Like skilled assassins, many diseases seem to know exactly what types of cells to attack.
While decimating one cadre of cells, diseases will inexplicably spare a seemingly identical group of neighbors. What makes cells vulnerable or not depends largely on the kinds and amounts of proteins they produce - their "translational profile," in the lingo of molecular biology. For this reason, scientists have struggled to parse the subtle molecular differences among the hundreds of specialized cell types that are tangled together in tissues like the brain.
Now, in back-to-back papers in the November 14 issue of the journal Cell, researchers at The Rockefeller University report a breakthrough in cellular analysis that slashes through this Gordian knot. The scientists have developed a method to reveal translational profiles by isolating the genetic messages that govern protein production in different cell types. The new method, translating ribosome affinity purification (TRAP), uses genetically engineered mice to capture these messages as they pass through the protein production factories called ribosomes. Because the mice have been made to express a specially tagged ribosome in only one particular cell type, the TRAP method can identify all the genetic messages that give that cell type its unique identity, including, perhaps, its susceptibility to disease.
So TRAP solves a problem that has been a fundamental barrier to a deeper understanding of the brain and how neurological diseases attack it. But because the method can be used to distinguish any type of cell in any tissue in any organ -- not just brain cells -- it has applications for research into afflictions as varied as cancer metastases, coronary artery disease and diabetes. The work is a collaboration between the labs of Rockefeller professors Nathaniel Heintz and Paul Greengard as well as colleagues at Northwestern University and the Translational Genomics Research Institute (TGen).
"We've created a novel, generally applicable tool that can be used by a broad spectrum of the scientific community," says Heintz, who is the James and Marilyn Simons Professor, head of the Laboratory of Molecular Biology and a Howard Hughes Medical Institute investigator. "I think it will rapidly spread into many of areas of biology."
Greengard, Vincent Astor Professor and head of the Laboratory of Molecular and Cellular Neuroscience, says about half of the research in his lab now employs the new technique to study the biochemical basis of Parkinson's, Alzheimer's and Huntington's diseases, as well as the still-mysterious ways in which psychoactive drugs fight schizophrenia and depression. TRAP should fundamentally change biochemical studies of the brain and the speed at which they yield results, he says.
"We can look at a thousand genes instead of one at a time, so things should clear a thousand times faster," says Greengard, who won the Nobel Prize in Physiology or Medicine in 2000 for research into how neurons communicate.
The TRAP method grew out of a project known as GENSAT (for Genetic Expression Nervous System Atlas) that Heintz and Rockefeller professor Mary Beth Hatten launched in 2000 to visualize the contributions of individual genes to the mouse brain. Heintz and his colleagues had developed a technique to engineer large pieces of DNA carried in bacterial artificial chromosomes (BACs), which can insinuate themselves into the genomes of other organisms. They were able to insert the genetic code for green fluorescent protein (EGFP) within the regulatory domain of any gene of interest. When one of these modified BACs is transferred into mice, expression of the EGFP mimics that of the gene of interest, lighting up cells with a green glow that shows researchers all of the cells in which that particular gene functions.
The GENSAT database laid out in glowing green myriad cell types of the mouse brain. And it provided genetic markers for each kind. But it was an accomplishment that was also a taunt. Ultimately, the researchers wanted to go deeper to understand the precise biochemical characteristics of the cell types they had brought into focus, to learn what makes cells vulnerable to attack - and possibly how to protect them from it - by discovering what's unique to the susceptible cells and the ones that are resistant. Enter TRAP.