{
  "question": [
    "How do telomeres affect the aging process?",
    "What role does DNA repair play in aging?",
    "Can genetic research lead to treatments that slow down aging?",
    "How does mitochondrial DNA influence aging?",
    "Are there any known genetic mutations that cause premature aging?"
  ],
  "answer": [
    "Telomeres play a central role in aging by adjusting the cellular response to stress and DNA damage. As cells divide, telomeres shorten, and when they become critically short, they can trigger cell cycle arrest, genomic instability, and cell death, a process known as senescence. This telomere shortening is considered a major cause of replicative senescence, which is linked to aging. Additionally, telomere dysfunction can lead to mitochondrial dysfunction, contributing to aging. However, the relationship between telomere length and aging is complex and not straightforward.",
    "DNA repair plays a significant role in aging. Evidence suggests that the rate of DNA repair declines with age, leading to an accumulation of DNA damage. This damage can cause changes in gene expression, cellular functions, and can lead to age-related diseases. Some studies also suggest that defects in DNA repair pathways can lead to premature aging. Furthermore, the balance between DNA damage and its repair is considered a major determinant of longevity and cell viability. Therefore, DNA repair mechanisms are crucial in maintaining genomic stability and cellular health, influencing the aging process.",
    "Yes, genetic research can potentially lead to treatments that slow down aging. Discoveries about the biological determinants of aging, such as gerontogenes, could lead to therapies that slow the aging process. Additionally, understanding how the environment modulates aging-related genes could lead to the creation of anti-aging therapies applicable to humans, potentially through diet, lifestyle, and pharmacological interventions.",
    "Mitochondrial DNA (mtDNA) influences aging through the accumulation of mutations and the reduction of mtDNA copy number over time. These changes disrupt mitochondrial energetics, which may contribute to aging and age-associated phenotypes. The accumulation of mtDNA mutations can compromise cellular energy metabolism and increase intracellular oxidative stress, leading to degenerative changes in tissues. Additionally, certain mtDNA polymorphisms have been associated with longevity and age-related diseases.",
    "Yes, there are several known genetic mutations that cause premature aging. These include mutations in genes involved in DNA metabolism or regulation, such as those seen in Werner syndrome (WS), Bloom syndrome (BLM), Cockayne syndrome (CS), ataxia-telangiectasia (AT), Hutchinson-Gilford progeria syndrome (HGPS), and restrictive dermopathy (RD). Other examples include mutations in the LMNA gene causing Hutchinson-Gilford progeria syndrome, and mutations in RecQ genes causing Werner syndrome, Bloom syndrome, and Rothmund-Thomson syndrome."
  ],
  "contexts": [
    [
      "\t\n\nIntegration of oxidative stress and cell senescence (and, by extension, telomere shortening and in vitro senescence in general) is thus very well established in vitro.The only question remaining is whether this relationship (and the underling phenomenon) is also true, and biologically significant, in vivo.Certain correlative data would point in that direction.Short telomeres have been identified as markers in human disease in which oxidative stress is also thought to be involved (for example, [311], reviewed in Ref. [312]).Even more interesting is the finding that telomere length is a statistical predictor of survival in humans over 60 [313] and mortality and morbidity in several age-related diseases [314].It is tempting to speculate that this may be the result of an underlying oxidative stress, though further work will be needed to prove this point.",
      "\t\n\nTelomeres play a central role in cell fate and aging by adjusting the cellular response to stress and growth stimulation on the basis of previous cell divisions and DNA damage.At least a few hundred nucleotides of telomere repeats must \"cap\" each chromosome end to avoid activation of DNA repair pathways.Repair of critically short or \"uncapped\" telomeres by telomerase or recombination is limited in most somatic cells and apoptosis or cellular senescence is triggered when too many \"uncapped\" telomeres accumulate.The chance of the latter increases as the average telomere length decreases.The average telomere length is set and maintained in cells of the germline which typically express high levels of telomerase.In somatic cells, telomere length is very heterogeneous but typically declines with age, posing a barrier to tumor growth but also contributing to loss of cells with age.Loss of (stem) cells via telomere attrition provides strong selection for abnormal and malignant cells, a process facilitated by the genome instability and aneuploidy triggered by dysfunctional telomeres.The crucial role of telomeres in cell turnover and aging is highlighted by patients with 50% of normal telomerase levels resulting from a mutation in one of the telomerase genes.Short telomeres in such patients are implicated in a variety of disorders including dyskeratosis congenita, aplastic anemia, pulmonary fibrosis, and cancer.Here the role of telomeres and telomerase in human aging and agingassociated diseases is reviewed.\t\nTelomeres play a central role in cell fate and aging by adjusting the cellular response to stress and growth stimulation on the basis of previous cell divisions and DNA damage.At least a few hundred nucleotides of telomere repeats must \"cap\" each chromosome end to avoid activation of DNA repair pathways.Repair of critically short or \"uncapped\" telomeres by telomerase or recombination is limited in most somatic cells and apoptosis or cellular senescence is triggered when too many \"uncapped\" telomeres accumulate.The chance of the latter increases as the average telomere length decreases.The average telomere length is set and maintained in cells of the germline which typically express high levels of telomerase.In somatic cells, telomere length is very heterogeneous but typically declines with age, posing a barrier to tumor growth but also contributing to loss of cells with age.Loss of (stem) cells via telomere attrition provides strong selection for abnormal and malignant cells, a process facilitated by the genome instability and aneuploidy triggered by dysfunctional telomeres.The crucial role of telomeres in cell turnover and aging is highlighted by patients with 50% of normal telomerase levels resulting from a mutation in one of the telomerase genes.Short telomeres in such patients are implicated in a variety of disorders including dyskeratosis congenita, aplastic anemia, pulmonary fibrosis, and cancer.Here the role of telomeres and telomerase in human aging and agingassociated diseases is reviewed.In the future attention undoubtedly will be centered on the genome, and with greater appreciation of its significance as a highly sensitive organ of the cell, monitoring genomic activities and correcting common errors, sensing the unusual and unexpected events, and responding to them, often by restructuring the genome.\t\n\nHigher \"background\" levels of activated p53 could decrease the threshold for activation of senescence or apoptosis in \"old\" cells, in line with the increased sensitivity to stress and more fragile nature of cells and tissues from the elderly.The role of telomeres in cellular aging relative to other proposed molecular mechanisms of aging including oxidative stress resulting from mitochondrial dysfunction or loss of ribosomal function remains to be precisely FIG. 4. Diagram of factors affecting the telomere length in primary somatic cells from human tissues.According to the model shown, telomeres in \"young\" somatic cells have long tracts of telomere repeats that favor folding into a \"closed\" structure that is invisible to the DNA damage response pathways and telomerase.As the telomere length at individual chromosome ends decreases, the likelihood that telomeres remain \"closed\" also decreases (see also Fig. 3).At one point telomeres become too short and indistinguishable from broken ends.Such ends will be processed by enzymes in the DNA repair compartment (proposed to occupy a different nuclear domain than long telomeres).Depending on the cell type and the genes that are expressed in the cell, a limited number of short ends can be elongated by limiting levels of telomerase or recombination.However, with continued cell division and telomere loss, eventually too many short ends accumulate for the limited capacity of these \"telomere salvage pathways. \"At this point, defective telomeres will trigger levels of DNA damage signals such as p53 to which cells respond by either apoptosis or senescence.Rare (mutant) cells that do not upregulate functional DNA damage responses (e.g., by loss of functional p53) continue cell divisions in the presence of dysfunctional telomeres causing genome instability via chromosome fusions, chromosome breaks, and repetitive break-fusion bridge cycles.delineated.The development of an integrated view of the various molecular mechanisms of aging that have been proposed remains as formidable a challenge.However, it has become clear that telomeres are directly responsible for sustained DNA damage signals in senescent cells (54,203), and DNA damage foci originating from telomeres in senescent cells can readily be detected in vivo (104).\tIII. LOSS OF TELOMERIC DNA WITH AGE: OVERVIEW\n\nLoss of telomeric DNA at the cellular level is well established and was shown to be related to replicative history and life span in somatic cells (see sect.II and Figs. 2 and 4).However, at the level of tissues or of the entire organism, what is the impact of telomere shortening?Does aging cause telomere shortening, or does telomere shortening cause aging (98)?The issue of organismal aging as a consequence of short telomeres was raised as a concern when Dolly, \"cloned\" by transfer of an adult mammary gland nucleus into an enucleated egg, was shown to have short telomeres (189).In contrast, nuclear transfer experiments using nuclei from senescent bovine fibroblasts yielded offspring with longer than expected telomeres and a \"youthful\" phenotype (117).Differences in donor nucleus cell type, nuclear transfer methodology, or species could explain these discrepant results (1,103,112).However, the \"immortal\" growth properties of embryonic stem cell lines derived from preimplantation embryos of many species suggest that telomere length can be maintained or telomere loss attenuated in early development.The loss of telomere repeats in human cells with age varies greatly between cells and tissues, and the amount of information for different tissues is often very limited.It has been proposed that the number of cell divisions in stem cells is 100 divisions over a human lifetime and that this efficiency is achieved by a strict hierarchy at the level of stem cells with the most primitive cells dividing the least and having the longest telomeres (115).A diagram representation of this model is shown in Figure 7.\t\n\nThe correlation between telomere length and replicative potential became a mechanistic link when it was demonstrated that the replicative potential of primary human fibroblasts can be extended indefinitely by artificially elongating telomeres.The latter was achieved in primary human fibroblasts by overexpression of the telomerase reverse transcriptase (hTERT) gene (25,211).These experiments established that progressive telomere loss is indeed the major cause of replicative senescence as had been proposed earlier (3,84).\tA. Telomeres From Cytogenetics to Replicative\n\nSenescence: Historic Background That chromosome ends play an important role in ensuring chromosome stability was first proposed in the 1930s by Barbara McClintock working with maize (142) and Hermann Muller working with fruitflies (155).Both investigators proposed that chromosome ends have special structures required for chromosome stability.Muller coined the term telomere, from the Greek for \"end\" (telos) and \"part\" (meros).McClintock noted that without these special end structures, chromosomes would fuse and often break upon mitosis, and she observed that the resulting chromosome instability was detrimental to cells.These pioneering studies established that functional \"telomeres\" are required to protect chromosome ends, to provide chromosome stability, and to ensure faithful segregation of genetic material into daughter cells upon cell division.These conclusions have stood the test of time, and since this work was published, an enormous amount of data on telomeres and their function have been produced.Some of the most striking contributions are reviewed here.However, despite this progress, it is also clear that many mysteries around telomeres and their function remain.The increasing amount of detail about individual molecules and pathways involved in telomere biology and DNA damage responses has not at all diminished the challenge of understanding how telomeres are integrated and involved in DNA damage responses, cellular fitness, and human aging.While it has become clear that telomeres play a central role in the cellular response to stress and DNA damage, neither the relative importance to other factors nor all the connections between proteins and signaling pathways that directly or indirectly involve telomeres are fully understood.The future of telomere research is bright!In the early 1960s, Leonard Hayflick observed that human cells placed in tissue culture stop dividing after a limited number of cell divisions by a process now known as replicative senescence (90,92;reviewed in Ref. 89).He proposed that the cell culture phenomenon could be used as a model to study human aging at a molecular and cellular level.However, the role of replicative senescence in human aging and the relevance of the in vitro studies remained subject to much debate.Cells presumably divide either to balance normal cell loss or in response to injury.Many cells in the human body can divide many more times than needed during a normal lifetime.A mitotic \"reserve capacity\" was used as an argument against the idea that replicative senescence has any relevance to human aging.However, one would not expect all (stem) cells in the body to have a similar replicative history (or potential), and cells that no longer exist (or can no longer divide) are easily overlooked.It has furthermore been difficult to estimate the actual turnover of the stem cells in tissues such as the intestine and hematopoietic stem cells over a normal lifetime with any degree of accuracy.Estimates range from more than 1,000 times for intestinal epithelial cells in rodents (170) to less than 100 times for hematopoietic stem cells in humans (115).Recent studies of the levels of 14 C remaining in tissues from nuclear weapons test during the Cold War have shown that the turnover of blood cells far exceeds that of the cells in the gut (197), and these data seem incompatible with thousands of cell divisions.Uncertainties about actual turnover and the fact that model organisms such as worms and flies clearly \"age\" without cell renewal being a major factor have been used to question the role of cell turnover and replicative senescence in human aging.However, as will be discussed, the tight association of telomeres to overall cellular fitness does not exclude a role for telomeres even in the aging of tissues that contain mostly long-lived postmitotic cells such as the brain, heart, or kidney.For example, it is possible that damage to telomeric DNA by reactive oxygen species (ROS) produced by either dysfunctional mitochondria (85,220) or by signaling pathways (e.g., overexpression of oncogenes such as Ras, Refs.152,239) contributes or predisposes cells to apoptosis and senescence.Thus DNA damage signals originating from telomeres could be replication independent, and the sensitivity of cells to DNA damage could increase as the overall telomere length declines.More information is needed on the role of telomeres in the cellular response to various types of insults (177).",
      "\tImpact on aging\n\nThere is no straightforward relationship between telomere length or stringency of control of telomerase expression and organismal life span (Campisi, 2001).On the other hand, two human syndromes with features of premature aging -Werner syndrome (WS) and dyskeratosis congenita (DKC) -have been linked directly (DKC) or indirectly (WRN) to telomere length and presumably telomere structure (Chang et al., 2004;Mitchell, Wood, & Collins, 1999).Thus, functional telomeres may directly increase longevity by maintaining genomic stability and suppressing cancer while also indirectly postponing aging phenotypes by preventing apoptosis and/or senescence (Blasco, 2003;Campisi, 2003aCampisi, , 2003b)).Whatever the case, the cellular responses to telomere dysfunction -apoptosis and senescence -have been proposed to contribute to aging phenotypes (Campisi, 2003a).",
      "\t\n\nRegarding cancer and aging, Serrano and Blasco (2007) suggested that an equilibrium between mechanisms diminishing cellular damage and mechanisms preventing excessive cellular proliferation is required between both processes [43].The authors argue that the p53 pathway may be seen as an anti-aging mechanism as it is a key defense mechanism against cellular damage protecting from both aging and cancer.One effect of aging at the cellular level is reduced telomerase activity and progressive shorter telomeres in somatic cells [45].Shortened telomeres are highly recombinogenic, leading to a genome-susceptible cancer development [46,47].Genomic instability driven by dysfunctional telomeres is also associated with the transition from benign to malignant tumors [48].Conversely, telomere dysfunction also acts to induce the p53 gene to suppress tumor development by initiating cell-cycle arrest, cellular senescence or, apoptosis.Our analysis has identified several genes involved in the regulation and activity of the p53 pathway as being affected by age.In skin, the telomerase reverse transcriptase (TERT) showed an age-related expression in association with a genetic variant (rs10866530).In addition p21, a gene directly regulated by p53 and also involved in telomere-driven aging, was shown to be differentially expressed with age [49].In brain, theZBTB16, CA9,and HEY2, genes associated to the p53 pathway directly or via SIRT1, all showed age-related expression.The activity of p53 has been shown to enhance the transcription of inhibitors of the insulin receptor pathway, preventing cell growth and division after stress signaling [50,51] and many genes from the insulin signaling pathway have been extensively associated with longevity in multiple studies and organisms.Our results suggest that the link between aging and cancer is evident in multiple tissues through differential expression of genes with age.",
