Genetic modifiers of Huntington disease differentially influence motor and cognitive domains

Abstract

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.

Keywords: CAG repeat; DNA maintenance; DNA repair; Huntington disease; age at onset; disease modification; genetic modifier; polyglutamine disease; somatic expansion; trinucleotide repeat.

Figure 1

Trajectory of HD clinical measures using HTT (CAG)₄₂ individuals as an example Proportion of the maximum sample value of the UHDRS SDMT (red), TFC (green), and TMS (blue) by age for CAG = 42. The black lines running left to right are based on the predicted mean trajectories from linear mixed models with cubic splines of age and the colored ribbons are bootstrapped 95% confidence bands. Each curve value indicates the proportion of the maximum sample value observed for the variable in our dataset, with max(SDMT) = 110, max(TFC) = 13, and max(TMS) = 107. The vertical black lines denote the age on the horizontal axis at which there is estimated to be 50% conversion, respectively, to DCL4 and TFC6 (median survival), with 95% confidence intervals. Median survival (and its confidence interval) was estimated with a parametric survival model (Weibull regression) that accommodated left truncation and right censoring.

Figure 2

GWAS of age at onset, age at DCL4, and age at TFC6 Stacked plots comparing GWASs show the −log10(p value) for SNV association with the Z score of CAG-specific age at onset, the Z score from age-at-DCL4 prediction, and the Z score from age-at-TFC6 prediction. The dotted red horizontal line shows the threshold for genome-wide significance (p value 5E−8). Solid arrows indicate loci that yield genome-wide significant signal with SNV of >1% MAF (with the exception of HTT), with candidate modifier genes all labeled in the top panel. One additional locus that awaits further confirmation is noted by a dashed arrow and its HD modifier effect designation (7BM1) based upon our standard nomenclature. Red labels indicate DNA maintenance genes.

Figure 3

Dichotomous GWAS of total motor score and symbol digit modalities test extremes Stacked plots of dichotomous GWASs (−log10(p value) for SNV association) comparing allele frequencies among HD subjects in the Registry study who represented consistent phenotypic extremes with respect to TMS (top) or SDMT (bottom). The dotted red horizontal line shows the threshold for genome-wide significance (p value 5E−8). Arrows mark the two loci that yielded genome-wide significant signal in at least one of the analyses with modifier gene labels denoted in the top panel.

Figure 4

GWAS of total motor score and symbol digit modalities test landmarks Stacked plots comparing GWAS analysis (−log10(p value) for SNV association) of age at TMS30 and age at SDMT30. Arrows indicate loci that yielded genome-wide significant signal for variants of >1% MAF (with the exception of HTT), with the candidate genes labeled in the top panel. The dotted red horizontal line shows the threshold for genome-wide significance (p value 5E−8). Red labels indicate DNA maintenance genes.

Figure 5

Age-at-TFC6 signal at MSH3 and FAN1 conditioned on other phenotypes Regional plots displaying age-at-TFC6 association significance (−log10(p value)) at MSH3 (left, chr 5) and FAN1 (right, chr 15) loci for the 4,879 participants for whom age at onset, age at DCL4, age at TFC6, age at TMS30, and age at SDMT30 were all available are shown above equivalent plots where the analysis was conditioned on each of the other age-at-landmark phenotypes. Each circle represents a different SNV with colored symbols indicating tag SNVs for particular modifier effects derived from the analysis of all 6,900 participants with age-at-TFC6 data: 5AM1, 5_79950781_A_G (red), 5AM2, 5_80086504_A_G (green); 5AM3, 5_79955360_G_GT (purple, peak SNV after conditioning on 5AM1 and 5AM2); 15AM1, 15_31202961_G_A (red), 15AM2, 15_31241346_G_A (green); 15AM3, 15_31197995_C_T (purple); 15AM5, 15_31282611_T_C (cyan).