Development of Synthetic Patient Populations and In Silico Clinical Trials

Drug development, which includes clinical trials, is a lengthy and expensive process that could significantly benefit from predictive modeling and in silico testing. Additionally, current treatments were designed based on the average patient using the “one size fits all” protocol. Therefore, they can be effective on some patients but not for others. There is an urgent need to replace such generalized approaches with personalized and predictive strategies that capture and analyze human diversity and variation at a resolution sufficient to identify and clinically validate personalized treatment paradigms. Utilization of heterogenous datasets, such as Electronic Health Records (EHRs), to build synthetic populations of patients and personalized, predictive models of response to therapy holds enormous promise in precipitating a revolution in precision medicine for IBD. In silico trials can be designed to include multi-modal data sources, including clinical trial data at the individual and aggregated levels, pre-clinical data from animal studies, as well as data from EHR. In silico clinical trials can help inform the design of clinical trials and make prediction at the population and individual level to increase the chances of success. This chapter discusses pioneering work on the use of in silico clinical trials to accelerate the development of new drugs.

[1]  H. Hotelling Analysis of a complex of statistical variables into principal components. , 1933 .

[2]  David S. Wishart,et al.  DrugBank 4.0: shedding new light on drug metabolism , 2013, Nucleic Acids Res..

[3]  G. Clermont,et al.  In silico design of clinical trials: A method coming of age , 2004, Critical care medicine.

[4]  Sean C. Bendall,et al.  Cytometry by time-of-flight shows combinatorial cytokine expression and virus-specific cell niches within a continuum of CD8+ T cell phenotypes. , 2012, Immunity.

[5]  Miquel Porta,et al.  A Dictionary of Epidemiology , 2008 .

[6]  Marylyn D. Ritchie,et al.  Distribution and clinical impact of functional variants in 50,726 whole-exome sequences from the DiscovEHR study , 2016, Science.

[7]  S. Piantadosi Clinical Trials : A Methodologic Perspective , 2005 .

[8]  H. Burger,et al.  Are we drawing the right conclusions from randomised placebo-controlled trials? A post-hoc analysis of data from a randomised controlled trial , 2009, BMC medical research methodology.

[9]  R. W. Hansen,et al.  Journal of Health Economics , 2016 .

[10]  Michael B. Yaffe,et al.  Data-driven modelling of signal-transduction networks , 2006, Nature Reviews Molecular Cell Biology.

[11]  Lucia Russo,et al.  Mathematical modeling of infectious disease dynamics , 2013, Virulence.

[12]  Danh V. Nguyen,et al.  Tumor classification by partial least squares using microarray gene expression data , 2002, Bioinform..

[13]  Ahmad Haidar,et al.  Stochastic Virtual Population of Subjects With Type 1 Diabetes for the Assessment of Closed-Loop Glucose Controllers , 2013, IEEE Transactions on Biomedical Engineering.

[14]  Jean-Marie Aerts,et al.  From data patterns to mechanistic models in acute critical illness. , 2014, Journal of critical care.

[15]  Patrick Royston,et al.  Multiple imputation using chained equations: Issues and guidance for practice , 2011, Statistics in medicine.

[16]  J. Bassaganya-Riera,et al.  Computational modeling of heterogeneity and function of CD4+ T cells , 2014, Front. Cell Dev. Biol..

[17]  Josep Bassaganya-Riera,et al.  Modeling new immunoregulatory therapeutics as antimicrobial alternatives for treating Clostridium difficile infection , 2017, Artif. Intell. Medicine.

[18]  Ziv Bar-Joseph,et al.  SMARTS: reconstructing disease response networks from multiple individuals using time series gene expression data , 2015, Bioinform..

[19]  M. Marathe,et al.  Predictive Computational Modeling of the Mucosal Immune Responses during Helicobacter pylori Infection , 2013, PloS one.

[20]  Marylyn D. Ritchie,et al.  Genetic identification of familial hypercholesterolemia within a single U.S. health care system , 2016, Science.

[21]  J C Gertrudes,et al.  Machine learning techniques and drug design. , 2012, Current medicinal chemistry.

