What have we learned from gene expression profiles in Huntington's disease?

Extensive changes in DNA methylation are associated with expression of mutant huntingtin

The earliest stages of Huntington disease are marked by changes in gene expression that are caused in an indirect and poorly understood manner by polyglutamine expansions in the huntingtin (HTT) protein. To explore the hypothesis that DNA methylation may be altered in cells expressing mutated HTT, we use reduced representation bisulfite sequencing (RRBS) to map sites of DNA methylation in cells carrying either wild-type or mutant HTT. We find that a large fraction of the genes that change in expression in the presence of mutant huntingtin demonstrate significant changes in DNA methylation. Regions with low CpG content, which have previously been shown to undergo methylation changes in response to neuronal activity, are disproportionately affected. On the basis of the sequence of regions that change in methylation, we identify AP-1 and SOX2 as transcriptional regulators associated with DNA methylation changes, and we confirm these hypotheses using genome-wide chromatin immunoprecipitation sequencing (ChIP-Seq). Our findings suggest new mechanisms for the effects of polyglutamine-expanded HTT. These results also raise important questions about the potential effects of changes in DNA methylation on neurogenesis and cognitive decline in patients with Huntington disease.

Neuronal Ca(2+) dyshomeostasis in Huntington disease

The expansion of the N-terminal poly-glutamine tract of the huntingtin (Htt) protein is responsible for Huntington disease (HD). A large number of studies have explored the neuronal phenotype of HD, but the molecular aethiology of the disease is still very poorly understood. This has hampered the development of an appropriate therapeutical strategy to at least alleviate its symptoms. In this short review, we have focused our attention on the alteration of a specific cellular mechanism common to all HD models, either genetic or induced by treatment with 3-NPA, i.e. the cellular dyshomeostasis of Ca(2+). We have highlighted the direct and indirect (i.e. transcriptionally mediated) effects of mutated Htt on the maintenance of the intracellular Ca(2+) balance, the correct modulation of which is fundamental to cell survival and the disturbance of which plays a key role in the death of the cell.

Mechanism(s) of alteration of micro RNA expressions in Huntington's disease and their possible contributions to the observed cellular and molecular dysfunctions in the disease

To identify the mechanism of deregulation of micro RNAs (miRNAs) altered in Huntington's disease (HD) and their possible contributions to the altered cellular and molecular functions observed in the disease, we analyzed the altered miRNAs in the postmortem brains of HD patients. There are 54 miRNAs differentially expressed in HD brains of which 30 are upregulated and 24 downregulated. Some of these miRNAs were also altered in various models of the disease. Regulation of these miRNAs was attributed to transcription factors and the host genes to which these miRNAs reside. We observed that transcription regulators TP53, E2F1, REST, and GATA4 together could regulate expressions of 26 miRNAs in HD. Altered expressions of 13 intronic miRNAs were correlated with the expressions of their host genes. From literature, we further collected 287 experimentally validated targets of miRNAs upregulated in HD, while 304 validated targets of downregulated miRNAs in HD. Analysis of these validated target genes of altered miRNAs by gene ontology (GO) revealed that these genes are significantly enriched in GO terms belonging to (1) apoptosis, (2) differentiation and development, (3) fatty acid, cholesterol, lipid, glucose, and carbohydrate metabolism, (4) cell cycle and growth, and (5) transcription regulation. Experimental evidences that these processes are altered in HD are provided from published reports. In conclusion, altered miRNAs in HD might target many genes and may contribute to the altered cellular and molecular functions observed in HD.

Genetic modifiers of Huntington’s disease: beyond CAG

Huntington’s disease (HD) is caused by the expansion of a CAG repeat within exon 1 of the huntingtin (HTT) gene. Although the variation in age at onset is partly explained by the lengths of the expanded repeat, the unexplained variation is heritable, emphasizing the role of the so-called genetic background on disease expression. Identification of modifier genes can confirm intracellular pathways already suspected to be involved in pathophysiological processes related to HD pathogenesis, but it may also point to completely new pathways and processes that have not yet been considered. Most importantly, confirmed modifier genes provide new targets for the development of therapies. Up to now, a wide range of susceptible HD modifier genes related to different biochemical pathways has been examined. On the basis of the published literature in this field, this review provides an overview of HD modifiers and integrates them into selected pathophysiology aspects.