Biology of Aging

Adult stem cells, or somatic stem cells, are undifferentiated cells residing in specific tissue niches that maintain and repair the tissue throughout life. Examples include hematopoietic, mesenchymal, intestinal, and neural stem cells. They are typically multipotent, generating the cell types of their tissue of origin. Their decline with age underlies stem cell exhaustion, making their preservation and rejuvenation a primary goal of longevity and regenerative medicine.

Advanced glycation end-products are stable, often crosslinked compounds formed when sugars react with proteins, lipids, or DNA over time. They accumulate in long-lived tissues such as skin, cartilage, and arterial walls, where they impair elasticity and function. AGEs activate the RAGE receptor, triggering inflammation and oxidative stress. Their build-up is linked to diabetes complications, atherosclerosis, kidney disease, and skin ageing.

The AGE-RAGE axis describes signalling initiated when advanced glycation end products (AGEs) and other endogenous ligands engage RAGE, a multiligand immunoglobulin-superfamily receptor encoded by the AGER gene. Besides AGEs, RAGE binds S100/calgranulin proteins, HMGB1, amyloid-beta peptides and certain beta-sheet fibrils. Ligand binding activates intracellular cascades involving NADPH oxidase, MAP kinases and NF-kB, leading to sustained pro-inflammatory and pro-oxidant gene expression in endothelial cells, vascular smooth muscle cells, macrophages and neurons. NF-kB also upregulates RAGE itself, generating a feed-forward loop. The axis is implicated in diabetic vascular complications, atherosclerosis, chronic kidney disease and neurodegeneration, and is regarded as one mechanistic bridge between hyperglycaemia, oxidative stress and chronic low-grade inflammation associated with biological ageing.

AMPK (AMP-activated protein kinase) is a cellular energy sensor activated when AMP and/or ADP relative to ATP rise, signaling low energy availability. Once active, it stimulates catabolic pathways like fatty acid oxidation and autophagy while inhibiting anabolic processes such as mTORC1-driven protein synthesis. AMPK activation mimics aspects of caloric restriction, and age-related changes in AMPK signaling can contribute to impaired metabolic regulation. Metformin and exercise are well-known indirect AMPK activators.

Apoptosis is a tightly regulated form of programmed cell death in which cells are dismantled in an orderly fashion via caspase activation, typically without triggering inflammation as it is non-lytic and anti-inflammatory relative to necrosis or pyroptosis. It eliminates damaged, infected, or surplus cells and is essential for development, tissue homeostasis, and tumor suppression. Tissue- and context-specific changes in apoptosis with age contribute to impaired clearance of damaged or senescent cells in some tissues and to atrophy and neurodegeneration in others.

Autophagy is a conserved lysosomal degradation pathway in which cells engulf damaged organelles, misfolded proteins, and other cytoplasmic material in double-membrane vesicles called autophagosomes for recycling (a process most precisely describing macroautophagy, the dominant subtype). By clearing dysfunctional components and recycling amino acids during nutrient stress, it maintains cellular homeostasis. Declining autophagic flux is widely observed with age, though the magnitude is tissue- and context-dependent, and its induction by fasting, exercise, and rapamycin is considered one of the major proposed longevity mechanisms.

Beclin-1 (encoded by BECN1) is a core component of the class III phosphatidylinositol 3-kinase (PI3K-III / VPS34) complex that nucleates phagophore membranes at the initiation step of macroautophagy, with its activity regulated by interactions with BCL-2 family proteins, UVRAG, and Rubicon. The broader ATG (AuTophaGy-related) gene family — comprising approximately 40 genes in yeast with conserved mammalian orthologues — encodes the machinery for phagophore elongation (ATG5, ATG12, ATG16L1), membrane lipidation (ATG7, ATG3), and closure (ATG2, ATG9). Beclin-1 is monoallelically deleted in many breast and ovarian cancers, implicating autophagy in tumour suppression, while global decline in Becn1 and other ATG gene expression in ageing tissues is proposed to contribute to the deterioration of autophagic flux observed with age.

Cathepsins are a family of lysosomal proteases — predominantly cysteine proteases (cathepsins B, C, H, K, L, S, V, X/Z) but also aspartyl (cathepsins D, E) and serine types (cathepsins A, G) — that collectively execute the terminal degradation of proteins delivered by autophagy, endocytosis, and phagocytosis in the acidic lysosomal lumen. Beyond lysosomal digestion, cathepsins can be secreted to remodel the extracellular matrix (cathepsin K is the primary bone collagenase), and cytosolic leakage of cathepsins — particularly cathepsin B — can trigger the NLRP3 inflammasome and initiate apoptosis, a pathway termed lysosomal membrane permeabilisation. Cathepsin activity declines with ageing in part due to impaired lysosomal acidification and altered cystatin inhibitor balance, impairing protein quality control and contributing to accumulation of undegraded material in long-lived post-mitotic cells such as neurons.

CD38 is a transmembrane glycoprotein with NAD+ glycohydrolase and ADP-ribosyl cyclase activity, expressed broadly but most abundantly on immune cells. It hydrolyses NAD+ to nicotinamide and ADP-ribose and can also generate cyclic ADP-ribose and NAADP, second messengers for calcium signalling. CD38 expression and activity rise with age, particularly in tissue-resident macrophages and other innate immune cells, where senescent cells and their secretome help drive its induction. Because CD38 is a dominant NAD+-consuming enzyme in many tissues, this age-related upregulation is a major mechanism behind systemic NAD+ decline and the associated drop in sirtuin activity and mitochondrial function. Genetic or pharmacological inhibition of CD38, for example with the selective inhibitor 78c, restores tissue NAD+ levels and improves metabolic phenotypes in aged mice.

Cellular reprogramming is the experimental conversion of one cell type into another, most often a differentiated somatic cell into a pluripotent stem cell, by forcing expression of specific transcription factors known as OSKM (Oct4, Sox2, Klf4, and c-Myc). The process resets the epigenome, including DNA methylation and histone marks; however, it is partial or cyclic reprogramming — rather than full iPSC induction — that is being explored as a route to rejuvenation, since complete reprogramming erases cell identity. It underpins iPSC technology and is being examined as a strategy for organ regeneration and systemic rejuvenation.

Cellular senescence is a stable cell-cycle arrest triggered by stressors such as DNA damage, telomere dysfunction, oncogene activation or oxidative stress. Senescent cells remain metabolically active and typically secrete a pro-inflammatory mixture of cytokines, chemokines and proteases known as the SASP. While senescence initially suppresses tumour formation and aids wound healing, the accumulation of senescent cells with age contributes to tissue dysfunction and age-related disease.

