diff options
Diffstat (limited to 'gnqa/data/study1/datasets/gpt4o/dataset_domainexpert_aging_2.json')
| -rw-r--r-- | gnqa/data/study1/datasets/gpt4o/dataset_domainexpert_aging_2.json | 109 |
1 files changed, 109 insertions, 0 deletions
diff --git a/gnqa/data/study1/datasets/gpt4o/dataset_domainexpert_aging_2.json b/gnqa/data/study1/datasets/gpt4o/dataset_domainexpert_aging_2.json new file mode 100644 index 0000000..dbaf184 --- /dev/null +++ b/gnqa/data/study1/datasets/gpt4o/dataset_domainexpert_aging_2.json @@ -0,0 +1,109 @@ +{ + "question": [ + "How do oxidative stress and the subsequent accumulation of damaged macromolecules contribute to cellular aging?", + "How are extracellular matrix remodeling and tissue stiffness implicated in the aging process?", + "How do recent developments in autophagy research contribute to our understanding of its role in aging and longevity?", + "What are the implications of age-related shifts in stem cell niche composition and function for tissue regeneration capacity?", + "How do cross-links and advanced glycation end-products (AGEs) accumulation affect the structural integrity and function of aging tissues?" + ], + "answer": [ + "Oxidative stress, primarily caused by reactive oxygen species (ROS) generated from cellular metabolism, leads to damage to various cellular components, including DNA, proteins, and lipids. This damage accumulates over time, leading to functional decline in cells. In particular, damage to DNA can lead to mutations and impaired cellular functions. The balance between DNA damage and its repair is a major determinant of cell longevity. Additionally, oxidative damage to mitochondria, a major source of ROS, can impair energy production and further contribute to aging. This process is supported by the oxidative stress theory of aging and the mitochondrial theory of aging.", + "Extracellular matrix (ECM) remodeling plays a significant role in the aging process. Aging results in changes in ECM biosynthesis, modifications of ECM components, and alterations of cell-matrix interactions, which contribute to age-related pathologies. The synthesis of many ECM components, such as elastin, declines with age, impairing the elasticity and resilience of tissues. Age-related ECM changes also alter vascular mechanotransduction, dysregulating cell responses to alterations in the environment. Additionally, aging and cellular senescence increase the secretion of matrix metalloproteinases (MMPs), which compromises the structural integrity of tissues and promotes pathological remodeling. This can lead to increased tissue stiffness, a common feature of aging tissues. Furthermore, dysregulated collagen synthesis contributes to vascular fibrosis and arterial stiffening.", + "Recent developments in autophagy research have shown that autophagy, a cellular degradation process, plays a crucial role in aging and longevity. Certain compounds like rapamycin, resveratrol, and polyamines can induce autophagy, with polyamines showing results in human clinical research. Autophagy is also linked to the regulation of various processes that contribute to aging, such as protein degradation, mitochondrial metabolism, and stress response. Studies have shown a decline in autophagy in aging mammals, and increased autophagy is required for lifespan extension in certain organisms. Furthermore, the up-regulation of autophagy by certain compounds has been associated with increased lifespan in various organisms. Dysfunctional autophagy is implicated in many age-related diseases, and the activation of autophagy has been linked with increasing lifespan in animal models.", + "Age-related shifts in stem cell niche composition and function can lead to a decrease in tissue regeneration capacity. This is because the stem cell's ability to self-renew and produce progeny to replenish worn-out and damaged cells in aged tissues may be compromised. This could result in a depletion of stem or progenitor cell pools, promoting age-related pathologies. Additionally, the induction of stem cell senescence may affect tissue renewal. Furthermore, the balance between stem cell proliferation and tissue regeneration, which is crucial for maximizing longevity, may be disrupted, leading to an aged phenotype.", + "Cross-links and AGEs accumulation can lead to several detrimental effects on aging tissues. They can cause structural changes in proteins, lipids, and nucleic acids, leading to altered function and potential damage. AGEs can mediate intracellular glycation of mitochondrial proteins, increasing ROS levels and triggering oxidative stress. They can also bind with RAGEs, activating signaling pathways that upregulate inflammatory cytokines and adhesion molecules. In the vascular system, AGEs can cause endothelial dysfunction, arterial stiffness, and increased capillary permeability. In the context of diabetes, AGEs can accelerate the death of certain cells, disrupt retinal vascular integrity, and induce neural cell dysfunction and death." + ], + "contexts": [ + [ + "\t\n\nCell senescence, telomere shortening, and oxidative stress Attempts at synthesizing two major areas of focus in aging research, cell senescence [287,288] and free radicals, have been made since the 1970s (for a recent review see [289,290]).Early results by Packer and Smith suggested that vitamin E treatment could completely prevent cell senescence [291]; however, this result proved to be irreproducible [292].Nevertheless, it was observed that decreasing oxygen tension, from the customary 21% O 2 to more physiological levels (3% O 2, as would be found in vivo) led to an increase in cell doublings before senescence (i.e., an increase in the Hayflick limit or replicative life span [293][294][295][296]).Similar effects were also reported using antioxidants [296][297][298].In the 1990s, von Zglinicki et al. reported that a mild increase in oxygen tension (40%) triggered senescence within 3 cell divisions in human fibroblasts [299].von Zglinicki and co-workers proposed that oxidative damage to telomeres was responsible for the rapid triggering of senescence [299][300][301] and recent studies show that telomeric DNA may be particularly sensitive to oxidative damage [302].Following von Zglinicki et al. 's report, other investigators, using different oxidative stressors and different cell types, have reported very similar results.Mild oxidative stress reduces clonal life span and conversely, reduction of oxidative stress extends clonal life span [303][304][305][306][307]. Guarente's lab has provided additional evidence in this general direction, with the demonstration that RNAi knockdown of Sod1 triggered early senescence in human fibroblasts [308].This result is consistent with the earlier report by Epstein's laboratory that fibroblasts derived from Sod1 / mice failed to grow at all in culture [188].A great breakthrough in this area occurred when Campisi's lab demonstrated that senescence could be prevented completely in primary mouse cells when the cells were grown at 3% oxygen, instead of the customary 21% [309].This also resulted in a dramatic reduction of oxidative damage-signature mutations [310].In other words, these investigators demonstrated that in vitro senescence in mice cells was directly related to oxygen toxicity, i.e., oxidative damage.", + "\t\n\nThe free radical theory of aging, first proposed by Harman in 1956 [21], has received a lot of attention over the years as indicated by the number of scientific reviews on antioxidant interventions in different animal models and human clinical trials.The mitochondrion has been identified as a major source of reactive oxygen species (ROS) and thus oxidative stress potentially contributing to the aging process, although several plasma membrane and cystosolic enzymes may also contribute to the increased intracellular pro-oxidant status observed during aging [22].In the mitochondrial respiratory chain, electrons entering complexes I and II are transferred to complex III, then IV where they are combined with molecular oxygen and hydrogen to form H 2 O. Redox reactions at respiratory complexes I, III, and IV are coupled to the extrusion of protons from the mitochondrial matrix into the intermembrane space.The re-entry of protons into the matrix is coupled to the synthesis of ATP from ADP and P i .This oxidative phosphorylation is responsible for the vast majority of ATP production and oxygen consumption in most types of animal cells [23].Up to 2% of oxygen used in this complex reaction undergoes monoelectronic reduction and results in the formation of superoxide anion and hydrogen peroxide, which can lead to the formation of the more toxic species hydroxyl radicals [24,25].Such reactive species can attack and modify genomic DNA.An important type of oxidative DNA lesion accumulating with age is 8-oxo-deoxyguanine [26].If unrepaired, this adduct in genomic DNA may lead to a point mutation upon DNA replication.During DNA replication, 8-oxo-deoxyguanines present on either strand of DNA can mispair with adenosines and lead to G:C T:A transversion mutations.A misincorporation of an 8-oxodeoxyguanine as a substrate nucleotide can also lead to the same type of mutational pattern [27].", + "\t\n\nOur results are consistent with the oxidative stress theory of aging originally proposed by Denham Harman [26], and the notion that a vicious cycle of ROS generation and oxidative damage is the ultimate driver of aging [27].Our data also indicate that endogenous nuclear DNA damage is able to trigger this cycle of escalating ROS abundance, oxidative damage, senescent cell accumulation and age-related pathology.\t\n\nTo determine if this oxidative stress is pathological, we suppressed it pharmacologically in Ercc1 -/ mice with the mitochondrial-targeted radical scavenger XJB-5-131.Chronic administration XJB-5-131 significantly reduced both oxidative DNA damage and senescence (Fig. 5).The reduced level of senescent cells corresponded to a reduction in agerelated morbidity.This is consistent with numerous recent studies demonstrating that genetic or pharmacologic elimination of senescent cells slows age-related decline [2,4,7,8,[84][85][86].The observation that suppressing oxidant production is sufficient to decreases senescence indicates that reactive species are required to ultimately cause or maintain senescence in response to genotoxic stress.", + "\t\n\nIntroduction as replication errors, spontaneous chemical changes to Although aging is nearly universally conserved among the DNA, programmed double-strand breaks (DSBs) (in eukaryotic organisms, the molecular mechanisms unlymphocyte development), and DNA damaging agents derlying aging are only beginning to be elucidated.A that are normally present in cells.The latter category useful conceptual framework for considering the probincludes reactive oxygen species (ROS), such as superlem of aging is the Disposable Soma model (Kirkwood oxide anion, hydroxyl radical, hydrogen peroxide, nitric and Holliday, 1979).This model proposes that organoxide, and others.Major sources of cellular ROS proisms only invest enough energy into maintenance of the duction are the mitochondria, peroxisomes, cytochrome soma to survive long enough to reproduce.Aging oc-p450 enzymes, and the antimicrobial oxidative burst of curs at least in part as a consequence of this imperfect phagocytic cells.ROS can cause lipid peroxidation, maintenance, rather than as a genetically programmed protein damage, and several types of DNA lesions: sinprocess.Although aging may involve damage to varigle-and double-strand breaks, adducts, and crossous cellular constituents, the imperfect maintenance of links.The situation in which ROS exceed cellular antinuclear DNA likely represents a critical contributor to oxidant defenses is termed oxidative stress.As normal aging.Unless precisely repaired, nuclear DNA damage byproducts of metabolism, ROS are a potential source can lead to mutation and/or other deleterious cellular of chronic, persistent DNA damage in all cells and may and organismal consequences.Damage to both nuclear contribute to aging (Sohal and Weindruch, 1996).The DNA, which encodes the vast majority of cellular RNA ROS theory of aging is discussed in depth in this issue and proteins, and mitochondrial DNA have been proof Cell by Balaban et al. (2005).In brief, longer-lived posed to contribute to aging (Karanjawala and Lieber, species generally show higher cellular oxidative stress 2004).The reader is referred to the review by Balaban resistance and lower levels of mitochondrial ROS proet al. in this issue of Cell concerning the potential role duction than shorter-lived species.Caloric restriction, of mitochondrial DNA damage in aging (Balaban et al.,", + "\t\n\nWe previously showed that superoxide plays a primary role in chronological age-dependent DNA damage and mutations.Our model is that the DNA damage caused by oxidative and other types of stress accumulated during aging in nondividing cells generates double-strand breaks during the fi rst round of replication after the exit from G 0 .Cells lacking SGS1 attempt to repair this damage by homologous recombination between sister chromatids but generate a large number of GCRs, especially at advanced age.", + "\t\n\nReactive oxygen species (ROS) have long been at the