Fang Lai

Discriminating two classes of toxicants through expression analysis of HepG2 cells with DNA arrays

Microarray technology provides a rapid and cost-effective method to associate specific cellular responses with unique gene expression patterns. If characteristic expression patterns of a small number of genes could be associated with drug toxicity, this association may be used for toxicity prediction, and thereby to reduce the need for traditional toxicity testing. To test this hypothesis, we have designed an array composed of 92 known human genes of toxicological interest (including seven housekeeping genes) and eight bacterial controls. HepG2 cells were treated with either ethanol or one of two quinone containing anticancer drugs, mitomycin C or doxorubicin. RNA was isolated from treated and untreated cells, differentially labeled with fluorescent dyes, and then hybridized to the array. Our results show that the expression patterns induced by ethanol and the anticancer drugs are different. Both of the anticancer drugs, but not ethanol had a differential effect on the regulation of several genes, including CYP4F2/3, CYP3A3, TNFRSF6 and CHES1, demonstrating that the two drugs might function through a similar mechanism, which differs from that of ethanol. These results suggest that microarray-based expression analysis may offer a rapid and efficient means for assessing drug toxicity.

A Reporter System for Reverse Transfection Cell Arrays

The incredible speed of gene cloning and sequencing brought about by the genomic revolution has begun to outpace conven tional gene discovery approaches in the pharmaceutical industry. High-throughput approaches for studying gene function in vivo are greatly needed. One potential answer to this challenge is reverse transfection, a high-throughput gene expression method for examining the function of hundreds to thousands of genes in parallel. One limitation of reverse transfection tech nology is the need for posttransfection processing of the arrays to analyze the activity of the expressed proteins. The authors have investigated the use of a reporter construct cotransfected with other genes of interest to monitor and screen gene function on reverse transfection microarrays. They developed a serum response element (SRE) reporter linked to the green fluorescent protein (GFP) that is cotransfected with target genes on reverse transfection arrays for monitoring mitogen-activated protein (MAP) kinase signaling by multiple targets in parallel. The authors show that this reporter system is able to detect inhibition of upstream MAP kinase signaling proteins by the MEK inhibitor U0126. The ability to monitor the activity of multiple signaling proteins in a multiwell format suggests the utility of reverse transfection reporter arrays for high-throughput screening applications.

G-protein-coupled receptor microarrays for multiplexed compound screening.

Conventional assay methods for discovering and profiling drug-target interactions are typically developed on a target-by-target basis and hence can be cumbersome to enable and orchestrate. Herein the authors report a solid-state ligand-binding assay that operates in a multiplexed mode to report compound activity against a micorarray-configured panel of G-protein-coupled receptor (GPCR) targets. The pharmacological fidelity of the system is high, and its miniaturized “plug-and-play” format provides improved efficiency both in terms of execution time and reagent consumption. Taken together, these features make the system ideally suited to explore the structure-activity relationship of compounds across a broad region of target class space.

Fabrication and Application of G Protein-Coupled Receptor Microarrays

The increased number of drug targets and compounds demands novel high-throughput screening technologies that could be used for parallel analysis of many genes and proteins. Protein microarrays are evolving promising technologies for the parallel analysis of many proteins with respect to their abundance, location, modifications, and interactions with other biological and chemical molecules. This chapter specifically describes the fabrication of G protein-coupled receptor (GPCR) microarrays, a unique subset of protein microarrays, using contact-pin printing technology. The bioassays and potential applications of GPCR microarrays for the determination of compound affinities and potencies are also included.

Development of multiplexed microarray binding assays for high-throughput drug discovery.

The ability to combine primary hit identification assays with target profiling would significantly streamline the current drug discovery process. Working towards this end, we report here the development of a microarray-based ligand binding assay that supports multiplexed analysis of G protein-coupled receptor systems in a 96-well microplate format that is compatible with the equipment and infrastructure typical of high-throughput screening laboratories. A prototype microarray was generated by pin-printing seven different receptors within the wells of a specially coated glass-bottom microplate and assaying with a cocktail of fluorescent ligands. Development of the multiplexed system included optimization of methods for depositing receptor membrane proteins and establishing a generic set of assay conditions that simultaneously satisfied the pharmacology requirements of all of the receptor systems included on the array. The multiplexed system is shown to produce valid pharmacological results as evidenced by its ability to report K(i) values for receptor-specific fluorescent ligands and rank ordered potencies for diagnostic displacing compounds comparable to values generated by conventional simplexed assays. Moreover, the results of a 40-compound mini-screen confirmed that the assay accurately identifies valid hits. The results suggest the assay may be immediately suitable for routine profiling tasks and demonstrate the potential of the format for high-throughput multiplexed drug discovery.

Cell-Based Co-transfection Microarrays for Use with HEK293T Cells on a Poly d -Lysine-Coated Polystyrene Microplate

Analysis of the human genome sequence has identified thousands of putative genes with unknown function; therefore, a new tool allowing for rapid identification of gene functions is needed. Reverse transfection microarray technology, which turns a DNA microarray into a cell-based microarray, has emerged for simultaneously studying the function of many genes. Since the initial demonstration in 2001, many variations have surfaced, making the technology more versatile for a broad range of applications. We have developed a protocol to make ready-to-transfect DNA microarrays in a 96-well microplate for co-transfection of two plasmids into HEK293T cells. This cell-based microarray in a microplate may be used for screening hundreds of analytes against multiple protein targets in parallel, providing a powerful tool for functional genomics and drug discovery.

Novel Surface Technologies for Genomics, Proteomics, and Drug Discovery

Following the recent progress in functional genomics and proteomics, and high-throughput screening (HTS) in drug discovery, evolving technologies over the last decade have offered a tremendous leap over the caveats of traditional techniques. In response to this metamorphosis of technologies through different platforms, Corning has introduced a suite of surface technologies with applications in microarray printing, enhanced attachment, and consumables in drug discovery. Microarrays generated on an ultra-flat glass substrate with GAPS coating exhibiting a robust chemistry and low surface background have led to higher sensitivity and reproducibility for the expression assay. Recent introduction of UltraGAPS™ surface enables oligo attachment for use in differential gene expression analysis. Various attachment surfaces to meet the needs of the applications in genomics, proteomics and drug discovery will be discussed.