The cGAS-STING pathway is an innate immune sensing mechanism in which cyclic GMP-AMP synthase (cGAS) detects cytosolic double-stranded DNA — a signal of viral infection, nuclear damage or mitochondrial DNA leakage — and synthesises the second messenger cGAMP, which activates the endoplasmic-reticulum adaptor protein STING (stimulator of interferon genes). STING then drives transcription of type-I interferons and pro-inflammatory NF-κB target genes, generating a potent immune response. In the context of ageing, the pathway is aberrantly activated by micronuclei, cytoplasmic chromatin fragments from ruptured senescent-cell nuclear envelopes, and leaked mitochondrial DNA, making cGAS-STING a key amplifier of inflammaging and the SASP; pharmacological STING inhibitors are under early investigation as potential modulators of age-related inflammation.

Chromatin is the complex of DNA, histones, and associated proteins that packages the genome inside the nucleus. Its basic unit, the nucleosome, can be tightly compacted as heterochromatin or loosely arranged as euchromatin, controlling which genes are accessible for transcription. Chromatin organisation safeguards genomic stability and cellular identity. Loss of heterochromatin and disorganised chromatin architecture are recognised hallmarks of ageing and contribute to cellular dysfunction.

Cuproptosis is a copper-dependent form of regulated cell death that is mechanistically distinct from apoptosis, ferroptosis, necroptosis and pyroptosis. When intracellular copper rises beyond the buffering capacity of chaperones such as ATOX1 and CCS, copper ions directly bind lipoylated components of the mitochondrial tricarboxylic acid (TCA) cycle, most notably dihydrolipoamide S-acetyltransferase (DLAT), and trigger their aggregation. This is accompanied by loss of iron-sulfur cluster proteins, leading to proteotoxic stress, mitochondrial dysfunction and cell death. The mitochondrial reductase FDX1 is required for protein lipoylation and acts as a key upstream regulator of cuproptosis. Cells with active oxidative phosphorylation and high lipoylated-protein content are particularly sensitive. Cuproptosis has attracted interest as a potential therapeutic vulnerability in copper-handling-altered cancers and is relevant to metabolic and neurodegenerative contexts.

DNA damage refers to chemical or structural alterations of the genome, including base modifications, single- and double-strand breaks, and crosslinks. It arises from reactive oxygen species, ionising radiation, UV light, and replication stress. Cells respond through DNA damage repair pathways; when overwhelmed, damage triggers senescence, apoptosis, or mutations. Genomic instability driven by accumulated DNA damage is a recognised hallmark of ageing and a cancer driver.

DNA methylation is an epigenetic modification in which methyl groups are added to cytosine bases, predominantly at CpG sites, by DNA methyltransferases. It regulates gene expression, X-inactivation, and genome stability without altering the underlying sequence. Methylation patterns shift predictably with age, forming the basis of epigenetic clocks such as Horvath's. Aberrant methylation contributes to cancer, immune dysfunction, and the broader epigenetic drift seen in ageing.

DNA methyltransferases (DNMTs) catalyse the transfer of a methyl group from S-adenosylmethionine to the 5-carbon of cytosine, primarily at CpG dinucleotides. In mammals, three catalytically active enzymes dominate. DNMT1, in cooperation with UHRF1, recognises hemi-methylated CpGs at the replication fork and copies parental methylation onto the nascent strand, providing maintenance methylation. DNMT3A and DNMT3B establish new methylation patterns during development and in adult stem cells (de novo methylation), with the accessory protein DNMT3L supporting activity in the germline. DNA methylation patterns shape gene expression, X-chromosome inactivation, imprinting and silencing of transposable elements. With ageing, methylation drift accumulates, and somatic DNMT3A loss-of-function mutations are a leading driver of clonal haematopoiesis, contributing to age-related disease.

Elastin is the extracellular matrix protein that confers recoil and elastic compliance to tissues under cyclical mechanical stress, particularly arterial walls, lungs, and skin; it is deposited almost exclusively during foetal and early postnatal development, and its half-life is estimated to exceed 70 years in humans, making post-synthetic preservation critical. With ageing, elastin fibres undergo progressive fragmentation driven by serine proteases (neutrophil elastase), cathepsins (cathepsin K, L), and matrix metalloproteinases (MMP-2, MMP-9, MMP-12), accompanied by loss of the microfibrillar scaffold of fibrillin-1 required for elastin assembly and repair. Accumulated elastin-derived peptides act as bioactive fragments that engage the elastin-binding protein (EBP) receptor to promote inflammation and MMP secretion, creating a pro-degradative feedback loop implicated in pulmonary emphysema, aortic aneurysm formation, and cutaneous ageing.

Epigenetic alterations are age-related changes in DNA methylation patterns, histone modifications, chromatin architecture and non-coding RNA expression that occur without changes to the underlying DNA sequence. With age, the epigenome typically shows global hypomethylation alongside focal hypermethylation, loss of heterochromatin and altered transcription. These shifts underpin epigenetic clocks: first-generation chronological-age estimators such as the Horvath clock, and second-generation clocks like PhenoAge and GrimAge that predict mortality and disease risk above and beyond chronological age.

Endoplasmic reticulum (ER) stress arises when the capacity of the ER to fold, modify, and quality-control secretory and membrane proteins is exceeded by the demand — triggered by misfolded protein accumulation, calcium depletion, lipid bilayer disequilibrium, or viral infection. Three ER-resident sensors — IRE1alpha, PERK, and ATF6 — detect luminal stress and activate the unfolded protein response (UPR) to restore ER homeostasis by attenuating global translation, upregulating chaperones, and expanding the ER. Chronic, unresolved ER stress, which increases with ageing due to diminished chaperone capacity and accumulated misfolded proteins, shifts UPR signalling toward pro-apoptotic and pro-inflammatory outputs, contributing to beta-cell loss in type 2 diabetes, neurodegeneration, and atherosclerosis.

The extracellular matrix (ECM) is the protein and proteoglycan scaffold that provides structural support and transmits biochemical and mechanical signals to resident cells; with age, it undergoes progressive stiffening, fragmentation, and compositional remodelling driven by accumulated crosslinks, glycation end-products, reduced matrix turnover, and dysregulated matrix metalloproteinase (MMP) and tissue inhibitor of metalloproteinase (TIMP) balance. ECM stiffening alters integrin-mediated mechanosignalling, promotes pro-fibrotic TGF-beta pathways, and has been shown to reinforce the SASP of senescent cells in a feed-forward loop. These changes impair tissue repair, compromise stem cell niches, and contribute to pathologies including cardiac fibrosis, osteoarthritis, and age-related pulmonary decline, making ECM integrity an emerging target for longevity-focused interventions.

Extracellular vesicles (EVs) are membrane-bound particles released by virtually all cell types and conventionally classified into exosomes (30–150 nm, endosomal origin via multivesicular bodies), microvesicles (100–1000 nm, direct plasma membrane budding), and apoptotic bodies (>1000 nm); MISEV2018/2023 guidelines recommend defining EVs operationally by physical properties (e.g., 'small EVs') unless biogenesis is directly demonstrated; they carry bioactive cargo including proteins, lipids, mRNA, microRNA, and DNA that can reprogram recipient cells upon uptake. EVs serve as key mediators of intercellular communication and are upregulated by senescent cells as part of the SASP, with aged plasma showing a distinct EV proteome and miRNA content that can accelerate senescence and inflammation when transferred to younger organisms in parabiosis-inspired experiments. Concurrently, EVs derived from young or stem cell sources are investigated as candidate therapeutic agents in regenerative medicine, with studies reporting improvements in muscle, cardiac, and cognitive function in aged rodent models, though mechanisms of selectivity and in vivo dosing remain areas of active investigation.