center of the debate on causes of aging and a central player in the free-radical theory of aging.One form of oxidative damage that is considered irreversible and has been correlated with age in various organisms, including replicative age in yeast, is protein carbonylation (Nystrom 2005).Protein carbonyls have been proposed as a yeast aging factor based on the observations that both protein carbonyls (Aguilaniu et al. 2003;Erjavec and Nystrom 2007) and aggregates containing heavily carbonylated proteins (Erjavec et al. 2007) are asymmetrically retained in mother cells during division.The proper asymmetric segregation of oxidatively damaged proteins appears to be dependent on a functioning actin cytoskeleton (Aguilaniu et al. 2003;Erjavec et al. 2007), which has independently been linked to ROS and life span through the actin bundling protein, Scp1 (Gourlay et al. 2004).", + "\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\nThere are many theoretical considerations on oxidative damage of mitochondria about aging.The \"free radical theory of aging,\" proposed by Harman in 1956 (138), that free radicals cause nonspecific damage to macromolecules, such as DNA, lipids, and proteins, has attracted much attention in recent years due to development in free radical biology.Harman (139) also proposed aging as consequences of mitochondrial aging that free radical reactions may contribute to changes in the mitochondrial inner membrane with age due to effects on both mtDNA and nDNA.Based on the observation of Drosophila, Miquel et al. (238) postulated that there is a distinct possibility of free radical-or lipid peroxide-induced inactivation of the mtDNA of fixed postmitotic cells with the passage of time.Fleming et al. (110) proposed that the site of irreversible injury is the mtDNA rather than the biomembranes.A two-step hypothesis on the mechanisms of in vitro cell aging, \"oxygen radical-mitochondrial injury hypothesis of cell aging,\" was proposed by Miquel and Fleming (239) that the fundamental cause of cell aging is an instability of the mitochondrial genome because of a lack of or balance between mitochondrial repair and the disorganizing effects of oxygen radicals.Thus, deprived of the ability to regenerate their mitochondrial populations, the cells will sustain an irreversible decline in their ability to synthesize ATP, with concomitant senescent degradation of physiological performance, and eventual death.Bandy and Davison (15) suggested that mitochondrial genome mutations may increase oxidative stress as implications for carcinogenesis and aging.", + "\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).", + "\tPrxs and the free radical hypothesis of aging\n\nThe evolved version of Harman's (Harman 2003) free radical theory of aging proposes that organisms age because the constituents of cells and tissues accumulate damage over time caused by reactive oxygen (and/or nitrogen) species originating from endogenous metabolism, including, among many other possible activities, mitochondrial respiration.At first glance, it appears that the data concerning Prxs and aging fit this theory like a glove, as Prxs become ''damaged'' (catalytically inactivated as a peroxidase) during aging due to a modification caused by a reactive oxygen species (ROS), specifically hydrogen peroxide (or organic hydroperoxides), and that counteracting this ''damage'' by elevating the levels of the ''repair'' enzyme Srx1 prolongs life span (Molin et al. 2011).Moreover, as the Prxs themselves act as enzymatic antioxidants and protect the genome against oxidative modifications (see below), it is possible that peroxidedependent inactivation of Prxs gives rise to a negative feedback loop with respect to the cell's capacity for ROS homeostasis.", + "\t\n\nAging is a dynamic and complex process defined as the time-dependent functional decline.With age, homeostasis declines and damage accumulates.One of prime candidates that induce macromolecular damage is oxidative stress from reactive oxygen species (ROS) generated from normal physiological activities.Indeed, many long-lived mutants are resistant to oxidative stress [53].Ferroptosis involves metabolic dysfunction that results in the production of both cytosolic and lipid ROS [36,38].Repression of SLC7A11 transcription by p53 results in reduction of cystine uptake.Because of less cystine uptake, the levels of intracellular glutathione (GSH) will be reduced and the cellular system for defending oxidative stress is abrogated.Thus, the sensitivity of ROS-induced ferroptosis is significantly increased in p53-activating cells.We showed that SLC7A11 is downregulated by p53 and that p53mediated ferroptosis is dramatically induced in the testis of p53 3KR/3KR Xrcc4 -/-mice.Thus, it is very likely that the combination of genomic instability and p53-mediated ferroptosis contributes significantly to the aging associated phenotypes observed in p53 3KR/3KR Xrcc4 -/-mice.", + "\tSources of Damage Increase with Age\n\nThe free radical theory of aging posits that aging is caused primarily by oxidative damage incurred by ROS that chemically modify critical cellular biomolecules (13).This theory has evolved over the years to become the oxidative stress theory of aging, but the principle is the same, in that the accumulation of oxidative damage drives aging.In support of this theory, a large body of literature indicates that oxidative damage to all cellular macromolecules increases with age.Furthermore, overexpression of antioxidant enzymes that detoxify ROS, such as copper-and zinc-containing superoxide dismutase (SOD), manganese-containing SOD, or catalase, increase the life span of Drosophila melanogaster by as much as 30% (14).Additionally, most long-lived mutants in D. melanogaster and Caenorhabditis elegans have increased resistance to oxidative stress.In mammals, the role of oxidative stress is less clear because overexpression of catalase, SOD1 (pancellular expression), or SOD2 (mitochondrial) does not extend the life span of mice (15).However, overexpression of catalase specifically targeted to the mitochondria does extend the life span of some mice up to 20% (16).Additionally, treatment with the antioxidant nordihydroguaiaretic acid (NDGA) and an activator of NRF2 (master regulator of antioxidant response) extends median life span in male mice (17).\t\n\nThe free radical theory of aging evolved to the mitochondrial theory of aging when mitochondria were implicated as the primary source of ROS.Electrons leaked from the electron transport chain at the inner mitochondrial membrane can react with molecular oxygen to produce a superoxide radical, which can be converted by SOD to yield hydrogen peroxide (H 2 O 2 ).In the presence of transition metal ions (e.g., Fe 2+ or Cu + ), H 2 O 2 can be further converted to the highly reactive hydroxyl radical via the Fenton-type reaction.These ROS react locally to damage genes or proteins necessary for oxidative phosphorylation, leading to further uncoupling of electron transport and increased ROS production in a feed-forward manner.Abundant evidence shows that ROS and oxidative damage increase as organisms age.But which cellular target of these damaging radicals and other reactive molecules is health and life limiting?If the answer is DNA, then one expects DNA damage to accumulate with age.", + "\tThe Free Radical Theory of Aging. The free radical theory of aging proposed by Denham Harman more than fifty years ago postulates that aging results from the accumulation of deleterious effects caused by free radicals, and the ability of an organism to cope with cellular damage induced by ROS plays an important role in determining organismal lifespan [3].In agreement with this theory, increased ROS production by mitochondria and increased 8-oxo-dG content in the mtDNA are frequently detected in aged tissues [40,[47][48][49][50], suggesting that progressive accumulation of oxidative DNA damage is a contributory factor to the aging process.Consistently, many studies have found that increased oxidative damage in cells is associated with aging [51][52][53].Furthermore, genetic studies in worm, fly, and mouse have linked enhanced stress resistance or reduced free radical production with increased lifespan [27].Mutant strains of C. elegans that are resistant to oxidative stress have extended lifespan, whereas those more susceptible to free radicals have shortened lifespan [54,55].Mice lacking the antioxidant enzyme superoxide dismutase 1 (SOD1) exhibit a 30% decrease in life expectancy [56].Conversely, simultaneous overexpression of SOD1 and catalase extends lifespan in Drosophila [57].Small synthetic mimetics of SOD/catalase increase lifespan in C. elegans [58], while treatment of antioxidant drugs in mice increases the median lifespan up to 25% [59,60].Further supporting this hypothesis, mice lacking Ogg1 and Myh, two enzymes of the base excision repair pathway that repairs oxidative DNA damage, show a 50% reduction in life expectancy [61].Collectively, these studies demonstrate that interplay between ROS and protective antioxidant responses is an important factor in determining aging and lifespan.\tMitochondria and Aging\n\n3.1.The Mitochondrial Theory of Aging.Because mitochondria are the major producer of ROS in mammalian cells, the close proximity to ROS places mitochondrial DNA (mtDNA) prone to oxidative damage [104].Consistently, many studies have shown that 8-oxo-dG, one of the common oxidative lesions, is detected at higher level in mtDNA than nuclear DNA, suggesting that mtDNA is more susceptible to oxidative damage [52,[105][106][107][108][109][110][111][112][113].As both the major producer and primary target of ROS, mitochondria are thought to play an important role in aging.The mitochondrial theory of aging, extended from the free radical theory, proposes that oxidative damage generated during oxidative phosphorylation of mitochondrial macromolecules such as mtDNA, proteins, or lipids is responsible for aging [114].As mtDNA encodes essential components of oxidative phosphorylation and protein synthesis machinery [115], oxidative damageinduced mtDNA mutations that impair either the assembly or the function of the respiratory chain will in turn trigger further accumulation of ROS, which results in a vicious cycle leading to energy depletion in the cell and ultimately cell death [104,114,[116][117][118].", + "\t\n\nThere is an emerging consensus that oxidative damage is of central importance to much of the age-related overall decline of animal cells, from yeast to humans [2][3][4][5][6][7] .Caloric restriction or environmental conditions that favour a decrease in oxidative metabolism also increase lifespan 8 , and transgenic or knockout animals with decreased oxidative metabolism have increased lifespans.For example, flies that consume oxygen at a high rate have a reduced lifespan, and low oxygen-consumption rates and cold temperatures favour a prolonged lifespan 9,10 .Lipids, proteins and DNA have all been argued to be Ageing, repetitive genomes and DNA damage Michael R. Lieber and Zarir E. Karanjawala www.nature.com/reviews/molcellbioP E R S P E C T I V E S to one another, thereby permitting a copying of information from one sister chromatid to the other.This typically restores the information content at the break site back to normal.", + "\t\n\nA key macromolecule at risk for ROS-mediated damage is nuclear DNA [1], which is evident from the wide range of oxidative DNA lesions that accumulate gradually in rodents and humans with advancing age [6,7].