Ultra-sensitive sequencing reveals an age-related increase in somatic mitochondrial mutations that are inconsistent with oxidative damage.

TitleUltra-sensitive sequencing reveals an age-related increase in somatic mitochondrial mutations that are inconsistent with oxidative damage.
Publication TypeJournal Article
Year of Publication2013
AuthorsKennedy, SR, Salk, JJ, Schmitt, MW, Loeb, LA
JournalPLoS Genet
Volume9
Issue9
Paginatione1003794
Date Published2013
ISSN1553-7404
KeywordsAged, Aged, 80 and over, Aging, Autopsy, Brain, DNA Damage, DNA, Mitochondrial, High-Throughput Nucleotide Sequencing, Humans, Infant, Infant, Newborn, Mitochondria, Mutagenesis, Mutation, Oxidative Stress, Reactive Oxygen Species
Abstract

Mitochondrial DNA (mtDNA) is believed to be highly vulnerable to age-associated damage and mutagenesis by reactive oxygen species (ROS). However, somatic mtDNA mutations have historically been difficult to study because of technical limitations in accurately quantifying rare mtDNA mutations. We have applied the highly sensitive Duplex Sequencing methodology, which can detect a single mutation among >10(7) wild type molecules, to sequence mtDNA purified from human brain tissue from both young and old individuals with unprecedented accuracy. We find that the frequency of point mutations increases ~5-fold over the course of 80 years of life. Overall, the mutation spectra of both groups are comprised predominantly of transition mutations, consistent with misincorporation by DNA polymerase γ or deamination of cytidine and adenosine as the primary mutagenic events in mtDNA. Surprisingly, G → T mutations, considered the hallmark of oxidative damage to DNA, do not significantly increase with age. We observe a non-uniform, age-independent distribution of mutations in mtDNA, with the D-loop exhibiting a significantly higher mutation frequency than the rest of the genome. The coding regions, but not the D-loop, exhibit a pronounced asymmetric accumulation of mutations between the two strands, with G → A and T → C mutations occurring more often on the light strand than the heavy strand. The patterns and biases we observe in our data closely mirror the mutational spectrum which has been reported in studies of human populations and closely related species. Overall our results argue against oxidative damage being a major driver of aging and suggest that replication errors by DNA polymerase γ and/or spontaneous base hydrolysis are responsible for the bulk of accumulating point mutations in mtDNA.

DOI10.1371/journal.pgen.1003794
Alternate JournalPLoS Genet.
Citation Key10.1371/journal.pgen.1003794
PubMed ID24086148
PubMed Central IDPMC3784509
Grant ListT32-AG000057 / AG / NIA NIH HHS / United States
P01-CA77852 / CA / NCI NIH HHS / United States
P01-AG01751 / AG / NIA NIH HHS / United States
P50AG05136 / AG / NIA NIH HHS / United States
T32 AG000057 / AG / NIA NIH HHS / United States
R01 CA160674 / CA / NCI NIH HHS / United States
T32 GM007266 / GM / NIGMS NIH HHS / United States
R01-CA102029 / CA / NCI NIH HHS / United States