NEW YORK(GenomeWeb) – Researchers at Leiden University Medical Center in The Netherlands have discovered a panel of five genes whose expression in whole blood correlates with progression of Huntington's disease.
In a study published online last week in The European Journal of Human Genetics, the group reported that transcriptome analysis of 91 Huntington's mutation carriers, about one third of whom were presymptomatic, and 33 controls yielded 167 differentially expressed genes. Twelve of the top 20 genes were validated using a different technique, and five of these proved significant in a smaller, independent cohort as well.
Presymptomatic testing can reveal expanded CAG repeats in theHuntingtongene, and symptom onset and rate of neurodegeneration vary with increasing repeats. There are currently a number of measures ofHuntington's-related pathology progression, including MRI, motor scores, and cognitive tests. "These can all follow the course of the disease, but there is no wet lab biomarker yet," Willeke van Roon-Mom, a geneticist at LUMC and corresponding author on the study, told GenomeWeb in an interview.
While there are a many pharmacological treatments for specific Huntington symptoms, van Roon-Mom said, "there haven't been many success stories" in trials of therapies that might slow progression or delay onset of the disease. "They always struggle to get a significant finding," she explained.
A relatively inexpensive, objective, and quantitative measure of disease progression may be particularly useful for clinical trials of drug treatments, providing "an extra read-out parameter to say if a treatment is effective or not," she said.
Van Roon-Mom and her colleagues are currently developing one such therapy, and a clinical trial of an anti-sense oligoneucleotide drug, the result of collaboration between Roche and Isis, is also slated to begin this year, she noted.
"That is an interesting trial, I think, because that is one of the first ones to actually target the real cause of the disease, which is the defective protein," van Roon-Mom said.
Her lab's Huntington's disease interventions are geared toward lowering expression of small, and very toxic, huntingtin protein fragments, while avoiding causing a decrease in overall levels of the protein, van Roon-Mom said. This could be important because huntingtin protein is also required for adult brain function, and lowering its levels may be harmful in the long term. This work is being undertaken with commercial partners, she said, but because it is in the early development stages she could not elaborate further.
The panel of biomarkers differentiating Huntington's disease gene carriers with and without symptoms from controls was developed using DeepSAGE sequencing and further validated using a Fluidigm RT-qPCR array. The researchers also confirmed the results using an independent cohort of 12 more symptomatic gene carriers and 11 controls. Differential expression levels were then correlated with scores of motor functioning.
The group used DeepSAGE-seq because it is a tag-based method that can quantify the number of transcripts expressed. At the time the study began, RNA-seq was not yet feasible on such a large sample size, van Roon-Mom said. The Fluidigm array, meanwhile, enabled the group to run many samples in parallel, and was "a really efficient way of testing a lot of genes on a lot of samples with quantitative RT-PCR," she said.
The exact relationship between neurodegeneration and transcript levels in blood is unknown, and van Roon-Mom said it is even possible the panel could generalize to other neurodegenerative disorders, such as Alzheimer's. Be that as it may, "We are quite confident that, forHuntington's, it is quite a robust panel," she said.
One mechanism explaining the potential correspondence between changes in blood and brain may be the fact that mutant huntingtin protein is present throughout the body, van Roon-Mom said, adding, "We know there is peripheral pathology in Huntington's disease as well, and that's related to expression of the mutant protein in the peripheral tissues."
The study was part of larger blood-based biomarker discovery efforts at LUMC, van Roon-Mom noted. "We have a big biosemantics research group here at the department, so they're looking with concept profile analysis and text mining to see if we can find out how different or how similar these disease signatures are," she said.
The next step will be to analyze blood samples that were collected four years later from the same cohort. This may allow the group to confirm the findings, and could provide data on how these biomarkers change with disease progression in individual patients.
The Roche-Isis oligo-based gene silencing drug, ISIS-HTTRx, is scheduled to enter Phase I clinical trials this year in Canadaand Europe, according to a recent statement released by the Huntington Society of Canada. Isis collaborators have also published results of an RNAi treatment in a mouse model of the disease. RNAi-based treatments from Genzyme are in the early stages, and a genome-wide RNAi screen two years ago revealed hundreds of potential drug targets for Huntington's.
Other groups, meanwhile, have been examining protein biomarkers of the disease. Notably, a collaboration between KineMed and the CHDI Foundation has been looking at hutingtin protein in axons. CHDI has also extended a collaboration that will support 52 full-time scientists at Evotec who will use high-throughput screening and proteomics platforms forHuntington's drug discovery.