\tIntroduction\n\nA prevailing hypothesis to explain the molecular basis of ageing is Harman's ''free-radical theory of ageing'', which states that endogenous reactive oxygen species (ROS), which result from cellular metabolism, continually damage biomolecules [1].In line with this hypothesis, it has been shown that increased resistance to oxidative stress (e.g., by improved antioxidant defense) extends the lifespan of Caenorhabditis elegans, Drosophila, and rodents [2][3][4], whereas hypersensitivity to oxygen considerably reduces the lifespan of nematodes [5].", + "\tReplication stress, mitochondria and growth signaling\n\nIncreased oxidative damage to DNA and other cellular constituents by ROS produced in dysfunctional mitochondria is an important component of modern versions of the 'free radical theory' of aging (3,71).It is often assumed that the production of ROS in mitochondria is directly proportional to the rate of mitochondrial respiration, and that increased respiration promotes aging.A number of recent studies in budding yeast and mammals argue that these long-held assumptions are incorrect (72).For example, caloric restriction and other experimental manipulations that enhance respiration in budding yeast reduce, rather than increase levels of ROS at the same time that they enhance life span (73).Similarly, budding yeast cells cultured in medium containing glycerol or ethanol, which are metabolized via respiratory pathways, exhibit a longer chronological life span (22).Furthermore, deletion of TOR1 extends chronological life span of budding yeast by enhancing respiration, but reducing ROS (21).As might be expected based on these reports, experimental manipulations that increase the production of ROS in mitochondria shorten the chronological life span of this organism (73,74)." + ], + [ + "\tSenescence and apoptosis are thought to contribute\nto aging and age-related disorders by decreasing the proliferative potential of progenitor\nstem cells, altering tissue regenerative capacity, decreasing tissue function and by altered\ntissue architecture and microenvironment caused by altered gene expression and secretion of\ninflammatory cytokines, growth factors, and proteases (Campisi 2003; Coppe et al. 2008;\nGarfinkel et al. 1994; Krtolica and Campisi 2002; Kuilman et al. 2008; Novakova et al. 2010; Ohtani and Hara 2013).", + "\t\n\nThere exists a substantial body of research addressing the tissue, cellular and molecular changes that accompany or directly contribute to aging in a range of model organisms (reviewed in [7]).However, the majority of data, generated in model organisms or in vitro (cellular senescence), has yet to be validated in human aging.Moreover the relative contribution of putative gerontogenes to human pathological agerelated processes is unknown.Age-associated impaired healing correlates with increased inflammation, increased matrix proteolysis and delayed re-epithelialization leading to chronic wound states, processes modulated by exogenous estrogen treatment [8].In a recent study we characterized estrogen-regulated changes in gene expression using a model of delayed wound healing in young mice that have been rendered hypogonadal by ovariectomization (hence removing any effects of 'intrinsic aging') [9].Thus, using comparative analysis we are now in a position to address the relative contributions of estrogen and aging to healing in elderly humans.", + "\t\nAging alters gene expression of growth and remodeling factors in human skeletal muscle both at rest and in response to acute resistance exercise.\t\n\nAging alters gene expression of growth and remodeling factors in human skeletal muscle both at rest and in response to acute resistance exercise.", + "\t\n\nStructural integrity of skeletal muscle.Some noteworthy genes that were differentially expressed only in older subjects after RL support the concept that the muscles of older subjects may have experienced a degree of stress far exceeding that in young subjects despite being exposed to the exact same stressor.For example, gene expression of MyBPH was robustly elevated (4.1-fold) in the old only, as was myosin head domain containing 1 (MYOHD1; 1.4-fold).MyBPH is an integral myosin binding partner in the A band of myofibrils that interacts with the myosin rods and titin to provide structural integrity to the contractile apparatus.Reduced MyBPH expression is associated with muscle weakness in age-related disorders (30).Interestingly, localization of MyBPH to the contractile apparatus is directed by its C terminal domain consisting of two fibronectin type III motifs (24), and our microarray analysis also revealed a 1.6-fold increase among the old in the expression of fibronectin type III domain containing 3B (FNDC3B).As shown in mice, MyBPH is upregulated in the young after more intense eccentric loading (5), again suggesting age differences in the degree of mechanical stress required to activate many of these transcriptional responses (with young muscles requiring greater stress than old).MyBPH expres-sion is modulated by the transcription factor SMARCA4 (SWI/ SNF-related, matrix-associated, actin-dependent regulator of chromatin, subfamily a, member 4), which was also significantly upregulated in the old only.Interestingly, SMARCA4 is activated by glucocorticoid receptor signaling and, in turn, regulates the expression of notable muscle-specific genes including myogenin, troponin T, and MyBPH.A strain on muscle integrity among the old was also suggested by significant downregulation (1.7-fold) of both type IV collagen 3 (COL4A3) and 4 (COL4A4) mRNA expression and 1.6-fold upregulation of TUBA8.Type IV collagen, a major constituent of basement membranes, is degraded by matrix metalloproteinases (MMP-2 and MMP-9) in response to muscle damage (49).These findings suggest that the muscles of the older subjects may have been attempting to launch a compensatory effort to maintain structural integrity-a response to this degree was apparently not sensed as necessary among the younger subjects.", + "\tRole of Extracellular Matrix Remodeling in Vascular Aging\n\nThe extracellular matrix (ECM) is an important contributor to health and longevity.This noncellular compartment, ubiquitous to all tissues and organs does not only provide essential mechanical scaffolding but mediates highly dynamic biomechanical and biochemical signals required for tissue homeostasis, morphogenesis, and cell differentiation.Studies on model organisms suggest that evolutionarily conserved pathways regulate ECM remodeling during aging and that promotion of ECM youthfulness by antiaging interventions is an essential signature of longevity assurance. 206Aging in mammals also results in significant changes in ECM biosynthesis, postsynthetic modifications of ECM components, and alterations of cell-matrix interactions, which contribute to the development of a spectrum of age-related pathologies. 207ge-related alterations of the ECM, including the subendothelial basement membrane, intima, media, adventitia, and interstitial matrix (which constitute more than half of the mass of the vascular tissue), play a fundamental role in impairment of both structural and regulatory homeostasis of the vasculature. 208With age, the expression of growth factors that regulate ECM biosynthesis is altered 45 and the synthesis of many ECM components (eg, elastin) declines, which impairs elasticity and resilience of the vascular wall to mechanical damage and rupture induced by bursts in wall tension because of pulsatile pressure waves. 208Age-related ECM changes also likely alter vascular mechanotransduction, dysregulating cell responses to alterations in the hemodynamic environment.Additionally, aging and cellular senescence alter the secretory phenotype of vascular endothelial and smooth muscle cells, increasing MMP secretion. 45This together with increased MMP activation 208 induced by high ROS levels compromises the structural integrity of the vasculature and promotes pathological remodeling (eg, in hypertension), resulting in increased likelihood of aneurysm formation and vessel rupture, including the development of cerebral microhemorrhages. 45The available evidence suggests that many of these age-related ECM alterations are governed by circulating factors and factors produced in the vascular wall, including the extended renin-angiotensin-aldosterone system (see above) and an age-related decline in circulating IGF-1. 209ollagen synthesis is also dysregulated with age in the vascular wall likely because of the effects of increased paracrine action of TGF- (transforming growth factor-), 123 which contributes to vascular fibrosis and arterial stiffening. 208Additional features that contribute to increased arterial stiffness include decreased elastin synthesis, elastin degradation and fragmentation, elastin calcification, alterations in cross-linking of extracellular matrix components (eg, by increased presence of advanced glycation end products). 208,210,211he pathophysiological consequences of age-related ECM remodeling and arterial stiffening have been the subject of a recent comprehensive review by AlGhatrif and Lakatta. 6In brief, as the large conduit arteries stiffen in aging, aortic pulse wave velocity, systolic pressure, and pulse pressure significantly increase, 212 whereas diastolic pressure decreases.Decreased diastolic pressure leads to a decline in coronary blood flow.Increased systolic pressure promotes left ventricular remodeling, diastolic dysfunction, and exacerbates atherogenesis.Because of the dilation of conduit arteries, wall tension significantly increases, contributing to the development of aneurysms.In addition to alterations in the biomechanical properties of large arteries, age-related ECM remodeling likely also affects microvascular transport and barrier functions. 213Age-related alteration of the ECM structure and composition are also manifested in the wall of veins, contributing to the pathogenesis of varicosities. 214\t\n\nFigure 4. Conceptual model for the pathogenic role of cellular senescence in vascular aging.The model predicts that increased presence of senescent endothelial or smooth muscle cells (SMCs) in the aged vasculature and their proinflammatory secretome (SASP [senescence-associated secretory phenotype]) contributes to impaired angiogenesis and microvascular rarefaction, pathological remodeling of the extracellular matrix (ECM), barrier disruption, chronic inflammation, and atherogenesis.MMP indicates matrix metalloproteinase.", + "\t\n\nAge-related transcriptional remodeling and mitochondria", + "\t\n\nChromatin remodeling in aging, J. G. Wood et al.", + "\tAging is only, in part, the result of crosslinking reactions\n\nWhile Bjorksten (1968) proposed that crosslinking was a major feature of the chemical aging of tissues, particularly of collagen, it has become apparent in recent years that many age-dependent chemical modifications of protein are monofunctional.These include oxidative modifications of phenylalanine, tyrosine and methionine residues (Table 1), carboxyalkylation of lysine (Table 4), and deamidation and racemization of amino acids.Extracellular matrix proteins accumulate higher levels of monofunctional chemical modifications, as well as crosslinks, not because they are uniquely sensitive to damage, but because they generally turnover more slowly.There are few quantitative studies on the age-dependent accumulation of biomarkers in intracellular proteins, even in proteins with long half-lives, such as contractile proteins in muscle or histones in post-mitotic cells.These proteins may be exposed to higher levels of reactive oxygen species generated in mitochondria or peroxisomes, or to higher levels of reactive carbonyl intermediates in glycolysis, but are also better protected by intracellular antioxidant and detoxification systems.", + "\t\n\nVarious extracellular matrix-related proteins were differentially regulated herein.Extracellular matrix proteins provide structural support, mechanical properties, and strength of tissues, including vocal folds, playing a pivotal role in phonation [62,71,72].Collagens XIV, XVIII, and Fibulin 5 were downregulated in older rabbit vocal folds compared to young tissue.To our knowledge, these specific collagen types have not been investigated in depth in vocal fold tissue; however, studies suggest that the changes in the collagen fiber density and arrangements within the lamina propria may affect phonation [73,74].Collagen type IV is exclusive to extracellular matrix basal membranes [75] and is present in the human vocal fold basal membrane providing support to epithelial and endothelial cells [76].Collagen type IV was upregulated in older rabbit vocal folds compared to young, an effect of aging observed in our study.The relationship between Collagen type IV and aging is not well established.Increased accumulation of Collagen type IV is reported in the basal lamina of cerebral microvessels in humans [77] but decreased in the skin of older adults [78].Conversely, several extracellular matrix proteins were upregulated, including Collagen type XVIII and Fibulin 5, in the presence of dehydration when observing the effect of hydration status alone.These protein changes may be related to the remodeling of the extracellular matrix [79] in response to dehydration.Moreover, the accumulation of collagens and the decrease of elastins may result in extracellular matrix stiffness in aging larynx and other organs [59,79].Finally, Lamin A was upregulated by dehydration, by a smaller magnitude, especially when observing the mean difference within the young groups.Previous data has identified that Lamin proteins A and C are important for imparting the nucleus with its stiffness, and their expression has been reported to scale with tissue stiffness [80].Thus, upregulation of this protein due to dehydration may be related to tissue stiffness in the vocal fold of rabbits.", + "\t\n\nRecently, collagen production and extracellular matrix remodeling were determined to be essential for longevity in C. elegans.Collagen may directly affect signaling processes associated with longevity in C. elegans, including signaling through SKN-1 [40,58].We note that HSF-1 was also recently shown to regulate cytoskeletal integrity in a process that can influence stress resistance and longevity in C. elegans [59].Thus, the linkage of both the extracellular matrix and the cytoskeleton to HSF-1 may provide a mechanism by which HSF-1 promotes longevity.