[22]  Raquel Hontecillas,et al.  Phase III Placebo-Controlled, Randomized Clinical Trial With Synthetic Crohn's Disease Patients to Evaluate Treatment Response , 2016 .

[23]  T. Deisboeck,et al.  Development of a three-dimensional multiscale agent-based tumor model: simulating gene-protein interaction profiles, cell phenotypes and multicellular patterns in brain cancer. , 2006, Journal of theoretical biology.

[24]  Raquel Hontecillas,et al.  Model of colonic inflammation: immune modulatory mechanisms in inflammatory bowel disease. , 2010, Journal of theoretical biology.

[25]  Michael Y. Galperin,et al.  The 2016 database issue of Nucleic Acids Research and an updated molecular biology database collection , 2015, Nucleic Acids Res..

[26]  B. Wells,et al.  Strategies for Handling Missing Data in Electronic Health Record Derived Data , 2013, EGEMS.

[27]  A. Alexandrov,et al.  Novel Screening Tool for Stroke Using Artificial Neural Network , 2017, Stroke.

[28]  Feilim Mac Gabhann,et al.  Molecular mechanism matters: Benefits of mechanistic computational models for drug development. , 2015, Pharmacological research.

[29]  J. Bassaganya-Riera,et al.  Modeling the Role of Lanthionine Synthetase C-Like 2 (LANCL2) in the Modulation of Immune Responses to Helicobacter pylori Infection , 2016, PloS one.

[30]  Marco Viceconti,et al.  In silico clinical trials: how computer simulation will transform the biomedical industry , 2016 .

[31]  Gilles Clermont,et al.  A Patient-Specific in silico Model of Inflammation and Healing Tested in Acute Vocal Fold Injury , 2008, PloS one.

[32]  Gang Fu,et al.  PubChem Substance and Compound databases , 2015, Nucleic Acids Res..

[33]  Jason A. Papin,et al.  Mechanistic systems modeling to guide drug discovery and development. , 2013, Drug discovery today.

[34]  D Polhamus,et al.  The future is now: Model‐based clinical trial design for Alzheimer's disease , 2015, Clinical pharmacology and therapeutics.

[35]  Stephanie Forrest,et al.  Infect Recognize Destroy , 1996 .

[36]  D. DeMets,et al.  Fundamentals of Clinical Trials , 1982 .

[37]  Miguel Rocha,et al.  Modeling formalisms in Systems Biology , 2011, AMB Express.

[38]  Chien-Chang Lee,et al.  Comparison of clinical manifestations and outcome of community-acquired bloodstream infections among the oldest old, elderly, and adult patients. , 2007 .

[39]  Vijay S. Pande,et al.  Massively Multitask Networks for Drug Discovery , 2015, ArXiv.

[40]  G. An In silico experiments of existing and hypothetical cytokine-directed clinical trials using agent-based modeling* , 2004, Critical care medicine.

[41]  R J Allen,et al.  Efficient Generation and Selection of Virtual Populations in Quantitative Systems Pharmacology Models , 2015, bioRxiv.

[42]  Fergal P. Casey,et al.  Alternate virtual populations elucidate the type I interferon signature predictive of the response to rituximab in rheumatoid arthritis , 2013, BMC Bioinformatics.

[43]  Y. Vodovotz,et al.  Trauma in silico: Individual-specific mathematical models and virtual clinical populations , 2015, Science Translational Medicine.

[44]  Yongguo Mei,et al.  Supervised learning methods in modeling of CD4+ T cell heterogeneity , 2015, BioData Mining.

[45]  Gary An,et al.  In silico augmentation of the drug development pipeline: examples from the study of acute inflammation , 2011, Drug development research.

[46]  Jose L. Segovia-Juarez,et al.  Identifying control mechanisms of granuloma formation during M. tuberculosis infection using an agent-based model. , 2004, Journal of theoretical biology.

[47]  T. Jensen,et al.  Randomised Controlled Trials May Underestimate Drug Effects: Balanced Placebo Trial Design , 2014, PloS one.

[48]  Mark Last,et al.  Differentiation between viral and bacterial acute infections using chemiluminescent signatures of circulating phagocytes. , 2011, Analytical chemistry.