      "\tevidence From In Vitro Studies\n\nIn most organisms, telomere elongation is controlled by the enzyme telomerase under tight regulation to ensure sufficient number of replications, yet when this number is reached, telomere elongation is seized (2,83).Once telomeres reach the critical length, the cells undergo senescence and stop proliferating (84).This process is believed to be the trigger for the aging process, according to the telomere theory (11,85,86).It is further supported by Bodnar et al. who proved that telomere elongation caused by ectopic expression of telomerase avoids the senescence phenotype (87).His work relied on one of the earliest studies linking telomere shortening to aging which was performed by Harley et al. on human fibroblast cells (88).In their paper, they describe the shortening of telomeres in aging fibroblasts alongside chromosomal abnormalities, specifically the fusion of two chromosomes at the telomeric region and chromosomal rearrangement, while hinting at a biological significance to the shortening process.Since this early study, numerous studies have emerged strengthening this association and aiming to elucidate the exact underlying mechanism of telomere shortening.Murillo-Ortiz et al. ( 89) studied telomere alterations using T, B, and NK cells from 20 to 25-year-old and 60 to 65-year-old donors.Treatment with concanavalin A (a mitogen of T cells) caused increase in telomere length and number of replications in the samples from the young donors, but did not improve the samples from the older donors, which exhibited loss of telomere parts, decrease in telomere length, and decreased proliferation potential (89).Age-related changes in telomere length were also established in bone marrow hMSC in a long-term in vitro study (90).COMET assay revealed higher levels of damage in cells from older donors (91).Similar results were obtained in the study of CD34  and CD34 + cells isolated from healthy donors of different ages.However, some of the cells exhibited telomere shortening that was not correlated with age.It seems that CD34 + cells from older donor suffer from increased non-telomeric DNA damage, but the variation among the cultures hints for multiple factors contributing to DNA damage (92).\t\n\nThe Question of Telomere-Related Senescence in S. cerevisiae For S. cerevisiae, various studies were performed on the effect of missing/broken telomere and mutated telomerase on the physiology of the organism.Genetic manipulations of S. cerevisiae cells caused decreased growth, irregular shape, and eventually, cellular senescence (69).Several genes, such as EST1 (telomere elongation protein), EST2 (telomere reverse transcriptase), EST3 (telomere replication protein), TLC1 (template RNA component), RAD9, RAP1 (DNA binding protein), CDC13 (cell division control protein 13), TEL1 (serine/threonine protein kinase), MEC1 (serine/ threonine protein kinase), and MRC1 (macrophage mannose receptor 1 precursor) were studied in connection to telomererelated senescence; however, despite the extensive experimental work put into using mutated cells, the role of eroded telomeres in \"natural\" cellular senescence in yeast remained questionable (93).For example, EST1-4 (ever short telomere) mutants began to lose viability after 60 doublings, but late knockout cultures continued to maintain proliferation potential (94).Cells with mutated telomerase exhibited irregular morphology and short telomeres, but these changes did not cause deadly damage and determinate senescence (95).One hypothesis connects aging to telomere erosion through the transcription of subtelomeric genes.Genes located in subtelomeric regions are affected by transcriptional silencing which was found to change in an age-related manner.Kim et al. (96) found that silencing of genes in subtelomeric regions declined during the cell's senescence, hinting at a connection between the transcription of subtelomeric regions and cellular senescence in yeast (96).The work of Austriaco and Guarente (97) reinforced this model, as they found that mutated telomerase extended life span (relatively to the wild type), probably by hanging the silencing procedure in the subtelomeric locations (97).\tCONCLUSiON\n\nHealthy aging and cellular senescence are complex processes of great interest to researchers.The multigenic nature of both of them complicates studies and necessitates creative and novel approaches in the path for understanding those phenomena.The three spear-headed strategies implemented for this purpose have brought forth much information and knowledge, yet there is still much to learn in these fields.The doubting and contradicting results in in vivo studies are influenced both by physiological and genetic differences between the model organisms and humans and the differences in the possible research methodologies between in vitro and in vivo studies.In many cases, the age-related phenotypes searched for and studied in vitro are not visible in vivo or not relevant for the model organism (Table 1. ).Molecular processes such as DNA damage repair, telomere shortening, and epigenetic alterations discussed earlier are the driving forces of the aging process in human, but their significance is varied in other organisms.Many evidence for age-related accumulation of DNA damage were found in in vitro studies, both in human and mice cell cultures.The connection between DNA damage and aging is emphasized by the secretion of senescenceassociated proteins during cellular senescence, a phenotype which is activated by DNA damage and is common for both human and mice.Human progeroid diseases also show the connection between early aging and faulty DNA repair.In yeast, flies and mice, however, although some evidence for age-related damage and faulty DNA repair mechanisms were found, contradicting and debating results highlight the complexity of the use of these model organisms in this aging research.The study of telomeres in relation to aging demonstrates the questions derived from both physiological differences between organisms and differences in research approaches.The connection between telomere attrition and aging is very present in human aging (both in in vitro studies and as telomeropathies such as DKC, Werner syndrome, and Hutchinson-Gilford progeria) but not relevant in model organisms.In C. elegans, the evidence are contradicting.In drosophila, maybe because of the unique telomere structure, there are no evidence connecting telomere attrition to aging.In yeast and mice, genetic manipulations enabled the study of telomere-aging relations, but such relations were not seen in wild-type subjects.The study of telomere-related aging in mice especially feature the difficulties of comparing human and model organisms, since the telomeres of most laboratory mice are 5-10 times longer than in humans, but their life span is much shorter.",
      "\t\n\nAnother attractive model of ageing is formulated by the ''telomere shortening theory'' [11].The activity of the telomerase enzyme complex responsible for maintaining the structure of the chromosome ends (telomeres) at each round of cell division likewise affects lifespan in a number of model organisms [11,12].Still, the ageing process of postmitotic cells (like neurons) contradicts the theory.Furthermore, the somatic cells of adult C. elegans do not divide, meaning that the shortening of telomeric regions is not an issue even in the case of a complete absence of telomerase activity [13].Regardless, the adult nematode ages and dies in about 2 weeks.Thus, the effect of telomere length on ageing appears to be rather complex.",
      "\t\n\nIn aging research there has been a great deal of interest in the idea that telomere shortening is a critical feature that leads to senescence.By contrast, the mitochondrial theory of aging posits that mitochondrial dysfunction is the cause of aging [56].Telomere processing and mitochondrial bioenergetics have so far been separate fields, with very limited interaction.The emerging evidence for some crosstalk between these fields of study is very exciting.Recently it has been shown that telomere dysfunction can lead to mitochondrial dysfunction [46] and vice versa [57].It is therefore of great interest that specific proteins, such as RECQL4, have now been identified that operate in both compartments.",
      "\t\n\nTelomere shortening is considered as the major cause of replicative senescence [82,83].It has been reported that the rate of telomere shortening is directly related to the cellular level of oxidative stress [84].Telomere shortening is significantly increased under mild oxidative stress as compared to that observed under normal conditions, whereas overexpression of the extracellular SOD in human fibroblasts decreases the peroxide content and the rate of telomere shortening [79].ROS can affect telomere maintenance at multiple levels.The presence of 8-oxoguanine (8-oxoG), an oxidative derivative of guanine, in telomeric repeat-containing DNA oligonucleotides has been shown to impair the formation of intramolecular G quadruplexes and reduces the affinity of telomeric DNA for telomerase, thereby interfering with telomerase-mediated extension of single-stranded telomeric DNA [85].ROS also affect telomeres indirectly through their interaction with the catalytic subunit of telomerase, telomerase reverse transcriptase (TERT).Increased intracellular ROS lead to loss of TERT activity, whereas ROS scavengers such as N-acetylcysteine (NAC) block ROSmediated reduction of TERT activity and delay the onset of cellular senescence [86].Furthermore, the presence of 8-oxoG in the telomeric sequence reduces the binding affinity of TRF1 and TRF2 to telomeres [87].TRF1 and TRF2 are components of the telomere-capping shelterin complex that protects the integrity of telomeres [88].In addition, ROS-induced DNA damage elicits a DNA damage response, leading to the activation of p53 [89], a critical regulator of senescence.It has been shown that p53 transactivates E3 ubiquitin ligase Siah1, which in turn mediates ubiquitination and degradation of TRF2.Consequently, knockdown of Siah1 expression stabilizes TRF2 and delays the onset of replicative senescence [90].The p53-Siah1-TRF2 regulatory axis places p53 both downstream and upstream of DNA damage signaling initiated by telomere dysfunction.By regulating telomere maintenance or integrity directly or indirectly, ROS plays a critical role in senescence.",
      "\tThe cell-autonomous theory on the\nother hand posits that individual cells are the targets of the aging process, via a timedependent increase in homeostatic dysfunction. The potential mechanisms include\nincreases in the production of reactive oxygen species, telomere shortening and, not\nsurprisingly, genomic instability. An implication of this theory is that long-lived cells in\nthe organism, such as neurons, muscle, and importantly stem cells, would be the\npredominant substrates of aging, while those cells that undergo rapid and continuous\nturnover would be removed before they could exert an effect on tissue function.",
      "\tTelomere Theory of Aging: Mitotic Clocks and Cancer\n\nTelomere stability has been implicated in the control of replicative senescence in human cells (Harley, 1995).The average telomere length of human germ cells is longer than that of differentiated somatic cells.As somatic cells age in vivo or in vitro, telomere arrays shorten in a progressive manner (Harley et al., 1990); telomere shortening in humans correlates with the developmental regulation of telomerase activity.Somatic cells have low or undetectable telomerase activity (Counter et al., 1992), and thus upon successive replication cycles, telomere sequences shorten as a result of incomplete replication of the 5 end of the daughter strand (Harley, 1995;Forsyth et al., 2002).Telomere shortening is proposed as the predominant \"mitotic clock\" that measures and controls the replicative life span of somatic cells.The telomere clock theory of aging states that erosion of the chromosome end triggers significant genome instability inducing cell senescence (Olovnikov, 1973;Hayflick, 1997).Numerous studies provide support for the telomere clock theory of cell aging (Harley et al., 1990;Harley, 1991;Harley, 1995;Forsyth et al., 2002).Telomere shortening is correlated with increased frequency of chromosome rearrangements (Counter et al., 1992) and p53-induced apoptosis (Karlseder et al., 1999).Of significant interest was the finding that telomerase activity resumes in the majority of immortalized cell lines and human tumors (Shay and Bacchetti, 1997) and that telomere array length stabilizes, and in some cases lengthens, in cancerous cells (Counter et al., 1992;Kim et al., 1994).Thus, telomere stabilization and abrogation of the normal telomere clock via abnormal telomerase activity (or an alternate pathway, see below) in cancerous cells may contribute to the immortalization capacity of metastatic cells (Harley et al., 1994; for a recent review, see Shay et al., 2001).Interestingly, transfection of TERT into human epithelial or fibroblast cells (Bodnar et al., 1998) has produced cell lines that are immortalized without being transformed.",
      "\tTelomeres and Reproductive Aging\n\n7][8] Telomeres are repetitive sequences and associated proteins, which cap and protect chromosome ends. 94][15] When telomeres become critically short, the uncapped, blunt chromosome end triggers cell cycle arrest, genomic instability, and cell death, a cellular process called senescence. 8,16elomere attrition plays a central role in oocyte aging. 5,17,18elomere length in most mouse strains is 5 to 10 times longer than that of humans, and intriguingly, most mouse strains do not exhibit appreciable oocyte aging.Rather, age-related changes in the uterus and/or hypothalamus precede oocyte aging. 19,20However, pharmacologic or genetic shortening of telomeres phenocopies the reproductive aging observed in women.As telomeres shorten in telomerase-null mice, their oocytes develop abnormal meiotic spindles, 21 arrested and fragmented embryos, 22 decreased chiasmata and synapsis, 23 and infertility. 24Observational studies in women have associated leukocyte telomere DNA attrition with earlier menopause, 25 recurrent miscarriage, 26 and Down syndrome. 27,28ocyte telomere length has been associated with failed in vitro fertilization (IVF) cycles, 29 embryo fragmentation, 22 and aneuploidy 30 in fertility treatment cycles.\t\n\nImplantation rate decreases and miscarriage rate increases with advancing maternal age.The oocyte must be the locus of reproductive aging because donation of oocytes from younger to older women abrogates the effects of aging on fecundity.Nuclear transfer experiments in a mouse model of reproductive aging show that the reproductive aging phenotype segregates with the nucleus rather than the cytoplasm.A number of factors within the nucleus have been hypothesized to mediate reproductive aging, including disruption of cohesions, reduced chiasma, aneuploidy, disrupted meiotic spindles, and DNA damage caused by chronic exposure to reactive oxygen species.We have proposed telomere attrition as a parsimonious way to explain these diverse effects of aging on oocyte function.Telomeres are repetitive sequences of DNA and associated proteins, which form a loop (t loop) at chromosome ends.Telomeres prevent the blunt end of DNA from triggering a DNA damage response.Previously, we showed that experimental telomere shortening phenocopies reproductive aging in mice.Telomere shortening causes reduced synapsis and chiasma, chromosome fusions, embryo arrest and fragmentation, and abnormal meiotic spindles.Telomere length of polar bodies predicts the fragmentation of human embryos.Telomerase, the reverse transcriptase capable of reconstituting shortened telomeres, is only minimally active in oocytes and preimplantation embryos.Intriguingly, during the first cell cycles following activation, telomeres robustly elongate via a DNA double-strand break mechanism called alternative lengthening of telomeres (ALTs).Alternative lengthening of telomere takes place even in telomerase-null mice.This mechanism of telomere elongation previously had been found only in cancer cells lacking telomerase activity.We propose that ALT elongates telomeres across generations but does so at the cost of extensive genomic instability in preimplantation embryos.",
      "\t\n\nWe examined the ant genomes and transcriptomes for signatures related to aging.Telomere shortening is a hallmark of cellular senescence in multicellular eukaryotes, and the enzyme telomerase (TERT), which counteracts telomere shortening, prolongs life span upon overexpression (8).TERT RNA levels were highest in eggs and lower in adults in both C. floridanus and H. saltator, but they were up-regulated in H. saltator gamergates (Fig. 3A).This may be explained by the gamergates acquiring many physiological characteristics of queens, including longer life span (9).Aging has also been linked to the sirtuin lysine deacetylases enzymes SIRT1 and SIRT6, homologous to the Saccharomyces cerevisiae Sir2p implicated in replicative senescence (10).In H. saltator gamergates, both of these genes are expressed at higher levels compared to workers (Fig. 3B).These results suggest that the regulation of life span in gamergates may share common mechanisms with other organisms."