Ferroptosis is a form of regulated cell death driven by iron-dependent accumulation of lipid peroxides to lethal levels, distinguishing it mechanistically from apoptosis, necroptosis and pyroptosis. The key regulatory node is glutathione peroxidase 4 (GPX4), which uses the antioxidant glutathione to reduce phospholipid hydroperoxides; when GPX4 activity is insufficient — due to glutathione depletion, GPX4 inhibition or excess labile iron — unreduced lipid peroxides propagate chain reactions that disrupt membrane integrity. Ferroptosis has been implicated in neurodegeneration, ischaemia-reperfusion injury and cancer cell death, and its relevance to tissue ageing is an active area of research, particularly in the context of declining GPX4 expression and iron accumulation observed with age.

FGF21 (fibroblast growth factor 21) is an endocrine member of the FGF superfamily secreted primarily by the liver in response to fasting, dietary protein restriction, and mitochondrial stress, acting on target tissues through FGFR1c/β-Klotho co-receptor complexes. It promotes fatty acid oxidation, ketogenesis, and insulin sensitisation, and suppresses growth hormone/IGF-1 axis activity. Transgenic mice overexpressing FGF21 show substantially extended median lifespan (Zhang 2012, ~30% in males and ~39% in females) with improvements in metabolic health and adiposity, while elevated circulating FGF21 in humans is paradoxically associated with metabolic disease and frailty, likely reflecting compensatory induction in states of metabolic stress rather than a direct pro-ageing role. Pharmacological FGF21 analogues are in clinical development for metabolic liver disease.

Fibrosis is the pathological excess deposition of extracellular matrix — predominantly fibrillar collagens type I and III — by activated myofibroblasts in response to chronic injury, inflammation, or senescent-cell SASP signalling, replacing normal parenchymal cells with a stiff, poorly vascularised scar. TGF-beta1 is the dominant pro-fibrotic cytokine, signalling through SMAD2/3 to transcriptionally activate collagen synthesis, suppress MMPs, and drive fibroblast-to-myofibroblast differentiation; IL-11, PDGF, and connective tissue growth factor (CTGF/CCN2) cooperate in a context-dependent manner. Age markedly increases fibrotic susceptibility because impaired senescent cell clearance sustains TGF-beta and SASP output, macrophage polarisation shifts toward pro-fibrotic M2 phenotypes, and regenerative responses become dysregulated, making liver cirrhosis, idiopathic pulmonary fibrosis, and cardiac fibrosis major determinants of age-related organ failure.

FOXO transcription factors (Forkhead box O) are downstream effectors of the insulin/IGF-1 pathway that regulate genes governing stress resistance, DNA repair, autophagy, and antioxidant defense. When insulin/IGF-1 signaling is low, FOXO enters the nucleus and activates protective transcriptional programs. FOXO3 variants are among the most reproducibly associated genetic markers of human exceptional longevity, observed across centenarian cohorts in multiple ethnicities.

Free radicals are atoms or molecules carrying one or more unpaired electrons, which makes them highly reactive. They arise from normal metabolism, immune activity, and external sources such as UV radiation, pollution, and tobacco smoke. By stealing electrons from neighbouring molecules, free radicals damage membranes, enzymes, and DNA. The free-radical theory of ageing posits that this cumulative damage contributes to functional decline and age-related disease; though historically influential, the theory is now considered an incomplete account of ageing, as supplemental antioxidants have not reliably extended lifespan in animal trials or human RCTs, and reactive oxygen species are increasingly recognised as signalling molecules as well as damaging agents.

GDF11 (growth differentiation factor 11) is a TGF-β superfamily ligand that plays an established role in axial patterning and organogenesis during embryonic development by signalling through activin type II receptors and SMAD2/3 transcription factors. Its role in adult ageing attracted intense interest following 2013–2014 parabiosis studies that reported circulating GDF11 levels decline with age and that supplementation reversed features of cardiac hypertrophy and muscle and brain ageing in mice; however, subsequent work raised significant questions about assay specificity, with some studies finding GDF11 levels actually increase with age, and others failing to replicate the rejuvenating effects. The current consensus is that GDF11's role as a systemic pro-youthful factor in adult mammals remains unresolved and contested, pending studies with validated, isoform-specific assays.

GDF15 (growth differentiation factor 15), also known as MIC-1, is a divergent TGF-β superfamily member that is expressed at low levels under homeostatic conditions but is strongly induced by mitochondrial stress, DNA damage, inflammation, and diverse cellular stressors. It signals through a dedicated receptor complex comprising GFRAL and RET in the hindbrain to suppress appetite and reduce body weight, a mechanism relevant to cancer cachexia and the metabolic effects of drugs such as metformin, which robustly elevates GDF15. Circulating GDF15 rises with age and is associated with markers of frailty, cardiovascular disease, and all-cause mortality; it is increasingly studied as a biomarker of mitochondrial stress and biological age, though its net role — detrimental stress signal or adaptive mediator — depends heavily on context.

Genomic instability is the progressive accumulation of damage to nuclear and mitochondrial DNA, including point mutations, chromosomal rearrangements, copy-number changes and retrotransposon activation. It arises from endogenous sources such as replication errors and reactive oxygen species as well as exogenous insults like UV light and toxins, and is exacerbated by declining DNA-repair capacity. As one of the primary hallmarks of ageing, it drives clonal expansion, cancer risk and tissue dysfunction.

Glutathione (GSH) is the most abundant intracellular low-molecular-weight thiol, synthesised in two ATP-dependent steps from glutamate, cysteine, and glycine by glutamate-cysteine ligase (GCL) and glutathione synthetase. It serves as a substrate for glutathione peroxidases (GPx) that neutralise hydrogen peroxide and lipid hydroperoxides, is conjugated to electrophilic toxins by glutathione S-transferases, and maintains the thiol-redox status of proteins. Total GSH declines with ageing in most tissues, due in part to reduced biosynthesis and increased oxidative load, and low GSH:GSSG (oxidised glutathione) ratios are associated with accelerated cellular senescence and disease risk; N-acetylcysteine and glycine supplementation are being evaluated as strategies to restore GSH levels in older adults.

Glycation is the non-enzymatic attachment of sugars such as glucose or fructose to proteins, lipids, or nucleic acids. Through the Maillard reaction it generates unstable Schiff bases, then Amadori products, and ultimately advanced glycation end-products. Glycation stiffens collagen, impairs enzyme activity, and disrupts cell signalling. Driven primarily by hyperglycaemia and elevated glycaemic load, it accelerates skin ageing, vascular stiffening, and diabetic complications.

