A probable cis-acting genetic modifier of Huntington disease frequent in individuals with African ancestry

Abstract

Huntington disease (HD)is a dominantly inherited neurodegenerative disorder caused by the expansion of a polyglutamine encoding CAG repeat in the huntingtin gene. Recently, it has been established that disease severity in HD is best predicted by the number of pure CAG repeats rather than total glutamines encoded. Along with uncovering DNA repair gene variants as trans-acting modifiers of HD severity, these data reveal somatic expansion of the CAG repeat as a key driver of HD onset. Using high-throughput DNA sequencing, we have determined the precise sequence and somatic expansion profiles of the HTT repeat tract of 68 HD-affected and 158 HD-unaffected African ancestry individuals. A high level of HTT repeat sequence diversity was observed, with three likely African-specific alleles identified. In the most common disease allele (30 out of 68), the typical proline-encoding CCGCCA sequence was absent. This CCGCCA-loss disease allele was associated with an earlier age of diagnosis of approximately 7.1 years and occurred exclusively on haplotype B2. Although somatic expansion was associated with an earlier age of diagnosis in the study overall, the CCGCCA-loss disease allele displayed reduced somatic expansion relative to the typical HTT expansions in blood DNA. We propose that the CCGCCA loss occurring on haplotype B2 is an African cis-acting modifier that appears to alter disease diagnosis of HD through a mechanism that is not driven by somatic expansion. The assessment of a group of individuals from an understudied population has highlighted population-specific differences that emphasize the importance of studying genetically diverse populations in the context of disease.

Keywords: African ancestry; CAG repeat; CCGCCA loss; Huntington disease; cis-acting modifier; genetically diverse.

Figure 1

The HTT disease and non-disease allele structures in African ancestry individuals Schematic representation of the HTT disease and non-disease allele structures defined for this study. The typical allele structures were grouped together as Q¹-2-2-P²-2, while the atypical allele structures are shown individually for deviations from the reference allele structure to be clearly demonstrated.

Figure 2

Frequency of the HTT haplotype B2 in the populations of the 1000 Genomes Project The African B2 haplotype was defined by SNPs rs2857936-rs762855-rs4690073 as described by Baine et al. The haplotype frequencies were obtained using the LDhap tool from the LDlink suite (ldlink.nci.nih.gov). Haplotype B2 was shown to have the highest frequencies among the African and African ancestry populations, ranging between 6.6% and 9.9%. Outside of the continental African populations, Puerto Rico (American) had the highest frequency of haplotype B2 (3.4%), followed by the five East Asian populations (range from 0.5% to 1.0%). The Columbian (American), Utah residents (European), and Sri Lankan (South Asian) populations had low frequencies (0.5%), and B2 was not detected in the rest of the populations analyzed. The results were comparable with the frequency of B2 in the African ancestry non-disease alleles included in this study. This indicates that, although this analysis was only conducted in non-disease alleles, haplotype B2 may be of an African origin and an African-specific haplotype.

Figure 3

The HTT allele structure associated with age at HD diagnosis and somatic expansion of the HD allele in blood DNA in African ancestry individuals (A) Linear regression analysis testing the association between the log transformed AoD and the inherited CAG repeat length for each disease allele structure revealed a significant association (r² = 0.61, p = 1.36 × 10⁻¹⁰). The Q¹-0-0-9-2 and Q¹-2-0-9-2 disease allele structures characterized by the loss of one or more of the intervening sequences had the earliest AoD. (B) The estimated marginal mean AoD for the disease allele structures, corrected for repeat size. The Q¹-2-0-9-2 allele structure had the earliest mean AoD (n = 30, 45.5 years: 95% CI = 43.0–48.2), followed by Q¹-0-0-9-2 (n = 2, 47.1 years: 95% CI = 38.1–58.1), Q¹-4-2-4-3 (n = 1, 50.4 years: 95% CI = 37.4–67.9), Q¹-2-2-P²-2 (n = 31, 53.0 years: 95% CI = 49.9–56.3), and Q¹-2-2-6-3 (n = 4, 56.9 years: 95% CI = 48.9–66.0). (C) Linear regression analysis testing the association between the log transformed AoD (corrected for CAG repeat length and allele structure) and expansion score. Overall, a significant association (p = 0.012) was identified. (D) The estimated marginal mean expansion score for the allele structures, corrected for CAG repeat length and age at sampling. The Q¹-0-0-9-2 (n = 2, 0.32: 95% CI = 0.227–0.458) and Q¹-2-0-9-2 (n = 30, 0.42: 95% CI = 0.380–0.460) allele structures had the lowest mean expansion score followed by Q¹-2-2-6-3 (n = 4, 0.44: 95% CI = 0.348–0.545), Q¹-4-2-4-3 (n = 1, 0.44: 95% CI = 0.288–0.680), and Q¹-2-2-P²-2 (n = 31, 0.60: 95% CI = 0.535–0.669).