    ],
    [
      "\t\nThe biology of aging is an area of intense research, and many questions remain about how and why cell and organismal functions decline over time.In mammalian cells, genomic instability and mitochondrial dysfunction are thought to be among the primary drivers of cellular aging.This review focuses on the interrelationship between genomic instability and mitochondrial dysfunction in mammalian cells and its relevance to age-related functional decline at the molecular and cellular level.The importance of oxidative stress and key DNA damage response (DDR) pathways in cellular aging is discussed, with a special focus on poly (ADP-ribose) polymerase 1, whose persistent activation depletes cellular energy reserves, leading to mitochondrial dysfunction, loss of energy homeostasis, and altered cellular metabolism.Elucidation of the relationship between genomic instability, mitochondrial dysfunction, and the signaling pathways that connect these pathways/processes are key to the future of research on human aging.An important component of mitochondrial health preservation is mitophagy, and this and other areas that are particularly ripe for future investigation will be discussed\nAccepted ArticleThis article is protected by copyright.All rights reserved.defects in DNA repair, and improved understanding of the signaling pathways that connect these processes are important for future research on human aging. DNA damage response pathwaysAll cells are continuously exposed to endogenous agents that cause DNA damage, including reactive oxygen species (ROS), reactive nitrogen species (RNS) and environmental sources of DNA damaging agents, such as radiation, chemical mutagens and carcinogens.It is estimated that approximately 10 5 DNA lesions accumulate in the human genome per cell per day [4].Figure 1 summarizes the classes of DNA damage and the primary cellular mechanism responsible for repairing each class of DNA damage [5].In mammalian cells, nucleotide excision repair (NER) is the primary pathway for repair of bulky DNA lesions, including those generated by ultraviolet light, environmental and chemical mutagens [6].Base excision repair (BER) removes damaged bases caused by oxidation, alkylation, deamination, and spontaneous hydrolysis of the glycosidic bond [7].Single-strand DNA breaks (SSBs) and double-strand DNA breaks (DSBs) are among the most genotoxic DNA lesions.DSBs can lead to chromosomal rearrangements and genomic instability that can trigger cell death and/or senescence [8].Mammalian cells express four distinct DSB repair (DSBR) pathways: homologous recombination (HR), non-homologous end joining (NHEJ), alternative end joining (Alt-EJ) and single strand annealing (SSA).Since NHEJ ligates free ends it is a mutagenic process whereas HR is thought to be error free.Notably, NHEJ is less mutagenic than Alt-EJ, and SSA pathways, which are highly error-prone and promote chromosomal rearrangements and genomic instability [9,10].The mechanisms and factors that determine which pathway repairs a specific DSB in a specific cell include cell cycle phase, efficiency of DNA end-resection, and status of RecQ helicase expression, and post-translational modification [9][10][11].When a cell's capacity to repair DNA lesions is compromised or exceeded, persistent DNA lesions can accumulate and block DNA replication forks and inhibit cell cycle progression in proliferating cells.Replication fork blockage can, in some cases, be overcome by activating secondary origins of replication or by enabling lesion bypass by an error-prone translesion DNA polymerases [12].Cells that harbor a defect in one or more DNA repair pathways, accumulate persistent DNA damage and typically exhibit an elevated mutation rate [2,13].Many theories have been advanced to explain why and how organisms age, and one of the prevalent ones proposes that time-dependent accumulation of DNA damage and genetic mutations plays a major causal role in aging.Consistent with this hypothesis, several heritable human disorders characterized by accelerated aging are caused by mutant alleles in DNA repair genes which impairs DNA repair capacity [14].Thus, human premature aging disorders are strongly associated with defects in DSBR,",
      "\t\n\nThe lacI/lacZ reporter gene mouse models have taught us that different tissues exhibit different mutation rates with age.Specific DNA repair pathways have been shown to decline with age, depending on the tissues.Except for the BER pathway, few studies have shown decline of other DNA repair pathways or repair enzymes in the mouse aging liver.As several DNA repair enzymes are posttranslationally modified upon DNA damage (thus altering their activities), appropriate experiments are warranted to follow such posttranslational changes at the protein levels in the liver of aging mice.Noteworthy, the genetic background of the mice under study and the husbandry conditions (including diet) will also impact on the phenotypes.Thus, depending on the stress imposed on mice, the severity of the phenotype will vary.Nevertheless, the control of ROS levels, structural changes at the telomere, DNA damage and mutation rate, mitochondrial dysfunction will ultimately impact on health, and such processes underline the complexity of aging.\t\n\nIt remains unclear why only certain DNA repair mutants show phenotypes related to premature aging.It is interesting to note that the DNA repair-deficient mouse models that exhibit reduced health and/or life span in addition to early appearance of age-related phenotypes also display major changes in the expression of liver genes involved in stress response, cell proliferation and apoptosis, glucose and/or lipid metabolism, and inflammatory response.This suggests that NEIL1 (associated with BER), CSB, ERCC1, XPA, XPD (associated with NER), DNA-PKcs/Ku complex (associated with NHEJ), and WRN (associated with NHEJ, HR, or BER) are also implicated (directly or indirectly) with the transcription of a subset of genes (or pathways) important for the aging phenotypes at least in the liver.Such data imply the possibility of targeting specific biochemical pathways (in addition to ROS levels, telomere structural changes, mitochondrial dysfunction) to control or slow down the progression of age-related diseases.The impact of calorie restriction, dietary restriction mimetics, or antioxidants is already under scrutiny in different mouse models of aging [129,130,137,138].",
      "\tDiscussion\n\nAlthough great attention has been paid to the potential relationship between aging and DNA DSB repair, the major descriptive and mechanistic studies were performed in rodent models. 3,4,6,11,17,23Relevant research in humans was mainly focused on age-related change in the recruitment kinetics of essential DNA damage response factors, assayed by immune-staining; 26 age-related change of genomic instability, measured by comet assay; 7 age-related change of expression profile of important DNA repair factors, analyzed by RNA array and proteomic tools. 27,28Although the previous work greatly advanced our understanding of age-associated changes of DNA DSB repair, due to a lack of proper tools for the analysis of NHEJ and HR efficiency and fidelity separately, and the hardship of acquiring a sufficient number of human samples, whether NHEJ efficiency and fidelity, and HR efficiency change with age in humans and the consequences of any such change, and its underlying molecular mechanism are not well understood.Here, we established 50 eyelids fibroblast cell lines derived from donors who are evenly distributed by age.With these cell lines, using our well-characterized reporters for the analysis of NHEJ and HR capacities, for the first time, we conclusively demonstrate that both DNA repair pathways decline with age.The impaired recruitment of Rad51 to DNA damage sites during aging hampers the ability of aged cells to choose the precise HR pathway, forcing cells to utilize the error-prone NHEJ pathway.Simultaneously, because of decreased expression of XRCC4, DNA Lig4 and DNA Lig3 during aging, NHEJ becomes more inefficient and inaccurate with age, leaving more damage sites repaired with a loss of more genetic information.The declined DNA DSB repair by both pathways then leads to accumulation of DNA mutations, posing more damages to both NHEJ and HR repair machineries, eventually exacerbating the age-related rise of genomic instability (Figure 8).Our previous reports indicate that the efficiency of DNA DSB repair by NHEJ and HR declines, and NHEJ becomes more error-prone with replicative cellular senescence. 21,29In presenescent cells, HR efficiency declines by 38-fold, whereas NHEJ changes by only ~two to threefold.Consistent with the above results, our current aging study also shows a sharp decline of HR efficiency during aging, with the biggest difference of an ~30-fold change, whereas the change of NHEJ with age is relatively mild, albeit statistically significant.However, contradictorily, knocking out major NHEJ factors, such as DNA-PKcs, Ku70, Ku80 or Artemis in mice leads to a phenotype of progeria, 4 whereas knocking out HR factors usually leads to a phenotype of embryonic lethality, 4,30,31 suggesting that NHEJ is more likely to be involved in aging.Considering an organism's life history is likely critical for reconciling these observations.During embryogenesis cells are rapidly dividing and therefore undergoing replication stress; complete loss of HR, which is a dominant pathway for relieving replication stress, 32 may cause cells to enter apoptosis by activating P53, leading to embryonic lethality.However, the embryonic lethality could mask the roles of HR in aging.Indeed, partial loss of HR might also lead to agingassociated phenotypes.For instance, BRCA1 heterozygous mice are short lived and have a premature aging phenotype in the ovaries. 33,34Intriguingly, once an organism has developed into adulthood, a gradual suppression of the HR pathway with age is needed to counteract the potential tumorigenesis as uncontrolled or overactive single-strand annealing (SSA), which shares almost identical repair machinery with the HR pathway, 35 may cause loss of large genomic fragments due to the prevalence of repetitive sequences in human genomes.",
      "\tPARP1 in DNA Repair. As discussed above, a substantial body of evidence demonstrates a causative role of DNA repair and genome maintenance mechanisms in mammalian longevity.",
      "\t\n\nA similar duality is emerging in mammals, where defective DNA repair is often associated with premature aging (Lombard et al., 2005), yet the lack of a DNA damage response can be beneficial in situations of chronic DNA damage due to telomere dysfunction (Choudhury et al., 2007;Schaetzlein et al., 2007).Furthermore, exposure to genotoxic stress early in life seems to accelerate changes in gene expression that have been associated with age-related diseases such as amyloidogenesis (Wu et al., 2008).Interestingly, we found that constitutive overexpression of a set of age-deregulated SIRT1 target genes promotes apoptosis in primary neurons (Figure S11); however more work is needed to determine the physiological relevance of this observation.\t\n\nThere is some evidence that related processes occur in mammals.First, cells damaged by oxidative stress in vitro undergo stochastic transcriptional changes that parallel those in aged heart tissue (Bahar et al., 2006).Second, a deficiency in the DNA repair factor ERCC1 accelerates aging phenotypes and generates gene expression profiles reminiscent of aged animals (Niedernhofer et al., 2006).Third, cells that senesce because of replicative aging in vitro or in aged tissues in vivo exhibit alterations in heterochromatin (Herbig et al., 2006;Narita et al., 2006) and secrete growth factors that can drive tumorigenesis (Campisi, 2005).Finally, oxidative DNA damage at promoters correlates with gene repression in the aging human brain (Lu et al., 2004) and has been linked to both transcriptional and epigenetic changes that may contribute to Alzheimer's disease (Wu et al., 2008).",
      "\t\n\nThe paradigm of the DNA damage theory of stem cell aging states that aging-associated changes in the DNA repair system in HSCs, together with changes in cell-cycle regulation due to increased DNA damage with age (Pietras et al., 2011;Rossi et al., 2007a), are thought to result in elevated DNA mutations, which then causally contribute to the decrease in HSC function with age.The paradigm is in part based on the finding that mice lacking a distinct set of DNA damage repair proteins display reduced function of HSCs, including an impaired repopulating potential and an overall depletion of the HSC pool (Ito et al., 2004;Navarro et al., 2006;Nijnik et al., 2007;Parmar et al., 2010;Prasher et al., 2005;Reese et al., 2003;Rossi et al., 2007a;Ruzankina et al., 2007;Zhang et al., 2010;Geiger et al., 2013), although in naturally aged mice, there is actually an expansion of the number of phenotypic stem cells instead of a depletion of the HSC pool.HSC aging also correlates with an increase in DNA double-strand breaks (DSBs).Both human and mouse HSCs present upon aging with a 2-to 3-fold elevated number of gH2AX foci, a bona fide surrogate marker for unresolved DSBs (Rossi et al., 2007a;R ube et al., 2011).Unresolved DSBs accumulated in quiescent, but not cycling, HSCs upon aging (Beerman et al., 2014).gH2AX foci though were very recently shown to co-localize in HSCs with proteins associated with replication and ribosomal biogenesis stress (Flach et al., 2014), rendering gH2AX foci as a general marker for persistent DNA DSBs in HSCs questionable.",
      "\tAging\n\nThe oxidative stress theory of aging proposes that accumulation of oxidative DNA damage over the life span of an organism leads to gradual decline of cellular functions and eventual death (Bohr, 2002).This model is supported by several circumstantial evidences including the observation that lower free radical production and/or antioxidant treatment protects against agerelated deterioration, and cognitive decline (Lemon et al., 2003).Further, deficit or decrease in the repair of oxidative DNA damage appears to correlate with premature aging and age-related diseases (Bohr et al., 2007).It appears likely that overall genome repair, specifically the balance between DNA damage and its repair is a major determinant of the longevity and cell viability.A specific defect in processing 5 0 dRP residue at the strand break in Sir2 (SIRT6 homolog)-deficient mice displayed age-related degenerative phenotype (Mostoslavsky et al., 2006).The activities of DGs OGG1, NTH1 and uracil DNA glycosylase (UNG) in brain mitochondria decrease significantly with age (Gredilla et al., 2010).",
