Analysis of PTRHD1 common and rare variants in European patients with Parkinson’s disease

Abstract

Three studies in Iranian and African families identified three different variants in the peptidyl-tRNA hydrolase domain containing 1 gene (PTRHD1) in patients affected by parkinsonism with intellectual impairment. In the current study, our objective was to investigate whether PTRHD1 variants are associated with Parkinson’s disease (PD) risk and age at onset (AAO). To evaluate the association between PTRHD1 and PD risk, we analyzed whole genome sequencing data of 1647 PD cases and 1050 healthy controls, as well as genome-wide imputed genotyping data on 14,671 PD cases and 17,667 controls, all of European ancestry. Furthermore, we examined the association of PTRHD1 with PD risk and AAO using summary statistics data from the most recent PD genome-wide association study meta-analyses. Our results show no association between PTRHD1 and PD risk or AAO. We conclude that PTRHD1 does not play a major role in PD in the European population. Further large-scale studies including subjects with different ancestry and family trios are required.

1. Introduction

Parkinson’s disease (PD) is a complex neurodegenerative disorder resulting from a variety of genetic and nongenetic risk factors. Three family studies nominated peptidyl-tRNA hydrolase domain containing 1 gene (PTRHD1) as a possible disease-causing gene in atypical parkinsonism Jaberi et al., 2016; Khodadadi et al., 2017; Kuipers et al., 2018). In particular, a study on Iranian families identified the homozygous PTRHD1 variant c.l57C>T (p.His53Tyr) in two siblings with cognitive impairment and successive development of parkinsonism at the third/fourth decade of life (Khodadadi et al., 2017). Likewise, two independent studies found that homozygous carriers of the PTRHD1 variant c.155G>A (p.Cys52Tyr) in an Iranian family (Jaberi et al., 2016) and of the homozygous deletion (c.l69_196del, p.Ala57Argfs*26) in an African family, showed similar symptoms, including intellectual disability and early onset parkinsonism (onset at the third decade of life for the Iranian family and first/third decade for the African family) (Kuipers et al., 2018).

Despite these findings, no large-scale study has been performed before in the European population to investigate the relationship between PTRHD1 and PD. To test this potential association, we examined the PTRHD1 region in Europeans using whole genome sequencing (WGS) from the Accelerating Medicines Partnership - Parkinson’s disease initiative (AMP-PD; www.amp-pd.org) and large-scale genome-wide association study (GWAS) data from the International Parkinson’s Disease Genomics Consortium (IPDGC).

2. Methods

To investigate the association of PTHRD1 common and rare variants with PD, we performed Fisher exact test and logistic regression in WGS AMP-PD data including 1647 PD cases and 1050 healthy controls of European descent (Supplementary Table S7). We repeated the analyses on a large European cohort using individual-level GWAS data including 14,671 PD cases and 17,667 controls from IPDGC (Supplementary Table S7). Logistic regression was adjusted for age, sex, and principal components. Summary statistics from the most recent GWAS meta-analysis on PD risk previously described (Nalls et al., 2019) excluding 23andMe data were also examined. In particular, the meta-analysis consisted of 15,056 PD cases, 18,618 UK Biobank proxy-cases (i.e., subjects with a first degree relative with PD) and 449,056 controls, all of European ancestry. As individuals carrying PTRHD1 variants displayed early onset parkinsonism we also assessed the most recent meta-analysis on PD AAO previously described (Blauwendraat et al., 2020), including 17,996 PD patients of European ancestry. Finally, as the PTRHD1 variants analyzed in the reported family studies were all rare, we evaluated the enrichment of PTRHD1 rare variants in WGS data using burden and kernel tests. The analyses on rare variants were first performed on all PTRHD1 rare variants that passed quality control, and then repeated only on the nonsynonymous rare variants. Bonferroni correction for multiple comparisons was applied as needed. Association analyses were performed using PLINK vl.9 (Chang et al., 2015) and burden analyses using software package RVTESTS v.2.1.0 (Zhan et al., 2016).

WGS data, processing and quality control pipelines can be found atwww.amp-pd.org. Quality control for GWAS data was performed as previously described (Nalls et al., 2019). For both genotyping and sequencing datasets, PTRHD1 region was annotated using ANNOVAR. To specifically analyze rare variants from WGS data, we selected variants with a minor allele frequency (MAF) <0.01.

3. Results

After Bonferroni correction, Fisher exact test and logistic regression showed no association between PTRHD1 variants and PD both using WGS and GWAS individual-level data (Supplementary Tables S1-S4). The analysis of the PD meta-analysis summary statistics confirmed such lack of association of PTRHD1 with PD risk (Fig. 1) as well as with PD AAO (Fig. 1). Finally, burden and kernel tests in WGS data did not show an enrichment of PTRHD1 rare variants in PD, compared to controls (Supplementary Table S5). As the previously identified PTRHD1 variants were all homozygous, we also assessed the number of homozygous/compound heterozygous carriers of at least one PTRHD1 coding variant, showing similar proportions of such carriers between PD patients and controls (Supplementary Table S6). Of note, the three PTRHD1 variants reported in the previous studies on Iranian and African families (Jaberi et al., 2016; Khodadadi et al., 2017; Kuipers et al., 2018) were not found in our dataset.

Fig. 1.

(A) Locus zoom plot of PTRHD1 variants versus PD risk. (B) Locus zoom plot of PTRHD1 variants versus PD AAO.

The position of the variants on the chromosome 2 (x axis) is plotted against the log10-scaled p-values (left y axis). The most strongly associated SNP is indicated by a purple diamond. Pairwise linkage disequilibrium scores are defined by different colors, explained by the legend on the upper right corner. The right vertical axis indicates the regional recombination rate (cM/Mb).

Abbreviations: chr, chromosome; cM, centimorgan; Mb, Megabase; PD, Parkinson’s disease; SNP, single nucleotide polymorphism.

4. Discussion

Herein, we did not find evidence for an association between PTRHD1 and PD in the European population. There are several reasons that might explain the discrepancy between our results and the previous findings on PTRHD1 in parkinsonian families (Jaberi et al., 2016; Khodadadi et al., 2017; Kuipers et al., 2018): 1) The findings from the family studies might not replicate on a large scale, suggesting that PTRHD1 variants might be either extremely rare in PD or not associated at all; 2) PTRHD1 carriers in the reported family studies manifested atypical parkinsonism with early-onset intellectual impairment, whereas our study was performed on patients with typical PD. Therefore, PTRHD1 variants might be associated with rare forms of atypical parkinsonism, rather than typical PD; 3) The family studies were performed in Iranian and African subjects, whereas our study was performed in European patients. These ethnic differences might as well explain the discrepancy between our and the three previous family studies on PTRHD1.

In conclusion, our results do not provide evidence for an association between PTRHD1 and PD in the European population. Larger studies on non-European ancestry populations and family trios are required to clarify the role of PTRHD1 in PD and atypical parkinsonism.