The Hallmarks of Aging are a set of interconnected biological processes proposed by López-Otín and colleagues to describe the molecular and cellular drivers of ageing. The 2023 update lists twelve hallmarks, including genomic instability, telomere attrition, epigenetic alterations, loss of proteostasis, deregulated nutrient sensing, mitochondrial dysfunction, cellular senescence, stem cell exhaustion, altered intercellular communication, disabled macroautophagy, chronic inflammation and dysbiosis. They serve as the dominant framework for longevity research and intervention design.

The Hayflick limit is the maximum number of times a normal human somatic cell can divide in culture, typically 40 to 60 times, before entering replicative senescence. Discovered by Leonard Hayflick in 1961, the limit is mechanistically explained by progressive telomere shortening with each division. It established that aging has a cell-intrinsic component and remains a foundational concept linking cellular replication, telomere biology, and organismal aging.

Heat shock proteins (HSPs) are a family of highly conserved molecular chaperones, named for their induction by heat but active under many forms of stress. They assist protein folding, prevent aggregation, attempt to refold denatured proteins when possible, and route irreparable ones for degradation. HSPs such as HSP70 and HSP90 are central to proteostasis, and HSP induction by exercise and heat exposure (including sauna) is studied as one contributing mechanism among many for their health effects.

Haematopoietic stem cells (HSCs) are rare, multipotent progenitors residing primarily in the bone marrow that sustain lifelong blood cell production through asymmetric self-renewal divisions and hierarchical differentiation into all lymphoid and myeloid lineages. With ageing, the HSC pool expands numerically but deteriorates functionally: aged HSCs show myeloid-biased output at the expense of lymphopoiesis, reduced engraftment efficiency, increased DNA damage, altered epigenetic landscapes, and mitochondrial dysfunction. Clonal haematopoiesis — the age-associated expansion of HSC clones carrying somatic mutations in epigenetic regulators such as DNMT3A, TET2, and ASXL1 — is present in approximately 10% of individuals over 70 with conventional sequencing depth (and substantially more on deep sequencing) and confers elevated risk of haematological malignancy, cardiovascular disease, and all-cause mortality, establishing HSC ageing as a direct contributor to systemic health decline.

Heterochromatin is the condensed, transcriptionally repressed fraction of chromatin marked by histone modifications such as H3K9me2/3 and H3K27me3, and maintained by factors including HP1 proteins, the polycomb repressive complexes and DNA methylation; it silences repetitive elements, maintains genome stability and enforces cell-type-specific gene expression patterns. With age, heterochromatin — particularly constitutive heterochromatin at pericentromeric and telomeric regions — undergoes progressive loss and spatial reorganisation, a process associated with de-repression of retrotransposons, ectopic gene expression and genomic instability. Lamin A dysfunction, HDAC sirtuin decline and the epigenetic drift captured by DNA methylation clocks all converge mechanistically on heterochromatin erosion, making it a proposed upstream driver linking multiple hallmarks of ageing.

HIF-1α (hypoxia-inducible factor 1α) is the oxygen-regulated subunit of the HIF-1 heterodimeric transcription factor that drives the cellular and systemic transcriptional response to low oxygen (hypoxia). Under normoxic conditions, HIF-1α is hydroxylated by prolyl hydroxylase domain enzymes (PHDs), recognised by the VHL E3 ubiquitin ligase, and rapidly proteasomally degraded; hypoxia inhibits PHD activity, allowing HIF-1α to accumulate, heterodimerize with HIF-1β (ARNT), and activate hypoxia response element (HRE)-driven genes for anaerobic glycolysis (GLUT1, LDHA), angiogenesis (VEGF), and erythropoiesis (EPO). In ageing, HIF-1α plays a contextually dual role: in C. elegans, both loss-of-function and gain-of-function HIF-1 mutations can extend lifespan depending on conditions such as temperature and oxygen tension, reflecting a context-dependent dual role; in mammals appropriate HIF-1α activity is required for hypoxic adaptation and ischemic preconditioning, and its dysregulation contributes to tumor progression, pulmonary hypertension, and potentially to age-related metabolic decline.

The Hippo pathway is a conserved kinase cascade — centred on MST1/2 and LATS1/2 kinases — that controls organ size, tissue homeostasis, and stem cell activity by phosphorylating and thereby inactivating the transcriptional co-activators YAP (Yes-associated protein) and TAZ (transcriptional co-activator with PDZ-binding motif). When Hippo signalling is active, phosphorylated YAP/TAZ are sequestered in the cytoplasm or degraded; when the pathway is off, YAP/TAZ translocate to the nucleus, associate with TEAD transcription factors, and drive pro-proliferative and anti-apoptotic gene programmes. Mechanical cues, cell density, extracellular matrix stiffness, and G-protein-coupled receptor signals converge on the pathway. In ageing, increased tissue stiffness and altered mechanical environments can dysregulate YAP/TAZ, contributing to impaired regeneration and fibrosis; YAP/TAZ are also implicated in the SASP and senescence-bypass phenotypes.

Histone modifications are reversible chemical changes to histone proteins around which DNA is wound, including acetylation, methylation, phosphorylation, and ubiquitination. They reshape chromatin structure and recruit regulatory complexes, thereby controlling gene transcription, DNA repair, and replication. The combined pattern is often called the histone code. Age-related shifts in histone marks contribute to epigenetic drift, loss of cellular identity, and dysregulated stress and longevity pathways.

Hormesis is a biphasic dose-response phenomenon in which a low or moderate dose of a stressor produces a beneficial adaptive effect, while higher doses are harmful. Mild stressors such as heat, cold, exercise, fasting, or certain phytochemicals can involve activation of defence and adaptive pathways such as Nrf2, heat-shock proteins and AMPK in some settings, with the precise response depending on dose, tissue and context. In longevity research, hormesis is one mechanistic framework, alongside others, for why intermittent stress can extend healthspan in model organisms.

IGF-1 signaling refers to the cascade triggered when insulin-like growth factor 1 binds the IGF-1 receptor, activating parallel PI3K/AKT and MAPK/ERK branches that promote cell growth, proliferation, and protein synthesis while suppressing FOXO-driven stress resistance. IGF-1 can also engage insulin/IGF-1R hybrid receptors at lower affinity. Reduced IGF-1 signaling extends lifespan in worms, flies, and mice, and lower circulating IGF-1 is observed in some long-lived human cohorts. The trade-off between growth/repair benefits and longevity costs remains actively debated.

Inflammaging describes the chronic, low-grade, sterile inflammation that develops with age in the absence of overt infection. It is characterised by often elevated baseline levels of pro-inflammatory mediators such as IL-6, TNF-alpha and CRP, driven by senescent cells, accumulated cellular debris, gut dysbiosis and immune dysregulation. Inflammaging is a recognised hallmark of ageing and, in many studies, an independent risk factor associated with increased risk of cardiovascular disease, neurodegeneration, frailty, sarcopenia and overall mortality.

