Million dollar grant boosts Epigenetics research

His research indicates that a number of complex diseases including schizophrenia may be the result of misreading of DNA sequences. Along with colleagues from Toronto, he has proposed an "Epigenetic Hypothesis for Schizophrenia". Which simply means that although the DNA sequence is fine, there is something that's causing misregulation or misexpression of some of the genes involved in schizophrenia. Their current focus is on the genes of chromosome 22.

This engaging premise has prompted the Ontario Mental Health Foundation to award Singh and Dr. Art Petronis, of the Centre for Addiction and Mental Health in Toronto, a grant of one million dollars to establish a ground rule and pursue this research.

"One thing that has been implicated in the expression of genes is DNA methylation" says Singh. In humans, the addition of methyl groups occurs on cytosines (C), most but not all located directly beside guanines (G) as the dinucleotide CG. "If that is the case we could technologically detect the methylation of CG in a given gene or set of genes, between a patient and a matched control."

In the past, the majority of genetic diseases were thought to be caused by errors in the DNA sequence itself due to deletions, substitutions or other mutations passed down through generations. The same mechanisms were believed to occur in complex multifactorial disorders such as cancers, high blood pressure and mental disorders such as schizophrenia since they tended to occur in families, and showed high correlations in twin studies. They all point to some genetic basis.

This realization and the subsequent breakthroughs in DNA technology encouraged the search for the genes of these diseases. However, the investment of 20 years and billions of dollars have little to show in the way of finding genes for complex multifactorial diseases.

"Here's the bottom line - we still do not have a single gene that causes any of the mental disorders," says Singh. "What has been found however, is that a number of chromosomes have been identified that have at least some genetic determinants that probably contributes to the development of schizophrenia." Of about 10 chromosomes that have been implicated in schizophrenia, the chromosome that invariably shows up most is chromosome 22.

Chromosome 22 was the first to be completely sequenced by the Human Genome Project in 1999. Yet we do not know the identity of the schizophrenia gene. Dr. Singh says: "For the last four or five years I've been arguing that it's not really the DNA mutation per se, rather it's the misexpression of the DNA that is involved in the causation of schizophrenia."

The grant will enable Singh to take the methylation analysis of DNA to the next level. "The next level to me, really, is producing and using a new kind of gene chip."

The procedure involves taking a single strand of DNA as a probe and placing it on a spot fixed on a slide. This process is repeated thousands of times for different probes and a matrix is set up this way. "We know at a given spot which gene it is, then we take our DNA, label it and hybridize. The ones that hybridize and form a duplex will give a signal, the rest will not." Theoretically, the concept is simple, but in practice the work is complex due to the sheer volume of numbers. Making some sense of all of the data involves bioinformatics which uses advanced computational methods to analyze biological problems.

Right now two types of gene chips are available. One is used to examine which genes are expressed in a given cell or tissue. The other is used for mutation analysis of the DNA. "What we want to do is to produce a chip that allows us to do a large-scale assessment of DNA methylation involving all the genes of chromosome 22."

Affinmetrix, a company that is a leader in this type of technology, will work with Dr. Singh and Dr. Petronis in the development of this novel gene chip to be used in testing the epigenetic hypothesis for schizophrenia. The method once established will be useful to variety of complex diseases including cancers.