Dynamics of the most common pathogenic mtDNA variant m.3243A > G demonstrate frequency-dependency in blood and positive selection in the germline

Abstract

The A-to-G point mutation at position 3243 in the human mitochondrial genome (m.3243A > G) is the most common pathogenic mtDNA variant responsible for disease in humans. It is widely accepted that m.3243A > G levels decrease in blood with age, and an age correction representing ~ 2% annual decline is often applied to account for this change in mutation level. Here we report that recent data indicate that the dynamics of m.3243A > G are more complex and depend on the mutation level in blood in a bi-phasic way. Consequently, the traditional 2% correction, which is adequate ‘on average’, creates opposite predictive biases at high and low mutation levels. Unbiased age correction is needed to circumvent these drawbacks of the standard model. We propose to eliminate both biases by using an approach where age correction depends on mutation level in a biphasic way to account for the dynamics of m.3243A > G in blood. The utility of this approach was further tested in estimating germline selection of m.3243A > G. The biphasic approach permitted us to uncover patterns consistent with the possibility of positive selection for m.3243A > G. Germline selection of m.3243A > G shows an ‘arching’ profile by which selection is positive at intermediate mutant fractions and declines at high and low mutant fractions. We conclude that use of this biphasic approach will greatly improve the accuracy of modelling changes in mtDNA mutation frequencies in the germline and in somatic cells during aging.

Reanalysis of mtDNA mutations of human primordial germ cells (PGCs) reveals NUMT contamination and suggests that selection in PGCs may be positive

“…The significance ceases at lower mutant fractions (see Supplementary Note 4). This is consistent with our previous findings of an 'arching' selection profile in human m.3243A>G mutation (Franco et al 2022). More generally, mutations at other mutant fractions, mutations of other types (e.g., highly detrimental mutations - (Fan et al 2008)), and at different stages of germline development may be subject to purifying selection so that overall balance of selection in the germline is negative despite some positive intervals.…”

Aneuploidy in human embryos is associated with a maternal age-independent increase in mitochondrial DNA content and an enrichment of ultra-rare mitochondrial DNA variants

“…The binary logic, above or below the phenotypically important heteroplasmic threshold, is commonly used for somatic mtDNA variants, and here we would like to use it for germline variants. There are several mechanisms, explaining how de novo or very rare deleterious mtDNA variants can affect the mitochondrial phenotype in the same generation: (i) a narrow stochastic mtDNA bottle-neck (about 20 inherited mtDNA copies) leads to a minimal heteroplasmy level of a deleterious variant of at least 5% or more; (ii) deterministic positive selection of deleterious variants in the germline (Franco et al 2022); (iii) some mutations with a dominant effect may affect a phenotype even at very low heteroplasmy level (Fan et al 2008); (iv) damage of oocytes in early life due to chemical or hormonal stresses can affect mtDNA nucleotide modifications, such as N-Deoxyadenosine methylation, having a pleiotropic effect on the whole mitochondria (Hao et al 2020). Altogether, we propose that the effect of the germ-line or early somatic deleterious variants, mediated by the increased mtDNA content, can be a common age-independent mechanism of some aneuploidies.…”

A novel, wave-shaped profile of germline selection of pathogenic mtDNA mutations is discovered by bypassing a classical statistical bias.

“…As schematically illustrated in Fig. 3 , blood heteroplasmy is separated from the ‘around-bottleneck’ heteroplasmy by changes in heteroplasmy during blood development and the lifelong cell dynamics in the blood (Rajasimha, Chinnery, and Samuels 2008), (Franco et al 2022; Grady et al 2018), which collectively represent a ‘somatic bottleneck’ (Barrett et al 2020). Given that these random changes take place in blood samples from both mothers and children, (H m +H ch )/2 must be a better proxy of heteroplasmy level at the point where selection is expected to take place than the conventionally used mother’s heteroplasmy in blood.…”