The insulin/IGF-1 pathway (often abbreviated IIS) is a conserved nutrient-sensing network in which insulin and IGF-1 bind tyrosine kinase receptors to activate PI3K, AKT, and mTOR while inhibiting FOXO. It coordinates glucose uptake, growth, and anabolic metabolism with nutrient availability. Loss-of-function mutations along this pathway dramatically extend lifespan in C. elegans (daf-2), Drosophila, and mice, establishing IIS as a foundational longevity pathway across the animal kingdom.

The integrated stress response (ISR) is a conserved eukaryotic signalling programme that converges on phosphorylation of the alpha subunit of eukaryotic initiation factor 2 (eIF2α) by any of four stress-sensing kinases — HRI (haem deficiency), PKR (double-stranded RNA), PERK (ER unfolded proteins) and GCN2 (uncharged tRNAs / amino acid deprivation). eIF2α phosphorylation globally suppresses cap-dependent translation while selectively enhancing translation of stress-response mRNAs containing upstream open reading frames, most notably ATF4, which orchestrates transcriptional adaptation to the specific stress. The ISR supports short-term adaptation but, when chronically active — as seen in neurodegenerative disease, obesity and ageing — impairs synaptic plasticity, memory, and protein synthesis capacity in post-mitotic tissues; small-molecule ISR inhibitors such as ISRIB, which antagonise the inhibitory effect of phospho-eIF2α on eIF2B thereby restoring translation capacity, show efficacy in preclinical models of neurodegeneration and cognitive decline.

Induced pluripotent stem cells (iPSCs) are adult somatic cells reprogrammed into a pluripotent state using factors such as OSKM (Oct4, Sox2, Klf4, c-Myc), capable of differentiating into any cell type of the body. They bypass the ethical concerns of embryonic stem cells and enable patient-specific disease modeling, drug screening, and autologous cell therapies. In aging research, iPSCs reset many epigenetic age markers, though epigenetic resetting is often incomplete and iPSCs can retain partial donor-cell epigenetic memory, providing a powerful platform to study and reverse cellular aging.

The JAK-STAT (Janus kinase – signal transducer and activator of transcription) pathway is a rapid, receptor-proximal signalling cascade through which cytokines and growth factors — including interferons, interleukins, and erythropoietin — transmit signals from the cell surface to the nucleus. Ligand binding induces receptor dimerisation and transphosphorylation of associated JAKs (JAK1, JAK2, JAK3, TYK2), which in turn phosphorylate STATs (STAT1–STAT6), enabling their dimerisation, nuclear translocation, and target gene activation. In ageing, elevated tonic JAK-STAT signalling driven by the SASP and inflammaging-associated cytokines (notably IL-6/JAK1/STAT3 and IL-6/JAK2/STAT3 axes) coexists with reduced cytokine-response amplitude, contributing to chronic tissue dysfunction; JAK1/2 inhibitors such as ruxolitinib have been shown to reduce SASP and improve healthspan parameters in aged mice, and clinical trials are underway.

Klotho (here referring to alpha-Klotho, distinct from beta-Klotho) is a transmembrane protein, predominantly expressed in the kidney and brain, that also circulates as a soluble hormone after cleavage. It regulates phosphate and vitamin D homeostasis via FGF23 co-receptor function and modulates several signaling pathways including insulin/IGF-1, Wnt, and others. Klotho-deficient mice show accelerated aging phenotypes, while Klotho overexpression extends lifespan. Higher circulating Klotho levels in humans are associated with better cognitive performance and reduced cardiovascular and renal disease risk.

Lamin A is a type-V intermediate filament protein and major structural component of the nuclear lamina — the meshwork underlying the inner nuclear membrane — that is essential for nuclear shape, chromatin organisation, DNA repair and gene regulation. It is encoded by LMNA and undergoes post-translational farnesylation and processing before its precursor, prelamin A, is cleaved by the endoprotease ZMPSTE24 to yield mature lamin A. Progerin is a truncated, permanently farnesylated isoform produced by a cryptic splice-site mutation in LMNA that causes the premature ageing syndrome Hutchinson-Gilford progeria; progerin accumulates at low levels during normal ageing and disrupts nuclear architecture, the DNA-damage response and heterochromatin, making it a model for studying molecular mechanisms of physiological ageing at the nuclear envelope.

LC3 lipidation is the covalent conjugation of the autophagy protein LC3 (microtubule-associated protein 1 light chain 3) to phosphatidylethanolamine (PE) in the phagophore and autophagosome membrane, converting cytosolic LC3-I to the membrane-anchored LC3-II form. The reaction is executed by a ubiquitin-like cascade involving the E1-like enzyme ATG7, the E2-like enzyme ATG3, and the E3-like ATG5-ATG12-ATG16L1 complex, and is dependent on prior phosphatidylinositol 3-phosphate (PI3P) generation by the Beclin-1/VPS34 complex. LC3-II density on autophagosomal membranes recruits selective autophagy receptors such as p62 and NDP52 and is the most widely used proxy for autophagosome abundance; the ratio of LC3-II to LC3-I, measured by immunoblot in the presence and absence of lysosomal inhibitors, is a standard method for estimating autophagic flux.

Long interspersed nuclear elements-1 (LINE-1, or L1) are autonomous retrotransposons that comprise roughly 17% of the human genome; they encode the proteins ORF1p and ORF2p, which mediate a copy-and-paste mechanism by which LINE-1 sequences can replicate via an RNA intermediate and insert new copies elsewhere in the genome. In somatic cells, LINE-1 elements are normally silenced through DNA methylation, H3K9me3 heterochromatin and the PIWI-piRNA system, but their repression weakens with age as heterochromatin erodes. Reactivated LINE-1 elements can trigger cGAS-STING innate immune sensing via cytosolic reverse-transcribed DNA, promote genomic instability through new insertions, and contribute to the inflammatory milieu of aged cells; reverse transcriptase inhibitors such as lamivudine have been shown in mouse models to suppress LINE-1-driven inflammation and extend healthspan in some settings.

Lipid peroxidation is an autocatalytic, radical-mediated oxidative degradation of polyunsaturated fatty acids (PUFAs) in cell membranes, lipoproteins, and lipid droplets, initiated when reactive oxygen species (ROS) or other radicals abstract a bis-allylic hydrogen atom from a PUFA chain. The resulting lipid radical reacts with molecular oxygen to form a lipid peroxyl radical, which propagates the chain reaction and yields end-products including malondialdehyde (MDA) and 4-hydroxynonenal (4-HNE) — reactive aldehydes that form adducts with proteins and DNA. Elevated lipid peroxidation is implicated in membrane dysfunction, mitochondrial damage, and ferroptosis, a form of regulated cell death driven by uncontrolled phospholipid peroxidation that is increasingly linked to neurodegenerative and cardiovascular ageing pathology.

