Nathaniel Heintz has a very ambitious goal: to characterize all the gene activity in each of what he estimates are the thousand types of neurons in the mammalian brain. By identifying the genetic signature of each of the brain's cell types, he then hopes to determine the molecular changes in the brain's circuitry that occur during learning, feeling, psychiatric illnesses, and a myriad other healthy and unhealthy mental processes. Although every cell in the brain contains the same genes, each cell type functions differently because unique subsets of these genes are expressed in it.
Heintz acknowledges that his objective to obtain a molecular atlas of the brain may be quixotic, but he feels it is necessary. Today, when scientists study a gene variation associated with a neurological or psychiatric disease in an animal model, Heintz explains, they may not know which neurons in the brain are impaired by the genetic change. Scientists can guess that a particular type of neuron is affected, he says, based on the gene's heightened expression in a cell. But they don't necessarily know how the genetic variant they are studying affects other genes in that cell or in the cells communicating with that neuron.
A genetic compendium for each cell type in the mouse brain would provide a baseline from which to start, says Heintz, who in his 25-year career has made seminal discoveries about the regulation of mammalian genes, identified genes in the developing and mature nervous system, and invented innovative methodologies to do his research.
Ever since Heintz was a graduate student in the late 1970s, he has wanted to study the brain in molecular detail. At that time, though, few organisms were amenable to precise molecular genetic analysis. Using the tools then available, he studied the genetics of viruses that infect bacteria for his doctorate. He moved to mammalian systems in 1982 for his postdoctoral fellowship in the laboratory of Robert Roeder, who was at the University of Washington in St. Louis. There, Heintz employed tissue culture techniques and biochemistry to analyze the regulation of the genes that encode histones, proteins that wind DNA to help form the structure of chromosomes.
Heintz went to Rockefeller University as an independent scientist in 1983 and continued to work with histones until the early 1990s, when he began studying genes expressed in the nervous system. Using animal models and cloning techniques, he found several genes important in the development and function of the mouse brain. The Blbp gene, for example, is used by immature nerve cells to give rise to mature nerve cells. Lynx1, which modulates the nicotinic receptors in the brain and peripheral nervous system, was the first gene identified that encodes an endogenous toxin-like protein in the nervous system. The molecule is related to snake venom poisons that cause paralysis. Lurcher plays a role in the function of the cerebellum's Purkinje neurons, which coordinate movement and become damaged in neurodegenerative diseases such as ataxia telangectasia.
To help him study how genes work in the different cells of the brain, in the late 1990s, Heintz developed a technique involving bacterial artificial chromosomes (BACs). The method allowed him to use large pieces of DNA—including the gene, its regulatory region, and reporter genes—that also could be easily manipulated in test tubes and in the genetic engineering of animals. Reporter genes fluoresce and make gene expression in different cells visible under the microscope.
By 2000, the BAC technique allowed him to begin to create a growing library that eventually will visualize the expression pattern of each of approximately 5,000 genes in the different cell types of the brain. The project, called GENSAT (Gene Expression Nervous System Atlas), was initiated by Heintz and his Rockefeller colleague Mary E. Hatten and is supported by the National Institutes of Health.
In the past few years, working in collaboration with Rockefeller scientist Paul Greengard, Heintz has adapted his BAC technique by adding microarrays, gene chips that analyze all the genes in a genome. They have used his "BAC-array" method to identify all the genes expressed in scores of different cell types of the brain. Using this strategy, Heintz has characterized a novel group of genes expressed in the Purkinje cells in a mouse model of ataxia telangectasia that have shed new light on the specificity of neurodegeneration in this disease.
Heintz believes his new methods may finally allow him to achieve what he has wanted to do for more than two decades: characterize all of the cell types in the nervous system at the molecular level. "It's going to take a while before we can understand the genetic circuits and subsystems in the brain's cells," Heintz says. "But the first few examples of these kinds of approaches are giving me confidence these new methods are going to be very powerful."