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Chips to Hits: Microarray and Microfluidic Technologies for High-Throughput Analysis and Drug Discovery

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Chips to Hits: Microarray and Microfluidic Technologies for High-Throughput Analysis and Drug Discovery Meeting Report automated manner. As emerging tools Chips to Hits: microarray and for proteomics, protein arrays have a number of advantages over conven- microfluidic technologies for tional methods of protein analysis using high-throughput analysis and 2D gel electrophoresis and mass spec- trometry, since they can be used to detect proteins with low concentrations drug discovery in a high-throughput manner. September12-15, 2005, MA, USA In general, there are two types of pro- Ali Khademhosseini tein microarrays: antibody microarrays and functional protein microarrays. Harvard-MIT Division of Health Sciences & Technology, Massachusetts Institute of Technology, Cambridge, Antibody microarrays are miniaturized MA 02139, USA; Department of Medicine, Brigham & Women’s Hospital, Harvard Medical School, Boston, enzyme-linked immunosorbent assays MA 02115, USA; Tel.: +1 617 253 3638; Fax: +1 617 258 8827; [email protected] that can be used to detect proteins with Expert Rev. Mol. Diagn. 5(6), 843–846 (2005) high sensitivity and selectivity. On the other hand, functional protein micro- arrays can be used to study protein inter- Methods of performing experiments One of the most successful applica- actions with other molecules. At Chips to cheaper, faster, easier, as well as with a tions of microarrays is for RNA analysis. Hits, Michael Snyder (Yale University, higher sensitivity and throughput, are This technology, which was pioneered USA) presented on the use of yeast pro- desirable for many scientific endeavors by Affimetrix, Inc., is now commonly tein microarrays to identify novel part- and commercial applications. In partic- used in many biologic and drug discov- ners within protein complexes, and to ular, improved technologies are benefi- ery studies to profile gene expression analyze the multifunctional nature of cial for the discovery of new drugs and within cells. DNA microarrays can be some proteins [1]. Using these assays, the analysis of biologic systems, where used to conduct large-scale quantitative novel functions could be found for even many different molecules must be ana- experiments that measure changes in well-studied proteins. Also, the use of lyzed in a combinatorial and concentra- gene expression for a particular tissue or protein arrays to understand phosphor- tion-dependant manner. A major cell type. The use of such technologies ylation mechanisms was demonstrated theme of the 2005 Chips to Hits confer- was a key aspect of the Chips to Hits by studying the binding of yeast protein ence recently held in Boston, Massa- conference, with many companies repre- kinases to large protein microarrays. chusetts, USA revolved around the senting their latest technologic advance- Using the data generated from pro- emergence of microarray and micro- ments and products. For example, Alan tein–protein, protein–DNA binding and fluidic technologies in addressing barriers Sachs (Merck Research Laboratories) phosphorylation experiments, network to high-throughput experimentation. presented on the use of DNA microar- maps could be generated that contain ray technology for enabling drug discov- much of the interaction and regulatory DNA & protein microarrays ery by using animal models and tumor pathways within a cell [2,3]. This ability Microarrays can be Authorused to perform samples to identify drug targets.Proofto construct regulato ry networks and to high-throughput experiments by localiz- Although gene arrays are good indica- analyze biologic systems may have great ing tests to small regions of a 2D sub- tors of RNA expression within a cell, implications in understanding the strate. By restricting the location of indi- they are not necessarily representative of underlying biologic mechanisms and vidual experiments, microarrays can the level of protein expression, due to identifying candidate drugs. dramatically miniaturize assays. Microar- complicated dynamics of translational Despite the remarkable potential of ray technologies have been widely used and post-translational modification proc- protein microarrays for understanding in academia and industry. It is estimated esses. Therefore, complementing gene biologic systems, significant technologi- that these technologies currently have a arrays with protein arrays is critical for cal challenges remain. Current research market of approximately 2 billion dollars producing a true picture of the state of thrusts in the area of microarrays involve with more than 350 companies selling the cell. It is envisioned that protein increasing the sensitivity of the assays, products. In addition, there are over arrays can be potentially used to perform