\tHSF-1 regulates collagen genes which may affect the aging process\n\nIt is interesting that cuticle structure genes constitute the largest overlap with aging-related genes.In humans, mutations in collagens lead to a large number of heritable human diseases such as osteoporosis and musculoskeletal diseases [53].Collagens are long-lived proteins known to accumulate damage during aging, leading to a decline in tissue health [54].Also, type I collagens become resistant to proteolysis upon age [55,56], affecting their turnover.Interestingly, mice expressing cleavageresistant type I collagen go through an accelerated aging process [57].Thus, cellular aging can be affected by the state of the extracellular matrix in mammals.", + "\t\n\nAn observation that is specific for males is the global downregulation with aging of genes involved in the synthesis of the ECM and in particular of different forms of collagen (Table 2).In addition, aging males but not females showed a decrease in collagen type III.Interestingly, collagen type III decreases the size of collagen bundles and thereby increases vascular elasticity (11).Therefore, a decreased expression of collagen type III can participate in the increased stiffness that characterizes the aging aorta (23).An interesting observation from our study that directly relates to the mechanism of vascular remodeling is the upregulation in aging males of the transcript encoding collagen type VIII (Table 3).That specific collagen type, which is upregulated in response to vascular injury (24), promotes VSMC migration (1).The upregulation of this transcript together with the downregulation of other isoforms in aging males again supports the notion that this group is more susceptible to neointimal proliferation, VSMC migration, and potentially atherosclerosis.\t\n\nOur study shows that the genomic adaptation to vascular aging involves not only the genes involved in ECM composition and VSMC differentiation and migration, but also many other categories of genes participating in intracellular functions, such as cell signaling, DNA repair, metabolism, and protein synthesis.Our study also illustrates that most of the changes in gene expression with aging differ between males and females and correspond to different sets of transcription factors.Indeed, 5% of the 600 genes that were regulated by aging were observed in both old males and females.GO analysis also shows that specific subsets of genes are regulated differently between sexes, especially the genes participating in ECM composition and VSMC phenotype.We therefore propose that these transcriptional differences may underlie the different physiological properties of aging arteries between males and females, as well as their different susceptibility to vascular complications, such as hypertension or atherosclerosis.Furthermore, the analyses in young monkeys demonstrated major differences in genes regulating vascular structure, implying that the sex differences in vascular stiffness that develop with aging are programmed at an early age.", + "\tChronic liver diseases are characterized by aberrant matrix deposition, calling for our\nattention to the role of ECM in resolution of liver fibrosis. Tissue remodeling is regulated by MMPs,\ninvolved in the ECM degradation, and TIMPs, their endogenous inhibitors. Their subtle balance\nmaintains liver fibrogenesis. Tissue homeostasis is further regulated by proteolytic activity of the\nPLAU/PLAT/plasmin, responsible for the maintenance of the physiologic levels of ECM (40). PLAU promotes ECM degradation through activation of MMPs (MMP-2, -3 and -9; (41, 42),\nincreases the differentiation of hepatic stem cells, and HGF-dependent regeneration of hepatocytes\n(43).", + "\t\n\nMechanistically, the age-related increase in elastin degradation may result from augmented activity of proteases with elastinolytic activity, including certain MMPs and cysteinyl cathepsins, enzymes that, in turn, are regulated by inflammatory mediators (54,55).Collagen catabolism falls in aging arteries.\t\n\nAugmented transforming growth factor (TGF)-b activity favors the accumulation of collagen in the aortic wall.The activity of various elastases, including matrix metalloproteinases (MMPs), such as MMP-9 and MMP-12, as well as overexpression of the cysteine proteinases cathepsins S, K, and L, and the serine proteinase neutrophil elastase, elaborated by inflammatory cells, can all contribute to depletion of elastin (11).These alterations in the aorta's extracellular matrix contribute importantly to its loss of distensibility.This increased stiffness raises reflected waves and elevates systolic pressure.Yet diastolic pressure tends to decline with age.As aortic pulse wave velocity increases, pulse pressure rises (12).Indeed, pulse pressure is an independent risk factor for CV events (13).Isolated systolic hypertension accounts for the majority of uncontrolled hypertension in Americans over 50 years of age (14,15).substantially stroke and total mortality, with lesser benefit for ischemic cardiac events (16).Avoiding excessive sodium intake may provide an additional, nonpharmacological intervention for control of hypertension in older individuals (17,18).Some have raised concerns regarding the safety of aggressive lowering of blood pressure in elderly patients, particularly those with concomitant coronary artery disease (19).Indeed, a J-shaped curve relating CV outcomes to blood pressure may pertain to this In addition to reducing stroke, a major impediment to independent living and function in older patients, antihypertensive therapy may limit the development of dementing illnesses, as shown in the Syst-Eur trial (27).Decreased dementia and cognitive decline accrue with longer duration of antihypertensive treatment (28).An asymmetric loss to follow-up of individuals with impaired cognition may have biased the results of dementia in the SHEP study to the null (29).With regard to the former, vascular aging alters the function of the endothelium, the cells that line the lumen of blood vessels.Endothelial dysfunction includes reduced vasodilatory and antithrombotic properties, with an increase in oxidative stress and inflammatory cytokines (33)(34)(35) favoring atherogenesis and thrombosis, and predisposing to CVD (36).Human and experimental studies concur that diminished bioavailability of nitric oxide (NO), a key mediator of vasorelaxation and antiatherogenic processes, underlies age-dependent endothelial dysfunction (37,38).Reduced NO bioavailability can occur due to decreased synthesis or increased degradation of NO.Under normal conditions, endothelial nitric oxide synthase (eNOS) produces NO from L-arginine in the presence of the cofactor tetrahydrobiopterin (BH4) (39).Although studies differ regarding eNOS protein expression with age (34,40,41), recent data suggest an age-related alteration in eNOS function, referred to as eNOS uncoupling (42).", + "\tBackground\n\nTissue aging is caused by intrinsic and extrinsic factors that induce complex molecular changes and, in turn, a deterioration of cellular structures and function.These changes are major causes of age-related diseases like cancer or cardiovascular disorders [1,2].The main molecular adaptations occurring during aging are loss of genomic stability due to reduced DNA repair capacities [3], loss of proliferative potential caused by increased senescence [1,4], and age-related alterations in the DNA-methylation patterns that affect cellular plasticity [5,6].Metabolic adaptations are also considered to play a major role in aging [7][8][9][10].For instance, the metabolic function of mitochondria is progressively impaired during aging in different tissues [8,11].This can result in increased generation of reactive oxygen species that foster genomic instability [8,12].Moreover, several studies reported that caloric restrictions and diet adaptations, such as supplementation of food with branched chain amino acids [13,14], can significantly increase lifespan [15].This suggests that metabolic activity as well as nutrient sensing pathways are highly relevant for cellular aging processes (reviewed in [10]).Accordingly, interference with the insulin/IGF1 and the mammalian target of rapamycin (mTOR) pathways increased lifespan in different model organisms [7,[16][17][18].", + "\t\n\nWe examined the list of 447 age-regulated genes for functional groups showing a consistent change with age.One group includes genes involved in the formation of the extracellular matrix, which show a consistent increase in expression in old age.Seven age-regulated genes encode proteins known to play key roles in maintaining epithelial polarity (three types of claudins, two cadherins, occludin, and a cell adhesion molecule), all but one of which increase expression in old age (see Table S4).Forty-nine age-regulated genes encode protein components of the extracellular matrix, all but four of which increase expression in old age.In the kidney, the extracellular matrix could play a key role in governing the filtration of blood via the basement membrane, a capacity that declines with age.The observation that genes involved in forming the extracellular matrix increase expression in the kidney with age may be directly relevant to the age-related decline in glomerular filtration rate." + ], + [ + "\tStochastic damage\n\nFigure 2. Longevity assurance, ageing and disease.New studies of the biology of ageing are revealing processes that control when and how fast ageing occurs, such as insulin-IGF-1 signalling [6], cellular senescence [4], protein refolding [43][44][45], autophagy [41] and phase 1 and 2 detoxification [36,37,52].These represent major points of intervention against ageing-related disease.As shown here, lifespan pathways control improved cellular maintenance, which leads to slowed ageing (e.g.slowed normal cognitive ageing) and protection against diseases of ageing (e.g.neurodegenerative diseases of ageing, such as Alzheimer's and Parkinson's disease, and cancer).Ageing can evolve via selection to reduce investment in energetically costly somatic maintenance processes and instead to increase early fitness traits such as growth and reproduction [50,51].Arrows denote stimulation, and T bars inhibition, of the process indicated.Red and green denote changes leading to ageing and longevity, respectively.", + "\t\n\nFig. 4. Schematic showing how some external interventions trigger longevity, often at least partly through stimulating autophagy.The pink writing refers to dietary, chemical, or therapeutic interventions that can extend life span, in at least some organisms (described in the text).Arrows indicate stimulating effects, and blocked lines indicate inhibitory effects.This schematic is not meant to be exhaustive but highlights the pathways that alter the epigenetic information and autophagy.", + "\t\n\nTORC1 regulates several downstream processes that may contribute to its role in aging, including protein degradation via autophagy, mitochondrial metabolism, stress response, and mRNA translation (Stanfel et al. 2009).Autophagy, which literally means \"self eating\", is a degradative process through which cellular components are engulfed by cytoplasmic vesicles and transported to the lysosome/vacuole for degradation (Klionsky 2007).Autophagy is repressed by TOR signaling and is induced in response to starvation or treatment with TOR inhibitors, such as rapamycin (Noda and Ohsumi 1998).A decline in the autophagic response has been reported in aging mammals (Cuervo and Dice 2000), and increased autophagy is required for life span extension in long-lived C. elegans mutants with reduced insulin/IGF-1-like signaling (Melendez et al. 2003).Several recent studies have also uncovered an important role for autophagy in the response to DR. DR induces autophagy in yeast, worms, and flies (Juhasz et al. 2007;Morck and Pilon 2006;Takeshige et al. 1992) and is reported to be required for life span extension from DR or TOR-inhibition in both worms and flies (Hansen et al. 2008;Jia and Levine 2007;Juhasz et al. 2007).Recently, up-regulation of autophagy by spermidine has also been shown to be associated with increased life span in yeast, nematodes, and flies (Eisenberg et al. 2009).", + "\tInductors of Autophagy and its Impact on Aging\n\nAutophagy has a role in homeostasis, which plays an essential role in the maintenance of cellular physiology and the prevention of cellular damage.Among the inducers of autophagy have been described the already-mentioned rapamycin, resveratrol, and polyamines; however, only polyamines have demonstrated results in clinical research in humans [65].It is known that these compounds can induce the canonical autophagy pathway, which includes inactivation of the mammalian objective of the rapamycin complex 1 (mTORC1), allowing phosphorylation and activation of the Unc-51 complex (Ulk1/2), where the cascade of the other members of the complex is subsequently activated, ULK as FIP200 and ATG13 [65].\t\n\nOn the other hand, interventions using chemical inducers of macroautophagy, such as rapamycin, an mTOR inhibitor, can increase the life span of middle-aged mice like that induced by spermidine or polyamine-producing gut flora supplementation [87].In an unexpected finding, aged cells showed an increased accumulation of protein aggregates, suggesting a decline in lysosome functionality during aging even though the number of lysosomes increased [72,88].This disparity could be due to changes in the pH, as suggested by the fact that the vacuolar V-type ATPase complex, which is responsible for maintaining vacuolar pH, decreased during aging, suggesting a mechanistic link between altered protein complex composition and lysosome dysfunction [72,88].The stress-induced synthesis of cytosolic and organelle-specific chaperones was also impaired in aging.Mutant mice that were deficient in a co-chaperone of the heat-shock family exhibited accelerated aging phenotypes, whereas long-lived mouse strains showed a marked upregulation of some heat-shock proteins [89].