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May 1, 2011 (Vol. 31, No. 9)

Protein Microarray Use Multiplies

Innovative Formats and Applications Extend Range Beyond Conventional Analyses

  • From Membrane to Microarray

    Although membrane-bound receptors comprise a major portion of the pharmaceutical industry’s target portfolio, they pose a challenge for microarrays. They are notoriously difficult to isolate, and the purified proteins are very likely to lose their function when they’re immobilized. GPCRs, for example, “have seven transmembrane domains that have to remain intact,” pointed out Fang Lai, Ph.D., research manager for Corning. “They have to remain associated with lipids to maintain their structure.”

    The Corning team has been developing technology for creating high-throughput ligand-binding assays for membrane proteins. By pin-printing nanogram quantities of commercially available membrane protein preparations onto the bottom of specially coated glass microwell plates—21 spots, for example, with three replicates of seven different proteins—they essentially create microarrays in the bottom of each well. The multiplex assays can then be performed using standard high-throughput screening automation.

    Dr. Lai described a ligand-displacement assay in which the control will be an array incubated with a cocktail of labeled ligands known to be able to bind to those receptors, and all the spots will be lit up by fluorescent signals. When an unlabeled ligand is added to the mix, if it is able to bind the GPCR it will compete with the labeled ligands for binding, and thus the fluorescent signal at that spot will disappear in a dose-dependent fashion. “In a microplate you can screen many, many compounds in this way,” she said. It enables a large amount of information to be garnered using minimal reagents while saving valuable time.

    Corning’s intention, Dr. Lai asserted, is more to provide a technology—in the surface chemistry suitable for immobilizing membrane proteins, and in the array-printing process that allows those proteins to remain functional—than to create assays themselves. It is actively seeking partners interested in marketing assays or providing services based on the technology.

  • Antibodies for All

    Click Image To Enlarge +
    The concept of next-generation plasma profiling, something that the Science for Life Laboratory is very interested in, is built on large and growing collections of affinity reagents that are implemented onto multiparallel platforms in order to analyze samples stored in biobanks in a hypothesis-free manner.

    Rather than printing spots on planar arrays or in microwells, Jochen Schwenk, Ph.D.’s group at the Science for Life Laboratory in Stockholm attaches antibodies to Luminex beads and queries the resulting suspension arrays with bodily fluids such as serum, plasma, urine, and cerebrospinal fluid.

    Luminex offers up to 500 uniquely identifiable “colors” of bead, each of which can be conjugated with a different antibody. “The number that we usually communicate is that we run 384 samples, and each of those samples we run with 384 antibodies, on a daily basis,” yielding about 150,000 immunoassays per day, Dr. Schwenk said.

    His work is an extension of that of the Human Protein Atlas, he explained, the stated goal of which is to explore the entirety of the human proteome using antibody-based proteomics. To date the HPA has produced antibodies against about 50%—roughly 10,000—of all nonredundant human proteins.

    With this many proteins and this many antibodies to deal with, “we cannot invest time into optimizing each protocol—addressing each of these targets with antibodies that we need to maturate or support—so we’ve chosen to adjust the sample to suit the antibody best,” he said.

    By heating biotin-labeled samples before mixing them with the antibody-coated beads, the epitopes of the proteins are often more exposed, and the functionality of the antibodies seems to be improved. Dr. Schwenk pointed out that “the advantage of using heat is that it’s something you can switch on or off, whereas if you add any chemical compound that would assist the denaturation, then you would need to remove that specific compound.” The group chose 56°C as “the balance between not too much and not too little—the problem is that for some targets if you heat the sample too much then you get precipitation and you lose some of the target.”

    What makes SciLifeLab unique is that in addition to performing directed discovery it “also performs undirected discovery approaches, where we only use antibodies based on quality criteria and not necessarily on which proteins they target,” Dr. Schwenk said. “We have the possibility to identify new protein/disease associations.” It recently conducted a pilot study in which 4,500 antibodies were used to screen 600 samples covering 24 different diseases including 12 cancers, cardiovascular, and neurodegenerative diseases, and it is currently crunching the data.

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