title: Deciphering the role of retrotransposon insertion polymorphisms as regulators of gene expression and as disease biomarker
Creators: name: Froehlich, Alexander
Publisher: name: University of Liverpool Repository
Year: 2024

description: Genome-wide association studies (GWAS) have demonstrated a significant genetic contribution for the development of multiple neurodegenerative disorders, including frontotemporal dementia (FTD) and Parkinson’s disease (PD), however, only a limited number of causative genetic variants have been identified. Transposable elements (TEs) represent one origin of genetic polymorphism within the human genome and have previously been proven to contribute to genome regulation and to have the potential to be involved in disease pathology and progression. Therefore, variation in the form of TEs can be an underappreciated source and a contributing factor to the genetic basis of complex diseases not captured in GWAS approaches. The main focus of the thesis was on a specific SINE-VNTR-Alu (SVA) retrotransposon (subclass element of TEs), termed SVA_67, which is located at the MAPT locus on chromosome 17, a genomic area associated with PD and FTD risk. The aim of this work was to broaden the understanding of SVA_67 as a regulatory domain to assess its association not only with differential transcriptomic gene profiles at this locus but
also with traits of disease progression. This targeted approach demonstrated that SVA_67 was not only polymorphic for presence or absence, termed retrotransposon insertion polymorphism, but also polymorphic for its central variable number tandem
repeat (VNTR) domain. Using a combination of wet lab and bioinformatic tools, SVA_67 was found to correlate with both regulatory capacities in an in vitro luciferase
reporter gene assay and changes in transcriptomic profiles of genes involved in pathogenic pathways of PD and FTD in vivo using transcriptomic datasets from both
the New York Genome Centre ALS Consortium and the Parkinson’s Progression Markers Initiative (PPMI) cohort. This regulatory potential as a genetic variant was validated using CRISPR technologies by generating SVA_67 knockout cell lines and quantifying expression changes in an otherwise genetically identical background by qPCR. Intriguingly, longitudinal analysis highlighted that SVA_67 VNTR polymorphism correlated with PD progression traits by using linear mixed-effects modelling and longitudinal clinical data from the PPMI cohort. The analysis was expanded to another class of retrotransposons, called long interspersed nuclear element (LINE-1/L1), whereby a global approach expanded the significant impact of TEs as expression quantitative trait loci and on PD progression.
Ultimately, this work highlights the plethora of phenotypic and transcriptomic changes linked with polymorphisms of transposable elements which should be considered when studying the missing heritability of neurodegenerative diseases. Therefore, this work can contribute to the identification of disease biomarkers that could be therapeutically targeted using technologies such as antisense oligonucleotides which are already in clinical trials for neurodegenerative disorders such as ALS.