\t\n\n2016;351:173-6.81.Koga H, Kaushik S, Cuervo AM.Protein homeostasis and aging: the importance of exquisite quality control.Ageing Res Rev. 2011;10:205-15.82.Labbadia J, Morimoto RI.The biology of proteostasis in aging and disease.Annu Rev Biochem.2015;84:435-64.83.Rubinsztein DC, Mario G, Kroemer G. Autophagy and aging.Cell.2011;146:682-95.84.Tomaru U, Takahashi S, Ishizu A, Miyatake Y, Gohda A, Suzuki S, et al.Decreased proteasomal activity causes age-related phenotypes and promotes the development of metabolic abnormalities.Am J Pathol.2012;180:963-72.85.Rodriguez KA, Edrey YH, Osmulski P, Gaczynska M, Buffenstein R. Altered composition of liver proteasome assemblies contributes to enhanced proteasome activity in the exceptionally long-lived naked mole-rat.Brodsky JL, editor.PLoS One.2012.https://doi.org/10.1371/journal.pone.0035890.86.Chondrogianni N, Georgila K, Kourtis N, Tavernarakis N, Gonos ES.Enhanced proteasome degradation extends Caenorhabditis elegans lifespan and alleviates aggregationrelated pathologies.Free Radic Biol Med.2014;75:S18.https://doi.org/10.1016/j.freeradbiomed.2014.10.632.87.91.Haigis MC, Yankner BA.The aging stress response.Mol Cell.2010;40:333-44.92.Johnson SC, Rabinovitch PS, Kaeberlein M. mTOR is a key modulator of ageing and agerelated disease.Nature.2013 Jan 16;493:338-45.93.Lamming DW, Ye L, Astle CM, Baur JA, Sabatini DM, Harrison DE.Young and old genetically heterogeneous HET3 mice on a rapamycin diet are glucose intolerant but insulin sensitive.Aging Cell.2013;12:712-8.\tConserved Metabolic Pathways Offer Clues to the Factors of Aging and Longevity\n\nEvolutionarily conserved pathways, from yeast to mammals, robustly correlate with aging and longevity, and their deregulation has been implied with the development of cellular aging and include the mechanistic target of rapamycin (mTOR), insulin/ insulin growth factor 1 signaling (IIS), AMPK sensing, and sirtuin (SIRT) pathways [90].The harmonized regulation of these metabolic pathways maintains cellular and organismal homeostasis, even in the presence of external perturbations like changes in nutrient availability, temperature, oxygen level, or internal alterations, including protein misfolding and DNA damage [91].", + "\t\n\npivotal in this aspect providing molecular insights and having huge conceptual contributions in the field.Characterising the contribution of individual mutants in ageing is a continuously active and informative activity in the field.On top of these studies, genome-wide screens have provided insights on the role of evolutionarily conserved processes and signalling pathways in ageing such as nutrient response [17,18], protein translation, oxidative damage [19,20], mitochondrial function [21,22] and autophagy [22,23] opening new avenues for biogerontology research.Yeasts have proved informative and helped in understanding mechanisms of highly conserved pathways (from yeast to human) in physiology, health and disease such as the Target of Rapamycin (TOR) [24], glucose sensing (PKA) and stress response pathways (Sty1/p38) [25].\t\n\nA competitive ageing assay was performed in budding yeast where samples from the ageing pool were collected at specific timepoints [58].Mutants were then detected using a microarray DNA hybridization technique that quantifies abundance of the barcode tags of each mutant.Using this approach multiple short-and long-lived mutants were identified with autophagy mutants being among the short-lived and mutants coding for proteins involved in de novo purine biosynthesis pathway, which ultimately produces IMP and AMP were among the long-lived ones [58].Validation experiments targeting autophagy or purine biosynthesis has the expected lifespan outcomes.In a similar approach, deletion of genes involved in protein sorting in vacuoles, autophagy and mitochondrial function shortened life span, confirming that respiration and degradation processes are essential for long-term survival.Among the genes whose deletion significantly extended life span were genes implicated in fatty acid transport and biosynthesis, cell signalling and transfer RNA (tRNA) methylation such as ACB1, CKA2 and TRM9, respectively [59].", + "\t\n\nWe have recently conducted a genome-wide screen using siRNA library to identify genes regulating autophagy in human cells under normal nutritional conditions (5).In this image-based screen we took advantage of the autophagy specific GFP-LC3 reporter whose translocation from the cytosol to autophagosomes can serve as a quantitative measure of autophagy.In this study, we specifically explore the mechanisms that regulate autophagy in neural cells using the hits identified in our screen.We demonstrate that reactive oxygen species (ROS) play a general function in mediation of autophagy upstream of the type III PI3 kinase and that this pathway is essential for the up-regulation of autophagy by A.Interestingly, our data show that genes regulating autophagy are differentially expressed in normal aging and in AD patient brains.Finally, we identify candidate molecular targets that may be safely manipulated to modulate autophagy to treat neurodegenerative diseases.\t\n\nConversely, expression of the key autophagy genes, such as Atg5 and Atg7, was down-regulated in aging.This is consistent with our previous data demonstrating transcriptional down-regulation of beclin 1, in normal human brain aging (11).Together, this suggests, that unlike AD, the normal aging process may lead to transcriptional down-regulation of autophagy.\t\n\nTo further define the biological processes affected by downregulation of autophagy in aging, we used gene ontology canonical pathway analysis.It revealed a significant enrichment in the \"Axon guidance\" (P = 0.0009) and \"Regulation of actin cytoskeleton\" (P = 0.038) pathways, suggesting a connection between regulation of autophagy, axon guidance and actin dynamics.Construction of protein-protein interaction networks anchored by the hit genes belonging to these pathways (12,13) revealed two related networks encompassing, respectively, 27 (11%) and 61 (26%) of the hit genes (Fig. S6 C and D).Importantly, both networks directly connect to the known autophagy machinery through the interaction of the RIP kinase (RIPK1) and PKC (PRKCZ) with p62/sequestrosome (SQSTM1).In addition, syndecan 2 (SDC2), a part of the \"Regulation of actin cytoskeleton\" network, interacts with syntenin, a binding partner of ULK1, the human ortholog of yeast Atg1 (14).ULK1 is known to play a role in the regulation of endocytic processes involved in axon guidance (15) and to promote synapse formation in Drosophila (16).These data suggest that some of the molecular networks involved in the regulation of autophagy are closely connected to those regulating endocytosis, actin dynamics, and neuronal axon guidance, and that autophagy may play a wider role in the development and maintenance of neuronal function.\t\n\nTranscriptional Regulation of Autophagy in Normal Brain Aging.To determine whether the regulation of autophagy may have wider implications in normal aging of the human brain, we analyzed expression of the autophagy screen hit genes in a set of younger versus older human brain samples (10).We observed differential expression of a large subset of genes, including a group of 32 genes significantly (P < 0.05) up-regulated and 46 down-regulated with age (Fig. 6A and Fig. S6 A and B and Table S9).Gene ontology biological process analysis revealed that the age up-regulated group was highly enriched in genes involved in mediation and regulation of the MAP kinase pathway (P = 1.6 10 4 ).An increase in the activity of MAP kinase pathway was predicted by our previous analysis to lead to the suppression of autophagy (5).\t\n\nDifferential Expression of Autophagy Regulators in Normal Aging and in AD.Our gene expression data suggest that autophagy is also differentially regulated at the transcriptional level in normal human brain aging versus in AD.Because autophagy is known to play a protective role against onset of neurodegeneration in animal models (2,3,20,21), its down-regulation in normal aging could contribute to the observed age-dependent predisposition to development of chronic neurodegenerative diseases.In addition, the extensive overlap of the autophagy screen hits with Fig. 6.Expression of autophagy screen hit genes in normal human aging.Clustering analysis (dChip) of mRNA expression levels of select autophagy hit genes in younger (40 y old) versus older (70 y old) human brain samples, based on (i) minimum 1.2-fold change between the average expression, and (ii) P value <0.05 using unpaired t test.\tDiscussion\n\nIn this study, we demonstrate that the type III PI3 kinase plays a fundamental role in the regulation of autophagy and that ROS function as general mediators of autophagy induction upstream of this kinase.This pathway has an essential function in the initiation of autophagy in response to mitochondrial damage following exposure to A, the main pathogen of AD.At the same time, A is able to slow down autophagic processing through ROS independent inhibition of lysosomal degradation.In addition, our analysis of expression of the autophagy screen hits suggests that autophagy is differentially regulated at the transcriptional level in normal human aging and in AD, with overall levels decreased in normal aging but elevated in AD.", + "\t\n\nAt least two aspects need to be addressed using a system biology approach in aging research.First, although many different pathways, compartments or processes are known to be closely related to aging, such as the IIS pathway, autophagy, mitochondria, oxidative stress response and so on, it remains unclear as to how they interact, are co-regulated and balanced during aging.To provide a glimpse of this problem, we visualized the network communities among the known aging regulators based on entries in the GenAge database [62,63] and controlling growth and proliferation (green nodes), DNA damage response for maintaining integrity of the genome (red nodes), mitochondria and oxidative stress response (yellow nodes), and ribosome and translation (blue nodes).It is obvious that the first two are intensively linked and closely entangled, while the latter two are relatively independent processes with only few links connected to the first two processes.Also, it is interesting to note that, by comparing the molecular interaction-based network with the co-citation network, the role of autophagy and protein transport in aging might be either overestimated due to study bias or under-estimated by the incompleteness of the molecular interactions among these genes.\tINTRODUCTION\n\nAging has fascinated researchers since ancient times.The hugely complicated process that has been revealed may be interpreted from different aspects, such as the accumulation of oxidative damage, shortening of telomeres, the costs of reproduction, metabolic rates, cellular senescence, etc., and these have in turn given rise to diverse theories of aging [1].However, thanks to forward and reverse genetic technologies, researchers in the recent decades have established that despite its complexity, a single or a few key genes in a few key pathways can modulate the aging rate.The most important players would appear to be those in nutrient sensing pathways or stress response pathways, such as DAF-2/IGF1R and DAF-16/FOXO in the Insulin/IGF like signaling pathway, AAK-2/AMPK in another nutrient sensing pathway, JNK in the stress response pathway, LET-363/mTOR as an inhibitor of autophagy and activator of translation and SIRT1/SIR2 in genome stability maintenance, to name a few [2,3].In addition to genetic perturbations, dietary perturbations, such as diet restriction (DR) are known to significantly extend lifespan in most organisms examined from yeasts to primates, although different pathways may act under different DR conditions, and alternative DR strategies also effect C.elegans lifespan in different ways [3,4].The main pathways revealed under different DR regimens are summarized in Fig. (1).In this small, convoluted DR response network, DAF-16 and ceTOR/LET-363 *Address correspondence to this author at the Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, 200031, China; Tel: 86-21-54920458; Fax: 86-21-54920451; E-mail: jdhan@picb.ac.cn These authors contributed equally to this work.", + "\t\n\nIn vitro and animal studies have reported a decline in autophagy with age [26,36,[40][41][42][43]; however, to our knowledge, only one other publication has reported an age-associated decline in expression of autophagy genes, which was carried out in a small number of human brain tissue samples [44].Overall, these findings for major components of core autophagy machinery and upstream regulators provide evidence for a transcriptional decline in autophagy gene expression with age in human monocytes.The identification of key genes contributing to a decline in autophagy are of great interest, as pharmacologic activation of autophagy has been linked with increasing lifespan in animal models, including mice [45].Further, dysfunctional autophagy is now widely implicated in pathophysiological processes of many age-related diseases such as cancer, Alzheimer's, diabetes, and cardiovascular diseases [46].However, longitudinal studies are necessary to validate the age-related transcriptional decline of autophagy gene expression in human monocytes, and to investigate the relationship between these age-related patterns and the development of age-associated diseases.", + "\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.", + "\tConcluding remarks and future perspectives\n\nAging research has rapidly expanded over the past two decades, with studies ranging from lifespan-extending [68,69,71].However, when their effect on cell death and senescence leads to stem cell loss and tissue degeneration, they might contribute to aging [66,67]." + ], + [ + "\tFurther evidence of age-related changes in stem cells include the finding that a\nhigher proportion of Thy-1loSca-1+Lin-Mac-1-CD4-c-kit+ cells from old mice are in\nS/G2/M phases of the cell cycle (Morrison, 1996), and the results of Henckaerts\net al. , who showed that the proliferative response of Lin-Sca-1+c-kit+ marrow cells\nto the early-acting cytokines KL, Flt3L and TPO, decreased dramatically with age\n(Henckaerts et al. 2002). As mentioned previously, the bone marrow niche is the optimal\nmicroenvironment for the growth and functional maintenance of HSCs (Moore\n2004; Nilsson et al. 2001).