      "\t\n\nPrevious evidence for an age-related decline in DNA repair was obtained largely from cell culture systems.For example, decreased repair has been observed in some but not all cases in mammalian cells undergoing senescence in culture [58,59], as well as cultures of primary cells taken from older versus younger individuals [26,[60][61][62][63][64].Additionally, there is a general correlation between mammalian lifespan and DNA repair (for review [65]).Further support for a relationship between DNA repair and aging comes from the existence of several human diseases caused by DNA repair defects that result in shortened lifespan in affected humans as well as rodent models, despite the much shorter normal rodent lifespan [24,25,66,67].Finally, a recent study reported that the in vivo repair of CPDs is decreased in the skin of old compared with that of young men, suggesting that the previous cell culture results are reflective of in vivo biology [27].\t\n\nWe also asked whether repair of UVC damage is less efficient in the nuclei of aging than in those of young adult C. elegans.There is evidence that nuclear genome integrity may be related to the aging process in mammals [24,25] and that repair rates decline in mammalian cells in culture [25,26].However, very few in vivo, whole organism data have been reported that address this hypothesis [27].Furthermore, there is little evidence to support the hypothesis that DNA repair capacity is related to age in C. elegans, despite the extensive use of this organism as a model for aging [5,6].In this study, we observed a 30% to 50% decrease in DNA repair in aging C. elegans (assayed at 6 days after L4 molt, corresponding to 60% of the population's mean adult lifespan), and then performed gene expression profiling in young and aging adults to generate hypotheses to explain the mechanism of that decline.\tRepair in nuclear genes is decreased in aging nematodes\n\nPrevious studies conducted in cells in culture have suggested that DNA repair declines with age in mammals [24,25].We found that repair in all ten nuclear targets was lower in aging (6 days after L4) adults than repair of those same targets in young (1 day after L4) glp-1 adults (P < 0.0001; Table 1).This difference was greatest in low and medium expression genes (about 50% decrease) but was also robust in high expression genes (about 33% decrease).We chose day 6 to represent the aging adult population because at this age more than 98% of the population is still alive, but the population as a whole has reached 60% of its mean adult lifespan (10 days; Figure 6) and 43% of its maximum adult lifespan (14 days; Figure 6).One-day-old adults have reached 10% of the mean adult lifespan, and 7% of the maximum adult lifespan.glp-1 adults raised at 25C exhibit signs of old age at 6 days, including constipation, cuticular blisters, and reduced mobility and feeding, but they have not yet begun to die in significant numbers (Figure 6 and Additional data file 2).It is therefore unlikely that repair rates are significantly confounded by DNA degradation occurring in dead animals.Initial lesion frequencies were not significantly different between young and aging adults (Table 1).",
      "\t\n\nAlthough these age-related diseases are strongly influenced by DNA damage, there is still much debate about the extent to which DNA damage contributes to ageing.On the one hand, there is a clear link between oxidative stress and lifespan in invertebrates.In mammals, calorie restriction -a dietary intervention known to extend lifespanreduces ROS production and increases the expression of enzymes that metabolize ROS, such as superoxide dismutases (SODs) and catalase (reviewed in Ref. 80) (see figure).Decreased DNA damage and increased lifespan have also been observed in mice that overexpress catalase in mitochondria 81 .Similarly, mice with mutations in DNA-repair enzymes that are involved in transcription-coupled repair or base-excision repair show signs of premature ageing 60,82 .In humans, several defective DNA-repair pathways can cause accelerated ageing (progeroid) syndromes.On the other hand, certain mouse strains with defective DNA-repair systems accumulate high levels of DNA damage and yet have a normal lifespan (reviewed in Ref. 83).Similarly, a reduction in SOD levels in mice leads to increased oxidative DNA damage but does not affect the ageing process 84 .",
      "\t\n\nThe role of faulty DNA repair machinery in age-related genomic instability was also found in S. cerevisiae and Drosophila.Mutations in the sgs1 and srs2 genes [encoding for RecQ helicase, homologous to the human WRN (43)] shortened S. cerevisiae life span through two distinct pathways: sgs1-and srs2-mutated cells stopped dividing randomly in an age-independent manner that required the RAD9 (cell cycle checkpoint control protein) DNA damage checkpoint, but late-generation sgs1-and srs2-mutated cells exhibited premature aging.The double sgs1/srs2-mutated yeast cells showed a high rate of terminal G2/M arrest.This arrest was suppressed by knockouts of RAD51 (DNA repair protein RAD51 homolog 1), RAD52 (DNA repair protein), and RAD57 (DNA repair protein), hinting for malfunctioning HR.In a similar study, knockout of DNA2, encoding RecQ helicase-like protein, caused premature aging phenotypes including longer cell cycle time, transcriptional silencing, genomic alterations, and eventually shorter life span (44).Shaposhnikov et al. (45) used D. melanogaster to evaluate the effect of overexpression of DNA repair genes in several locations in the body and several time points during the life period on the Drosophila life span.Beneficial effects on life span were observed with overexpression of Hus1 (checkpoint clamp component), mnk (MAPK interacting protein kinases), mei-9 (meiotic 9, D. melanogaster), mus210 (Xeroderma pigmentosum, complementation group C, D. melanogaster), spn-B (spindle B, D. melanogaster), and WRNexo (WRN exonuclease, D. melanogaster), which control the processes of DNA damage recognition and repair (45).Myc, a key regulator protein of cell growth and proliferation, was shown to act as a pro-aging factor, probably by its ability to increase genomic instability.Overexpression of Myc in Drosophila increased the frequency of large genome rearrangements associated with faulty repair of DNA DSBs and decreased adult life span.Myc knockdowns demonstrated reduced mutation rate and extended life span (46).In aged mice, increased levels of DNA breaks or unrepaired DNA damage as illustrated by the formation of H2AX (phosphorylated variant histone H2A) foci were observed (47)(48)(49).A positive effect on longevity was observed with overexpression of the human enzyme hMTH1 (MutT Human Homolog 1), which eliminates oxidized purine18 and deacetylase Sirt6 (50).Overexpression of SIRT6 promotes DSB repair by the activation of PARP1 [Poly (ADP-ribose) polymerase 1] and facilitating the recruitment of Rad51 (51) and NBS1 (Nijmegen Breakage Syndrome 1) (52) to DNA lesions.",
      "\t\n\n40.Goukassian D, Gad F, Yaar M, Eller MS, Nehal US, Gilchrest BA. 2000.Mechanisms and implications of the age-associated decrease in DNA repair capacity.FASEB J. 14:1325-34",
      "\tHow does the rate of DNA damage accumulation influence ovarian ageing? Detailed analysis of full genome expression profiles of multiple organs in a variety of DNA repair-deficient, progeroid mouse models has disclosed that these mutants strongly resemble genome-wide expression profiles of normal ageing, capturing a tremendous amount of underlying biological processes, which are shared between accelerated and natural ageing [31,39,40].This is consistent with the numerous parallels at the pathological, histological, physiological and functional levels, supporting the notion that the accelerated ageing to a large extent resembles the normal ageing process.The expression profile analysis also revealed that repair-deficient, premature ageing mouse mutants systemically suppress key somato-, lacto-and thyrotrophic hormonal axes, including the GH/IGF1 pathway, explaining why all progeroid repair mice -and the corresponding human patients-show dramatic early cessation of growth.Attenuation of the GH/IGF1 axis is also found with normal ageing [41].Energy appears to be redirected from growth to maintenance and defence mechanisms, such as the NRF2-controlled anti-oxidant system and stress resistance.This so-called 'survival' response resembles the response triggered by dietary restriction, which is for long known to retard the process of ageing and promote longevity in a very wide variety of organisms, ranging from yeast to mammals, including in one study non-human primates [42].Persistent DNA damage even triggers this response at the level of individual cells in culture, indicating its universal, highly conserved nature [43].The most plausible interpretation of this response is that organisms facing accelerated ageing due to rapid accumulation of DNA damage, caused by an inborn DNA repair deficiency, attempt in this way to delay ageing in order to extend their short lifespan and live as long as possible.This finding provided a link between high DNA damage loads and the insulin/IGF1 signal transduction pathway, which controls, metabolism, growth and lifespan and influences the ageing process.",
      "\t\n\nIt is well known that a link between DNA damage and mammalian ageing exists (Sedelnikova et al., 2004;Karanjawala and Lieber, 2004;Lans and Hoeijmakers, 2006).Recent studies have shown that double-strand breaks (DSBs) typically accumulate in HGPS and RD cells and that the resultant genome instability might contribute to premature aging (Liu et al., 2005;Manju et al., 2006).DNA repair pathway defects were observed in HGPS and in a RD mouse model (Zmpste24/).Prelamin A accumulation was also associated with impairing of DNA repair factors recruitment at damage sites (Liu et al., 2005).A second study identified the overexpression of many essential p53 targets in the Zmpste24/ mouse model, which caused at least part of their Progeria-like phenotype (Bergo et al., 2002;Penda s et al., 2002;Varela et al., 2005).Indeed, double knock-out Zmpste24/, p53/ mice showed a partially rescued phenotype (Varela et al., 2005).It is known indeed that p53 activation is triggered by DNA damage (Burma et al., 1999;d'Adda di Fagagna et al., 2003), and that, to some extent, p53 activation can have deleterious effects on bone development, as observed in Progeria (Zambetti et al., 2006).Further proofs of the links existing between altered bone development, DNA repair, accelerated aging, and reduced cancer are the phenotypes of several DNA repair mouse models, as XPD mutant mice (de Boer et al., 2002), Ku80 defective mice (Difilippantonio et al., 2000) and p53 truncation mutants (Tyner et al., 2002).Furthermore, Manju et al. demonstrated that several Lamin mutants causing Progeria and muscle-specific disorders induce defects in ATR signaling pathways such as reduced phosphorylation of g-H2AX and inadequate recruitment of 53BP1 to repair sites in response to DNA damage in cultured cells (Manju et al., 2006).More recently, it has been shown that whereas DSBs repair proteins Rad51 and Rad50 were absent at Laminopathy-related DNA damage sites in patients' cells, xeroderma pigmentosum group A (XPA) protein, a unique nucleotide excisionrepair protein, colocalizes with DSB sites (Liu et al., 2007), maybe pointing to ''unifying'' pathophysiologic clues between different disorders characterized by features of premature ageing.",
      "\t\n\nOther modulators of the DNA damage response appear to impact aging.For example, inhibition of PARP1 leads to lifespan extension in certain model organisms [21].Concomitant with the age-associated activation of PARP1 is the observation that persistent DNA damage foci containing the proteins 53BP1, gH2AX, and FOXO4 accumulate in aging cells [4,60].Notably, signaling from these foci may contribute to the senescence-associated secretory phenotype [47].Another approach to tackle this signaling cascade is therefore to break up these foci.Treatment with a FOXO4mimicking peptide leads to the removal of p53-and FOXO4-containing foci, thus facilitating apoptosis of senescent cells, regrowth of lost hair, and lifespan extension in models of severe premature aging [60].",
      "\tCONCLUSION\n\nAccumulation of DNA lesions during aging is likely a major driver of aging and age-related diseases.Known prolongevity interventions and pathways could reduce DNA damage load.Dissecting these mechanisms might facilitate the development of novel age-related intervention strategies.Conversely, elucidating the downstream molecular and cellular mechanisms by which DNA damage drives aging and age-related diseases might also lead to novel antiaging therapies.The use of mouse models that mimic progeroid syndromes can dramatically accelerate aging research, not only by shedding light on the molecular mechanisms underlying the aging process, but also by screening for novel interventions.For instance, premature aging Ercc1 / mice with a life span of 0.5 year have the broadest spectrum of age-related pathologies recorded, which also includes the progressive frailty that is frequently observed in natural human aging.Ercc1 / mice could be used to systematically screen interventions for their ability to reduce age-related pathology much faster than in wild-type mice.\t\n\nrepair capacity and thereby reduce DNA damage load and its consequences could be promising.DNA repair, however, is comprised of multiple, complex pathways for which capacity-limiting proteins have not been identified; this hampers the development of interventions that enhance repair.If DNA damage is a main driver of aging, then known life span-extending pathways and interventions might promote longevity by reducing DNA damage load.Several lines of evidence support this hypothesis.Dietary restriction (DR), reduced calorie intake without malnutrition, is the only robust universal intervention with widespread documented longevity-and health-promoting effects in numerous species (117).DR reduces mutation accumulation (118), which suggests improved DNA repair or reduced generation of endogenous genotoxic metabolic (by-)products by direct DR-mediated alterations in metabolism.Suppression of insulin and IGF1 signaling are among the best-documented prolongevity pathways in model organisms ranging from worms and flies to mammals (119).These pathways also directly impinge on energy metabolism; hence, generation of genotoxic metabolic (by-)products could be reduced.Additionally, insulin/IGF1 longevity pathways can also impinge on DNA repair to provide a complementary protective mechanism against aging.Insulin/IGF1 signaling is reduced by DR in long-lived mouse mutants with defects in these signaling pathways (120), which leads to reduced AKT activity.AKT activity needs both T308 and S473 phosphorylation (121); insulin/IGF1 signaling induces T308 phosphorylation (121).The proteins responsible for S473 phosphorylation are less clear, but DSB-induced checkpoint kinases DNA-PK and ATM can phosphorylate AKT at S473 (122)(123)(124)(125)(126). Thus, DNA damage repair and signaling might be integrated with nutrient status.Indeed, active AKT negatively modulates DNA repair (127) by inhibiting p53 activity (128).Also, the FoxO transcription factors, repressed by AKT (129), have also been implicated in promoting DNA repair (130,131).This provides yet another mechanism by which repair might be affected by DR.Furthermore, AKT has been shown to phosphorylate and inhibit several key DDR factors including Chk1 and TopBP1 (127).Thus, DR could improve DNA repair or signaling via altered insulin/IGF1 signal transduction pathways.This could provide opportunities to improve DNA repair via existing prolongevity mechanisms."