minimizing false positives and increasing 150 academic institutes and approxi- protein–protein, protein–DNA, pro- the throughput of the assays. For exam- mately 10,000 researchers conducting tein–drug, or enzyme substrate screen- ple, since protein–protein interactions research in this field. ing assays in a sensitive, parallel and are complicated by the existence of many 10.1586/14737159.5.6.843 © 2005 Future Drugs Ltd ISSN 1473-7159 843 Khademhosseini post-translational modifications, such as the identification of cues that induce identifying drug target interactions and phosphorylation and glycosylation, pro- desired cell responses. Also, the materials for evaluating phenotypic changes result- tein arrays must be fabricated that can that yield desired responses could be used ing from the expression of specific pro- sense such interactions by using post- as templates for tissue engineering scaf- teins in the cells. translationally modified proteins or spe- folds. Such an approach is a radical Other types of cell microarrays have cific antibodies. Also, technological bar- change from traditional methods of also been developed in which cells are riers exist for protein arrays that must be developing new biomaterials, where pol- patterned on surfaces comprised of adhe- optimized to further facilitate their wide- ymers have been individually developed sive or nonadhesive regions. As adhesive spread use for biologic studies. Current and tested for their effect on cells. In cells are seeded on these substrates, they research ranges from enhancing the func- addition, the effect of natural ECM mol- adhere to the patterned regions. Alterna- tionality of proteins by using spacer mol- ecules on cell fate can be evaluated in a tively, microwells have been used, in ecules, to minimizing nonspecific protein high-throughput manner. For example, which cells, including nonadhesive cells, adsorption through surface modification. combinatorial matrices of various natural are plated within the microwells and For example, Jason Armstrong (Bio- ECM proteins were tested for their abil- remain physically separated from each Layer, Austria), presented the use of bio- ity to maintain the function of differenti- other. Cell arrays have been used to study mimetic surfaces to improve various ated hepatocytes and to induce hepatic cell behavior in a clonal manner [14,15] or assays in the range of 6- to 50-fold. differentiation from murine ES cells [9]. to study the effects of drugs on cells in a These technologies may provide addi- Other emerging microarray technolo- high-throughput manner [16,17]. Current tional functionality and sensitivity to gies include patterned polysaccharide limitations with cell array technologies today’s microarray technology. and bead arrays [10]. Polysaccharide arrays include lack of suitable technologies to can be used to study the interaction of assay for many different chemicals as well Other polymeric microarrays chemical libraries or drugs with polysac- as maintaining proper cellular phenotype Microarrays fabricated from polymers or charides. Such interactions will be partic- in culture. Methods of integrating cell extracellular matrix (ECM) proteins can ularly important in finding new drugs arrays within microfluidic channels, gen- also be used to test extracellular condi- that interact with the cell surface polysac- erating patterned co-cultures and multi- tions on cellular behavior or to test charide molecules, and are potentially phenotype cell arrays are emerging fea- molecular libraries. Such libraries are use- important tools for understanding the tures which may solve these challenges. ful for tissue engineering and have interaction of sugars with other mole- The cell array technology requires further already yielded candidates that have been cules in the emerging filed of glycomics. development, but has the potential to shown to induce osteogenesis [4] and car- lend itself to a broad range of functional diomyogenesis [5] from embryonic stem Cell microarrays ultrahigh-throughput cell-based assays. (ES) cells as well as the dedifferentiation Cellular micropatterning can be used to of committed cells [6]. Recently, research- control cell shape and subsequent behav- Microfluidics ers in Robert Langer and Sangeeta Bha- ior (i.e., migration, proliferation, differ- Microfluidics is a potentially powerful tia’s groups (Massachusetts Institute of entiation and apoptosis) [11,12]. Cell method of performing high-throughput Technology, USA) have used robotic arrays are also a potentially powerful tool experiments that encompass a series of spotters capable of dispensing and for performing high-throughput bio- techniques used for controlling the flow immobilizing nanoliters of material to logic studies. There have been a number and reaction of minute amounts of liq- fabricate microarrays, where cell–matrix of studies that have demonstrated
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