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Swedish Researchers Ready 'World's Largest Protein Array' for Autoimmunity Screening

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Though protein microarrays have arguably lagged nucleic acid arrays in terms of adoption and commercialization, technology development continues apace.

According to Peter Nilsson, protein and peptide platform array manager at Sweden's Science for Life Laboratory, or SciLifeLab, it is "no longer early days" for protein array technology, and his lab is in the process of spotting what he believes is the highest-density protein array available to date.

Nilsson spoke earlier this month with BioArray News during a visit to SciLifeLab's Stockholm facility. He said at the time that his lab was preparing to produce an array containing about 21,120 proteins spread across 55 separate 384-well plates.

"That will be significantly larger than [Life Technologies'] ProtoArrays, and it will be larger than the arrays from CDI [Laboratories]," said Nilsson. Life Tech's ProtoArray Human Protein Microarrays currently contain about 9,000 proteins, according to the company's website. Meantime, CDI's HumanProt microarray contains "17,239 and counting," according to its website.

CDI CEO Scott Paschke told BioArray News separately this week that the company plans to update the HuProt array to contain 20,000 proteins in the next couple of months. But until that time, and perhaps beyond, Nilsson's lab may boast the array with the most proteins.

"Numbers count," said Nilsson, "and to my knowledge this is the world's largest protein array."

Nilsson and colleagues will use this array, manufactured using an Arrayjet inkjet spotter, to validate the antibodies that are used within the Swedish Human Protein Atlas, a scientific research program that aims to explore the human proteome using antibody-based proteomics. As part of the project, Nilsson's lab has access to the purified proteins it needs to construct its arrays.

According to Nilsson, the new array is made up of purified protein fragments that overlap, meaning that there is more than one fragment arrayed for each unique protein. In total, between 13,000 and 14,000 proteins are covered by the new array, Nilsson said.

The array is being generated mainly for autoimmunity screening, he said, although it will also be used for antibody validation, "to see in a much larger context how these antibodies behave in terms of outside interactions." The antibodies run on the array will be selected from a larger set in order to maximize the use of the new resource, as it will take about a week to make the array, Nilsson said.

According to Nilsson, all antibody variation data generated on the new array will be made available to researchers via the Human Protein Atlas project. In terms of autoimmunity screening, he said data might not be published until Nilsson's lab and its partners identify interesting targets that have been fully understood and verified.

"We have quite a few [targets] in the pipeline, but [are] being very careful in terms of requiring much validation and verification data," he said.

Last month, Nilsson and colleagues discussed the use of their protein microarrays in a study featured in Molecular & Cellular Proteomics. In the paper, the authors showcased the use of arrays containing 11,520 protein fragments to screen for profiles of IgG in human plasma from 90 individuals with multiple-sclerosis-related diagnoses.

Nilsson and colleagues used reactivity distributions among multiple sclerosis subgroups to select 384 antigens, then re-evaluated these on planar microarrays, corroborated this with Luminex suspension bead arrays in a larger cohort, and confirmed for specificity in inhibition assays. Among the heterogeneous patterns within and across multiple sclerosis subtypes, differences in recognition frequencies were found for 51 antigens, which were enriched for proteins of transcriptional regulation, the authors wrote in the paper.

Nilsson said that the project is now entering a new phase. In coming months, the researchers will screen 4,000 multiple sclerosis samples using a set of 300 highly selected proteins.

"That is something totally unique within the autoimmunity profiling area," said Nilsson. "That is something that I am really excited about."

17,239 and counting...

While Nilsson's lab scales up its protein array resources, CDI Labs is doing the same. Based in Baltimore and Puerto Rico, CDI offers protein array services based on technology developed at Johns Hopkins University. On its website, CDI claims the number of proteins on its HuProt Microarray is currently "17,239 and counting," but that will change soon, according to Paschke.

"We will increase the content on our array to up to 20,000 fully folded proteins in the next couple months," he said.

Paschke said that he is familiar with Nilsson's work and that CDI and SciLifeLab have been cooperating on certain projects. While he praised Nilsson's activities, he said that there are "significant differences" between CDI's array and the one in production at SciLifeLab. For instance, CDI's arrays contain fully folded proteins, while SciLifeLab's array will contain protein fragments. Looking at full-length proteins, as opposed to smaller protein fragments, can "give you certain advantages in certain assays," he noted.

Like Nilsson's lab, CDI's clients use its arrays for antibody validation and autoimmune screening. The company markets its array screening services together with a menu of "microarray-powered" monoclonal antibodies and services.

According to Paschke, while there is some interest in high-density protein arrays such as CDI's or SciLifeLab's, there could be more interest. He said that CDI will need to reach out to more researchers in the future to make them aware of the information that their technology can provide.

"Microarrays in proteomics have lagged nucleic acid arrays," said Paschke, "And some people need to be educated and convinced of the things that you can do with an array that has 20,000 proteins on it."

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