Huntington's disease (HD) is a progressive neurodegenerative disorder with autosomal dominant inheritance. It is caused by a singular mutation in exon 1 of the HD gene encoding an abnormal polyglutamine (polyQ) expansion in the N-terminal region of the huntingtin (htt) protein. HD is associated with severe motor, cognitive and psychiatric symptoms, and death occurs within one to two decades. Postmortem analysis of the brains of affected patients reveals proteinaceous inclusions, marked striatal atrophy, and extensive transcriptional dysregulation in the caudate, putamen and cerebral cortex. Both wild-type and mutant htt physically interact with numerous transcription factors, coactivators and repressors, implying aberrant protein-protein interactions and sequestration as a possible cause for the manifest gene expression alterations. The well-established and robust gene expression changes in the HD brain motivated our investigation of potential transcriptomic biomarkers in peripheral blood. The ultimate aim was to identify surrogate markers which can discriminate between different HD states, and thereby be valuable in evaluating the possible effects of new candidate HD therapeutics. Chapter 5.1. describes the result of a cross-sectional analysis of human HD samples using microarray and real-time PCR techniques. We identified one RNA, IER3, which showed significantly higher expression levels in HD than control and tracked with disease progression. In contrast, potential RNA biomarkers identified in a previous study were not differentially expressed between HD and controls in our sample set. Transcriptomic changes in HD can be seen as a composite representation of distinct, parallel disease mechanisms involving both cell-autonomous and trans-cellular effects. Primary striatal neuron models of HD comprised of rat ganglionic eminence cells transduced with lentiviral expression vectors delivering different lengths and dosages of htt protein have been extensively characterized in our lab (described in chapter 5.2.). Gene expression profiling of these in vitro HD models demonstrated high concordance with human HD. Disease-related effects on the transcriptome were dependent on the length of the polyQ repeat and time of mutant htt exposure. Importantly, the observed changes occurred in the absence of brain circuitry, and also in the absence of brain-derived neurotrophic factor, indicating that the transcriptomic level effects arise from direct actions of mutant htt in medium spiny neurons. The transcriptomic signatures of cultured neurons have also been employed as readout of neuroprotective effects of sirtuin 2 (SIRT2) inhibitors (see chapter 5.3.). Sirtuins comprise Class III histone deacetylases and thus have potential gene regulatory effects through transcription factor and chromatin modifications. Biological pathway analysis within the Gene Ontology framework showed that acute treatment with novel small-molecule SIRT2 inhibitors caused the downregulation of genes associated with sterol and lipid metabolism in both wild-type and polyQ htt expressing cells. In contrast, SIRT2 inhibition did not reverse polyglutamine-induced transcriptional dysregulation, suggesting that it works through an alternate mechanism. These results build on the current evidence supporting that sirtuins comprise interesting targets for anti-neurodegenerative drug development and suggest new candidate mechanisms for their therapeutic effects in neurons.