Lipofuscin is a yellow-brown, autofluorescent pigment composed of cross-linked oxidised proteins, peroxidised lipids, sugar adducts and redox-active metals such as iron. It forms within lysosomes from material that escapes complete degradation, particularly under conditions of oxidative stress and limited autophagic flux. Because lipofuscin is essentially non-degradable and cannot be exported from the cell, it accumulates progressively in long-lived post-mitotic cells, including neurons, cardiomyocytes, skeletal muscle fibres and retinal pigment epithelial cells. The accumulating granules occupy lysosomal volume, blunt autophagy and base-line proteolytic capacity, and contribute to age-related declines in proteostasis. Lipofuscin is widely used as a histological biomarker of cellular ageing and senescence and is implicated in age-related macular degeneration and certain neurodegenerative conditions.

Loss of proteostasis is one of the established hallmarks of aging and describes the age-related decline of the protein quality control network. Chaperones become less efficient, the proteasome and autophagy slow down, and misfolded or aggregation-prone proteins accumulate. The resulting proteotoxicity contributes to neurodegenerative disorders, cardiac amyloidosis, and cellular dysfunction across tissues, making proteostasis enhancers an active longevity research target.

The lysosome is a membrane-bound organelle filled with acidic hydrolases that degrade proteins, lipids, nucleic acids, and carbohydrates delivered via endocytosis, phagocytosis, or autophagy. Beyond digestion, it acts as a metabolic and signaling hub that senses nutrients through the mTORC1 pathway. Lysosomal dysfunction underlies storage diseases and contributes to aging by impairing autophagy, clearance of lipofuscin, and overall cellular waste management.

Mitochondrial biogenesis is the process by which cells increase mitochondrial mass and capacity by coordinating the expression of nuclear and mitochondrial genes. The transcriptional coactivator PGC-1-alpha is a key nodal regulator, regulated by AMPK and SIRT1 among other signals. Endurance exercise, caloric restriction, and cold exposure are well-established physiological stimuli, and robust biogenesis is associated with muscular endurance, metabolic flexibility, and healthy aging.

Mitochondrial DNA (mtDNA) is a circular, double-stranded genome of approximately 16,569 base pairs present in multiple copies per cell that encodes 13 essential subunits of the oxidative phosphorylation complexes, 22 transfer RNAs and 2 ribosomal RNAs required for their mitochondria-local translation. Unlike nuclear DNA, mtDNA is packaged in nucleoids without protective histones, is physically proximate to the electron transport chain — a major ROS source — and relies on a distinct and less-redundant set of repair enzymes, making it more susceptible to oxidative damage. Somatic mtDNA mutations and deletions accumulate with age and are elevated in post-mitotic tissues such as muscle and brain; their functional significance ranges from contributing to mitochondrial dysfunction when heteroplasmy crosses threshold levels to triggering cGAS-STING innate immune activation when cytosolic mtDNA is released during cellular stress.

Mitochondrial dysfunction refers to a decline in mitochondrial efficiency, including reduced ATP output, impaired electron transport chain activity, increased reactive oxygen species, and altered mitochondrial dynamics. It is recognized as a hallmark of aging and is implicated in sarcopenia, type 2 diabetes, neurodegeneration, and cardiovascular disease. Interventions under study include exercise, NAD+ precursors, urolithin A, and senolytics, while extreme antioxidant supplementation has not shown longevity benefit.

The mitochondrial unfolded protein response (mtUPR) is a stress-signalling pathway activated when the capacity of mitochondrial chaperones — including HSP60, HSP70 and the AAA+ protease ClpP — is overwhelmed by misfolded or aggregated proteins within the mitochondrial matrix. In Caenorhabditis elegans, mtUPR is mediated by the transcription factor ATFS-1, which under stress traffics to the nucleus rather than being imported into mitochondria; in mammals, the homologous pathway involves ATF5 along with other transcription factors including ATF4 and CHOP. Activation of the mtUPR upregulates mitochondrial chaperones, proteases and metabolic genes to restore organelle homeostasis, and its induction by interventions such as NAD+ precursors and mild mitochondrial stress has been linked to lifespan extension in model organisms, though the translation to mammals is not fully established.

Mitophagy is the selective form of autophagy that targets damaged or depolarized mitochondria for lysosomal degradation, with the PINK1/Parkin pathway being the best-characterized route alongside PINK1/Parkin-independent receptor pathways. By removing dysfunctional mitochondria, it can help limit oxidative stress and support bioenergetic function. Impaired mitophagy is linked to neurodegeneration, sarcopenia, and cardiovascular aging, and compounds such as urolithin A are studied for effects consistent with enhanced mitophagy markers, including in older and middle-aged adults.

mTOR (mechanistic target of rapamycin) is a serine/threonine kinase that integrates signals from amino acids, growth factors, and cellular energy status to regulate protein synthesis, cell growth, and autophagy. It functions in two complexes, mTORC1 and mTORC2. Chronic mTORC1 hyperactivation accelerates aging phenotypes, while pharmacologic inhibition with rapamycin extends lifespan in multiple model organisms, making mTOR one of the most validated longevity targets.

The mechanistic target of rapamycin (mTOR) kinase assembles into two structurally and functionally distinct multi-protein complexes: mTORC1, defined by its scaffold subunit Raptor, and mTORC2, defined by Rictor. mTORC1 integrates signals from amino acids, insulin, energy status and growth factors to promote anabolic processes — principally ribosome biogenesis via S6K1 and 4E-BP1 phosphorylation — and to suppress autophagy by phosphorylating ULK1; it is acutely sensitive to allosteric inhibition by rapamycin. mTORC2, by contrast, is rapamycin-insensitive under standard conditions, phosphorylates AKT at Ser473 to regulate cell survival and cytoskeletal organisation, and feeds into the PI3K/AKT/FOXO axis. In the context of ageing, chronic mTORC1 hyperactivity is considered a principal driver of anabolic imbalance and suppressed autophagy, while the differential contributions of each complex to lifespan extension — particularly when mTOR is inhibited globally — remain an active area of investigation.

NAD+ (nicotinamide adenine dinucleotide, oxidized form) is a coenzyme central to redox reactions in energy metabolism and a required substrate for sirtuins, PARPs, and CD38. Cellular NAD+ levels decline substantially with age across tissues, impairing mitochondrial function, DNA repair, and sirtuin activity. NAD+ precursors such as NR (nicotinamide riboside) and NMN (nicotinamide mononucleotide) are studied as supplements aimed at restoring tissue NAD+, with mixed clinical evidence.

NADH is the reduced form of NAD+, generated when NAD+ accepts electrons during glycolysis, the citric acid cycle, and fatty acid oxidation. It delivers electrons to the mitochondrial electron transport chain, driving ATP synthesis. The cellular NAD+/NADH ratio reflects metabolic state and influences sirtuin activity, redox signaling, and substrate selection. A shifted ratio toward NADH, often observed in aging and metabolic disease, is associated with reductive stress and mitochondrial dysfunction.

