Genetic factors modulating mitochondrial DNA copy number

Abstract

Mitochondria are dynamic organelles whose principal role is the generation of cellular energy (ATP) through oxidative phosphorylation (OXPHOS). 13 OXPHOS subunits are encoded by the mitochondrion’s polyploid circular genome (mtDNA), and the nuclear genome (nDNA) encodes the remaining subunits as well as proteins required for mtDNA maintenance. In addition to mitochondrial number, mtDNA copy number (mtDNA CN) varies between cell and tissue type, depending on metabolic demand and baseline mtDNA quality, and ranges from hundreds to thousands of copies per cell. mtDNA CN is often linked to mitochondrial dysfunction and the ubiquity of mitochondria results in a broad spectrum of dysfunction and clinical phenotypes; ranging from primary mitochondrial disorders to complex diseases such as cancer, type 2 diabetes, and Parkinson’s disease. Given the variability in mtDNA between individuals, it is possible that mtDNA CN is influenced by secondary factors. I hypothesise that nDNA diversity is a major component of mtDNA variability between individuals and will test this hypothesis by conducting a genome wide association study (GWAS) in a large, European, asymptomatic cohort (>8000 individuals), comparing nDNA genotype to mtDNA copy-number as a QTL. Peripheral blood mtDNA CN was correlated to array-based and imputed nDNA genotype in a two-stage QTL analysis, utilising three independent replicative cohorts: UKBS, Newcastle, and ALPAC. In addition the effect of potential confounding biological variables such as age, gender, blood count, and potential methodological confounders such as assay variation, technical and biological replicate numbers, and differences in genotype platform were all assessed and used to improve the GWAS analysis. Individual cohort analysis identified nuclear gene UNC13C (Unc-13 Homolog C), two intergenic, and one intronic SNP, which is in close proximity to PSMD3 (Proteasome 26S Subunit, Non-ATPase 3), to be genome wide significant (GWS) (p< 1.00E-07) in individual cohort analysis. However these hits could not be replicated in meta-analysis. mtDNA variant analysis in all three cohorts revealed that mtDNA SNPs G5460A and G5046A, which identify as mitochondrial haplogroup W, were significantly associated to a significant reduction in mtDNA CN. Furthermore, our work identified gender-specific genetic differences, which was supported by a Preliminary iv significant decrease in mtDNA CN in males with age, but not females, and significant changes in mtDNA CN relative to blood cell type and proportions highlighted the importance of regulating for cellular heterogeneity. Additionally, no difference in mtDNA CN was observed between pre- and post-menopausal women. This work indicates that there are likely genetic variants present at the population level modulating mtDNA CN, but that this process is complex and multifaceted.