    ],
    [
      "\t\n\nBackground: Genetic research on longevity has provided important insights into the mechanism of aging and aging-related diseases.Pinpointing import genetic variants associated with aging could provide insights for aging research.\t\nBackground: Genetic research on longevity has provided important insights into the mechanism of aging and aging-related diseases.Pinpointing import genetic variants associated with aging could provide insights for aging research.Methods: We performed a whole-genome sequencing in 19 centenarians to establish the genetic basis of human longevity.Results: Using SKAT analysis, we found 41 significantly correlated genes in centenarians as compared to control genomes.Pathway enrichment analysis of these genes showed that immune-related pathways were enriched, suggesting that immune pathways might be critically involved in aging.HLA typing was next performed based on the whole-genome sequencing data obtained.We discovered that several HLA subtypes were significantly overrepresented.Conclusions: Our study indicated a new mechanism of longevity, suggesting potential genetic variants for further study.\tIntroduction\n\nWith the development of human genomics research, a large number of studies of the genetics of longevity have been conducted.Scientists from various countries have proposed many different theories concerning the mechanisms of aging from different perspectives, involving oxidative stress, energy metabolism, signal transduction pathways, immune response, etc. [1,2].These mechanisms interact with each other and are influenced by heredity to some degree [2,3].The identification of longevity-related biological markers is critical to an indepth understanding of the mechanisms of carrier protection against common disease and/or of the retardation of the process of aging.",
      "\tConclusions\n\nIn the absence of a consensus phenotype for aging, genetic research is impeded (Melzer et al. 2007).At present, it is difficult to determine whether preventative and therapeutic strategies (such as calorie restriction) have beneficial effects in humans because there are no validated biomarkers that can serve as surrogate markers of aging (Matkovic et al. 1990).To have the \"phenome of aging\" (Xue et al. 2007) much better defined, we propose using the musculoskeletal aging phenotypes as an example and starting point.",
      "\t\nStudies of the basic biology of aging have identified several genetic and pharmacological interventions that appear to modulate the rate of aging in laboratory model organisms, but a barrier to further progress has been the challenge of moving beyond these laboratory discoveries to impact health and quality of life for people.The domestic dog, Canis familiaris, offers a unique opportunity for surmounting this barrier in the near future.In particular, companion dogs share our environment and play an important role in improving the quality of life for millions of people.Here, we present a rationale for increasing the role of companion dogs as an animal model for both basic and clinical geroscience and describe complementary approaches and ongoing projects aimed at achieving this goal.",
      "\t\n\nOn the other hand, the same evolutionary-motivated strategy suggesting to focus on more heterogeneous phenotypes (as opposite to more homogenous) can be highly beneficial for unraveling genetic predisposition to fundamental mechanisms of intrinsic biological aging and, consequently, to geriatric diseases.Indeed, aging is associated with systemic remodeling of an organism's functioning which increases chances of virtually all geriatric disorders (Franco et al. 2009;Franceschi et al. 2000;Martin et al. 2007;Cutler and Mattson 2006).Experiments with laboratory animals (Johnson 2006) and heritability estimates in humans (Christensen et al. 2006;Iachine et al. 1998) show that aging can be genetically regulated (Finch and Tanzi 1997;Martin et al. 2007;Vaupel 2010).Accordingly, yielding insights in genetic predisposition to aging-related processes in an organism could be a major breakthrough in preventing and/or ameliorating not one geriatric trait, but perhaps a major subset of such traits (Martin et al. 2007) that can greatly advance progress in solving the problem of extending healthy lifespan in humans.",
      "\t\n\nThe studies in lower animals made in recent years that have led to the view that genes are involved in aging have not revealed a reversal or arrest of the inexorable expression of molecular disorder that is the hallmark of aging.These studies are more accurately interpreted to have impact on our understanding of longevity determination because all of the experimental results have altered biological variables before the aging process begins.None of these studies in invertebrates has demonstrated that the manipulation of genes has slowed, stopped, or reversed recognized biomarkers of the aging process.",
      "\t\n\nAny discovery about the biological determinants of the rate of aging raises the possibility of therapies to slow aging.Therefore the discovery of a gerontogene with even very rare mutations that increased longevity would cause speculation about future trends in mortality.However, the discovery of such a gene would be relevant only to long-term (and, therefore, very speculative) projections.\tGENETIC ANALYSIS OF LONGEVITY, OF AGING, AND OF AGE-SENSITIVE TRAITS IN MICE\n\nBiogerontology has just begun to benefit from the attention and skills of professional geneticists.Geneticists can attack problems of aging from several related but fundamentally distinct directions.Studies of rare mutations at individual loci, such as the Werner's syndrome locus WRN, whose mutant form produces, in middle-aged people, several of the diseases typically not seen until old age, can give attractive points of entry into the pathophysiology of age-related diseases.In mice there are now four reports of mutations-two naturally occurring and two artificially produced-that lead to impressive increases in mean and maximal longevity (Miskin and Masos, 1997;Brown-Borg et al., 1996;Miller, 1999;Migliaccio et al., 1999), and thus provide extremely valuable models for testing mechanistic ideas and the control of aging.Some of these, such as the dw/dw and df/df dwarfing mutations that affect levels of growth hormone and thyroid hormone, provide clues to endocrine-dependent pathways that could regulate age effects in multiple cells and tissues.The recent report (Migliaccio et al., 1999) that mouse life span can be extended by an induced mutation that diminishes cell susceptibility to apoptotic death after injury should stimulate new inquiries into the effects of altered cell turnover on age-dependent changes.Each of these mutations, however, is exceptionally rare in natural populations; despite their effect on longevity, perhaps mediated by a direct effect on aging, each of the mutations is likely to have, overall, a negative effect on reproductive success and thus fail to become fixed in natural mouse populations.",
      "\t\n\nIn 2021, Science published a special issue entitled \"125 Questions: Exploration and Discovery.\" One of these 125 questions was \"Can we stop ourselves from aging? \"The U.S. National Institute on Aging (NIA) at the National Institutes of Health (NIH) states that \"aging is associated with changes in dynamic biological, physiological, environmental, psychological, behavioral, and social processes.\" Although geneticists and epidemiologists have long debated the relative importance of the role played by genotype or the environment in the development of age-related diseases, it is apparent that both can play substantial roles in this process [6,7].However, most etiological studies have concentrated on the role of genotype and have considered the environment to play a secondary role.Nevertheless, an analysis of GBD data showed that nearly 50% of deaths worldwide are attributable to environmental exposure, primarily exposure to airborne particulates (including household air pollution and occupational exposure; 14% of all deaths), smoking and secondhand smoke (13%), plasma sodium concentrations (6%), and alcohol consumption (5%) [8].In contrast, a recent analysis of 28 chronic diseases in identical twins showed that the genetic-related risks of developing one of five age-related diseases were 33.3%, 10.6%, 36.3%, 19.5%, and 33.9% for AD, PD, CAD, COPD, and T2DM, respectively, with a mean of only 26% [9].The results of over 400 genome-wide association studies (GWASs) have also elucidated that the heritability of degenerative diseases is only approximately 10% [10,11].Consequently, nongenetic drivers, such as environmental factors, are now recognized as major risk factors for age-related diseases.The contributions of environmental factors to the development of age-related diseases can be revealed by analyses of all of the factors to which individuals are exposed in their life and the relationships between these exposures and age-related diseases [12,13].",
      "\t\n\nWith an aging population, there is a great and urgent need to develop approaches and therapies targeting the aging process and age-related diseases (Butler et al., 2008).Delaying the process of aging, even slightly, would have profound social, medical and economic benefits (Olshansky et al., 2006;Butler et al., 2008).For example, slowing aging by a mere 7 years would cut mortality of age-related diseases by half at every age.Therefore, the potential benefits from research on the basic biology and genetics of aging are unparalleled in terms of improving quality of life and health.Although much debate remains regarding the molecular causes of aging, findings from model organisms show that aging is surprisingly plastic and can be manipulated by both genetic and environmental factors (Finch and Ruvkun, 2001;Kenyon, 2010).In principle, therefore, it is possible to manipulate human aging.Unlocking this capacity to manipulate aging in people would result in unprecedented human health benefits, and it opens new opportunities for industry.\tIV. Genome-Environment Interactions as Targets for Dietary Interventions and Drug Discovery\n\n\"[It's] possible that we could change a human gene and double our life span. \"-CynthiaKenyon (Duncan, 2004) According to the GenAge database of aging-related genes (http://genomics.senescence.info/genes/),more than 700 genes have been identified that regulate lifespan in model organisms (de Magalha es et al., 2009a).Many of these genes and their associated pathways-such as the insulin/IGF1/GH pathway-have been shown to affect longevity across different model organisms (Kenyon, 2010).Therefore, at least some mechanisms of aging are evolutionarily conserved and may have potential therapeutic applications (Baur et al., 2006).For example, evidence suggests the use of lowered IGF signaling (e.g., by targeting IGF receptors) to treat certain age-related diseases such as cancer (Pollak et al., 2004), Alzheimer's disease (Cohen et al., 2009), and autoimmune diseases (Smith, 2010).Moreover, a number of genes and pathways associated with longevity and CR are part of nutrient-sensing pathways that also regulate growth and development, including the insulin/IGF1/GH pathway (Narasimhan et al., 2009;Stanfel et al., 2009).Many of these genes modulate the response to environmental signals, such as food availability, and act in signaling pathways that if understood can be targeted (Fig. 1).The genetic regulation of aging is therefore an emerging field with multiple applications in the human nutrition, cosmetic, and pharmaceutical industries.\t\n\nThe remarkable discoveries of the past 2 decades showing that single genes can regulate aging in model organisms demonstrate that aging can be genetically manipulated (Finch and Ruvkun, 2001;Kenyon, 2010).Hundreds of genes that modulate longevity have now been identified in model organisms (de Magalha es et al., 2009a).In some cases (e.g., in worms), mutations in single genes can extend lifespan by almost 10-fold (Ayyadevara et al., 2008).Nonetheless, aging is a complex process that derives not from single genes but from the interactions of multiple genes with each other and with the environment.Evidence from animal systems shows a major impact of the environment on aging, yet environmental manipulations of aging act through genes and proteins, usually by triggering signaling pathways and modulating gene expression.In fact, some genes have been shown in model organisms to have varying effects on lifespan depending on diet (Heikkinen et al., 2009).Genes that can regulate aging in model organisms cannot be directly applied to humans through genetic manipulations for numerous legal, ethical, and technical reasons.If we could understand how the environment modulates these aging-related genes, we might be able to create antiaging therapies applicable to humans, potentially through diet, lifestyle, and even pharmacological interventions.Therefore, understanding genome-environment interactions in the context of aging can be a powerful approach to identify attractive targets for drug design.\t\n\nEven if sirtuins and resveratrol do not live up to their expectations, this research is pioneering in terms of genome-environment interactions and nutritional manipulations of aging.These studies also show the path from basic discovery on the biology of aging to potential antiaging and pharmacological interventions and can therefore be applied to other genes and pathways.The lessons learned from the pitfalls of SIRT1 and resveratrol research can also help others to translate basic research on the biology of aging to the clinic, such as avoiding the use of short-lived rodent strains (e.g., by using unhealthy diets), which may lead to findings that only apply to a subset of individuals.\t\n\nIt seems that organisms from yeast to mammals have evolved genetic programs to cope with periods of starvation that can also postpone aging and age-related diseases, but how can we take advantage of those mechanisms to improve human health?Because assaying the longevity effects of CR in humans is practically impossible, studying its molecular mechanisms in lower life forms could be beneficial to humans through the identification of candidate genes, pathways and molecular mechanisms.Although CR will not be suitable for everyone, targeting its mechanisms and developing CR mimetics may lead to drug development for a number of age-related and metabolic diseases.",
      "\t\n\nMany factors contribute to aging, including genes.This is the first article in a 10-part series that highlight some of what is known about the influence of genes on aging and emerging treatment options that may slow down or potentially reverse the aging process.The series will address \\genes, adducts, and telomeres, decreased immune defenses, oxidation and inefficient mitochondria, toxins and radiation, glycosylation, caloric intake and sirtuin production, neurotransmitter imbalance, hormone mechanisms, reduced nitric oxide, and stem cell slowdown.Underpinning these factors are wear and tear on cells and aging as a result of inability to repair or replace these affected cells.These topics have been addressed in research, health magazines, and even by talk show hosts.There is even a LongevityMap website addressing significant and nonsignificant genetic association studies in aging across the human genome (http://genomics.senescence.info/longevity/).The series will address a scientific and clinical approach to genome-related aging topics.\tRelevance to nurse practitioner practice\n\nCurrently, there is no cure for genetic variants associated with rapid aging, but novel agents that may slow down the aging process are being tested.The authors of this article advocate individual participation in association studies of aging and pharmacologic risk mitigation or reversal of symptoms for those with known genetic disease risk.Direct to consumer epigenetic biological aging tests and telomere length tests are available; but they are not approved by the Food and Drug Administration.Health care providers may want to consider the simple but key clinical and personal changes, suggested above, to enhance DNA health, wellness, and longevity.Simple mindful changes in behavior, environmental exposure, food/supplement use, weight loss, and regular exercise can reduce adduct exposure damage and impact telomere length, potentially increasing longevity.A Mediterranean diet containing fruits and whole grains along with fiber, antioxidants, soy protein, and healthy fats (from avocados, fish, flax, and walnuts) is suggested to reduce DNA adducts and protect telomeres.In light of our current pandemic, focus on population health, and restrictions to health care access, especially in rural communities, health care providers could incorporate these lifestyle and dietary principles in telehealth visits with patients to reduce disease risk and optimize healthy aging.",
      "\t\n\nTaking advantage of advances in genomics and bioinformatics, we have used the evidence available to argue for a new theory of aging.To test that theory, still more sophisticated experiments and analyses will be necessary, but we are sure that the talented and dedicated scientists of the future will rise to the challenge.Regardless of what they find, we are now seeing the dawn of a new age in aging research.Borrowing elements from both Szilard's and Orgel's models, somatic mutations increase at an accelerating rate with age, a feedback loop mediated partially by altered protein sequences but primarily by a dysregulation of gene expression.The redundancy of the organism, both cellular and genetic, may inhibit these consequences of somatic mutations from directly contributing to aging, but is itself subject to degradation by somatic mutations.This model may most accurately reflect human aging, predicting both a period of latency (reflecting the lack of an aging phenotype during development and early adulthood) and an accelerating decline afterwards (reflecting the slow-thenrapid deterioration that begins in middle age).",
      "\t\n\nWith modern genomic technologies and largescale data analysis methods, it is possible to sift through the genes of populations to find the loci that act to postpone aging. [3]There are uncertainties with the comparison of populations with different rates of aging.However, it is superior to experimental designs that only consider age-dependence or dietary-response, without determining causal mechanisms.\tCONCLUSION: AGING DOES NOT HAVE TO BE UNSTOPPABLE\n\nThirty years ago, the genetic or biochemical postponement of aging was regarded as impossible in any organism.But the last few decades have seen aging become an easily ameliorated condition in model organisms, especially Drosophila.The toy electrical machines of Michael Faraday pointed to the future electrification of industry.The rockets of Robert Godard pointed toward space travel.Likewise, tiny Methuselahs show that aging can be substantially postponed.There is no biological necessity to any particular rate of aging, only the practical difficulty of changing that rate."