Necroptosis is a form of programmed necrotic cell death that proceeds through a defined molecular pathway involving receptor-interacting protein kinases RIPK1 and RIPK3 and the pseudokinase MLKL; when apoptosis is blocked or overwhelmed, RIPK3-mediated phosphorylation of MLKL drives its oligomerisation and plasma-membrane translocation, causing lytic membrane disruption and the release of damage-associated molecular patterns (DAMPs). Unlike apoptosis, necroptosis is inherently inflammatory due to this DAMP release, and it can be triggered by death-receptor ligands, viral sensors and toll-like receptors. Emerging evidence links necroptosis to age-related pathologies including neurodegeneration, ischaemic injury and inflammatory bowel disease, though its specific contribution to physiological ageing versus acute disease remains under investigation.

NF-κB (nuclear factor kappa-light-chain-enhancer of activated B cells) is a family of transcription factors — comprising RelA, RelB, c-Rel, p50 and p52 subunits — that regulate the expression of hundreds of genes involved in inflammation, immunity, cell survival and proliferation. In the canonical pathway, pro-inflammatory signals such as TNF-α, IL-1β, lipopolysaccharide or reactive oxygen species trigger IκB kinase-mediated degradation of inhibitory IκB proteins, releasing NF-κB dimers to translocate to the nucleus and drive target gene expression. NF-κB activity increases with age in multiple tissues and is considered a principal driver of inflammaging, the SASP and age-related immune dysregulation; its activation is also downstream of the cGAS-STING pathway, linking cytosolic DNA sensing to chronic inflammation.

The NLRP3 inflammasome is a multiprotein cytosolic complex — composed of the sensor protein NLRP3, the adaptor ASC and pro-caspase-1 — that assembles in response to a broad range of danger signals including ATP, uric acid crystals, cholesterol crystals, saturated fatty acids and mitochondrial ROS. Upon assembly, the complex drives auto-proteolytic caspase-1 activation, which in turn cleaves pro-IL-1β and pro-IL-18 into their mature secreted forms and cleaves gasdermin D to initiate pyroptosis. NLRP3 inflammasome activity increases with age in multiple tissues, contributes to inflammaging and is mechanistically linked to atherosclerosis, type 2 diabetes, gout and Alzheimer's disease; clinical trials are evaluating novel selective small-molecule NLRP3 inhibitors (e.g. MCC950 analogues, inzomelid) and downstream IL-1β antagonists such as canakinumab, as well as colchicine — which suppresses NLRP3-driven inflammation indirectly via microtubule disruption rather than selective NLRP3 blockade — in several of these conditions.

While advanced glycation end-products (AGEs) are one well-known source of collagen crosslinks, a distinct class of enzyme-mediated crosslinks is introduced by lysyl oxidase (LOX) and its paralogues (LOXL1–4), copper-dependent amine oxidases that oxidise specific lysine and hydroxylysine residues in newly secreted collagen and elastin to reactive aldehydes, which then condense spontaneously to form covalent intramolecular and intermolecular crosslinks — pyridinoline and deoxypyridinoline in collagen, and desmosine and isodesmosine in elastin. LOX-mediated crosslinking is essential for tensile strength and tissue integrity during development, but pathological upregulation — driven by TGF-beta, hypoxia, and PDGF signalling in fibrotic and tumour microenvironments — produces excessive matrix stiffness that drives fibrosis, impairs cellular mechanosensing, and promotes tumour invasion. Unlike AGE crosslinks, LOX-mediated bonds are in principle modifiable by LOX inhibitors such as beta-aminopropionitrile (BAPN), making this pathway a pharmacological target distinct from the AGE/RAGE axis.

Notch signaling is a conserved juxtacrine pathway that governs cell-fate decisions, differentiation, and tissue homeostasis through direct cell-to-cell contact. Binding of Delta-like or Jagged ligands on signal-sending cells to Notch receptors (NOTCH1–4) on receiving cells triggers sequential proteolytic cleavages — first by ADAM metalloproteases (S2 cleavage), then by the γ-secretase complex (S3 cleavage) — releasing the Notch intracellular domain (NICD), which translocates to the nucleus and activates transcription via the CSL/RBPJ complex. Notch is a key regulator of satellite cell quiescence and muscle regeneration, neural progenitor specification, and T-cell development; its activity declines with age in multiple tissue compartments, impairing regenerative responses, and dysregulation in either direction — gain or loss of function — is associated with pathological ageing phenotypes and cancer.

NRF2 (nuclear factor erythroid 2-related factor 2) is a transcription factor that orchestrates the cellular antioxidant and cytoprotective response by binding antioxidant response elements (AREs) in the promoters of genes encoding detoxification enzymes, glutathione synthesis components, proteasome subunits, and anti-inflammatory mediators. Under homeostatic conditions, NRF2 is continuously ubiquitinated by KEAP1 (Kelch-like ECH-associated protein 1), an adaptor for CUL3-based E3 ligase, and targeted for proteasomal degradation; oxidative stress or electrophilic compounds modify critical cysteine residues on KEAP1, impairing its ability to present NRF2 for ubiquitination and allowing NRF2 to accumulate and translocate to the nucleus. NRF2 activity declines with age in multiple tissues, contributing to increased oxidative burden and inflammation; natural compounds such as sulforaphane and pharmacological NRF2 activators are studied for their ability to restore cytoprotective capacity, though the distinction between hormetic activation and potentially tumour-promoting chronic activation warrants caution.

One-carbon metabolism is an interconnected network of folate and methionine cycles that transfers single-carbon units for the biosynthesis of nucleotides, the remethylation of homocysteine to methionine, and the production of S-adenosylmethionine (SAM), the universal methyl donor for DNA, RNA, histone, and lipid methylation. Dietary inputs — including folate, choline, betaine, methionine, vitamins B2, B6, and B12 — feed the network at multiple entry points, making its output sensitive to nutritional status. With ageing, dysregulation of one-carbon flux is associated with elevated plasma homocysteine, global DNA hypomethylation, and impaired epigenetic maintenance, linking the pathway mechanistically to two recognised hallmarks of ageing: epigenetic alterations and genomic instability.

Oxidative stress is an imbalance between reactive oxygen species production and the body's antioxidant defences, leading to oxidative damage of biomolecules. It impairs mitochondrial function, accelerates telomere attrition, and drives chronic low-grade inflammation. Implicated in many hallmarks of ageing, oxidative stress is associated with cardiovascular disease, neurodegeneration, diabetes, and cancer, and is modulated by diet, exercise, sleep, and environmental exposures.

p16INK4a is a cyclin-dependent kinase inhibitor encoded by the CDKN2A locus that blocks CDK4/6, halting cell cycle progression and enforcing cellular senescence. Its expression rises markedly with chronological age across many tissues, making it a widely used biomarker of senescent cell burden and biological aging. Selective elimination of p16-positive senescent cells (senolysis) extends healthspan in mice, motivating ongoing senolytic drug development for age-related disease.

