Functional genomics and proteomics: application in neurosciences.(Neuroscience for Neurologists)

J Neurol Neurosurg Psychiatry 2004;75:529-538. doi: 10.1136/jnnp.2003.026260

The sequencing of the complete genome for many organisms, including man, has opened the door to the systematic understanding of how complex structures such as the brain integrate and function, not only in health but also in disease. This blueprint, however, means that the piecemeal analysis regimes of the past are being rapidly superseded by new methods that analyse not just tens of genes or proteins at any one time, but thousands, if not the entire repertoire of a cell population or tissue under investigation. Using the most appropriate method of analysis to maximise the available data therefore becomes vital if a complete picture is to be obtained of how a system or individual cell is affected by a treatment or disease. This review examines what methods are currently available for the large scale analysis of gene and protein expression, and what are their limitations.

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    "The Blind Man and the Elephant" 
    And so these men of Indostan 
    Disputed loud and long, 
    Each in his own opinion ~ Exceeding stiff and strong, 
    Though each was partly in the right ~ And all were in the wrong! 
    John Godfrey Saxe 

Many of the currently used methods for the analysis of function in a cell or tissue rely on measuring one single analyte at a time, with the analysis being based on a prior hypothesis of mechanisms of action or biology. By measuring only one analyte, only a limited picture is gained of the complexities of an often very dynamic situation. Rather like the tale of the six blind men and the elephant, by observing only one facet at a time, a distorted view of the situation can be achieved, and the real answer to the problem remains hidden. With the advent of whole genome maps for several key organisms including man, and the use of methods for profiling all the changes that occur in cells or tissues, it is now possible to stand back and take an unbiased view of biological processes. This is particularly the case for neuropsychiatric disease, where the complexities of the brain, its multitude of connections, and the dynamic interplay between neurones and glia make an unbiased view of disease processes particularly important. (1) Two emerging fields are now coming into general use where the global approach to gaining insight into brain function can be applied. Functional genomics is the generic term used to describe methods that analyse the various genes expressed by a cell or tissue, while proteomics aims to define the protein complement. These technologies now allow an almost complete examination of gene and protein expression using single techniques. Our aim in this article is to provide an overview of the specialised methodologies and to point out the potential pitfalls and limitations of these techniques, with particular reference to investigations on human postmortem brain samples.

FUNCTIONAL GENOMICS

Cellular function is mediated through gene expression involving the production of messenger RNA. Several methods can be employed to profile gene expression in neurological and psychiatric disorders, including differential display and microarrays, ideally coupled with real time quantitative polymerase chain reaction (Q-PCR) cross validation. These technologies can be used independently or in parallel, where they investigate mRNA transcripts quantitatively by amplification of RNA from disease and control samples, and then detection of specific complementary DNA (cDNA) or antisense RNA (aRNA) species. It is hoped that pathologically relevant pathways and disease mechanisms involved in neurological and psychiatric disorders can be revealed with these techniques.