Exploring the role of SVA retrotransposons in the risk and progression of motor neurone disease

Description

We and others have demonstrated that SVA retrotransposons are modulators of gene function, influencing gene expression, methylation, splicing and 3D chromatin architectures, particularly in the field of neurodegeneration. This includes associations of SVA retrotransposons, as well as other family members such as LINE1 and Alu, in neurodegenerative disorders including Parkinson’s disease, amyotrophic lateral sclerosis (ALS) (the most common form of MND) and X-linked dystonia Parkinsonism (XDP). In XDP, a single SVA insertion within an intron of the TAF1 gene is linked with development of XDP and polymorphisms within the primary sequence of the SVA is associated with age of onset. In the case of ALS, recent research has indicated significant links between iron regulation and metabolism with ALS, including the identification of serum ferritin levels as a potential biomarker. We identified the presence of an SVA RIP within the 3’ UTR of the TF gene and showed differential gene expression of TF in the presence/absence of the SVA. The TF gene encodes a glycoprotein which transports ions of ferric iron (Fe3+) to cells throughout the body. Our hypothesis is that the SVA within the TF gene can modulate expression of TF and thus have an impact on iron homeostasis regulation. This effect would have an influence with ALS disease mechanisms.

OBJECTIVES:

This proposal aims to better understand the genetic underpinning of complex disorders including ALS, by targeting the SVA within the TF gene in iPSC derived neuronal disease models. Using molecular approaches, we will analyse the function of the SVA on TF modulation and its role in ALS.

NOVELTY:

The field of retrotransposon involvement in complex neurodegenerative disorders is still in the early stages, but the evidence that these elements are involved in disease onset and/or progression is growing. Understanding the processes by which these elements are regulated, and the consequence of such regulation, is key to allow the development of novel therapeutic approaches to target SVAs, such as the use of antisense oligonucleotides (ASO).

EXPERIMENTAL APPROACH:

We will identify a suitable iPS cell model that contains the TF SVA using PCR genotyping, followed by CRISPR of the SVA within the selected line. The iPSCs will be differentiated into both generic glutamatergic neurons and motor neurons which we will then perform qPCR-based gene expression analysis of TF, comparing the difference between unmodified and CRISPR modified iPSCs and induced neurons. Further analysis will be performed including ChIP and luciferase reporter gene assays to assess function of the SVA on modulation of TF. Validation of differential gene expression could also be performed using RNA-seq.

POTENTIAL IMPACT:

If the TF SVA contributes to the regulation of the TF gene within neuronal models, we can design ASOs to target the SVA directly and modulate the behaviour of the SVA on TF expression. ASOs have been proven as a clinically effective and safe therapeutic and are currently in trials for use in ALS with Tofersen and Jacifusen. We are currently using ASOs to target transcription factors and will use the same protocols.

 

Applicants wishing to apply should send their CV and covering letters to Dr Ben Middlehurst at the email address benmidd2@liverpool.ac.uk. Eligible candidates will be asked to make formal applications through the University of Liverpool online application form.

Availability

Open to UK applicants

Funding information

Funded studentship

This project is fully funded through the University of Liverpool’s Faculty Supported Studentship scheme supported also by the Motor Neurone Disease Association (MNDA) and private charitable donations. This includes a stipend of £18,622 per year, postgraduate tuition fees (standard UK rate) and a research budget. This application is only open to UK based students.

Supervisors

References

  1. Pfaff AL, Bubb VJ, Quinn JP, Koks S. A Genome-Wide Screen for the Exonisation of Reference SINE-VNTR-Alus and Their Expression in CNS Tissues of Individuals with Amyotrophic Lateral Sclerosis. Int J Mol Sci. 2023;24(14).
  2. Hall A, Middlehurst B, Cadogan MAM, Reed X, Billingsley KJ, Bubb VJ, Quinn JP. A SINE-VNTR-Alu at the LRIG2 locus is associated with proximal and distal gene expression in CRISPR and population models. Scientific reports. 2024;14(1):792.
  3. Frohlich A, Hughes LS, Middlehurst B, Pfaff AL, Bubb VJ, Koks S, Quinn JP. CRISPR deletion of a SINE-VNTR-Alu (SVA_67) retrotransposon demonstrates its ability to differentially modulate gene expression at the MAPT locus. Front Neurol. 2023;14:1273036.
  4. Aneichyk T, Hendriks WT, Yadav R, Shin D, Gao D, Vaine CA, et al. Dissecting the Causal Mechanism of X-Linked Dystonia-Parkinsonism by Integrating Genome and Transcriptome Assembly. Cell. 2018;172(5):897-909 e21.