\t17\nAging Effects on Hematopoietic Stem Cells and Bone Marrow Niche\nAs discussed above, HSC expansion and transplantation is clinically\nimportant to treat patients with hematological and non-hematological disorders. It\nis also well known that cancer risk increases in older people (Balducci and\nExtermann FEB 2000). Therefore, understanding aging effects on hematopoietic\nsystem, especially on HSCs and their bone marrow microenvironment (niche),\nmay not only help to prevent malignant transformation, but also to determine\nefficacy of aging stem cells for transplantation (Pinto et al. 2003; Van Zant and\nLiang 2003) .", + "\t\n\nMost mammalian tissues can be described as being comprised of two major cellular components: stem or progenitor cells, which are responsible for regenerative capacity or repair after injury, and differentiated somatic cells, responsible for adult stem cell support and specialized tissue/organ functions.Based on this classification, two major mechanisms can account for tissue degeneration associated with age: loss of stem cell pool division potential (loss of regenerative capacity) and loss of differentiated somatic cell function, which directly leads to loss of organ function.Loss of differentiated somatic cell function can additionally indirectly affect adult stem and progenitor cells by altering the tissue microenvironment that is essential for stem cell support (the stem cell niche).In general, loss of stem cell pool division potential can occur through multiple mechanisms including stem cell senescence, death or dysfunction of the niche.One specific mechanism that can account for the loss of both stem cell and differentiated somatic cell function is the gradual accumulation of persistent DNA damage.Persistent DNA damage and its erroneous resolution *To whom correspondence should be addressed.Tel: +1 415 209 2042; Fax: 415-209-22232; Email: dbhaumik@buckinstitute.org 2007 The Author(s) This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/ by-nc/2.0/uk/)which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.include telomeric dysfunction (9)(10)(11) and somatic mutations (12), both of which increase with age; both also have been proposed to contribute to the loss of stem and differentiated somatic cell function with age (13,14).DNA damage accumulation in stem cells has been detected in mice and clearly contributes to the attrition of stem cell division potential during aging (15).Thus, it is likely that DNA damage contributes to aging by limiting stem cell division potential and by also interfering with somatic tissue functions, including stem cell niches.", + "\t\n\nA diminished capacity to maintain tissue homeostasis is a central physiological characteristic of ageing.As stem cells regulate tissue homeostasis, depletion of stem cell reserves and/or diminished stem cell function have been postulated to contribute to ageing 1 .It has further been suggested that accumulated DNA damage could be a principal mechanism underlying age-dependent stem cell decline 2 .We have tested these hypotheses by examining haematopoietic stem cell reserves and function with age in mice deficient in several genomic maintenance pathways including nucleotide excision repair 3,4 , telomere maintenance 5,6 and non-homologous end-joining 7,8 .Here we show that although deficiencies in these pathways did not deplete stem cell reserves with age, stem cell functional capacity was severely affected under conditions of stress, leading to loss of reconstitution and proliferative potential, diminished self-renewal, increased apoptosis and, ultimately, functional exhaustion.Moreover, we provide evidence that endogenous DNA damage accumulates with age in wild-type stem cells.These data are consistent with DNA damage accrual being a physiological mechanism of stem cell ageing that may contribute to the diminished capacity of aged tissues to return to homeostasis after exposure to acute stress or injury.", + "\tSeveral studies have shown\nthat the systemic milieu regulates stem cell decline during aging. Liang et al. showed\nthat HSCs have a reduced ability to home to the bone marrow and spleen after\ntransplantation into old versus young recipients (Liang et al. , 2005). Further experiments\ndemonstrated that the muscle stem cell niche adversely effects stem cell function as\nevidenced by the restoration of old stem cell regenerative potential upon exposure to a\nyoung systemic microenvironment (Conboy et al. , 2005; Conboy and Rando, 2005).\tSince stem cells\nare capable of self-renewal and produce progeny to replenish worn-out and damaged cells\nin aged tissues, the induction of stem cell senescence may compromise tissue renewal by\ndepletion of stem or progenitor cell pools and thus promote age-related pathologies. 6\nIt is apparent that the HSC compartment undergoes considerable age-related\nchanges, however it is not yet clear whether theses changes are intrinsic to the cells\nthemselves or whether they occur due to alterations in the hematopoietic\nmicroenvironment, commonly referred to as the HSC niche.\tHowever, studies do indicate that aged tissues have a diminished capacity to return to a\nhomeostatic state after exposure to stress or injury, therefore indicating a defect in stem\ncell function during the aging process. Since the HSC population provides an ideal\nmodel to study stem cell aging, it is necessary to elucidate the mechanisms of\nhematopoietic aging and expand the findings to other tissues and organ systems. Theories of Aging and Age Related Epigenomic Changes\nThere are two major theories of organismal aging: evolutionary and damage\nbased.\tWith\nthis in mind, it has been hypothesized that the aging or functional failure of tissuespecific stem cells, which fulfill this job, may limit tissue repair and renewal, therefore\ncontributing to overall organismal aging (Krtolica, 2005; Van Zant and Liang, 2003). Because of the unprecedented experimental model systems that are available for the\nexploration of HSCs, stem cell aging research in the field of hematology has been the\nsubject of extensive studies. Indeed, the hematopoietic system has served as an important\nmodel for advancing our understanding of stem cell biology and its association with\naging.\tIn view of the importance of stem cells for maintaining\nimmune function and in a broader sense tissue homeostasis and longevity, there is a\ncritical need to better understand the mechanisms involved in HSC aging. 17\nFigure 1.1 The HSC hierarchy. The HSC compartment can be functionally divided into three populations; long-term\nHSCs, which have extensive self-renewal capacity, short-term HSCs, which have limited\nself-renewal capacity, and multipotent progenitor cells which cannot self-renew and give\nrise to common lymphoid progenitors (CLP) and common myeloid progenitors (CMP).", + "\tIn other words, lower HSC proliferation results in a\nmore youthful stem cell, but poorer tissue regeneration, and\nconsequently an aged phenotype; this indicates that stem cell\nproliferation and tissue regeneration are nely balanced to\nmaximize longevity, so that cell cycle disruption results in an\nuncoupling of tissue and organismal aging from the aging of\nthe resident stem cell. Finally, three lines of evidence in our work indicate broad\nchanges in epigenetic regulation with age.\tIf the rejuvenating effect of stem cells were perfect, senescing cells would be\nreplaced indenitely; but even in highly regenerative tissues\nsuch as the skin, the gut, and the hematopoietic system, agerelated decline in function is well established [1]. Still unclear\nare the effects of aging on the stem cells themselves, which\ncould contribute to inferior tissue repair. Hematopoietic stem cells (HSCs) continuously replenish\nthe blood and immune system throughout life. Data from\nmice support an age-related decline in stem cell function [1],\nsuggesting that older HSCs are inadequate to cope with the\ndemands of blood production.", + "\tFurthermore, the differentiation potential of the HSC compartment\nappears to become skewed toward the myeloid lineage with age\n(26 28). As HSC have been shown to cycle (29), replicative stress,\neven in the absence of detectable telomere erosion (30, 31), may\nunderlie at least some of the age-related changes in HSC (32). Many traits affecting the hemopoietic stem and progenitor cell\ncompartments also change with age in a mouse strain-dependent\nfashion (2123, 3234) and have been implicated in organismal\nlife span (21, 3234). The responsiveness of LSK cells to TGF-2\nshowed mouse strain-dependent variation in young mice.", + "\tFurther evidence of age-related changes in stem cells include the finding that a\nhigher proportion of Thy-1loSca-1+Lin-Mac-1-CD4-c-kit+ cells from old mice are in\nS/G2/M phases of the cell cycle (Morrison, 1996), and the results of Henckaerts\net al. , who showed that the proliferative response of Lin-Sca-1+c-kit+ marrow cells\nto the early-acting cytokines KL, Flt3L and TPO, decreased dramatically with age\n(Henckaerts et al. 2002). As mentioned previously, the bone marrow niche is the optimal\nmicroenvironment for the growth and functional maintenance of HSCs (Moore\n2004; Nilsson et al. 2001).\t17\nAging Effects on Hematopoietic Stem Cells and Bone Marrow Niche\nAs discussed above, HSC expansion and transplantation is clinically\nimportant to treat patients with hematological and non-hematological disorders. It\nis also well known that cancer risk increases in older people (Balducci and\nExtermann FEB 2000). Therefore, understanding aging effects on hematopoietic\nsystem, especially on HSCs and their bone marrow microenvironment (niche),\nmay not only help to prevent malignant transformation, but also to determine\nefficacy of aging stem cells for transplantation (Pinto et al. 2003; Van Zant and\nLiang 2003) .", + "\tIntroduction\n\nThe regenerative potential of our body decreases upon aging.Regenerative tissues depend on specialized adult stem cells, thus aging in these tissues can be interpreted as signs of aging in somatic stem cells [1].Adult stem cells are characterized by the dual function to differentiate into different cell lineages and to selfrenew for maintenance of the stem cell pool.It is, however, still controversial if this self-renewal also includes juvenation or if adult stem cells are doomed to undergo aging upon each cell division.It is unclear if adult stem cells undergo functional and molecular changes, if their number decreases because of aging, or if aging is due to extrinsic environmental factors without any effect on the stem cell pool [2,3].\t\n\nThere is emerging evidence that aging is not purely a cell intrinsic process, but rather regulated by interaction with the cellular microenvironment.For example, Ju and co-workers have demonstrated that telomere dysfunction induces alterations in the microenvironment that affect aging of the hematopoietic system [55].In general, adult stem cells have a slow turnover and reside in specialized niches, protected from the environment and only a few are activated at a time [33,56].By keeping adult stem cells in a quiescent state, the stem cell niche might also play a crucial role in regulating replicative senescence.Strong experimental data for this hypothesis derives form serial transplantation experiments of HSC in mice.The reconstituting ability declines continuously within 4 to 5 transfers [57,58] and this decline is thought to be telomereindependent [59], although it has been reported that telomere length decreases by serial transplantation [60].Recently, Wilson and co-workers have demonstrated that there is a dormantfraction of HSC that divides only five times during the lifetime of mice and especially these dormant HSC posses repopulating activity upon serial transplantation [61].The stem cell niche could therefore play a central role in maintaining a dormant pool of HSC to prevent replicative senescence over the lifetime of the organism [62].