Investigating the Protective Role of the Mitochondrial 2158 T > C Variant in Parkinson's Disease

Abstract

A considerable portion of the risk for Parkinson's disease (PD) is attributed to genetic factors.^{1, 2} Several monogenic forms of PD have been associated with mutations in genes encoding proteins involved in mitochondrial function including PRKN and PINK1.^{1, 3, 4} Furthermore, human cell culture studies and animal models have offered evidence supporting the presence of mitochondrial disturbances in PD.⁵

Hudson et al. proposed a protective role of two mitochondrial DNA variants in PD etiology.⁶ In an array-based genotyping study, the authors showed that the m.2158 T > C (p.Lys4Arg, rs41349444) variant in SHLP2 is associated with reduced risk for PD (P-value = 2 × 10⁻², OR = 0.32). A follow-up functional study by Kim et al. demonstrated that the mutated protein was protective against mitochondrial dysfunction in both in vitro and in vivo models of PD.⁷ Nevertheless, the association of this variant with reduced risk of PD has not been confirmed in large-scale sequencing datasets.

To further investigate the association between m.2158 T > C and PD, we conducted an extensive genetic characterization utilizing large-scale genome sequencing (GS) datasets, totaling 4358 PD cases and 16,609 controls. Additionally, we included 779 maternal PD proxies from All of Us, considering the maternal transmission of mitochondrial DNA. The homoplasmic allele frequency (AF) of m.2158 T > C variant is reported as 0.0066 in gnomAD v.4.0.0.⁸ Considering the limited capture of rare variants by genotyping arrays, the challenge becomes more substantial for a variant in mitochondrial DNA. GS offers a comprehensive, accurate, and high-resolution approach to explore mitochondrial DNA, making it the preferred method for researchers studying the complexity of mitochondrial genetics and associated diseases. Worldwide and extensive efforts, exemplified by initiatives such as the Global Parkinson's Genetics Program (GP2; https://gp2.org/), enable us to conduct large-scale and unbiased screenings, facilitating genetic associations with significant statistical power.

First, we genotyped the m.2158 T > C variant from alignment files using the mitochondrial mode.⁹ Details regarding sequencing, which includes sample and variant-level quality control procedures, are presented in the supplementary materials. The homoplasmic AF of the m.2158 T > C variant was 0.012, 0.010, 0.010, and 0.013 in All of Us, AMP-PD, GP2, and 100KGP, respectively. Subsequently, we performed per-cohort logistic regression analyses adjusted by age at onset for cases and age for controls, sex, and the first 10 principal components using PLINK v.2.0 (https://www.cog-genomics.org/plink/2.0/).¹⁰ Our inverse-variance weighted meta-analysis¹¹ did not identify an association between SHLP2 m.2158 T > C and reduced risk of developing PD in the cohorts under study (Table 1).

Our study, which utilized large-scale GS data from various datasets while considering covariates such as sex and age, did not support the findings reported by Kim et al. in 2024, suggesting that previous associations may represent a type 1 error. Our investigation focused on evaluating the association of the m.2158 T > C variant with PD, accounting for potential confounders. Utilizing genomes of more than 20,000 individuals provided a statistical power of over 95% to detect an association with a minimum relative risk of 1.5 (https://csg.sph.umich.edu/abecasis/cats/gas_power_calculator/). Our results underscore the significance of leveraging multiple datasets encompassing diverse populations to validate genetic associations before embarking on extensive functional follow-up studies.

F.A. and V.v.M. wrote the initial draft. F.A. and S.C.A. performed or contributed to the statistical analysis. S.C.A., M.B.M., and J.D.R. assisted in data acquisition and statistical analysis. Z.-H.F. performed the analysis and quality control of the raw genome sequencing data in the GP2. S.B.-C. conceptualized, designed, and supervised the project. All authors edited and reviewed the final manuscript.