Genetic modifiers of risk and age at onset in GBA associated Parkinson's disease and Lewy body dementia

Abstract

Parkinson's disease is a genetically complex disorder. Multiple genes have been shown to contribute to the risk of Parkinson's disease, and currently 90 independent risk variants have been identified by genome-wide association studies. Thus far, a number of genes (including SNCA, LRRK2, and GBA) have been shown to contain variability across a spectrum of frequency and effect, from rare, highly penetrant variants to common risk alleles with small effect sizes. Variants in GBA, encoding the enzyme glucocerebrosidase, are associated with Lewy body diseases such as Parkinson's disease and Lewy body dementia. These variants, which reduce or abolish enzymatic activity, confer a spectrum of disease risk, from 1.4- to >10-fold. An outstanding question in the field is what other genetic factors that influence GBA-associated risk for disease, and whether these overlap with known Parkinson's disease risk variants. Using multiple, large case-control datasets, totalling 217 165 individuals (22 757 Parkinson's disease cases, 13 431 Parkinson's disease proxy cases, 622 Lewy body dementia cases and 180 355 controls), we identified 1691 Parkinson's disease cases, 81 Lewy body dementia cases, 711 proxy cases and 7624 controls with a GBA variant (p.E326K, p.T369M or p.N370S). We performed a genome-wide association study and analysed the most recent Parkinson's disease-associated genetic risk score to detect genetic influences on GBA risk and age at onset. We attempted to replicate our findings in two independent datasets, including the personal genetics company 23andMe, Inc. and whole-genome sequencing data. Our analysis showed that the overall Parkinson's disease genetic risk score modifies risk for disease and decreases age at onset in carriers of GBA variants. Notably, this effect was consistent across all tested GBA risk variants. Dissecting this signal demonstrated that variants in close proximity to SNCA and CTSB (encoding cathepsin B) are the most significant contributors. Risk variants in the CTSB locus were identified to decrease mRNA expression of CTSB. Additional analyses suggest a possible genetic interaction between GBA and CTSB and GBA p.N370S induced pluripotent cell-derived neurons were shown to have decreased cathepsin B expression compared to controls. These data provide a genetic basis for modification of GBA-associated Parkinson's disease risk and age at onset, although the total contribution of common genetics variants is not large. We further demonstrate that common variability at genes implicated in lysosomal function exerts the largest effect on GBA associated risk for disease. Further, these results have implications for selection of GBA carriers for therapeutic interventions.

Keywords: CTSB; GBA; Parkinson’s disease; SNCA; modifiers.

Figure 1

Parkinson disease GRS box plots divided by disease status and GBA carrier status. GRS differences between GBA negative controls, GBA negative Parkinson’s disease or LBD cases, GBA positive controls and GBA positive cases. In each dataset, a highly similar effect is observed clearly separating the subgroups. PD = Parkinson’s disease.

Figure 2

Parkinson disease GRS box plots divided by disease status and GBA carrier status excluding GBA in the GRS calculation. GRS differences between GBA negative controls, GBA negative Parkinson’s disease or Lewy body dementia cases, GBA positive controls and GBA positive cases when excluding the GBA region and LRRK2 p.G2019S from the calculations. In each dataset, a highly similar effect is observed clearly separating the cases and controls. However, there is no clear separation between GBA cases and GBA negative cases or GBA negative controls and GBA positive controls. PD = Parkinson’s disease.

Figure 3

Genetic dissection of the CTSB locus. (A) LocusZoom plot of the CTSB region from the latest Parkinson’s disease GWAS (Nalls et al., 2018). (B) LocusZoom plot of the CTSB region from the latest current GBA carrier GWAS. (C) LocusCompare plot of the CTSB region showing high correlation between the Parkinson’s disease GWAS (x-axis) and the GBA carrier GWAS (y-axis). (D) LocusCompare plot of the CTSB region showing high correlation between the Parkinson’s disease GWAS (x-axis) and the brain QTL data (Qi et al., 2018) (y-axis).

Figure 4

Cathepsin B protein expression is decreased in iPSC derived neurons from GBA p.N370S carriers. Forebrain neurons differentiated from patient iPSCs with GBA mutations have decreased cathepsin B protein expression. (A) Representative western blot showing protein levels of active cathepsin B (CTSB, 24 and 29 kDa) and neuron associated β-III tubulin (50 kDa) in forebrain neurons differentiated from individuals with and without Parkinson’s disease-associated GBA variants (n = 2 lines from each genotype; all lines tested are heterozygous at rs1293298). (B) Quantification of the mean active cathepsin B protein levels relative to β-III tubulin shows a significant decrease (*P < 0.05; unpaired t-test, n = 2 lines of each genotype with three technical replicates each) in cathepsin B levels in forebrain neurons differentiated from GBA p.N370S carriers compared to neurons from wild-type (WT) GBA carriers. M = protein marker; error bars represent standard error of the mean. Note that both the heavy chain and heavy plus light chain bands were quantified in this analysis.

Figure 5

Parkinson’s disease GRS significantly influences the age at onset of GBA positive cases. Parkinson’s disease cases carrying a GBA variant were grouped by ages and a clear and significant decline was seen for the GRS. PD = Parkinson’s disease.