The Age is in the Nucleus

Abstract

Nuclear DNA damage has detrimental effects on cellular homoeostasis and accelerates the aging process. A new study causally links error-prone mitochondrial replication to increased nuclear DNA damage, thereby drawing the hallmarks of aging closer to nuclear genome instability as a unifying denominator of the aging process.

A wide range of progeroid syndromes has been linked to nuclear DNA damage. Causal mutations range from defects in the Werner’s or Bloom’s helicases, double strand break repair factors and nucleotide excision repair (NER) to nuclear lamin defects that all fuel instability in the nuclear genome¹. However, also mitochondrial defects have been linked to accelerated aging. The role of mitochondria in driving the aging process has been boosted by studies of a mitochondrial DNA (mtDNA) mutator mouse that carries a defect in the proof reading activity of the mitochondrial DNA polymerase. The deficient proof reading activity leads to elevated mitochondrial mutation rates and causes overt signs of premature aging². While at first sight the progeroid mutator phenotype could lend support to the Harman theory of free radicals that originate from dysfunctional mitochondria and promote the aging process, closer inspection has indicated that there was no elevated oxidative damage in those animals. Also, mutation frequencies in tissues of these mice, which can live for more than a year, were one to two orders of magnitude higher than in normally aged mice³. A new study brings a possible answer to the question as to the mechanism of premature aging in the mtDNA mutator mice and it does not reside in mitochondria. In a provocative article in this issue of Nature Metabolism Hämäläinen et al.⁴ show that mtDNA mutator stem cells carry increased nuclear DNA damage. This was linked to impaired replication and depleted pools of dNTPs. In contrast to the impaired nuclear replication, mitochondrial replicative activity was elevated along with increased mitochondrial dNTP pools. Reduction of mitochondrial replication through elevated Tfam expression could indeed alleviate nuclear DNA damage. These results suggest that instead of a direct effect of mitochondrial defects on aging, the exacerbated mitochondrial replication in these cells drains dNTP pools from the nucleus. Reduced dNTP availability in the nucleus is a common cause of replicative impediments, which in turn could result in replication fork stalling and eventually in fork breakdown, thus precipitating nuclear genome instability.

Thus, the quest for a unifying mechanism of aging has once more pointed to a central role for nuclear genome instability. Such a central role has been difficult to accept and instead aging is attributed to multiple processes, so-called hallmarks of aging⁵, that each contribute to the functional decline and the buildup of pathology during aging. However, by now each single one of those hallmarks has been connected to nuclear genome instability⁶. Telomere attrition becomes detrimental when a critically shortened telomere is sensed as a double strand break (DSB) instead of a protected telomere. The DNA damage response (DDR) affects epigenetic modifications when chromatin remodelers provide access to the repair machineries and subsequently restore chromatin organization. Chronic DDR drives cellular senescence. Cellular senescence in combination with another DDR output, apoptosis, can drive stem cell exhaustion⁷.

A growing body of evidence also suggests alterations in intercellular communication, i.e. non-cell-autonomous consequences, resulting from the DDR, as for instance inflammatory responses have been observed in several DNA repair-deficient mouse models. In addition, senescent cells secrete cytokines that can have detrimental consequences for the aging organism, including stimulating cancerous cell growth. Nuclear genome instability could even cause loss of proteostasis, another hallmark of aging, when DNA damage or mutations cause a stoichiometric imbalance in the assembly of multiprotein complexes. Proteostatic factors have also been mechanistically implicated in the actual DNA repair process such as DSB repair or NER. In addition, some aspects of the DDR might also cause protein folding stress. For instance the rampant secretion of inflammatory cytokines might burden the unfolded protein response in the endoplasmic reticulum and the ubiquitin proteasome system. Also metabolic dysfunctions have been observed in progeroid DNA repair deficient animals even though it remains to be explored whether this might be a consequence of organ dysfunction through elevated cellular senescence and apoptosis or a direct regulatory output of the DDR⁸. Hence, virtually all hallmarks of aging can now be causally linked to nuclear DNA damage (Figure 1).

Figure 1. Nuclear DNA damage integrates the multiple hallmarks of aging.

Endogenous and exogenous genotoxic sources cause DNA damage such as DNA adducts, crosslinks and breaks, apurinic/apyrimidinic (AP) sites, base modifications, and critically shortened telomeres. DNA damage causes cellular dysfunction thus driving the organism’s functional decline during aging. Erroneous DNA repair or lesion bypass can lead to point mutations, chromosomal aberrations, deletions, as well as to copy number variations (CNVs) and retrotranspositions. Mutations that alter the function of tumor suppressor genes or oncogenes can cause cancer development. While the multiple hallmarks of aging can result from nuclear DNA damage, telomere attrition and epigenetic alterations can in themselves destabilize the genome. Hämäläinen et al. now show that error-prone mtDNA replication could deprive nuclear dNTP pools consequently leading to replication stress in the nucleus that causes genome instability thus linking mitochondrial alterations via nuclear DNA damage to the aging process.

Hämäläinen et al. have provided yet another piece of the puzzle by showing how defects in mtDNA replication could cause nuclear DNA damage through deprivation of cellular dNTP pools, which in turn triggers nuclear replication stress. One limitation of the study is the lack of evidence that this newly discovered mechanism is also active during normal in vivo aging. Their findings also do not rule out a role for mtDNA mutations, probably mostly deletions, in causing respiratory chain deficiencies during normal aging. What the study does offer almost immediately is the possibility of intervention at the level of mitochondrial dNTP pools. It will be interesting to explore whether for instance NAD+ supplementation that has recently been implicated as healthspan extension intervention⁹, could augment mtDNA metabolism and consequently alleviate nuclear replication stress.