Genome-wide Association and Meta-analysis of Age at Onset in Parkinson Disease

Discussion

The identification of genetic determinants that modify the disease progression will not only help to increase our understanding of PD etiopathogenesis but also enable the development of strategies that could be used for therapeutic intervention for at-risk carriers. Our study not only validates previously reported AAO PD loci in the COURAGE-PD dataset, but our meta-analysis with IPDGC data also provides the first genome-wide significant evidence that the known BST1 PD risk locus affects AAO. Of interest, the variant, rs4698412, representing the BST1 locus, showed a similar large effect in COURAGE-PD and IPDGC, providing strong evidence that this is a bona fide genetic locus for PD AAO. Finally, using significant SNVs from the meta-analysis of COURAGE-PD and IPDGC case-control datasets, we demonstrate an inverse association between a PD PRS and AAO of PD.

Numerous genetic loci for familial and sporadic PD have been well characterized. The existence of overlapping loci between familial and sporadic PD suggests a complex but interconnected relationship between PD and age. Several meta-analyses of candidate genes and GWAS have previously recognized the BST1 locus as a locus that could influence the development of sporadic late-onset PD.^6,22,-,24 Notably, the BST1 locus has been demonstrated to play a role in both Asian and European PD populations.^6,22,-,24 The genome-wide significant BST1 variant, rs4698412 observed in our AAO meta-analysis, is also identical to the top BST1 variant reported in the latest PD GWAS meta-analysis.⁶ Of interest, regional plots showed that the genome-wide significant variant, rs4694812, was neither the top genetic variant in the BST1 locus in IPDGC nor COURAGE AAO PD datasets. Although rs4694819 (r² with rs4694812 < 0.6) was the most significant variant in the COURAGE AAO dataset, rs11724635 (r² with rs4698412 = 1.0) was the most significant variant in the IPDGC AAO dataset (eFigure 2B, links.lww.com/WNL/C86).

BST1 was first identified as a gene encoding a cell surface receptor on bone marrow stromal cells (bone marrow stromal cell antigen 1) with a role in promoting the growth of hematopoietic stromal cells.²⁵ In addition to its role as a receptor, it also exhibits ADP-ribosyl cyclase activity, leading to the generation of cyclic ADP-ribose, with a role in intrinsic Ca²⁺ regulation.²⁶ The dual functional protein, a highly conserved glycosylphosphatidylinositol-anchored glycoprotein (also known as CD157), is now known to be expressed in a wide variety of tissues, including the vascular endothelium and follicular dendritic cells, with an ability to perform a wide variety of immune system– and inflammation-related cellular functions.²⁷ The initial identification of BST1/CD157 as a potential risk locus for sporadic late-onset PD in a GWAS in the Japanese population led to several functional studies aimed at deciphering its potential neuronal role in influencing the PD phenotype.²² Several knockout mouse model studies have shown that BST1 can influence social behavior. However, the studies failed to demonstrate any influence on motor functioning, the cardinal feature that is impaired in patients with PD.^28,29 The eQTL analysis demonstrated a highly significant effect of the BST1 locus, rs4694812, on gene expression, with the A allele resulting in a decreased expression of CD38, a paralog of CD157, in a dose-dependent manner. CD38 and CD157 are contiguous gene duplicates, which belong to the same gene family with a similar role of dual functional protein and an ability to modulate social behavior.^30,31 Of interest, unlike CD157, CD38 knockout mice have been shown to have higher locomotor activity.³² Furthermore, the highly significant increased expression of CD38 was mainly observed in the striatum, a region directly implicated in motor dysfunction in PD. Of interest, a statistically underpowered brain imaging study in humans suggested that allele A of BST1 SNV rs4698412 leads to deficits in the right lingual gyrus region in the brain during the progression of PD.³³ This brain region is known to play a role in spatial orientation and visuospatial information processing. However, specific molecular and neuronal pathways influenced by altered CD38 expression in basal ganglia, with a potential role in triggering earlier AAO in sporadic PD, remain unclear.

