Leveraging single-nucleus RNA sequencing data to dissect mechanisms of polyglutamine toxicity in Huntington’s disease

Project supervisors:

• Professor Flaviano Giorgini
• Professor Ed Hollox

Project Description:

The project is open to UK applicants only.

HD is an inherited neurodegenerative disorder caused by the expansion of a CAG repeat in the HTT gene and is associated with brain pathology in the striatum within the basal ganglia. This CAG region encodes an expanded polyglutamine (polyQ) tract within the HTT protein, which is the primary driver of toxicity in HD. The inherited CAG length by itself is not enough to cause disease, but instead, the allele appears to be somatically unstable if >38-40 repeats, expanding in length over time in susceptible cells [e.g. medium spiny neurons (MSN) within the striatum]. Single-nucleus RNA sequencing (snRNA-seq) studies from postmortem HD brains support the idea that dysregulation occurs when the CAG length at the HTT locus exceeds ~140-150 repeats, eliciting a transcriptional response that reflects loss of neuronal identity, i.e., loss of cell type specific transcripts and upregulation of ubiquitous genes.

A related triplet repeat disease (Spinocerebellar ataxia 1, SCA1) is caused by an expansion of a CAG repeat in the ATXN1 gene. Intriguingly a recent report showed that this disease gene is also susceptible to somatic expansion in similar brain cells, and while the clinical symptoms arise from brainstem and cerebellar nuclei that succumb following CAG expansion, the MSNs in the striatum are also exposed to expanded ATXN1 gene product. Transcriptional dysregulation in these SCA1 MSNs is highly correlated to changes seen in HD, giving rise to the hypothesis that these diseases share largely overlapping agents of toxicity (polyQ protein localized to the nucleus) and that transcriptional loss of cellular identity is a shared feature resultant of this event.

The project will focus on the characteristics shared by triplet repeat disease transcriptional dysregulation in the MSNs and attempt to deeply understand the apparent loss of cell identity genes. For example, is the loss of cell identity unique to polyQ toxicity or a transcriptional program commonly seen in neurons facing cell demise? The fraction of transcriptional responses in MSNs not shared between SCA1 and HD brains would also give insights into understanding what separates the two diseases that gives rise to distinct clinical features. In parallel, additional datasets of vulnerable cell types from other CAG repeat disorders will be cross-compared to the MSN data in order to further test the specificity of these transcriptional signatures. This project will utilise unique data sets generated by or available to CHDI, as well as published data sets from clinical and preclinical models of triplet repeat disorders. The candidate will employ bioinformatics pipelines/expertise available at Leicester to deeply analyse the transcriptomic profiles in key brain regions of these two disorders across stages of disease and key regions of the brain as well as representative peripheral tissues. “Starting” CAG repeat length from blood or other genetically stable sources of DNA as well as somatic instability of the repeat will also be considered. Downstream gene ontology and network analyses of the differentially expressed transcriptome will be performed to ascertain similarities and differences between these disorders, which will help identify key aspects of the pathology which could be targeted for therapeutic intervention.

References:

Bates et al., Nature Reviews Disease Primers 2015

Matsushima et al., Nat Comm 2023

Tejwani et al., Neuron 2024