Investigating Trans-acting Genetic Modifier Variants’ Association with Loss of Interruption (LOI) Variants and Impacts on Age of Onset in Relation to Canonical Alleles.

Huntington’s disease (HD) age of onset is primarily determined by the CAG repeat length in the huntingtin gene (HTT); however, CAG repeat length does not fully explain the variability in age of onset observed between HD affected individuals. Approximately a dozen HD genetic modifiers have been identified through genome-wide association studies (GWAS) that alter the onset and severity of disease to varying degrees. The most significant signals are found in genes involved in DNA mismatch repair and maintenance, including RRM2B (chr 8), FAN1 (chr 15), MSH3 (chr 5), PMS1 (chr 2), PMS2 (chr 7), LIG1 (chr 19), and MLH1 (chr 3). These are known as trans-acting genetic modifiers as these genes, which encode for proteins, are located at a physical distance relative to the HTT gene, while cis-acting modifiers are sequence variants located within the HTT repeat tract. The most impactful cis-modifiers are loss of interruption (LOI) variants, which lack one or both interrupting codons that are present in the canonical sequence.

Canonical alleles consist of CAG repeats with an interrupting penultimate CAA codon that together encode for polyglutamine as well as CCG repeats with a second interrupting CCA codon and downstream CCT codons that together encode for polyproline. LOI variants are classified based on the interruption loss: both interrupting codons in CAG and CCG repeats are absent in CAG-CCG LOI; only CCG repeats are uninterrupted in CCG LOI; and only CAG repeats are uninterrupted in CAG LOI.

Although LOI variants are associated with a significantly hastened onset and progression of disease, they do not fully explain the observed variability in age of onset. Additionally, some individuals within the UBC HD Biobank notably show significantly earlier onset despite having a canonical sequence, suggesting the presence of additional trans-acting genetic modifiers. This project thus aims to investigate whether trans-acting genetic modifiers are associated with LOI variants, and whether these modifiers could explain an earlier than expected age of onset in HD patients with canonical alleles.

This project will genotype validated onset-modifying variants in DNA mismatch repair genes using TaqMan assays and assess their association with age of onset in canonical and LOI variant patients. Onset hastening variants that will be investigated include DHFR; LINC01337

(rs701383) which is essential for DNA synthesis, RRM2B (rs79136984) which is crucial for mediating deoxyribonucleotide synthesis for DNA repair, and MTMR10; FAN1 (rs150393409) and FAN1 (rs151322829) which are both associated with DNA repair nucleases. By correlating trans-acting modifier genotypes with clinical onset data, this work aims to clarify the genetic sources of residual onset variability, advance understanding of how cis- and trans-acting mechanisms interact, and inform investigations into disease mechanisms.