Antibodies for All
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.