Work

Assessing the NOTCH2NLC GGC expansion in European patients with essential tremor

Year: 2020

Type: letter

Abstract: Currently, there have been several genes implicated in essential tremor, such as FUS, STK32B and TENM4 (Merner et al., 2012; Hor et al., 2015; Müller et al., 2016; Liao et al., 2019). Other studies have investigated the cerebellar transcriptome and also found potentially relevant genes such as SHF and CACNA1A (Liao et al., 2020). However, some of these results have been inconsistent across cohorts, suggesting genetic and clinical heterogeneity, which may be influenced by misdiagnosis (Louis, 2014; Clark and Louis, 2015; Houle et al., 2017). We recently read with interest the article published in Brain by Sun et al. (2020) titled ‘Expansion of GGC repeat in the human-specific NOTCH2NLC gene is associated with essential tremor', which implicates a novel gene of interest for essential tremor (Sun et al., 2020). The authors screened 197 Chinese pedigrees and found that the NOTCH2NLC 5ʹ UTR expansion co-segregated in ∼5–6% of essential tremor families. Furthermore, cases carrying an expansion had a more severe tremor phenotype with lower quality of life. The pathogenic repeat size in expanded families was estimated to be 81 to 138 with a mean of 108.67 ± 22.24 GGC repeats. The healthy cohorts had a mean repeat size of 16.19 ± 5.21. The authors concluded that the GGC expansion may point towards a subset of essential tremor pedigrees with anticipation due to NOTCH2NLC. These observations led us to investigate whether this expansion is found in essential tremor individuals and control subjects with European ancestry. We screened whole-genome sequences of 204 beta-blocker responsive essential tremor cases with European ancestry and 406 control subjects with European ancestry and found no pathogenic NOTCH2NLC expansion in the control or case cohorts. Consent was acquired from all individuals participating in the study and the review board at the McGill University Health Center Research Ethics Board (MUHC REB) approved the study protocols (reference number IRB00010120). Beta-blocker response was defined as any individual who is currently on beta-blockers for essential tremor and/or responded positively to the drug with reduced tremor. This criterion was used in an attempt to increase clinical homogeneity for essential tremor. For instance, previous drug-responsive stratification for disorders, such as bipolar disorder, has led to increased genetic homogeneity (Hou et al., 2016). Samples were whole-genome sequenced on the Illumina NovaSeq 6000 at 30× and aligned using the Illumina DRAGEN Bio-IT pipeline using the hg38 build. European ancestry was confirmed by taking the average principal component 1 and 2 in the European 1000 Genomes Project cohort and removing individuals who deviated more than 3 standard deviations for either principal component. Highly related individuals with a p̂ > 0.125 were excluded. ExpansionHunter was used to estimate repeat sizes for the short-tandem repeat, GGC, in the region chr1:149390802-149390842 (hg38) with a region extension length of 1000 base pairs (bp). The region extension length specifies how far on and off target regions should be used to search for informative reads. The mean expansion size in controls was 20.32 (20.02, 20.63) and a median of 21 whereas the mean expansion size in cases was 20.60 (20.20, 21.10) with a median of 21 (Fig. 1). The mean confidence intervals were calculated using 1000 bootstraps and are reported as bias-corrected and accelerated bootstrap intervals (BCa). No cases or controls had pathogenic repeat sizes. Next, a two-sample Kolmogorov-Smirnov test was done, and it was found that the two probability distributions did not differ significantly (D = 0.52, P = 0.48), suggesting that they are comparable. Density distribution of NOTCH2NLC expansion sizes in essential tremor cases and control subjects. Bins were set to 20 for both groups. Density distribution of NOTCH2NLC expansion sizes in essential tremor cases and control subjects. Bins were set to 20 for both groups. Given that the pathogenic expansion frequency was 5–6% in Chinese essential tremor cases, we expected to find ∼10 samples with a pathogenic expansion (Sun et al., 2020). However, none of the European essential tremor cases or control subjects had a large repeat. The differences may suggest that the pathogenic expansion is rarer in European populations and points towards an ancestry-specific repeat implicated in essential tremor. Furthermore, we failed to find any differences between case-control repeat size distributions, suggesting that both cohorts have similar shape and spread, with no evident positive right shift in case repeat distribution. Future studies could evaluate larger essential tremor cohorts and assess whether the repeat is expanded in essential tremor patients with European ancestry. In conclusion, our results do not support a significant association between NOTCH2NLC 5ʹ UTR expansions and essential tremor risk in European ancestry. Future studies should investigate the role of expansions in essential tremor as typical mutation searches have not had a high yield and anticipation is seen in some families. The authors confirm that the data supporting the findings of this study are available within the article. We thank all the participants in the study. C.L. is funded by the Vanier Graduate Scholarship from the Canadian Institutes of Health (CIHR). G.A.R. holds a Canada Research Chair in Genetics of the Nervous System and the Wilder Penfield Chair in Neurosciences and is supported by a Canadian Institutes of Health Research Foundation Scheme Grant #332971. The authors report no competing interests.

Source: Brain

DOI: 10.1093/brain/awaa291