A recent publication by Vogt and colleagues illustrates both the power and pitfalls of using gene expression profiling of neurodegenerative disease (24). ‘Neurodegeneration’ is a generic term which describes the death of neurons, and, as such, could be applied to acute injury such as brain trauma. In contrast, the term ‘neurodegenerative disease’ connotes those disorders in which an endogenous process produces dysfunction and death of neurons over the course of years. In the past decade, there has been increasing recognition of the remarkable similarities among the neurodegenerative diseases (2,13,17, 20). For many of these disorders, genetic forms of the disease have been identified (6,8,12, 19,23). For many of these disorders, there are characteristic proteinaceous aggregates: amyloid plaques in Alzheimer's disease, Lewy bodies in Parkinson's disease (PD), neuronal intranuclear inclusions in Huntington's disease, Bunina bodies in amyotrophic lateral sclerosis, and glial cytoplasmic inclusions in multiple system atrophy (MSA) and progressive supranuclear palsy. Interestingly, it is not known if these characteristic proteins aggregates are in themselves toxic, or if they represent a compensatory cellular response. Another recent realization is that abnormal symptoms may not result purely from neuronal death, but may reflect abnormal functioning of the remaining neurons. Thus, defining the scope of neuronal dysfunction is critical in unraveling these disorders. Brain cells – neurons – are unique in that these post-mitotic cells encode experience-dependent alterations in their activity, so-called synaptic plasticity. Whereas a decade ago, the prevailing theory was that synaptic plasticity was a phenomenon that occurred primarily at the synapse, there is increasing realization that transcriptional events are critical to the encoding and maintenance of synaptic plasticity. What neurons do is alter their activity in response to external signals; we now understand that this type of lifelong plasticity depends on a continual interrogation of the genome. Transcription is the process whereby cells read specified portions of the DNA. Thus, increasing evidence demonstrates that neurons depend on transcriptional events in order to function normally. Expression profiling is the technique that permits simultaneous assessment of expression levels of thousands of genes. Using DNA microarrays, one can obtain an instantaneous snapshot of cellular activity. These measurements can often lead to novel hypotheses regarding pathogenesis. The first application of DNA microarrays to human neurologic disease revealed gene expression abnormalities in a transgenic mouse model of Huntington's disease (HD) (15). Subsequently, gene expression abnormalities have been found in a number of neurodegenerative diseases, including AD (1), ALS (5), PD (9,10,16), prion diseases (25), frontotemporal dementia and PSP (10), and multiple sclerosis (22), suggesting that impacting the genome is another common feature of these disorders. These studies of human
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