jagasia MH, Stuart RK, Ganguly S, Avigan D, Craig M, Collins R, Maris MB, Kovacsovics T, Goldberg S, Seiter K, Hari P, Ravandi F, Wang ES, Eckert S, Huebner D, Kantarjian H. Clofarabine plus cytarabine compared to cytarabine alone in older patients with relapsed or refractory (R/R) acute myelogenous leukemia (AML): Results from the phase III CLASSIC 1 trial. J Clin Oncol 2011. [DOI: 10.1200/jco.2011.29.15_suppl.6503] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Awan FT, Osman S, Kochuparambil ST, Gibson L, Remick SC, Abraham J, Craig M, Jillella A, Hamadani M. Impact of response to thalidomide-, lenalidomide- or bortezomib- containing induction therapy on the outcomes of multiple myeloma patients undergoing autologous transplantation. Bone Marrow Transplant 2011; 47:146-8. [DOI: 10.1038/bmt.2011.18] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Kanate A, Chaudhary L, Cumpston A, Leadmon S, Bunner P, Bulian D, Gibson L, Tse W, Abraham J, Remick S, Craig M, Hamadani M. High Rates of Non-Relapse Mortality and Graft-Versus-Host Disease in Patient Undergoing Allogeneic Stem Cell Transplantation (ASCT) Following Non-Myeloablative (NMA) Conditioning With TLI/ATG. Biol Blood Marrow Transplant 2011. [DOI: 10.1016/j.bbmt.2010.12.476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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