Discovery of a low order drug-cell response surface for applications in personalized medicine

The cell is a complex system involving numerous components, which may often interact in a non-linear dynamic manner. Diseases at the cellular level are thus likely to involve multiple cellular constituents and pathways. As some drugs, or drug combinations, may act synergistically on these multiple pathways, they might be more effective than the respective single target agents. Optimizing a drug mixture for a given disease in a particular patient is particularly challenging due to both the difficulty in the selection of the drug mixture components to start out with, and the all-important doses of these drugs to be applied. For n concentrations of m drugs, in principle, n(m) combinations will have to be tested. As this may lead to a costly and time-consuming investigation for each individual patient, we have developed a Feedback System Control (FSC) technique which can rapidly select the optimal drug-dose combination from the often millions of possible combinations. By testing this FSC technique in a number of experimental systems representing different disease states, we found that the response of cells to multiple drugs is well described by a low order, rather smooth, drug-mixture-input/drug-effect-output multidimensional surface. The main consequences of this are that optimal drug combinations can be found in a surprisingly small number of tests, and that translation from in vitro to in vivo is simplified. This points to the possibility of personalized optimal drug mixtures in the near future. This unexpectedly simple input-output relationship may also lead to a simple solution for handling the issue of human diversity in cancer therapeutics.

[1]  Peter Imming,et al.  Drugs, their targets and the nature and number of drug targets , 2007, Nature Reviews Drug Discovery.

[2]  E. Parati,et al.  Isolation and Cloning of Multipotential Stem Cells from the Embryonic Human CNS and Establishment of Transplantable Human Neural Stem Cell Lines by Epigenetic Stimulation , 1999, Experimental Neurology.

[3]  Chih-Ming Ho,et al.  Cascade search for HSV-1 combinatorial drugs with high antiviral efficacy and low toxicity , 2012, International journal of nanomedicine.

[4]  D. V. Steward,et al.  The design structure system: A method for managing the design of complex systems , 1981, IEEE Transactions on Engineering Management.

[5]  S. Morrison,et al.  Heterogeneity in Cancer: Cancer Stem Cells versus Clonal Evolution , 2009, Cell.

[6]  S. Fields,et al.  A novel genetic system to detect protein–protein interactions , 1989, Nature.

[7]  J. Lupski,et al.  The complete genome of an individual by massively parallel DNA sequencing , 2008, Nature.

[8]  Chih-Ming Ho,et al.  Optimizing Combinations of Flavonoids Deriving from Astragali Radix in Activating the Regulatory Element of Erythropoietin by a Feedback System Control Scheme , 2013, Evidence-based complementary and alternative medicine : eCAM.

[9]  C. S. Allardyce,et al.  [Ru(η6-p-cymene)Cl2(pta)] (pta = 1,3,5-triaza-7-phosphatricyclo- [3.3.1.1]decane): a water soluble compound that exhibits pH dependent DNA binding providing selectivity for diseased cells , 2001 .

[10]  Qunyuan Xu,et al.  Long-term expansion of human neural progenitor cells by epigenetic stimulation in vitro , 2005, Neuroscience Research.

[11]  Michael E Phelps,et al.  Systems Biology and New Technologies Enable Predictive and Preventative Medicine , 2004, Science.

[12]  Erik De Clercq,et al.  Antiviral drugs in current clinical use. , 2004 .

[13]  U. Alon Biological Networks: The Tinkerer as an Engineer , 2003, Science.

[14]  R. Sun,et al.  Closed-loop control of cellular functions using combinatory drugs guided by a stochastic search algorithm , 2008, Proceedings of the National Academy of Sciences.

[15]  Rainer Breitling,et al.  What is Systems Biology? , 2010, Front. Physiology.

[16]  Xianting Ding,et al.  Guiding the osteogenic fate of mouse and human mesenchymal stem cells through feedback system control , 2013, Scientific Reports.

[17]  Weng Kee Wong,et al.  Application of fractional factorial designs to study drug combinations , 2013, Statistics in medicine.

[18]  Jeff S. Shamma,et al.  Systematic quantitative characterization of cellular responses induced by multiple signals , 2011, BMC Systems Biology.

[19]  Francesca Aloisi,et al.  Chemokines and Glial Cells: A Complex Network in the Central Nervous System , 2004, Neurochemical Research.

[20]  E. Lemarié,et al.  A Phase II Study of Navelbine (Vinorelbine) in the Treatment of Non‐Small‐Cell Lung Cancer , 1991, American journal of clinical oncology.

[21]  Chih-Ming Ho,et al.  An optimized small molecule inhibitor cocktail supports long-term maintenance of human embryonic stem cells. , 2011, Nature communications.

[22]  Y. Z. Chen,et al.  Therapeutic Targets: Progress of Their Exploration and Investigation of Their Characteristics , 2006, Pharmacological Reviews.

[23]  J Chang-Claude,et al.  Genetic heterogeneity and penetrance analysis of the BRCA1 and BRCA2 genes in breast cancer families. The Breast Cancer Linkage Consortium. , 1998, American journal of human genetics.

[24]  N. Stoecklein,et al.  Genetic heterogeneity of single disseminated tumour cells in minimal residual cancer , 2002, The Lancet.

[25]  R. Steinman,et al.  The dendritic cell system and its role in immunogenicity. , 1991, Annual review of immunology.

[26]  Jian Yang,et al.  Use of Fractional Factorial Designs in Antiviral Drug Studies , 2013, Qual. Reliab. Eng. Int..

[27]  A. Tarakanova,et al.  Molecular modeling of protein materials: case study of elastin , 2013 .

[28]  P. Sorger,et al.  Systems biology and combination therapy in the quest for clinical efficacy , 2006, Nature chemical biology.