Googling brain proteins with 3-D goggles

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RICHLAND, Wash. — The Allen Brain Atlas, a genome-wide map of the mouse brain on the Internet, has been hailed as “Google of the brain.” The atlas now has a companion or the brain’s working molecules, a sort of pop-up book of the proteins, or proteome map, that those genes express.

The protein map is “the first to apply quantitative proteomics to imaging,” said Richard D. Smith, Battelle Fellow at the Department of Energy’s Pacific Northwest National Laboratory, who led the mapping effort with Desmond Smith of UCLA’s David Geffen School of Medicine.
“Proteins are the lead actors, the most important part of the picture,” PNNL’s Smith said. “They are the molecules that do the work of the cells.”

Fine-tuning such proteome maps will enable comparisons of healthy brains with others whose protein portraits look different. Contrasts in location and abundance of proteins may display the earliest detectable stages of Alzheimer’s, Parkinson’s and other neurological diseases. They hope such diseases might be curbed if caught and treated early enough.

The National Institutes of Health-funded study, performed at DOE’s Environmental Molecular Sciences Laboratory on PNNL’s campus, is published in the advance online edition of Genome Research and featured in current Nature online Neuroscience Gateway (http://www.brainatlas.org). PNNL staff scientists Vladislav A. Petyuk, Wei-Jun Qian and UCLA’s Mark Chin are co-lead authors.

To produce the map, the team characterized center-brain slices as several dozen 1 millimeter cubes, or “voxels,” to “show us where proteins appear in the brain and where they vary in abundance,” PNNL’s Smith said. “We labeled all the proteins so we would have reference points so we know we’re looking at the same protein between different parts of the brain and from one mouse to another.”

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