Random intracellular drift explains the clonal expansion of mitochondrial DNA mutations with age

Abstract

Human tissues acquire somatic mitochondrial DNA (mtDNA) mutations with age. Very high levels of specific mtDNA mutations accumulate within individual cells, causing a defect of mitochondrial oxidative metabolism. This is a fundamental property of nondividing tissues, but it is not known how it comes about. To explore this problem, we developed a model of mtDNA replication within single human cells. Using this model, we show that relaxed replication of mtDNA alone can lead, through random genetic drift, to the clonal expansion of single mutant events during human life. Significant expansions primarily develop from mutations acquired during a critical period in childhood or early adult life.

Figure 1

A, Proportion of mutant mtDNA in single simulated cells. Each simulated cell contained 1,000 mtDNAs and had a half-life, T_1/2, of 10 d and a copy-error (mutation) probability of 10⁻⁵ (measurements taken monthly for 30 years). For illustration, we have shown the results of 24 simulations from a total of 600. In the 600 cells, one mutant event went to fixation (trace at the back) and three others showed a significant expansion (one shown), but, in most, the mutations were rapidly lost. When these simulations were continued for a full 120 years (not shown on the graph), a mean of only 31.27 mutations occurred per cell, corresponding to the value predicted by the equation N_mut={N_mtDNAP_mutt ln(2)}/T_1/2, where N_mut is the number of mutation events and t is the duration of the simulation in d. Many of these mutations were lost almost instantaneously (41% were lost within one T_1/2, and 88% were lost within 10 T_1/2), but, in some cells, the proportion of mutant mtDNA increased. B, Proportion of cells containing >60% mutant mtDNA (^SimCOX_neg cells) accumulates with age. Each line represents 600 simulated cells, followed for 120 years, containing a given number of mtDNA molecules, N, and with a copy-error (mutation) probability 5 x 10⁻⁵ and a T_1/2 of 10 d (measurements taken every 10 years). The proportion of ^SimCOX_neg cells increases with age. Similar rates of accumulation of ^SimCOX_neg cells were seen for N=100 and N=1,000. Greater numbers of N were associated with a lower number of ^SimCOX_neg cells at each age. C, Effect of P_mut on the proportion of cells containing >60% mutant mtDNA (^SimCOX_neg cells). Each line represents 600 simulated cells followed for 120 years. For cells containing 1,000 mtDNA molecules and a T_1/2 of 10 d, low mutation probabilities (P_mut of 10⁻⁷ and 10⁻⁶) are associated with a very low or undetectable incidence of ^SimCOX_neg cells throughout life. Higher mutation probabilities lead to a greater number of ^SimCOX_neg cells accumulating throughout a simulated human life. D, Proportion of clonally expanded mutant mtDNA in simulated cells with different copy-error (mutation) probabilities. Each data point represents 1,000–2,000 simulated cells, each containing 1,000 or 5,000 mtDNA molecules (see legend on graph) with a T_1/2 of 10 d. The ordinate shows the proportion of mtDNA that was the most populous mutant allele (clonally expanded mtDNA) at 80 years. For moderate mutation probabilities (P_mut of 10⁻⁵ to 10⁻⁴), the vast majority of mutant mtDNA within a single simulated cell is identical (clonal expansion). For much higher mutation probabilities (P_mut >10⁻⁴), a mixture of mutant species is seen within the simulated cells. E, Age when mtDNA copy errors (mutations) occurred, which led to significant clonal expansions by age 80 years. Of 32,000 simulated cells containing 5,000 mtDNA with a copy-error (mutation) probability 10⁻⁵ and T_1/2 of 10 d, 123 contained >60% mutant mtDNA (^SimCOX_neg cells) at age 80 years. The percentage distribution of the age at which these mutations occurred is shown in the figure. Seventy-eight percent of the original copy errors occurred in the first three decades of life, and 46% began at age <15 years. F, Effect of mitochondrial proliferation on the rate of accumulation of ^SimCOX_neg cells with age. These simulations were based on the assumption that nondividing cells maintain an optimal number of wild-type mtDNA molecules (Chinnery and Samuels 1999). If the number of wild-type molecules is reduced by mutation, the cell responds by the nonselective proliferation of all mtDNA molecules to redress the balance. The maximum level of mtDNA proliferation, α, times the normal mtDNA number, was based on the maximum degree of mitochondrial proliferation measured in skeletal muscle fibers from patients harboring high levels of mutant mtDNA (see Chinnery and Samuels 1999). We studied the effect of varying α by simulating 1,000 postmitotic cells containing 100 mtDNA molecules with a T_1/2 of 10 d over a human life span of 120 years, with a P_mut of 5×10^-5. Proliferation had no significant effect on the rate of accumulation of ^SimCOX_neg cells with age.