    ],
    [
      "\tOxidative stress and mitochondrial DNA\n\nNot long after it was discovered that mitochondria have their own genetic apparatus, Harman proposed that mitochondria play a central role in the free radical theory of aging [16].This idea was developed further by Miquel et al. [330], and the notion that mtDNA mutagenesis played a role in aging took hold.The phenotypical importance of mutations in mtDNA was demonstrated by Wallace et al. [331] and Holt et al. [332], who first showed that Leber's hereditary optic neuropathy and mitochondrial myopathies were caused by mtDNA mutations (reviewed in [333]).Because mtDNA is so close to the site of mitochondrial ROS production, it is exposed to considerably higher oxidative stress, resulting in 3-fold higher levels of DNA oxidative damage (the previously quoted 20-fold figure is apparently due to an isolation artifact [334,335]).In the 1990s a series of papers reported that the frequency of mitochondrial DNA deletions increases dramatically with age, being essentially undetectable in young individuals and reaching levels as high as 2% of mtDNA in old individuals.This age-related increase in mtDNA deletions was found in organisms as diverse as worms, mice, and humans (reviewed in [24,336]).The same is also true with mtDNA point mutations [337,338].Certain mtDNA polymorphisms have been found in increased frequency in centenarians, implying a protective effect during aging [339][340][341].Similar protective effects of mtDNA polymorphisms have been reported for the age-related neurodegenerative condition, Parkinson's disease [342].",
      "\t\n\ndoi: 10.1196/annals.1293.002cells and individuals.We previously identified a mitochondrial genotype, 5178C~A (ND2, Leu237Met), representing haplogroup D, to be associated with longevity in Japanese centenarians.Our proposal that certain mitochondrial polymorphisms are associated with longevity is further supported by observations that haplogroups J and U are overrepresented in European centenarians. 2Based on these findings, we have hypothesized that other haplogroups are associated with age-related neurodegeneration in Parkinson's disease or Alzheimer's disease.We also postulated that common metabolic disorders, such as obesity and type-2 diabetes mellitus, are attributable at least in part to mitochondrial polymorphisms.To examine these hypotheses, we have started comprehensive sequence analysis of the entire mitochondrial genome of centenarians, young obese or non-obese adults, patients with Parkinson's disease or Alzheimer's disease, and diabetic patients with or without angiopathy, using 96 individuals for each of these groups",
      "\t\n\nBuilding on previous work in this system, the current study tests three primary hypotheses about how variation in mtDNA and mitochondrial function relate to variation in life-history traits and aging within this system (Fig. 1): (1) First, we test whether rates of cellular oxygen consumption in isolated immune cells exhibit patterns that are consistent with the hypothesis that cellular processes drive whole-organism senescence and aging, and if these patterns differ between the SA and FA ecotypes and between sexes.By measuring basal, ATP-production associated, and maximal rates of cellular oxygen consumption, we further test for evidence that phenotypic divergence is dependent on a specific aspect of oxidative phosphorylation within immune cells.The energetics of these cells are particularly important given their essential role in modulating disease and infection, important factors contributing to senescence (Metcalf et al., 2019).We predict that SA snakes will maintain levels of cellular oxygen consumption across age, whereas the FA snakes will show a decline with age, especially in ATP-associated rates, possibly due to continual degradation of electron transport chain functionality from accumulating oxidative damage and reduced DNA repair mechanisms (Robert and Bronikowski, 2010;Schwartz and Bronikowski, 2013). ( 2) Second, we expand our mitochondrial genomics dataset to quantify mtDNA genetic structure across the landscape and test whether mtDNA haplotypes, and alleles at a nonsynonymous SNP in the Cytochrome B (CytB) gene correlate with aging ecotypes. (3) Third, we test the hypothesis that variation in mtDNA correlates with whole-organism variation in metabolic rates, suggesting a pathway linking mitochondrial genetic variation in mtDNA to whole-organism energetics.We first test whether different haplotypes differ in resting metabolic rate.Then, we test the effects of the nonsynonymous SNP in CytB on resting metabolic rate.The CytB gene encodes a component of complex III of the ETC, and was previously found to segregate between these life-history ecotypes (Schwartz et al., 2015).This SNP results in an amino acid substitution from isoleucine (aliphatic, hydrophobic) to threonine (hydrophilic) on a region that comes into close contact with a nuclear-encoded subunit (Schwartz et al., 2015).We combine previously published and new data on whole-organism resting metabolic rates (oxygen consumption) to test for the effects of this nonsynonymous mutation in three populations where we find heterogeneity at this nucleotide, thus allowing us to disentangle the effects of shared environment (population) from sequence variation (SNP).We predict that this SNP will correlate with variation in whole-organism metabolic rate, demonstrating a putatively adaptive difference between the derived and ancestral sequence.By utilizing this integrative data setfrom genes to organelles to whole organisms to populationsin a known life-history context, we are able to test hypotheses across levels of organization to provide a more complete picture of the complicated story of mitochondria and life history (Havird et al., 2019).",
      "\t\n\nEven with these levels of mtDNA protection, mtDNA mutation frequency increases with age in animal models and humans alike (Cortopassi and Arnheim 1990;Larsson 2010), although the role of mtDNA mutations remains unclear (Khrapko and Vijg 2009;Pohjoismaki et al. 2018;Theurey and Pizzo 2018).However, recent reports have shown that mtDNA point mutations in aged tissues largely arise from replication infidelity (i.e., DNA polymerase errors), rather than ROS-induced damage (Ameur et al. 2011;Kennedy et al. 2013;Vermulst et al. 2007).To test if replicative infidelity causes aging, mice with mutant mitochondrial DNA polymerase  that are deficient in proofreading during DNA replication, causing supraphysiological mutation loads (roughly 2500-fold in the homozygous polg mut/mut compared to 500-fold higher in the polg +/mut ), were examined (Vermulst et al. 2007).While the homozygous mice (polg mut/mut ) showed signs of accelerated aging phenotypes and significantly reduced lifespan, the heterozygous mice (polg +/mut ) had a normal lifespan albeit exhibiting premature aging phenotypes (Trifunovic et al. 2004).One plausible explanation for this discrepancy lies with increased mtDNA deletions in the homozygous mice (polg mut/mut ) (Vermulst et al. 2007(Vermulst et al. , 2008)).These cumulative results suggest that the connections between oxidative stress, mtDNA mutations, and aging are more complicated than originally appreciated and require further investigation to fully understand their relation (Pomatto and Davies 2018).It is evident, however, that the mtDNA mutations are linked to more than 300 diseases connected to aging, including Alzheimer's Disease, and that proper communication between the mitochondria and the nucleus plays a key role (DeBalsi et al. 2017;Grazina et al. 2006;Lane 2011;Onyango et al. 2006;Quirs et al. 2016;Swerdlow et al. 2017).",
      "\t\n\nConclusions: Our population-based study indicates that both mtDNA quality and quantity are influenced by age.An open question for the future is whether interventions that would contribute to maintain optimal mtDNA copy number and prevent the expansion of heteroplasmy could promote healthy aging.\t\nBackground: The accumulation of mitochondrial DNA (mtDNA) mutations, and the reduction of mtDNA copy number, both disrupt mitochondrial energetics, and may contribute to aging and age-associated phenotypes.However, there are few genetic and epidemiological studies on the spectra of blood mtDNA heteroplasmies, and the distribution of mtDNA copy numbers in different age groups and their impact on age-related phenotypes.In this work, we used whole-genome sequencing data of isolated peripheral blood mononuclear cells (PBMCs) from the UK10K project to investigate in parallel mtDNA heteroplasmy and copy number in 1511 women, between 17 and 85 years old, recruited in the TwinsUK cohorts.Results: We report a high prevalence of pathogenic mtDNA heteroplasmies in this population.We also find an increase in mtDNA heteroplasmies with age ( = 0.011, P = 5.77e-6), and showed that, on average, individuals aged 70-years or older had 58.5% more mtDNA heteroplasmies than those under 40-years old.Conversely, mtDNA copy number decreased by an average of 0.4 copies per year ( = 0.395,P = 0.0097).Multiple regression analyses also showed that age had independent effects on mtDNA copy number decrease and heteroplasmy accumulation.Finally, mtDNA copy number was positively associated with serum bicarbonate level (P = 4.46e-5), and inversely correlated with white blood cell count (P = 0.0006).Moreover, the aggregated heteroplasmy load was associated with blood apolipoprotein B level (P = 1.33e-5), linking the accumulation of mtDNA mutations to age-related physiological markers.Conclusions: Our population-based study indicates that both mtDNA quality and quantity are influenced by age.An open question for the future is whether interventions that would contribute to maintain optimal mtDNA copy number and prevent the expansion of heteroplasmy could promote healthy aging.\t\n\nAging is commonly characterized as a time-dependent progressive loss of physiological integrity, leading to impaired function and increased vulnerability to death [14].One important factor in aging is the accumulation of DNA damage over time [15].mtDNA has been considered a major target of aging-associated mutation accumulation, possibly because it experiences higher oxidative damages, more turnover, and has lower replication fidelity compared to nuclear DNA (nDNA) [16][17][18].Mice carrying elevated mtDNA mutation burden present premature signs of aging including hair loss, kyphosis, and premature death (lifespan shortened by up to 50%) [19,20].In human studies, mtDNA heteroplasmy incidence increases with age [21][22][23], while lower mtDNA copy number has been reported in aged populations [12,24].Ding et al. reported an trend of increased heteroplasmies and decreased mtDNA copy number with age in their study population [25].However, previous studies were limited in one or more ways: i) limited power in detecting low-to-medium frequency heteroplasmies in blood due to low sequencing depth; ii) relatively small sample sizes, limiting statistical power; iii) small age range; iv) whole blood as the source of DNA, which contains several sources of contaminants for mtDNA analysis; and/or v) assessing either mtDNA mutation or copy number, but not both in the same biological samples.Thus, it is largely unknown whether the impacts of age on mtDNA mutation burden and on copy number are independent from each other.\t\n\nBackground: The accumulation of mitochondrial DNA (mtDNA) mutations, and the reduction of mtDNA copy number, both disrupt mitochondrial energetics, and may contribute to aging and age-associated phenotypes.However, there are few genetic and epidemiological studies on the spectra of blood mtDNA heteroplasmies, and the distribution of mtDNA copy numbers in different age groups and their impact on age-related phenotypes.In this work, we used whole-genome sequencing data of isolated peripheral blood mononuclear cells (PBMCs) from the UK10K project to investigate in parallel mtDNA heteroplasmy and copy number in 1511 women, between 17 and 85 years old, recruited in the TwinsUK cohorts.",
      "\t\n\nHence, progressive age-dependent damage in mitochondrial genomes and functions is an important contributor to human aging.\t\n\nIn 1989, based on expanding molecular biology studies of diseases caused by mtDNA mutations, my colleagues and I (216) proposed the \"mitochondrial theory of aging\" that the somatic accumulation of mitochondrial mutations and the subsequent cytoplasmic segregation of these mutations during life is a major contributor to the gradual loss of cellular bioenergetic capacity within tissues and organs associated with general senescence and diseases of aging.The hypothesis encompasses the concept that a decline in bioenergetic capacity in tissues will contribute to age-associated diseases, such as those that affect the cardiac, vascular, and neuromuscular systems.\t\n\nAccumulated evidence to date exhorts to unify both ideas of the free radical theory of aging and mitochondrial theory of aging to be \"the redox mechanism of mitochondrial aging\" (281), that the mtDNA's oxidative damage results in cumulative increase in somatic mutations in mtDNA leading to bioenergetic deficit, cell death, and aging.The germline mutations in mtDNA as well as nDNA specific for the patients with mitochondrial diseases accelerate the oxidative damage and somatic mutations synergistically leading to their phenotypic expression as premature aging or death.",
      "\t\n\nAging is a complex process as a time-dependent progressive loss of physiological integrity, leading to impaired function and increased vulnerability to death [74], and as we described above, aging is highly associated with mtDNA mutations; in fact heteroplasmy incidence increases with age, while lower mtDNA copy number has been reported in aged populations as well as mitochondria morphology, abundance, and oxidative phosphorylation activity [75,76].Interestingly, in aging the significant amount of these mutations converges in sites that encode structural subunits of the ETC such as complexes I and III [77], leading to OxPhos uncoupling and mitochondrial dysfunction in aged population.Since there are several limitations to study mitochondrial metabolism in human samples, in this section we briefly described the implications of mitochondrial metabolism for aging in the most studied and high energy demand human tissues, such as skeletal muscle, heart, and brain.",
      "\tINTRODUCTION\n\nAbout 10 years ago it was proposed that aging is caused by life-long accumulation of somatic mitochondrial DNA (mtDNA) mutations (1), which compromises cellular energy metabolism and/or increases intracellular oxidative stress (2).Ultimately, this could result in the development of the multiple degenerative changes in tissues that become manifest in old age.It has been shown that mtDNA deletions and, with less certainty, mtDNA point mutations, increase with advancing age (recently reviewed in 3,4).These data are consistent with the mitochondrial theory of aging but do not exclude the possibility that accumulation of mtDNA mutations accompanies, but does not cause aging.",
      "\t\nAging is an intricate phenomenon characterized by progressive decline in physiological functions and increase in mortality that is often accompanied by many pathological diseases.Although aging is almost universally conserved among all organisms, the underlying molecular mechanisms of aging remain largely elusive.Many theories of aging have been proposed, including the freeradical and mitochondrial theories of aging.Both theories speculate that cumulative damage to mitochondria and mitochondrial DNA (mtDNA) caused by reactive oxygen species (ROS) is one of the causes of aging.Oxidative damage affects replication and transcription of mtDNA and results in a decline in mitochondrial function which in turn leads to enhanced ROS production and further damage to mtDNA.In this paper, we will present the current understanding of the interplay between ROS and mitochondria and will discuss their potential impact on aging and age-related diseases.\t\n\nAging is an intricate phenomenon characterized by progressive decline in physiological functions and increase in mortality that is often accompanied by many pathological diseases.Although aging is almost universally conserved among all organisms, the underlying molecular mechanisms of aging remain largely elusive.Many theories of aging have been proposed, including the freeradical and mitochondrial theories of aging.Both theories speculate that cumulative damage to mitochondria and mitochondrial DNA (mtDNA) caused by reactive oxygen species (ROS) is one of the causes of aging.Oxidative damage affects replication and transcription of mtDNA and results in a decline in mitochondrial function which in turn leads to enhanced ROS production and further damage to mtDNA.In this paper, we will present the current understanding of the interplay between ROS and mitochondria and will discuss their potential impact on aging and age-related diseases.",