SNCA is one of the most consistently observed significant loci in both early- and late-onset PD and has been suggested to play a critical role in the age-related hierarchy of disease onset. Although monogenic PD, often with relatively early onset, is attributed to rare point mutations and multiple copies of the SNCA gene, susceptibility to late-onset PD is attributed to common variants.^6,10,34,-,36 In addition to being a leading locus in the largest GWAS of sporadic PD to date, the locus was also recently reported to be a top locus in influencing AAO in Europeans in meta-analyses comprising IPDGC and 23andMe datasets (n = 28,568).⁷ An SNV present toward the 3′ end (rs356203) of the SNCA gene was observed as the strongest genome-wide significant variant originating from the region (p = 1.9 × 10⁻¹²). Based on the conditional analysis, the study also identified an independent signal at the 5′ end of the gene, rs983361 (p = 6.8 × 10⁻⁶). A recent GWAS of AAO in 5,166 East Asian (Chinese) patients with PD further reported a slightly weaker signal originating from another independent SNCA variant, rs3775458 (p = 9.92 × 10⁻⁷).⁹ Using the 1000 genome phase 3 dataset, we failed to detect any LD among the 3 variants in both European and East Asian populations (data not shown here). On screening the SNCA locus in the COURAGE-PD dataset, we observed nominal significance of all the 3 variants (P_{COURAGE (rs356203)} = 0.035, P_{COURAGE (rs3775458)} = 0.005, and P_{COURAGE (rs983361)} = 0.022), possibly suggesting a consistence influence of different loci around the SNCA region in determining AAO in different worldwide PD populations. The combination of our dataset with IPDGC further showed an independent genome-wide significant signal originating from the 3′ end of the SNCA gene (rs983361), as shown in the Results section above. Notably, we also observed an independent signal at the 5′ end (rs356203). However, the variant was excluded for further interpretation because of high heterogeneity observed when combining IPDGC and COURAGE datasets (β(SE)_{COURAGE+IPDGC} = −0.591(0.097), P_{COURAGE+IPDGC} = 9.28 × 10⁻¹⁰; I² = 61.9%).

Another PD locus, TMEM175, was previously shown to reach genome-wide significance in an AAO study.³⁷ Similar to SNCA, our study also demonstrated replication of the TMEM175 locus in the COURAGE-PD AAO dataset with a nominal level of significance (p = 0.018). The subsequent combination of the nonsynonymous coding variant, rs3431186 (p.M393T), representing the genome-wide significant locus, in the IPDGC dataset with the COURAGE-PD, resulted in the suggestive level of association without any underlying heterogeneity (P_{COURAGE+IPDGC} = 2.64 × 10⁻⁷; I² = 0.0). On the contrary, a recent East Asian GWAS failed to observe any signal originating from the locus, possibly suggesting the contribution of the locus mainly in the European populations.⁹ A previous study also reported a borderline significant association of the variant rs429358, representing the APOE ε4 locus with PD-AAO (p = 5.69 × 10⁻⁸) in a combined dataset (n = 28,568) comprising IPDGC and 23andMe datasets.⁷ The study, however, suggested that the association at the locus could be an age-related effect, with a highly significant association with the age of controls (p = 1.49 × 10⁻⁵). The variant also resulted in a suggestive association on merging of the COURAGE-PD European dataset only with the IPDGC dataset (p = 9.3 × 10⁻⁷). These findings are consistent with the failure to detect the association of APOE ε4 locus with PD-AAO in the recently reported East Asian GWAS.⁹ However, being a longevity marker, the suggestive finding of the APOE ε4 locus in Europeans must be interpreted with caution.

Our study has several strengths and limitations. Our study provides the largest independent dataset for testing the reliability of previously discovered AAO loci in a highly diverse and predominantly European population. Another strength of our study was the availability of data on AAO on all the study participants as opposed to the age at diagnosis, often used as a proxy for AAO. One of the significant limitations of our findings was the lack of ready access to the recently published East Asian AAO GWAS dataset that prevented us from drawing any conclusion on the validity of the novel BST1 locus in the East Asian population. Likewise, the unavailability of the 23andMe dataset to us has precluded us from making an unequivocal claim on our BST1 findings. Hopefully, the inclusion of other datasets, such as 23andMe and East Asian GWAS datasets, will help further to refine the signals originating from the BST1 locus. We also suggest that loci identified through meta-analysis in the COURAGE-PD dataset (PDZPH1P) and subsequent stratification by gender (RHEB, MTHFD1L, and KNH3) and ethnicity (MOAP1/TMEM251 and SUGCT) be meta-analyzed with these unavailable datasets. Another limitation was our inability to conduct gene-gene interaction because of the limited sample size in this study. The possibility of complex interactions among various loci on Chr 4 in modulating AAO cannot be ruled out. A recent study showed the association of several genome-wide significant loci on the X Chr with PD.³⁸ It is also possible that some of these variants may also modulate AAO. However, owing to potential analytic challenges from calling and imputation of X Chr genotypes, to model uncertainty associated with random X Chr inactivation, we excluded the X Chr variants from the present analysis.³⁹ And finally, it is hoped that in the future, the availability of a larger dataset would enable us to integrate additional layers of genetic data, including rare and copy number variants.⁴⁰

Our findings clearly highlight the importance of combining GWAS from diverse populations, representative of worldwide populations, to refine the genetic architecture underlying a complex trait such as AAO. Our COURAGE-PD dataset suggests a role for additional pathways in addition to α-synuclein mechanisms of modulating PD pathogenesis and influencing AAO in worldwide PD populations.