The multi-tissue landscape of somatic mtDNA mutations indicates tissue-specific accumulation and removal in aging

Abstract

Accumulation of somatic mutations in the mitochondrial genome (mtDNA) has long been proposed as a possible mechanism of mitochondrial and tissue dysfunction that occurs during aging. A thorough characterization of age-associated mtDNA somatic mutations has been hampered by the limited ability to detect low frequency mutations. Here, we used Duplex Sequencing on eight tissues of an aged mouse cohort to detect >89,000 independent somatic mtDNA mutations and show significant tissue-specific increases during aging across all tissues examined which did not correlate with mitochondrial content and tissue function. G→A/C→T substitutions, indicative of replication errors and/or cytidine deamination, were the predominant mutation type across all tissues and increased with age, whereas G→T/C→A substitutions, indicative of oxidative damage, were the second most common mutation type, but did not increase with age regardless of tissue. We also show that clonal expansions of mtDNA mutations with age is tissue and mutation type dependent. Unexpectedly, mutations associated with oxidative damage rarely formed clones in any tissue and were significantly reduced in the hearts and kidneys of aged mice treated at late age with Elamipretide or nicotinamide mononucleotide. Thus, the lack of accumulation of oxidative damage-linked mutations with age suggests a life-long dynamic clearance of either the oxidative lesions or mtDNA genomes harboring oxidative damage.

Single-strand mismatch and damage patterns revealed by single-molecule DNA sequencing

“…However, the mechanism by which the mitochondrial genome mutates remains unclear 76-81 . While it was long assumed to be due to oxidative damage from mitochondrial oxidative metabolism 78,82 , recent studies have not identified oxidation-related mutational signatures such as G>T mutations from 8-oxoguanine, and instead have found patterns supporting a mechanism closely linked to replication 76-78,80,83,84 . Specifically, A>G and C>T dsDNA mutations are highly enriched on the mitochondrial heavy strand (the G+T-rich ‘-‘ strand of the reference genome, which is the template strand for most genes)—i.e., A>G and C>T changes on the heavy strand with complementary changes on the opposite light strand— with a gradient in frequency that decreases with distance from the origin of replication in the direction of heavy strand synthesis 76,77,80,83 .…”

The ‘Stem’ and the ‘Workers’ of the mtDNA population of the cell. Evidence from mutational analysis

“…Importantly, because mtDNA is highly damaged such a separation of responsibilities could help greatly reduce the conversion of DNA damage into real inheritable mutations. An unexpected twist in the resolution of this problem has been brought about by a recent high-precision analysis of mtDNA mutations (Sanchez-Contreras et al 2023). They discovered that certain transversion mutations, unlike more common transitions, are not accumulating with age in mice.…”

“…An unexpected twist to this problem has been brought about by a recent study of mtDNA mutations (Sanchez-Contreras 2023).…”

“…To further clarify this relationship, we re-analyzed mutational data reported by (Sanchez-Contreras 2023).…”

Are some mutations more equal than others?

“…This means that damaged nucleotides – which, in vivo, would have likely been repaired prior to replication or excluded from replication – end up getting erroneously copied and eventually converted into artificial double-stranded mutations that are indistinguishable from genuine ones. Now, in eLife, Scott Kennedy and colleagues from the University of Washington – including Monica Sanchez-Contreras and Mariya Sweetwyne as joint first authors – report how they used a technique called duplex sequencing, which excludes these artificial mutations, to study how mtDNA mutations accumulate with age in mice ( Sanchez-Contreras et al, 2023 ).…”