      "\t\n\nMitochondrial genomes harboring large deletions are known to accumulate both in patients with heteroplasmic mtDNA mutations and in normal individuals during aging, particularly in postmitotic tissues such as muscle and brain (3).These observations support the mitochondrial theory of aging, which states that the slow accumulation of impaired mitochondria is the driving force of the aging process.This idea is attractive because it can be reconciled with the free radical theory of aging, which argues that oxidative damage plays a key role in senescence.Among the numerous mechanisms known to generate oxidants, leakage of superoxide anion and hydrogen peroxide from the mitochondrial electron transport chain are the chief candidates.Increased damage to mtDNA could exacerbate this leakage of reactive oxygen species (ROS) (4).",
      "\t\n\nMitochondrial DNA (mtDNA) rearrangements have been shown to accumulate with age in the post-mitotic tissues of a variety of animals and have been hypothesized to result in the age-related decline of mitochondrial bioenergetics leading to tissue and organ failure.Caloric restriction in rodents has been shown to extend life span supporting an association between bioenergetics and senescence.In the present study, we use full length mtDNA amplification by long-extension polymerase chain reaction (LX-PCR) to demonstrate that mice accumulate a wide variety of mtDNA rearrangements with age in post mitotic tissues.Similarly, using an alternative PCR strategy, we have found that 2-4 kb minicircles containing the origin of heavy-strand replication accumulate with age in heart but not brain.Analysis of mtDNA structure and conformation by Southern blots of unrestricted DNA resolved by field inversion gel electrophoresis have revealed that the brain mtDNAs of young animals contain the traditional linear, nicked, and supercoiled mtDNAs while old animals accumulate substantial levels of a slower migrating species we designate age-specific mtDNAs.In old caloric restricted animals, a wide variety of rearranged mtDNAs can be detected by LX-PCR in post mitotic tissues, but Southern blots of unrestricted DNA reveals a marked reduction in the levels of the agespecific mtDNA species.These observations confirm that mtDNA mutations accumulate with age in mice and suggest that caloric restriction impedes this progress.\t\n\nIt has often been hypothesized that quantitation of a single mtDNA deletion from old tissue represents 'the tip of the iceberg', and that the cumulative mitochondrial somatic mutational load is large in senescent organisms (1).By observing an array of mitochondrial sequence rearrangements with age, our data lend strong experimental support to this hypothesis.Further, the observation that there are substantial mtDNA conformational variants with age, and that the regimen of CR can modulate the level of the conformational variant in the brain, may indicate that mtDNA from the brain is more sensitive to oxidative damage as a result of ROS production.The current results in mouse are consistent with our previous studies in aging humans, in skeletal muscle (10), heart (15), and brain (5).The association of somatic mtDNA changes with age regardless of organismal maximum or mean lifespan, and modulation of some of these changes via CR, are consistent with the hypothesis that mtDNA changes with age may play a role in the senescence of multicellular organisms.\t\n\nAs a further step toward determining if mtDNA rearrangements play a significant role in senescence, it would be important to demonstrate that the accumulation of mtDNA rearrangements is retarded when mortality rate is reduced through genetic, or environmental modifications which extend lifespan.One of the few experimental aging models in which lifespan can be genetically extended is the age-1 mutant of Caenorhabditis elegans.In this mutant, mtDNA rearrangements have been observed to accumulate at a slower rate than in wild-type animals (9).In mammals, the only reproducible treatment to date which extends lifespan is that of CR (32).When the total number of calories consumed by the animal is reduced over the lifespan relative to AL fed animals, the mean and maximum lifespan can be extended by up to 50% (33).The mechanism by which CR extends lifespan is unknown, but CR is associated with a decrease in total body fat, increased fitness, and decreased pathology.\t\nMitochondrial DNA (mtDNA) rearrangements have been shown to accumulate with age in the post-mitotic tissues of a variety of animals and have been hypothesized to result in the age-related decline of mitochondrial bioenergetics leading to tissue and organ failure.Caloric restriction in rodents has been shown to extend life span supporting an association between bioenergetics and senescence.In the present study, we use full length mtDNA amplification by long-extension polymerase chain reaction (LX-PCR) to demonstrate that mice accumulate a wide variety of mtDNA rearrangements with age in post mitotic tissues.Similarly, using an alternative PCR strategy, we have found that 2-4 kb minicircles containing the origin of heavy-strand replication accumulate with age in heart but not brain.Analysis of mtDNA structure and conformation by Southern blots of unrestricted DNA resolved by field inversion gel electrophoresis have revealed that the brain mtDNAs of young animals contain the traditional linear, nicked, and supercoiled mtDNAs while old animals accumulate substantial levels of a slower migrating species we designate age-specific mtDNAs.In old caloric restricted animals, a wide variety of rearranged mtDNAs can be detected by LX-PCR in post mitotic tissues, but Southern blots of unrestricted DNA reveals a marked reduction in the levels of the agespecific mtDNA species.These observations confirm that mtDNA mutations accumulate with age in mice and suggest that caloric restriction impedes this progress."
    ],
    [
      "\t\n\nStudies of genes and molecular processes that are associated with segmental progeroid disorders, such as Hutchinson-Gilford progeria syndrome (HGPS, progeria, OMIM#176670), could be of importance when studying the genetic mechanisms of aging (Martin, 2005;Baker et al., 1981).For example, most cases of HGPS are caused by a de novo point mutation in the LMNA gene (LMNA c.1824C>T; p.G608G).This mutation activates a cryptic splice site that results in aberrant splicing of the lamin A transcript (Eriksson et al., 2003).Interestingly, it has been shown that the products of this aberrant splicing, the truncated transcript and resultant protein (named progerin), increase in number with aging in HGPS (Goldman et al., 2004;Cao et al., 2007;Rodriguez et al., 2009).In addition, several reports have found progerin, and increasing levels of progerin, in normal cells over the course of normal aging (Scaffidi & Misteli, 2006;McClintock et al., 2007;Cao et al., 2007;Rodriguez et al., 2009), which suggests a similar genetic mechanism in HGPS and normal aging.Moreover, genome-scale expression profiling in cells from HGPS patients, as well as in physiological aging, has revealed widespread transcriptional misregulation in multiple mammalian tissues (Ly et al., 2000;Csoka et al., 2004;Zahn et al., 2007;Scaffidi & Misteli, 2008;Cao et al., 2011;McCord et al., 2013).",
      "\tDNA Repair and Accelerated Aging Syndromes\n\nThe association of human syndromes of accelerated aging with inherited mutations in DNA repair genes strongly implicates DNA damage in the human aging process.These disorders, known as segmental progeroid syndromes, are characterized by accelerated onset of a subset of human aging phenotypes that frequently include neurodegeneration (50).Mutations in genes involved in singleor double-strand DNA break repair result in cerebellar degenerative syndromes known as ataxias, which are manifested by movement disorders.The continued proliferation of cerebellar granule cells during postnatal development may underlie the vulnerability of the cerebellum to inherited deficits in genome stability.In contrast, inherited mutations in DNA helicases, such as Werner and Rothmund-Thomson syndromes, give rise to features of accelerated aging that often do not include nervous system dysfunction.This may reflect the role of RecQ-like helicases in recombinant events in replicating cells.Inherited mutations in enzymes involved in nucleotide and base excision repair, including xeroderma pigmentosum and Cockayne syndrome, are characterized by accelerated aging phenotypes that include neurodegeneration, mental retardation, and delayed psychomotor development (50).A new human progeroid syndrome that is caused by a loss of function mutation in the XPF-ERCC1 endonuclease that repairs helix-distorting DNA lesions was recently described.Mice deficient in ERCC1 recapitulate the progeroid features and exhibit a gene expression profile in the liver that overlaps with that of normal aging mice (correlation coefficient 0.32), suggesting that this type of DNA damage may contribute to the aging process (51).Segmental progerias typically have a short life span of less than 20 years, which may account for the absence of Alzheimer-type neuropathological Double-strand break (DSB): a severe form of DNA damage involving scission of both DNA strands, usually induced by ionizing radiation or ROS NHEJ: nonhomologous end joining changes.However, individuals with Werner syndrome, a longer-lived progeroid syndrome, can have variable neuropathology, with one 57-year-old case reportedly showing unusually high levels of amyloid -protein deposition in the brain (52).",
      "\t\n\nHutchinson-Gilford progeria syndrome (HGPS) and Werner syndrome are rare human genetic disorders characterized by premature aging phenotypes with a shortened life span.This group of diseases resembles physiological aging to a certain extent, serving as excellent models to gain insight into the biology of aging in humans (24,25).These diseases are due to either a mutation in genes encoding the DNA repair machinery or the A-type lamin, leading to disorganized chromatin structures.The causative mutations behind these progeria syndromes indicate that genomic instability and chromatin deterioration are causes of human aging.Furthermore, the knowledge we gain from understanding the molecular pathology of these human premature aging diseases provides us with useful information to understand the complex aging process.Individuals with HGPS do not recapitulate all aging phenotypes because they usually show segmental progeria affecting multiple tissues.By recapitulating some molecular and cellular changes that are characteristics of the natural aging process, these models provide us with a unique opportunity to understand the aging process in a human model (24,25).",
      "\t\n\nResearchers in recent studies have focused on gene mutations accompanying known progeroid syndromes, such as Hutchinson-Gilford progeria, Werner syndrome, Rothmund-Thomson syndrome, Cockayne syndrome, ataxia telangiectasia, and Down syndrome. 143The most common skin disorders of these syndromes, which are characterized by an acceleration of the aging phenotype, are alopecia, skin atrophy and sclerosis, telangiectasia, poikiloderma, thinning and graying of hair, and several malignancies.Most of these syndromes are inherited in an autosomal recessive way and mostly display defects in DNA replication, recombination, repair, and transcription.Expression gene patterns of skin cells derived from old and young donors with Werner syndrome, 144 show that 91% of the analyzed genes have similar expression changes in Werner syndrome and in normal aging, implying transcription alterations common to Werner syndrome and normal aging represent general events in the aging process.",
      "\tDNA Repair-Related Progeroid Syndromes\n\nAs mentioned previously, premature aging syndromes are often caused by mutations in genes whose function is to preserve genomic integrity.In this respect, the RecQ family of DNA helicases has been found to function in DNA damage repair, including base excision repair and in DNA double-strand break (DBS) repair, as well as in DNA replication subjected to a normal or stressed state [36].Mutations in three RecQ genes (WRN, BLM, and RECQL4) give rise to the Werner syndrome (WS), Bloom syndrome (BS), and Rothmund-Thomson syndrome (RTS), respectively [37].Additional genetic defects in the DNA damage repair system also cause the following disorders: Cockayne syndrome (CS), xeroderma pigmentosum (XP), and trichothiodystrophy (TTD).\t\n\nAn alternative strategy to the investigation of aging using the humans themselves is the study of progeroid syndromes, a group of very rare genetic disorders characterized by accelerated aging and the presence of clinical features that resemble physiological aging, including osteoarthritis and osteoporosis, loss of muscle mass, hair loss, short stature, skin tightness, and cardiovascular diseases [4].In addition to the genuine medical interest in improving the quality of life of these patients, the study of progeroid syndromes has attracted great interest in the past 10 years, in that they constitute an invaluable source of information for understanding the molecular basis of human aging.\tConclusions\n\nRecent advances in the study of progeroid syndromes, especially HGPS, have provided novel insights into our understanding of the aging process in humans.The main progeroid syndromes revised in this chapter are caused by mutations in genes encoding for DNA repair enzymes or the nuclear lamina protein lamin A, which reinforces the notion that genome instability is a critical determinant of aging.The study models that recapitulate progeroid syndromes have dramatically stimulated aging research; while cellular models have allowed the dissection of basic cellular and molecular processes linked to aging, mice models have facilitated screening of therapeutic drugs.It is expected that upcoming technologies and the design of novel optimized animal models will help to accomplish a translational medicine approach in aging research, with HGPS being the ideal model for such a goal.",
