2007 Progress Report - Executive Summary
Medication empowers the biological system (body, organ or cell) to combat infections or genetic defects in an attempt to bring the system back to a homeostatic state. Drug cocktails, which simultaneously affect several pathways of the overall system, have been shown to be extremely powerful in controlling complex diseases such as AIDS, the HIV infection. Figure on the right shows the historical AIDS clinical data that illustrates the revolutionary impact of using drugs in combination, noting the nearly 60% reduction of deaths after the appearance of the first HIV drug combination in 1995. However, the roadblock is finding a cocktail with the most effective drug concentration from millions of possible combinations, a proverbial daunting task of finding a needle in the haystack.
The Center for Cell Control (CCC, CenterForCellControl.org) has demonstrated that smart search algorithms can efficiently identify the most potent drug cocktail in tens of iterations from a large number of possible combinations. In addition, the concentrations of the drugs combined together require significantly lower dosages, one tenth or less when compared to single drug administration, to prohibit 100% viral replication. The explanation for the power of drug combinations lies in the complexity of signaling pathways within the cell, normal or diseased. A cell consists of millions of intracellular molecules, which serve as building blocks for its structure and functions. Interactions among these building blocks display the property of self organization which intrinsically serves as the foundation of the networks of signaling and regulatory pathways. It is through these intrinsically interconnected networks that a cell, the basic unit of life, senses, responses and adapts its environment. These three characteristics (large number of building blocks, self-organization due to interactions and adaptation) are commonly observed in all complex systems. The goal of CCC is to apply an unprecedented approach towards efficiently searching the potent drug cocktail for guiding biological systems to a directed phenotype. We then use nanoscale modalities, molecular sensors, to understand the signal pathways responses under the influence of the combinatory drugs. This approach will introduce engineering systems that can be applied towards the regulation of a spectrum of cellular functions, such as cancer eradication, controlling viral infection onset, and stem cell differentiation.
This highly interdisciplinary approach demands strong synergetic collaboration between biologists, engineers and clinical doctors at the University of California, Los Angeles and the University of California at Berkeley. CCC also started collaborations with other NDC, including the NDC for the Optical Control of Biological Function at Lawrence Berkeley National Laboratory and the Nanomedicine Center for Nucleoprotein Machines at Georgia Institute of Technology.
The projects at CCC are focused on two application areas important for the overarching goals of the NIH Nanomedicine program: (1) monitor key elements in signal initiation and interrogate cascades of pathway under drug cocktail stimulation in a smart Petri-dish. This technology platform consists of nano modalities including microfluidic circuitries integrated with optoelectrical tweezers (OET), tunable nano plasmonic resonators (TNPR) and molecular cleavage machine (MCM) (2) demonstrate capability to control and elicit desired cellular phenotypes by determining optimal drug combination for pathogenic diseases, cancer and directing differentiation of stem cells.
Three biological systems, stem cell, cancer and viral infection, have been proposed in the CCC project. Due to the interesting feature of circuit reprogramming, we will use stem cells as the first system for monitoring and interrogating the reactions in the network of pathways in the early phase. Viral infection and cancer cells will first be used in drug combinatory studies. As the program becomes more mature, the networks of all three systems will be interrogated by nano tools under the potent drug cocktails. We have made significant progress in optimizing the stem cell culture in a controlled micro fluidic environment, especially in large array forms which will give a well defined starting point for the delicate stem cell research. The capability of operating OET in high ionic fluid has removed the main roadblock for applications in biological studies. Progress has also been made in further developing of TNPR and in the uptake of nanoparticles in cells.
We characterized the different sizes of cell clusters that yield optimal embryoid body (EB) for controlled tissue differentiation. In order to find the best surface condition to grow the optimal size of EB, we performed contact angle hydrophobicity measurement of the surfaces in which EB are cultured and determined the proper surface coating required. We also designed and fabricated an EB array based on microfluidic systems to be used for the systematic study of stem cells. This array is currently being tested. We have extended the capability of our Optoelectronic Tweezers for massively parallel single-cell manipulation, enabling the technique to efficiently function in highly ionic solution of typical cell culture media. We also improved our Tunable Nanoparticle Plasmon Resonance platform for kinase assay in small sample amounts, demonstrating significantly higher signal to noise in our Raman Scattering Spectra of Jak3 kinase.
For optimal multiple-drug combination as potential therapeutic drug cocktail in pathogenic disease and cancer, we focused in the past year on searching for potent drug cocktails of controlling viral diseases. We have demonstrated the success of our drug combination optimization methodology on cellular models for (1) the reactivation of Kaposi’s Sacroma-associated Herpesvirun (KSHV) in a GFP transfected body cavity-based lymphoma cell line (BC-3), (2) the inhibition of Vesicular Somatitis Virus on NIH 3T3 fibroblast cells, (3) positive preliminary results of inhibiting HSV infection supported by the supplementary fund, and finally also in a cancer in vitro model, (4) enhanced NFkB actives in 293 T cells (supported by other funding source). By using the search scheme, we have demonstrated in several different biological systems that twenty to thirty iterations is sufficient in finding the optimal drug cocktail within millions of possible combinations. Plans for in vivo animal validation of our in vitro results have been proposed as supplemental research. Also, we are in the process of generating a cancer model with the p21 promoter linked to a GFP reporter to drive HCT116 colon cancer cells into maximal p21 expressions using the system control approach.
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