\t\nThe regenerative potential diminishes with age and this has been ascribed to functional impairments of adult stem cells.Cells in culture undergo senescence after a certain number of cell divisions whereby the cells enlarge and finally stop proliferation.This observation of replicative senescence has been extrapolated to somatic stem cells in vivo and might reflect the aging process of the whole organism.In this study we have analyzed the effect of aging on gene expression profiles of human mesenchymal stromal cells (MSC) and human hematopoietic progenitor cells (HPC).MSC were isolated from bone marrow of donors between 21 and 92 years old.67 genes were age-induced and 60 were age-repressed.HPC were isolated from cord blood or from mobilized peripheral blood of donors between 27 and 73 years and 432 genes were age-induced and 495 were age-repressed.The overlap of age-associated differential gene expression in HPC and MSC was moderate.However, it was striking that several age-related gene expression changes in both MSC and HPC were also differentially expressed upon replicative senescence of MSC in vitro.Especially genes involved in genomic integrity and regulation of transcription were age-repressed.Although telomerase activity and telomere length varied in HPC particularly from older donors, an age-dependent decline was not significant arguing against telomere exhaustion as being causal for the aging phenotype.These studies have demonstrated that aging causes gene expression changes in human MSC and HPC that vary between the two different cell types.Changes upon aging of MSC and HPC are related to those of replicative senescence of MSC in vitro and this indicates that our stem and progenitor cells undergo a similar process also in vivo.\t\n\nThe regenerative potential diminishes with age and this has been ascribed to functional impairments of adult stem cells.Cells in culture undergo senescence after a certain number of cell divisions whereby the cells enlarge and finally stop proliferation.This observation of replicative senescence has been extrapolated to somatic stem cells in vivo and might reflect the aging process of the whole organism.In this study we have analyzed the effect of aging on gene expression profiles of human mesenchymal stromal cells (MSC) and human hematopoietic progenitor cells (HPC).MSC were isolated from bone marrow of donors between 21 and 92 years old.67 genes were age-induced and 60 were age-repressed.HPC were isolated from cord blood or from mobilized peripheral blood of donors between 27 and 73 years and 432 genes were age-induced and 495 were age-repressed.The overlap of age-associated differential gene expression in HPC and MSC was moderate.However, it was striking that several age-related gene expression changes in both MSC and HPC were also differentially expressed upon replicative senescence of MSC in vitro.Especially genes involved in genomic integrity and regulation of transcription were age-repressed.Although telomerase activity and telomere length varied in HPC particularly from older donors, an age-dependent decline was not significant arguing against telomere exhaustion as being causal for the aging phenotype.These studies have demonstrated that aging causes gene expression changes in human MSC and HPC that vary between the two different cell types.Changes upon aging of MSC and HPC are related to those of replicative senescence of MSC in vitro and this indicates that our stem and progenitor cells undergo a similar process also in vivo.\tDiscussion\n\nThe deterioration of the regenerative potential upon aging might be due to functional changes in adult stem cells.To test this hypothesis we have investigated differential gene expression in primary, human MSC and HPC derived from different age groups.In this study, we demonstrate for the first time age-related gene expression changes in human MSC and HPC and that there is a moderate but significant concordance in the expression profiles upon aging in vivo and replicative senescence in vitro.It needs to be pointed out, that chronological age and biological age do not necessarily coincide.Multiparametric assessment of biological age might be valuable in this context.Furthermore, MSC and HPC preparations are heterogeneous and it is conceivable that they represent a mixture of different aged or senescent subsets.Further research will be necessary to address age-related changes on a single cell level to investigate the heterogeneity of aging within cell populations.activating complex, polypeptide 5 (SNAPC5) and peroxisome proliferator-activated receptor gamma (PPARG) were age-repressed.Furthermore, we have validated age associated changes in HPC for 9 genes (B): S100 calcium binding protein A10 (S100A10); vimentin (VIM); myeloid-associated differentiation marker (MYADM); pim-1 oncogene (PIM1) and annexin A2 (ANXA2) were age-induced.Timeless interacting protein (TIPIN); myosin regulatory light chain interacting protein (MYLIP); lymphocyte transmembrane adaptor 1 (LAX1) and Early growth response 1 (ERG1) were agerepressed.Protocadherin 9 (PCDH9) was not amplified in HPC from elderly donors whereas interleukine 7 receptor (IL7R) was not amplified in young samples (not presented in the figure).Differential gene expression was always calculated in relation to the mean of young samples.The mean foldratio (6SD) is demonstrated for median aged and old donor samples.RT-PCR results (red) were always in line with microarray data (blue) for all genes tested.doi:10.1371/journal.pone.0005846.g003", + "\tFor instance, mice null for the repair\nprotein Ercc1 show progressive marrow failure resulting in a pancytopenia, while the\nmice exhibit several symptoms of premature aging (Prasher, Lalai et al. 2005). However,\nno studies to date have demonstrated conclusively that diminished DNA repair capacity\nof HSCs with age results in their functional impairment, much less a decreased ability to\nrepair DNA lesions with age. 10\nGenetic regulation of stem cell proliferation\n\nThese many ramifications of the proliferative nature of hematopoietic stem cells\nbegs the question of what are the key molecules regulating this vital feature." + ], + [ + "\tHowever, under diabetic conditions, AGEs generated by the exposure of proteins and lipids\nto high glucose levels crosslink ECM proteins, impair ECM degradation by MMPs and\nincrease cardiac stiffness, which together manifest as early diastolic dysfunction33,5254. AGEs can also promote the differentiation of fibroblasts into myofibroblasts, which\nproliferate and induce ECM dyshomeostasis by secreting profibrotic cytokines and matrix\nproteins. Furthermore, the altered cardiac mechanics lead to the release of other stimuli\nincluding transforming growth factor- (TGF), tumour necrosis factor (TNF), angiotensin\nII and various interleukins, which activate profibrotic responses in fibroblasts and\nmyofibroblasts55.", + "\t\n\nMuch work has focused on molecular features often observed with advanced age-cellular senescence, autophagy, oxidative stress, and epigenetic changes.Vascular remodeling, as a consequence of these features, is well documented leading to endothelial dysfunction and arterial stiffness.Although such features are also invoked in other conditions such as heart failure with preserved ejection fraction and valvular calcification, disentangling the key causal features suitable for therapeutic modulation remains elusive.", + "\t\n\nNonenzymatic glycation of proteins and lipids occurs with aging, a process that is accelerated in the setting of glucose dysregulation, such as diabetes mellitus [7].Advanced glycation end products (AGEs) formation has been implicated in a number of pathological processes associated with micro-and macrovascular diabetic complications [8][9][10].It has been demonstrated that the effects of AGEs are partially mediated through their interactions with cell surface receptor, the receptor for advanced glycation end products (RAGE) [11].The soluble form of RAGE (sRAGE) is a proteolytic cleavage product of RAGE, which has AGE-binding property but lacks the signaling cascade [12].In Caucasians without T2DM, sRAGE has been associated with decreased renal function assessed by estimated glomerular filtration rate (eGFR) or serum creatinine level [13][14][15].In Caucasian T2DM patients, sRAGE has been associated with albuminuria [16], decreased eGFR [17] and new or worsening kidney diseases and mortality [18].However, to date, only two studies reported associations of sRAGE level with renal function in Asians with T2DM [19,20].Although sRAGE is increasingly gaining importance as a biomarker in diabetic complications, it is not clear how sRAGE level is regulated and why it varies among studies.In addition, genetic studies of sRAGE remain very limited.", + "\t\n\nAdvanced glycation end-products (AGE) are the result of nonenzymatic glycation, which produces heterogeneous bioactive molecules, such as lipids, proteins, and nucleic acids [59].The accumulation of AGEs in aged tissues leads to several processes, such as inflammation, obesity, apoptosis, and other adverse processes related to ageing [47].These AGEs are detected by various techniques, such as gas chromatography, high-performance liquid chromatography, spectrometry, and immunochemical technique [60], which make them robust biomarkers that can be analyzed by different methodologies.", + "\t\n\nCritical areas of vascular aging research include the role of senescence, epigenetics, stress resilience, inflammation, macromolecular damage, proteostasis, mitochondrial and metabolic dysfunction, and impaired stem cell biology.The specific roles for cell-autonomous and noncell-autonomous mechanisms contributing to vascular aging need to be elucidated further.The role of signal transduction pathways linked to regulation of cellular energetics in the vascular aging process should be better defined.Future studies should also lead to improved understanding of the role circadian clocks to vascular aging.New studies investigating cellular heterogeneity in vascular aging are warranted.Stochastic macromolecular damage leads to regional variability in the presence of senescent cells, cells with altered metabolism, mitochondrial dysfunction, and increased ROS production.Such regional variability likely contributes to the focal development of vascular pathologies, ranging from atherosclerotic plaques to microhemorrhages.Single-cell gene expression analysis should facilitate better understanding of the pathophysiological role of functional heterogeneity.Finally, how environmental factors and lifestyle choice impact the vascular aging processes should be better understood.", + "\t\n\nThe characteristics of the second pathway include the formation of advanced glycation end-products (AGEs) from excessive imbibing of glucose [7].The AGEs via interaction with their receptor, RAGE, transduce a complex series of signaling events that result in cellular dysfunctions, thus generating an inflammatory response and reactive oxygen species (ROS), which in turn cause oxidative stress [7].Both in vitro and in vivo studies support the relevance of this pathway in the pathogenesis of diabetic nephropathy [7].The fact that several inhibitors of AGEs, such as pyridoxamine, LR-90 and KIOM-79, have been demonstrated to be beneficial in various murine models of diabetes emphasizes the role of AGE:RAGE interactions [8][9][10].Although these inhibitors may be effective in murine models, their efficacy certainly needs to be evaluated in diabetic nephropathy in humans.", + "\tAging is only, in part, the result of oxidative, free radical chemistry\n\nThe free radical theory of aging (Harman 1992) proposes that reactive oxygen is the major culprit in aging, leading to age-dependent oxidative modification, crosslinking and denaturation of proteins, with resultant loss of protein and enzyme structure and function.This theory has been expanded in recent years to include not only direct oxidation of proteins by reactive oxygen, but also the modification of proteins by Maillard reaction products, AGEs and ALEs (Thorpe and Baynes 1996).The majority of AGEs that are known to accumulate with age in tissue proteins are glycoxidation products, formed by combined glycation and oxidation reactions of precursors, such as glucose or ascorbate (Baynes 1991).In non-diabetic patients, levels of the glycoxidation products CML and pentosidine correlate with levels of methionine sulfoxide and o-tyrosine in skin collagen, indicating that these products are formed in parallel with one another (Wells-Knecht et al. 1997).Although oxidation appears to be important in the formation of AGEs and crosslinking of protein by glucose and ascorbate (Fu et al. 1994), some AGEs, such as pyrraline and crosslines, are formed non-oxidatively from glucose.The crosslines increase in lens proteins with age (Obayashi et al. 1996), so that oxidation is not essential for an age-dependent increase in crosslinking of protein by carbohydrates.In contrast to AGEs, ALEs require oxidative conditions for their formation -the first intermediate in ALE formation is a lipid peroxide, formed from a polyunsaturated fatty acid (PUFA) by an enzymatic or non-enzymatic autoxidation reaction involving molecular oxygen.The EAGLEs, CEL and MOLD, increase with age in collagen and crystallins, but cannot be classified as oxidative or nonoxidative since they may be formed either oxidatively during peroxidation of PUFA (Fu et al. 1996) or non-oxidatively from glyceraldehyde 3-phosphate or dihydroxyacetone phosphate formed during anaerobic glycolysis (Ahmed et al. 1997).Other modifications of amino acids, including deamidation, racemization and formation of hydroxykynurenine adducts are also age-dependent, non-crosslinking modifications of proteins.