      "\tProgeroid syndromes\n\nPatients suffering from progeroid syndromes, or accelerated aging phenotypes, display an array of physical and biological features that vary widely between tissues and diseases and among individuals.Some of the main characteristics for the specific disorders of interest to this review are cited below (for further review of molecules involved and clinical presentation, see Ref. 96).A general dilemma in studies on the role of telomeres in progeroid syndromes (and aging) is that telomere involvement could be direct as well as indirect.For example, the increased cell death resulting from defective DNA repair could result in telomere shortening via increased compensatory (stem) cell turnover or via direct effects on (repair of) telomeric DNA.For many segmental aging disorders, it has proven to be very difficult to distinguish between direct and indirect effects on telomere length.Perhaps phenotypically the most striking segmental aging genetic disorder in humans, Hutchinson-Gilford Progeria syndrome (HGPS), is caused by point mutations in lamin A, a key component of nuclear scaffolding (34,72).Lamin A deficiency results in absence of hair, craniofacial deformities (\"pinched\" facial features), emaciated and wrinkled appearance, as well as cardiovascular defects that eventually lead to stroke or heart attack at a very young age.The disease is characterized by specific defects in FIG. 8. Defects in human telomerase.The human telomerase complex is minimally composed of two proteins, telomerase reverse transcriptase (hTERT, green) and dyskerin (or DKC1, blue), that both bind specifically to a folded RNA molecule (or hTERC, black) containing a telomere repeat anchoring sequence and a template (red box).Known mutations in each component have now been linked to autosomal dominant dyskeratosis congenita (AD DC), bone marrow failure (BMF), and idiopathic pulmonary fibrosis (IPF) (6,63,127,134,151,217,231,234).The telomerase complex is thought to dimerize, bind to the single-strand G-rich telomere end, and catalyze the addition of new repeats (see also Figs. 3 and 4).The complex translocates along (newly added) telomere tracts for further elongation.Mutations affecting telomerase function lead to failure to assemble a functional complex.In the majority of cases, the level of telomerase activity is reduced by 50%.Such a reduction in telomerase activity compromises telomere length maintenance and increases apoptosis and senescence in proliferating cells (see Fig. 4).nuclear shape (183).Because expression of (defective) lamin A is limited to certain cell types, some cells and tissues are more affected than others.While there is evidence that DNA damage responses in cells expressing mutant lamin A are abnormal (133), the role of telomeres in this disorders (if any) remains to be clarified.A number of other segmental aging disorders have been more directly linked to telomere (dys)function.Among these, Fanconi anemia (FA) and ataxia telangiectasia (AT) are generally autosomal recessive diseases caused by mutations in, respectively, Fanconi genes (encoding any of 12 Fanconi anemia complementation group proteins) and the ataxia telangiectasia mutated gene (encoding the ATM protein).These proteins are implicated in DNA damage and repair pathways; in addition, ATM is known to phosphorylate FANCD2 (for reviews, see Refs.64,118,190).Both diseases are associated with accelerated telomere shortening (29,121,123,146), and abnormalities in telomere replication or repair are thought to play a role in the pathogenesis, particularly in the progression of the disease to immunodeficiency and bone marrow failure, as well as in the increased predisposition to malignancy in young adults.Other syndromes related to the Fanconi DNA damage response pathway include Nijmegen breakage syndrome (NBS) and Seckel syndrome.Other \"progeroid\" genes that have been implicated in DNA replication and repair are the family of genes encoding the RecQ DNA helicases.One of the functions of these enzymes is to assist in the resolution and repair of broken or stalled replication forks.Telomeric DNA is known to readily form higher order DNA structures such as G quadruplex structures in vitro (159), and it seems plausible, based on work in C. elegans (42), that specialized helicases are required to resolve structures of G-rich DNA arising sporadically during lagging strand DNA synthesis (62).Helicases that could be involved include RecQ protein-like 2 (RecQL2), RecQL3, and RecQL4 with known mutations that give rise to Werner (WRN), Bloom (BLM), and Rothmund Thompson syndromes, respectively.Accelerated telomere shortening is observed in Werner's syndrome (51), and pathology in animal model systems is accentuated in the context of telomerase deficiency (40,156).",
      "\t\n\nThe relationship between DNA damage accumulation and aging has gained maximum credibility through studies conducted on various human progeria syndromes, which are genetic disorders where patients precociously develop features resembling natural aging.Most of the reported progeria syndromes, including Werner syndrome (WS), Bloom's syndrome (BS), Rothmund-Thomson syndrome (RTS), Cockayne syndrome type A and type B (CSA and CSB), Xeroderma pigmentosum (XP), Trichothiodystrophy (TTD) and Hutchinson-Gilford progeria syndrome (HGPS) are caused by mutations of genes that are directly or indirectly involved in DNA repair.Of these, WS, BS and RTS are associated with defects in RecQ helicases, i.e.RECQL2 (WRN), RECQL3 (BLM) and RECQL4 respectively, whereas CS, XP and TTD shared similar defects in NER pathway.RecQ helicases are a group of highly conserved proteins from bacteria to humans.The roles of RecQ helicases in DNA metabolism, including DNA replication, transcription, repair and recombination, have been extensively investigated and are demonstrated to be the underlying pathological basis of WS, BS and RTS [139][140][141][142].Most recently, delayed DNA damage checkpoint response and defective DNA repair were found to contribute to the progeria phenotypes in HGPS as well [143].",
      "\t\n\nThey arise from mutations in one or several genes involved in DNA metabolism or in its regulation.Accelerated aging also may result from partial genome imbalances as seen in the chromosomal disorders of Down, Klinefelter and Turner syndromes.\t\n\nThese defects result in part from accumulated damage to DNA.Such damage may result inability to maintain replicative fidelity of the genome [2][3][4].Thus, organisms with mutations to genes directly involved in basic genome structure, maintenance and replicative fidelity would understandably have an accelerated aging phenotype and/or shortened life spans.Individuals with a progeroid syndrome have a premature aging phenotype and, depending on the specific mutations involved, the effects on lifespan may range from moderate to severe.Examples include Werner syndrome (WS), Bloom syndrome (BLM), Cockayne syndrome (CS), ataxia-telangiectasia (AT), Hutchinson-Gilford progeria syndrome (HGPS), and restrictive dermopathy (RD).",
      "\t\n\nThe identification of these diseases spurred the creation of numerous animal models, and the characterization of engineered laboratory mutants led to the identification of many new human diseases of systemic and segmental accelerated aging.The animal models are useful for discovering how, when, and where (in what tissues) DNA damage contributes to aging, an area in which much work is still needed.The models, because of their accelerated aging, are useful for rapid hypothesis and drug testing.The models for the large part faithfully recapitulate the human genetic diseases; however, it is notable that mice tend to display a milder phenotype than humans.This might arise from the environmental contribution to human disease, which is not well reproduced in experimental model systems.Collectively, however, these human diseases and their conservation in multiple animal model systems strongly support the role of DNA damage as a proximal contributor to aging.",
      "\t\n\nThe number of identified genes associated with progeroid syndromes has increased in recent years, possibly shedding light as well on mechanisms underlying ageing in general.\t\n\nSeveral heritable premature aging syndromes have for a long time been linked to defects in genome maintenance, due to altered DNA repair mechanisms.These mainly include the following autosomal recessive syndromes: (i) Werner syndrome, due to mutations in RecQL2 DNA helicase; (ii) Cockayne syndrome (CS) type A and B, due to mutations in the genes encoding the group 8 or 6 excision-repair cross-complementing proteins (ERCC8 and ERCC6), respectively; (iii) Rothmund-Thomson syndrome (RTS), due to RecQL4 mutations; (iv) trichothiodystrophy (TTD), due to mutations in the genes ERCC2/XPD and ERCC3/XPB, encoding the two helicase subunits of the transcription/repair factor TFIIH, as well as in TFB5, encoding the tenth subunit of TFIIH (Giglia-Mari et al., 2004); (v) ataxia-telangiectasia, due to mutations in the ataxia-telangiectasia mutated gene (ATM); (vi) xeroderma pigmentosum (XP), a genetically heterogeneous autosomal recessive disorder in which can be distinguished at least seven complementation groups, due to mutations of different DNA excisionrepair proteins (Hasty et al., 2003;Kipling et al., 2004).All these progeroid diseases, involving heritable defects in DNA repair, suggest a central role of genome integrity maintenance in the aging process.\tConclusion\n\nFrom a pathophysiological point of view, the known Progeroid syndromes are caused either by mutations in genes encoding DNA repair proteins, such as in WS, Bloom syndrome (BS), Rothmund-Thomson syndrome, Cockayne syndrome, xeroderma pigmentosum or trichothiodystrophy (Hasty et al., 2003;Wood et al., 2005), or by mutations in genes encoding Lamins A/C or partners involved in their biological pathway, such as HGPS or RD (De Sandre-Giovannoli et al., 2003;Eriksson et al., 2003;Navarro et al., 2004Navarro et al., , 2005)).\t\nProgeroid syndromes are heritable human disorders displaying features that recall premature ageing.In these syndromes, premature aging is defined as ''segmental'' since only some of its features are accelerated.A number of cellular biological pathways have been linked to aging, including regulation of the insulin/growth hormone axis, pathways involving ROS metabolism, caloric restriction, and DNA repair.Different animal models, ranging from yeast, to nematodes, to mice, have been instrumental in obtaining evidence for these connections (Hasty et al., 2003).Several heritable premature aging syndromes have for a long time been linked to defects in genome maintenance, due to altered DNA repair mechanisms.These mainly include the following autosomal recessive syndromes: (i) Werner syndrome, due to mutations in RecQL2 DNA helicase; (ii) Cockayne syndrome (CS) type A and B, due to mutations in the genes encoding the group 8 or 6 excision-repair cross-complementing proteins (ERCC8 and ERCC6), respectively; (iii) Rothmund-Thomson syndrome (RTS), due to RecQL4 mutations; (iv) trichothiodystrophy (TTD), due to mutations in the genes ERCC2/XPD and ERCC3/XPB, encoding the two helicase subunits of the transcription/repair factor TFIIH, as well as in TFB5, encoding the tenth subunit of TFIIH (Giglia-Mari et al., 2004); (v) ataxia-telangiectasia, due to mutations in the ataxia-telangiectasia mutated gene (ATM); (vi) xeroderma pigmentosum (XP), a genetically heterogeneous autosomal recessive disorder in which can be distinguished at least seven complementation groups, due to mutations of different DNA excisionrepair proteins (Hasty et al., 2003;Kipling et al., 2004).All these progeroid diseases, involving heritable defects in DNA repair, suggest a central role of genome integrity maintenance in the aging process.The number of identified genes associated with progeroid syndromes has increased in recent years, possibly shedding light as well on mechanisms underlying ageing in general.Among these, premature aging syndromes related to alterations of the LMNA gene have recently been identified.LMNA encodes Lamins A/C, ubiquitous nuclear proteins belonging to the intermediate filament superfamily.These premature aging disorders have thus been classified as ''Laminopathies'', the large group of diseases associated to Lamin A/C defects.This group of heterogeneous disorders includes three main subgroups: (1) neuromuscular disorders (Emery-Dreifuss muscular dystrophy, limb-girdle",
      "\t\n\nHowever, only those genetic disorders that exhibit premature aging, neurodegeneration (mental defects), and some form of chromosomal/DNA damage all together will be empha-sized here.Perhaps the most appropriate disorder under this category is Down's syndrome.It has several features of premature aging and the genetic defect is trisomy of the distal part of the long arm of chromosome 21.The critical segment of chromosome 21 is shown to have three genes coding for copper-and zinc-dependent superoxide dismutase, oncogene ets-2, and cystathione ~-synthase (Delabar et al., 1987).Since elevated levels of superoxide dismutase are found in various tissues of these individuals, it is postulated that the accelerated aging of these patients may be caused by overproduction of superoxide dismutase, which is responsible for the production of H20 2 while scavenging the oxygen-free radicals.The brains of Down's syndrome individuals are particularly vulnerable to oxidative DNA damage because the high levels of superoxide dismutase found in this tissue are not accompanied by an elevation in the glutathione peroxidase and catalase (Balazs and Brookshank, 1985) that would have normally helped in removing the overproduced H202.Other genetic syndromes characterized by signs of nervous debility, premature aging, and DNA damage/ decreased DNA-repair capacity, are Ataxia Telangiectasia (AT) and Cockayne syndrome (CS).",
      "\tRare genetic disorders of aging\n\nProgeria, also known as Hutchinson-Gilford progeria syndrome, affects one in four million births worldwide with equal distribution between sex and race, causing a child's body to age more rapidly (Genetics Home Reference, 2019a).Symptoms typically occur within the first year of life, and most children do not live past 13 years.Mutation in the LMNA gene (not an adduct or telomere factor) contributes to abnormal lamin A protein, called progerin, causing cell instability and cells to easily breakdown (Genetics Home Reference, 2019a).There is no current cure for progeria but farnesyltransferase inhibitors, a cancer drug, has shown promise in reversing cell damage (Genetics Home Reference, 2019a).Other supportive treatments include cardiovascular diseaserelated issues, growth hormones, and bone/joint health.Adalia Rose has taken to social media, with multiple YouTube and Facebook postings, to help others understand her case of progeria.",
      "\t\n\nMitochondrial DNA (mtDNA) mutations are thought to have a causal role in many age-related pathologies.Here we identify mtDNA deletions as a driving force behind the premature aging phenotype of mitochondrial mutator mice, and provide evidence for a homology-directed DNA repair mechanism in mitochondria that is directly linked to the formation of mtDNA deletions.In addition, our results demonstrate that the rate at which mtDNA mutations reach phenotypic expression differs markedly among tissues, which may be an important factor in determining the tolerance of a tissue to random mitochondrial mutagenesis.",
      "\tINTRODUCTION\n\nIn genetics, identification of genotype-phenotype relationships relies on generated or selected mutants, which highlight underlying mechanisms.For the biology of aging, mutants that display delayed or accelerated aging have been invaluable.Rare heritable syndromes have been identified in the human population that exhibit multiple features of premature aging.A search in the Online Mendelian Inheritance in Man database (OMIM version February 25, 2015) using the keywords \"premature aging,\" \"progeria,\" or \"progeroid\" yielded 20 syndromes with at least one known mutated gene.Certainly this list is far from complete; for example, ataxia telangiectasia, fanconi anemia, and maternally transmitted mitochondrial syndromes such as maternally inherited diabetes and deafness and mitochondrial encephalomyopathy (MIDD/MELAS) are missing.Additionally, many more conditions await identification as unrecognized progeroid syndrome.The application of powerful exome and whole genome sequencing technologies will dramatically accelerate molecular resolution of genetic defects in rare patients with features of accelerated aging, and through this process, many new genes underlying these conditions will be identified.However, when we assign a primary function to each of the causally mutated genes in the known syndromes, it appears that the majority is linked to perturbed genome integrity, a second class represents metabolism, and one syndrome appears connected with cell adhesion (Figure 1).Recently, evidence has emerged for bidirectional interactions between the main aging-related processes: For instance, most DNA damage is derived from endogenous metabolic sources, and compromised genome function indirectly affects many cellular processes including metabolism (1, 2).This suggests the existence of a tightly interwoven network that underlies aging, which is the focus of this review.Progeria-associated syndromes classified by primary function of the causal genetic defect.These 20 human syndromes, listed outside of the circle, were selected from the OMIM database using the keywords \"premature aging,\" \"progeria,\" and \"progeroid. \"Related primary functions were combined in the categories genome integrity, metabolism, and adhesion (inner circle).Abbreviations: DSB, DNA double-strand break; MDPL, mandibular hypoplasia, deafness, progeroid features, and lipodystrophy; PI3K, phosphoinositide-3-kinase; PS, phosphatidylserine; XFE, XpF-Ercc1.GAPO indicates growth retardation, alopecia, pseudoanodontia, and optic atrophy.SHORT indicates short stature, hyperextensibility, hernia, ocular depression, Rieger anomaly, and teething delay."
    ]
  ]
}