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Many Mendelian disorders, such as Huntington's disease (HD) and spinocerebellar ataxias, arise from expansions of CAG trinucleotide repeats. Despite the clear genetic causes, additional genetic factors may influence the rate of those monogenic disorders. Notably, genome-wide association studies discovered somewhat expected modifiers, particularly mismatch repair genes involved in the CAG repeat instability, impacting age at onset of HD. Strikingly, FAN1, previously unrelated to repeat instability, produced the strongest HD modification signals. Diverse FAN1 haplotypes independently modify HD, with rare genetic variants diminishing DNA binding or nuclease activity of the FAN1 protein, hastening HD onset. However, the mechanism behind the frequent and the most significant onset-delaying FAN1 haplotype lacking missense variations has remained elusive. Here, we illustrated that a microRNA acting on 3'-UTR (untranslated region) SNP rs3512, rather than transcriptional regulation, is responsible for the significant FAN1 expression quantitative trait loci signal and allelic imbalance in FAN1 messenger ribonucleic acid (mRNA), accounting for the most significant and frequent onset-delaying modifier haplotype in HD. Specifically, miR-124-3p selectively targets the reference allele at rs3512, diminishing the stability of FAN1 mRNA harboring that allele and consequently reducing its levels. Subsequent validation analyses, including the use of antagomir and 3'-UTR reporter vectors with swapped alleles, confirmed the specificity of miR-124-3p at rs3512. Together, these findings indicate that the alternative allele at rs3512 renders the FAN1 mRNA less susceptible to miR-124-3p-mediated posttranscriptional regulation, resulting in increased FAN1 levels and a subsequent delay in HD onset by mitigating CAG repeat instability. [ABSTRACT FROM AUTHOR]

Genome-wide association studies (GWASs) of Huntington disease (HD) have identified six DNA maintenance gene loci (among others) as modifiers and implicated a two step-mechanism of pathogenesis: somatic instability of the causative HTT CAG repeat with subsequent triggering of neuronal damage. The largest studies have been limited to HD individuals with a rater-estimated age at motor onset. To capitalize on the wealth of phenotypic data in several large HD natural history studies, we have performed algorithmic prediction by using common motor and cognitive measures to predict age at other disease landmarks as additional phenotypes for GWASs. Combined with imputation with the Trans-Omics for Precision Medicine reference panel, predictions using integrated measures provided objective landmark phenotypes with greater power to detect most modifier loci. Importantly, substantial differences in the relative modifier signal across loci, highlighted by comparing common modifiers at MSH3 and FAN1, revealed that individual modifier effects can act preferentially in the motor or cognitive domains. Individual components of the DNA maintenance modifier mechanisms may therefore act differentially on the neuronal circuits underlying the corresponding clinical measures. In addition, we identified additional modifier effects at the PMS1 and PMS2 loci and implicated a potential second locus on chromosome 7. These findings indicate that broadened discovery and characterization of HD genetic modifiers based on additional quantitative or qualitative phenotypes offers not only the promise of in-human validated therapeutic targets but also a route to dissecting the mechanisms and cell types involved in both the somatic instability and toxicity components of HD pathogenesis., Competing Interests: Declaration of interests J.M.L. serves on the scientific advisory board of GenEdit Inc. V.C.W. is a scientific advisory board member of Triplet Therapeutics Inc., a company developing new therapeutic approaches to address triplet repeat disorders such as Huntington disease and myotonic dystrophy. Her financial interests in Triplet Therapeutics were reviewed and are managed by Massachusetts General Hospital and Mass General Brigham in accordance with their conflict of interest policies. She is a scientific advisory board member of LoQus23 Therapeutics Ltd and has provided paid consulting services to Acadia Pharmaceuticals Inc., Alnylam Inc., and Biogen Inc. She has also received research support from Pfizer Inc. J.A.M. is a paid consultant for PTC Therapeutics Inc. and Behavioral Diagnostics Inc. and has also been a consultant for Wave Life Sciences USA Inc. T.H.M. is an associate member of the scientific advisory board of LoQus23 Therapeutics Ltd. G.B.L. has provided consulting services, advisory board functions, clinical trial services, and lectures for Acadia, Affiris, Allergan, Alnylam, Amarin, AOP Orphan Pharmaceuticals AG, Bayer Pharma AG, Boehringer-Ingelheim, CHDI Foundation, GlaxoSmithKline, Hoffmann-LaRoche, Ipsen, ISIS (Ionis) Pharma, Lundbeck, Neurosearch Inc., Medesis, Medivation, Medtronic, NeuraMetrix, Novartis, Pfizer, Prana Biotechnology, PTC Therapeutics, Raptor, Remix, Sangamo/Shire, Sanofi-Aventis, Siena Biotech, Takeda, Temmler Pharma GmbH, Teva Pharmaceuticals and Triplet Therapeutics. J.S.P. is a paid consultant for Acadia Pharmaceuticals and Wave Life Sciences USA Inc. E.R.D. has received research support from Wave Life Sciences USA Inc. D.G.M. has been a scientific consultant and/or received honoraria/stock options from AMO Pharma, Charles River, LoQus23, Small Molecule RNA, Triplet Therapeutics, and Vertex Pharmaceuticals and held research contracts with AMO Pharma and Vertex Pharmaceuticals within the last 5 years. L.J. is a member of the scientific advisory boards of LoQus23 Therapeutics Ltd and Triplet Therapeutics Inc. and a member of the executive committee of the European Huntington Disease Network. J.D.L. is a paid advisory board member for F. Hoffmann-La Roche Ltd and UniQure, and he is a paid consultant for Triplet Therapeutics, PTC Therapeutics, and Remix Therapeutics. J.F.G. is a scientific advisory board member and has a financial interest in Triplet Therapeutics Inc. His NIH-funded project is using genetic and genomic approaches to uncover other genes that significantly influence when diagnosable symptoms emerge and how rapidly they worsen in Huntington disease. The company is developing new therapeutic approaches to address triplet repeat disorders such Huntington disease, myotonic dystrophy, and spinocerebellar ataxias. His interests were reviewed and are managed by Massachusetts General Hospital and Mass General Brigham in accordance with their conflict of interest policies. J.F.G. has also been a consultant for Wave Life Sciences USA Inc., Biogen Inc., and Pfizer Inc., (Copyright © 2022 American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.)

Huntington's disease (HD) is caused by a CAG repeat expansion in the HTT gene. Repeat length can change over time, both in individual cells and between generations, and longer repeats may drive pathology. Cellular DNA repair systems have long been implicated in CAG repeat instability but recent genetic evidence from humans linking DNA repair variants to HD onset and progression has reignited interest in this area. The DNA damage response plays an essential role in maintaining genome stability, but may also license repeat expansions in the context of HD. In this chapter we summarize the methods developed to assay CAG repeat expansion/contraction in vitro and in cells, and review the DNA repair genes tested in mouse models of HD. While none of these systems is currently ideal, new technologies, such as long-read DNA sequencing, should improve the sensitivity of assays to assess the effects of DNA repair pathways in HD. Improved assays will be essential precursors to high-throughput testing of small molecules that can alter specific steps in DNA repair pathways and perhaps ameliorate expansion or enhance contraction of the HTT CAG repeat.