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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.

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.

A genome-wide association study recently identified an MSH3/DHFR locus associated with Huntington’s disease progression. Flower, Lomeikaite et al. identify tandem repeat variants at this locus, and show that a three-repeat allele is associated with reduced somatic expansion, delayed onset and slower progression in Huntington’s disease and myotonic dystrophy type 1., The mismatch repair gene MSH3 has been implicated as a genetic modifier of the CAG·CTG repeat expansion disorders Huntington’s disease and myotonic dystrophy type 1. A recent Huntington’s disease genome-wide association study found rs557874766, an imputed single nucleotide polymorphism located within a polymorphic 9 bp tandem repeat in MSH3/DHFR, as the variant most significantly associated with progression in Huntington’s disease. Using Illumina sequencing in Huntington’s disease and myotonic dystrophy type 1 subjects, we show that rs557874766 is an alignment artefact, the minor allele for which corresponds to a three-repeat allele in MSH3 exon 1 that is associated with a reduced rate of somatic CAG·CTG expansion (P = 0.004) and delayed disease onset (P = 0.003) in both Huntington’s disease and myotonic dystrophy type 1, and slower progression (P = 3.86 × 10−7) in Huntington’s disease. RNA-Seq of whole blood in the Huntington’s disease subjects found that repeat variants are associated with MSH3 and DHFR expression. A transcriptome-wide association study in the Huntington’s disease cohort found increased MSH3 and DHFR expression are associated with disease progression. These results suggest that variation in the MSH3 exon 1 repeat region influences somatic expansion and disease phenotype in Huntington’s disease and myotonic dystrophy type 1, and suggests a common DNA repair mechanism operates in both repeat expansion diseases.

Background Both male and female tsetse flies, haematophagous insects, transmit trypanosomes between hosts and are the cyclical vectors for Human African Trypanosomiasis (HAT) and Animal African Trypanosomiasis (AAT). Trypanosomes responsible for AAT can be transmitted by tsetse between wild animals and livestock. However, the degree of connectivity between the sylvatic and domestic cycles is unknown. The objectives of this study were to investigate patterns of host feeding in relationship to trypanosome prevalence among Kenyan populations of G. pallidipes at the livestock-wildlife interface. Methodology/Principal Findings Sources of blood meals of Glossina pallidipes were identified by polymerase chain reaction amplification and sequencing of the mitochondrial cytochrome b gene and compared with previous characterization of trypanosome prevalence from the same flies. In the Nguruman region in southern Kenya, the majority (98%) of the 148 flies for which dominant hosts could be resolved fed on single host species and only a single fly had fed on a domestic host; intriguingly this was the only fly confirmed to have fed on cattle. In contrast, in the Shimba Hills region (South Coast), multiple host feeding was more common: 42% inside a fenced wildlife protected area, where 35% of dominant hosts were domestic animals or humans, compared with 62% from traps set along the border to an adjacent village, which was dominated by domestic hosts (77%). Across sites, 44% of flies tested positive for trypanosomes (28/50 domestic hosts; 78/193 wild hosts). Multiple Correspondence Analysis revealed strong correlations between feeding pattern, host type and site but these were resolved along a different dimension than trypanosome status. Conclusions/Significance Our results suggest that host fidelity when feeding on wild hosts in G. pallidipes could reduce risk of transmission of trypanosomes to domestic hosts in interface areas and emphasise the importance of considering vector behaviour when designing management interventions. Author Summary Tsetse flies are the main vectors transmitting trypanosomes, which cause disease in both humans and animals. Since tsetse flies feed on a wide range of vertebrate hosts, there is the potential for transmission between wild and domestic animals in regions where their ranges overlap. In this study, we used molecular methods to determine the hosts fed on by tsetse flies sampled from three sites in Kenya at the wildlife-livestock interface. In areas where wildlife dominated, tsetse tended to feed on single host species, whereas in areas with more domesticated animals, they tended to feed on multiple hosts. These results suggest either that tsetse flies get interrupted more while feeding on domestic hosts or that they prefer to feed on wildlife and so switch hosts more often when feeding on less desirable hosts. Using data from a previous study on the same samples, we found that trypanosome prevalence was not correlated with the type or number of hosts fed on. These results have important implications for understanding the risk of transmission between wildlife and livestock in regions bordering protected areas but the high host fidelity for wild hosts suggests that tsetse feeding preferences could reduce risks of disease transmission to livestock.