\tAging may be accelerated by inflammation and disease\n\nThe relationship between aging and age-related, chronic disease is complex.Healthy aging generally leads to a longer life, while chronic disease and associated inflammatory processes generally accelerate the aging process, i.e. shorten life span.The relationship between aging and chronic disease may be illustrated by diabetes, a disease in which the accumulation of AGEs in tissue proteins is accelerated by hyperglycemia.CML and pentosidine are biomarkers of normal aging of tissue collagens, and their accelerated accumulation in collagen in diabetes is de facto evidence that diabetes is a disease characterized by accelerated aging of collagen (Dyer et al. 1993).The acceleration of protein aging in diabetes is apparent, not only by the increase in AGEs, but also by increases in browning and fluorescence of collagen, and decreased solubility, decreased elasticity and increased thickness of basement membranes in diabetes (Baynes and Thorpe 1999).Notably, the rates of accumulation of other biomarkers, such as o-tyrosine and methionine sulfoxide in skin collagen, do not change significantly in diabetes (Wells-Knecht et al. 1997).Thus, the acceleration of chemical aging of collagen in diabetes is unbalanced or 'pathologic' in nature, apparently driven by the increase in circulating levels of oxidizable substrates (carbohydrates and lipids) (Baynes 1991(Baynes , 1999;;Baynes and Thorpe 1999a, b), rather than an increase in oxidative stress.Diabetes also increases the risk for cardiovascular disease, the major cause of mortality in the western world, while the increased risk for cataracts in diabetes may result from increases in both glycation and oxidative stress in the lens (Stevens 1998).", + "\tMG is elevated in the diabetic state and is\nthought to contribute to the development of diabetic complications, particularly through the\nformation of AGEs (60). AGE modification of vascular extracellular matrix proteins causes\n\nW\n\ncross-linking, which alters elastic properties and traps low-density lipoprotein in the vessel wall\n(60). Upon ligating RAGE, AGEs cause endothelial dysfunction, activation of NF-B, release of\n\nIE\n\npro-inflammatory molecules, and formation of vessel-damaging ROS (60). Through detoxifying\nMG, GLO1 is thought to protect against diabetic complications.", + "\tIt is based on the tendency of glucose to\nundergo oxydation in the presence of traces of heavy metal\nions, thus creating reactive ketoaldehydes, hydrogen peroxyde, and free radicals. It is clear now that the rearrangement of Schiff bases, Amadori products and/or AGEs is\naccompanied by generation of reactive oxygen species that\ncause conformational changes and fragmentation of the\nglycated proteins (11, 12). The proteins modified by AGEs\nare shown to be toxic, immunogenic, and capable of triggering cellular injury responses after binding to specific\nreceptors (1315).\tTaking into consideration that glycation is a slow process, it has always been regarded as typical for the longliving organisms and as affecting the long-living proteins\n(haemoglobin, crystalline, etc.)only. Surprisingly, our\nrecent studies indicated that glycation takes place also in\nE. coli and affects both the host bacterial and recombinant\nproteins (16, 17). Once started in vivo, glycation can not\nbe stopped after isolation and purification of the protein. Accumulation of AGEs continues even when pure protein preparations are stored in deep frozen solutions. A\ngreat number of studies have been dedicated to the search\nfor inhibitors of glycation.\tMullarkey CJ, Edelstein D, Brownlee M (1990) Free radical generation by early glycation products: a mechanism for accelerated atherogenesis in diabetes. Biochem Biophys Res Commun\n173:932939. Sakurai T, Tsuchiya S (1988) Superoxide production from nonenzymatically glycated protein. FEBS Lett 236:406410\nWendt T, Tanji N, Guo J, Hudson BI, Bierhaus A, Ramasamy R,\nArnold B, Nawroth PP, Yan SF, DAgati V, Schmidt AM (2003)\nGlucose, glycation, and RAGE: implications for amplification of\ncellular dysfunction in diabetic nephropathy. J Am Soc Nephrol\n14:13831395. Wautier JL, Schmidt AM (2004) Protein glycation: a firm link to\nendothelial cell dysfunction. Circ Res 95:233238.", + "\t\n\nFigure 15: Aspects of hyperglycemia-related vascular cell dysfunction.Hyperglycemia-induces a range of pathways in cells such as endothelium, and these include the polyol pathway, reactive oxygen species (ROS) formation, and advanced glycation endproducts (AGEs) formation.Excess glucose in endothelial cells enters polyol pathway; the electron donors like reduced nicotinamide adenine dinucleotide (NADH) and Flavin adenine dinucleotide (FADH2) accumulate in the mitochondria, thus affecting the electron transport chain; the excess electrons increase ROS in mitochondria; ROS triggers accumulation of AGEs; ROS and AGEs create mitochondrial DNA damage and mitochondrial dysfunction; protein kinase C (PKC) and AGE mediated activation of nuclear factor kappa B (NFB) activate the expression of inflammation proteins, tumor suppressor p53, and inducible nitric oxide synthase (iNOS); increased nitric oxide (NO) by iNOS is highly reactive with superoxide anions; the peroxynitrite thus generated acts as a strong oxidant and completes the vicious cycle of oxidative stress by increasing ROS production; accumulation of AGEs also increases ROS production independent of glucose levels\tM A N U S C R I P T A C C E P T E D ACCEPTED MANUSCRIPT 50\n\nglycation and lipoxidation end-products and upregulation of the receptor for AGEs (RAGE) has a key role in the hyperglycemia-induced activation of Mller glia and downstream cytokine production in the context of diabetic retinopathy (Berner et al., 2012;Curtis et al., 2011;Yong et al., 2010;Zong et al., 2010).Diabetes has also been reported to accelerate death of Mller glia (Feenstra et al., 2013;Hammes et al., 1995), an effect which has recently been linked to the disruption of retinal vascular integrity and the induction of neural cell dysfunction and death (Shen et al., 2012).A schematic diagram summarising how Mller glia changes are believed to contribute to the sight threatening complications of diabetic retinopathy is presented in Figure 11.Apart from the Mller cells, activated microglial cells adjacent to the vessels also appear to have a key role in vasoregression, the vascular hallmark of the early stages of diabetic retinopathy in both animal models (McVicar et al., 2015) and diabetic patients (Scott et al., 2014b).", + "\tTaking into consideration that glycation is a slow process, it has always been regarded as typical for the longliving organisms and as affecting the long-living proteins\n(haemoglobin, crystalline, etc.)only. Surprisingly, our\nrecent studies indicated that glycation takes place also in\nE. coli and affects both the host bacterial and recombinant\nproteins (16, 17). Once started in vivo, glycation can not\nbe stopped after isolation and purification of the protein. Accumulation of AGEs continues even when pure protein preparations are stored in deep frozen solutions. A\ngreat number of studies have been dedicated to the search\nfor inhibitors of glycation.\tMullarkey CJ, Edelstein D, Brownlee M (1990) Free radical generation by early glycation products: a mechanism for accelerated atherogenesis in diabetes. Biochem Biophys Res Commun\n173:932939. Sakurai T, Tsuchiya S (1988) Superoxide production from nonenzymatically glycated protein. FEBS Lett 236:406410\nWendt T, Tanji N, Guo J, Hudson BI, Bierhaus A, Ramasamy R,\nArnold B, Nawroth PP, Yan SF, DAgati V, Schmidt AM (2003)\nGlucose, glycation, and RAGE: implications for amplification of\ncellular dysfunction in diabetic nephropathy. J Am Soc Nephrol\n14:13831395. Wautier JL, Schmidt AM (2004) Protein glycation: a firm link to\nendothelial cell dysfunction. Circ Res 95:233238.\tIt is based on the tendency of glucose to\nundergo oxydation in the presence of traces of heavy metal\nions, thus creating reactive ketoaldehydes, hydrogen peroxyde, and free radicals. It is clear now that the rearrangement of Schiff bases, Amadori products and/or AGEs is\naccompanied by generation of reactive oxygen species that\ncause conformational changes and fragmentation of the\nglycated proteins (11, 12). The proteins modified by AGEs\nare shown to be toxic, immunogenic, and capable of triggering cellular injury responses after binding to specific\nreceptors (1315).", + "\tVascular endothelial dysfunction. In diabetes, endothelial dysfunction is linked to the accumulation of toxic lipids 90 , AGEs 91 and/or aggregated proteins 59 in the vasculature.Proteinaceous deposition on blood vessel walls damages endothelial cells 59,91 , increases the production of reactive oxygen species (ROS) 92,93 and impairs production of vasodilatory substances 92 , which results in a reduced cerebral blood flow.Stalled blood flow can lead to neurovascular uncoupling and hypoxic neuronal injury [92][93][94] .Elevated ROS production can further damage cellular structures and activate matrix metalloproteinases, inducing cytoskeletal reorganization and vascular remodelling 93 .Cytoskeletal reorganization affects the stability of tight junction proteins, resulting in increased capillary permeability, depletion of energy resources and altered neural viability 92,93 .", + "\t\n\nAdvanced glycation end products (AGEs) are a heterogeneous group of macromolecules that are formed by the nonenzymatic glycation of proteins, lipids, and nucleic acids.Overproduction of AGEs is considered the most important pathophysiological mechanism that induces diabetic complications (Semba et al. 2010).On one hand, AGEs mediate intracellular glycation of mitochondrial respiratory chain proteins and increase ROS levels, thus triggering oxidative stress (Coughlan et al. 2009) and endoplasmic reticulum stress (Piperi et al. 2012).On the other hand, binding of AGEs with receptors for advanced glycation end products (RAGEs) activates the AGE signalling axis to induce activation of NF-KB signalling and JAK/STAT signalling, which upregulate inflammatory cytokines and adhesion molecules (Basta 2008;Basta et al. 2004).The evidence indicates that exposure to AGEs is connected with the risk of adverse ageing-related outcomes.Akt1, Bsk, and P38b have been found to be crucial in the regulation of the AGE-RAGE-signalling pathway.Transforming growth factor beta (TGF-beta) is a major growth factor in joints that is crucial in maintaining chondrocyte homeostasis.However, the TGF-beta-signalling pathway changes with ageing, resulting in an age-related decline in the anabolic response that favours hypertrophy of chondrocytes and the development of osteoarthritis (Baug et al. 2014).In addition, Upadhyay et al. also reviewed the important role of TGF in the developmental processes of D. melanogaster and the role of TGF in regulating hormones, neurons and innate immunity (Upadhyay et al. 2017).Therefore, ageing-induced TGF-beta dysregulation is associated with deleterious effects on longevity and ageing itself.Dpp, Mad, and S6k are functionally crucial in the TGF-beta-signalling pathway.", + "\tIntroduction\n\nIn individuals with diabetes, nonenzymatic glycation of proteins leads to the formation of advanced glycation end products (AGE) and this process occurs at an accelerated rate in chronic hyperglycaemia 1 , and also the levels are found to be increased in complications of diabetes, such as diabetic retinopathy (DR). 2 AGE induces a variety of pathological changes, such as increased basement membrane thickening, arterial stiffness, and glomerular sclerosis. 3,4AGEs bind to a specific receptor known as receptor for advanced glycation end products (RAGE).RAGE is expressed in many of the cell types, such as the endothelial cells, monocytes, and lymphocytes, including the beta cells of the pancreas.RAGE-mediated signaling leads to the activation of transcription factors, such as NF-kB, AP-1, and STAT-1, 5,6 the adhesion molecules VCAM, ICAM, and tissue factor, 7,8 which promote a procoagulant state in the microcapillaries of the retina.This results in a hypoxic state that leads to the initiation of the angiogenic process in proliferative DR." + ] + ], + "task_id": [ + { + "task_id": "A05D259409652DBA4BBB171E44BC0E4A" + }, + { + "task_id": "92D5CE6EE0709DACC5A0B1DAFC050200" + }, + { + "task_id": "82159196857E23B681446BAEAD1E37B8" + }, + { + "task_id": "62833A83C24DBF2F02AB95C0D6E00814" + }, + { + "task_id": "0BF2D6A0BF2A7B5B35D42D578BF25E9E" + } + ] +}
\ No newline at end of file |