Figure S1. Probability of T. congolense presence in tsetse samples from the best-fitting model (Model 3). pos_Sodalis: S. glossinidius-positive status. neg_Sodalis: S. glossinidius-negative status. This analysis shows the significant three-way interaction between sex, age and S. glossinidius status. (PDF 93 kb)

Table S4. Comparison of the target location, amplification product size for the three PCR primer pairs tested (pSG2-Farikou, GPO1 and Hem) for the detection of S. glossinidius in tsetse flies. (DOCX 57 kb)

Figure S5. The modified collection cage used with NG2G traps in this study. (PDF 2992 kb)

Figure S2. Probability of T. brucei presence in tsetse samples from the best-fitting model (Model 4), showing complex interactions. Predicted values are shown for males and females in the seven subpopulations: (a) G. pallidipes from Buffalo Ridge. (b) G. brevipalpis from Buffalo Ridge. (c) G. pallidipes from Zungu Luka. (d) G. austeni from Zungu Luka. (e) G. pallidipes from Mukinyo. (f) G. longipennis from Mukinyo. (g) G. longipennis from Sampu. (PDF 140 kb)

Table S2. Adjusted Eta2 for the combination of variables in dimensions 1â 3 in the Multiple Correspondence Analysis 1. (DOCX 13 kb)

Figure S3. Dimensions 1 and 2 of the Multiple Correspondence Analysis 1 showing the relationships between the trypanosome status of tsetse flies and their biological traits. Sex (male and female), age (young, juvenile and old) and S. glossinidius status (negative and positive) of the seven subpopulations were plotted for describing associations with the trypanosome status of tsetse flies (Tryp_negative and Tryp_positive). BRGp: G. pallidipes from Buffalo Ridge; BRGb: G. brevipalpis from Buffalo Ridge; ZuGp: G. pallidipes from Zungu Luka; ZuGa: G. austeni from Zungu Luka; MuGp: G. pallidipes from Mukinyo; MuGl: G. longipennis from Mukinyo; SaGl: G. longipennis from Sampu. (PDF 163 kb)

Summary of additional GLM analyses performed to consider: A) the tsetse-specific factors that affect presence or absence of Sodalis glossinidius, without taking into account trypanosome presence; B) the effects of site on Sodalis glossinidius, tested by considering only G. pallidipes; and C) the effects of site on trypanosome prevalence by focusing only on G. pallidipes. (DOCX 23 kb)

Figure S4. Dimension 3 and 4 of the Multiple Correspondence Analysis 1 for explaining relationships between the trypanosome status of tsetse flies and their biological traits. (PDF 89 kb)

Background: \ud Animal African Trypanosomiasis (AAT) is caused by several species of trypanosomes including Trypanosoma congolense, T. vivax, T. godfreyi, T. simiae and T. brucei. Two of the subspecies of T. brucei also cause Human African Trypanosomiasis. Although some of them can be mechanically transmitted by biting flies; these trypanosomes are all transmitted by tsetse flies which are the cyclical vectors of Trypanosoma congolense, T. godfreyi, T. simiae and T. brucei. We present here the first report assessing the prevalence of trypanosomes in tsetse flies in Nigeria using molecular tools.\ud \ud Methods: \ud 488 tsetse flies of three species, Glossina palpalis palpalis, G. tachinoides and G. morsitans submorsitans were collected from Wuya, Niger State and Yankari National Park, Bauchi State in 2012. Trypanosomes were detected and identified using an ITS1 PCR assay on DNA purified from the ‘head plus proboscis’ (H + P) and abdomen (ABD) parts of each fly.\ud \ud Results: \ud T. vivax and T. congolense Savannah were the major parasites detected. Trypanosomes prevalence was 7.1 % in G. p. palpalis, 11.9 % in G. tachinoides and 13.5 % in G. m. submorsitans. Prevalences of T. congolense Savannah ranged from 2.5 to 6.7 % and of T. vivax were approximately 4.5 %. Trypanosoma congolense Forest, T. godfreyi and T. simiae were also detected in the site of Yankari. The main biological and ecological determinants of trypanosome prevalence were the fly sex, with more trypanosomes found in females than males, and the site, with T. congolense subspp. being more abundant in Yankari than in Wuya. As expected, the trypanosome species diversity was higher in Yankari National Park than in the more agricultural site of Wuya where vertebrate host species diversity is lower.\ud \ud Conclusions: \ud Our results show that T. congolense Savannah and T. vivax are the main species of parasite potentially causing AAT in the two study sites and that Yankari National Park is a potential reservoir of trypanosomes both in terms of parasite abundance and species diversity.