p21, encoded by CDKN1A (cyclin-dependent kinase inhibitor 1A), is a potent inhibitor of cyclin-CDK complexes — particularly CDK2 — that enforces G1 and S phase cell-cycle arrest in response to p53 activation, DNA damage and other stressors. By halting replication in damaged cells, p21 provides time for repair; if damage is irreparable, sustained p21 expression can stabilise the senescent state. p21 levels rise with age in multiple tissues and its expression is used as one biomarker of the senescent cell burden, though p21 induction is not exclusive to senescence and can be context-dependent. Genetic experiments in mice show that modulating CDKN1A influences both cancer susceptibility and tissue homeostasis in opposing directions, underscoring its context-dependent biology.

p38 MAPK (p38 mitogen-activated protein kinase), comprising four isoforms (α, β, γ, δ) with p38α being the predominant and most studied form, is a stress-activated kinase that is phosphorylated and activated by upstream MAP2Ks (MKK3 and MKK6) in response to inflammatory cytokines, oxidative stress, UV irradiation, and osmotic shock. It phosphorylates a wide range of substrates including the downstream kinase MK2, transcription factors ATF2 and MEF2, and AU-rich element-binding proteins that stabilise pro-inflammatory mRNAs such as TNF-α. In ageing biology, p38α drives the SASP in senescent cells via NF-κB and MK2/tristetraprolin, suppresses satellite cell self-renewal by phosphorylating MyoD and disrupting quiescence, and mediates inflammatory amplification in inflammaging; pharmacological p38α inhibition has been shown to restore muscle regeneration in aged mice.

p53 is a tumour-suppressor protein encoded by the TP53 gene that acts as a central transcription factor in the cellular response to genotoxic stress, hypoxia, oncogene activation and nutrient deprivation. Upon activation, it induces transcriptional programmes that can drive cell-cycle arrest, DNA repair, apoptosis or senescence, with the outcome depending on stress intensity, cell type and co-regulatory context. Because p53-dependent senescence and apoptosis both limit the proliferation of damaged cells, p53 plays a dual role in ageing: it suppresses tumours yet, when chronically active, can deplete stem-cell pools and reinforce senescent-cell accumulation. Germline TP53 variants and somatic TP53 mutations are the most common alterations found in human cancers, and altered p53 activity is implicated in multiple age-related pathologies beyond malignancy.

p62, encoded by the SQSTM1 gene, is a multifunctional scaffold and selective autophagy receptor that recognises ubiquitinated cargo through its UBA domain and delivers it to autophagosomes by simultaneously binding LC3/GABARAP proteins via its LC3-interacting region (LIR). Beyond cargo triage, p62 integrates cellular stress signals: it activates the Nrf2 antioxidant response by sequestering the Keap1 adaptor and promotes mTORC1 activity by recruiting TRAF6 to catalyse K63-ubiquitination of mTOR (facilitating lysosomal translocation) and by amino-acid-dependent scaffolding of Raptor. Because autophagic flux normally degrades p62, its cytoplasmic accumulation — observed in aged tissues, alcoholic liver disease, and many cancers — serves as a practical readout of impaired autophagy and is a histopathological hallmark of ubiquitin-positive inclusion bodies.

Parkin, encoded by the PRKN gene (formerly PARK2), is a RING-between-RING E3 ubiquitin ligase that operates at the centre of mitochondrial quality control. In the cytosol it is held in an autoinhibited conformation. When PINK1 accumulates on damaged mitochondria, it phosphorylates ubiquitin and the ubiquitin-like (Ubl) domain of Parkin at Ser65, releasing autoinhibition and recruiting Parkin to the outer mitochondrial membrane. Activated Parkin builds ubiquitin chains, enriched in K6, K11 and K63 linkages, on outer-membrane substrates such as MFN1/2, MIRO and VDAC1. These chains attract autophagy receptors including OPTN, NDP52 and p62, leading to engulfment of the mitochondrion by an autophagosome. Loss-of-function PRKN mutations cause autosomal recessive juvenile parkinsonism, linking impaired mitophagy to neurodegeneration.

PARP1 (poly(ADP-ribose) polymerase 1) is a nuclear enzyme and central sensor of DNA damage, especially single-strand breaks. When activated, it cleaves NAD+ and transfers ADP-ribose units onto itself and onto target proteins to build branched poly(ADP-ribose) (PAR) chains. PAR signals recruit base excision repair factors, modulate chromatin structure and coordinate the early DNA damage response. Because PARP1 consumes substantial amounts of NAD+, chronic or excessive activation in ageing tissues with accumulating DNA damage can deplete cellular NAD+ pools, reducing the activity of NAD+-dependent enzymes such as sirtuins and impairing mitochondrial function. The NAD+-PARP1-sirtuin axis is therefore a central node connecting genome maintenance, energy metabolism and ageing, and is a target of NAD+ precursor and PARP inhibitor strategies.

Partial reprogramming uses transient or low-dose expression of Yamanaka factors to rejuvenate cells without erasing their differentiated identity or inducing pluripotency. Studies in mice show restoration of youthful epigenetic patterns, improved tissue regeneration, and extended healthspan. Because full reprogramming risks teratoma formation, partial protocols aim to capture rejuvenation benefits while preserving cell function. It is an active and contested frontier in longevity research, with safety and durability still under investigation. In January 2026, Life Biosciences' ER-100 — a gene therapy expressing three Yamanaka factors (Oct4, Sox2, Klf4; c-Myc omitted), administered by intravitreal injection — became the first cellular-rejuvenation therapy using epigenetic reprogramming to receive FDA IND clearance; a Phase 1 first-in-human trial (NCT07290244) is enrolling patients with non-arteritic anterior ischemic optic neuropathy (NAION) and open-angle glaucoma.

PGC-1α (peroxisome proliferator-activated receptor gamma coactivator 1-alpha) is a transcriptional co-activator and master regulator of mitochondrial biogenesis and oxidative metabolism that lacks intrinsic DNA-binding activity and instead coordinates transcription by interacting with nuclear receptors (PPARα, ERRα) and other transcription factors (NRF1, NRF2, TFAM). Note: the nuclear respiratory factors NRF1/NRF2 are distinct from the antioxidant transcription factor Nrf2/NFE2L2 covered in the nrf2-keap1 entry. It is induced by exercise, cold exposure, fasting, and AMPK or SIRT1 activation, and drives the expression of the mitochondrial genome replication machinery and enzymes of fatty acid oxidation and the tricarboxylic acid cycle. PGC-1α expression and activity decline in aged skeletal muscle and heart, contributing to mitochondrial dysfunction and metabolic inflexibility; its overexpression or pharmacological induction has extended healthspan and delayed age-related muscle wasting in several animal models, making it a prominent target in longevity pharmacology.

The PI3K/AKT pathway is a central intracellular signalling axis activated by receptor tyrosine kinases (including the insulin and IGF-1 receptors), G-protein-coupled receptors, and other stimuli. Phosphoinositide 3-kinase (PI3K) phosphorylates PIP2 to generate PIP3 at the plasma membrane, recruiting AKT (also called protein kinase B) and its activating kinase PDK1; AKT is further activated by mTORC2-mediated phosphorylation at Ser473. Activated AKT phosphorylates a broad set of substrates — including FOXO transcription factors (promoting their nuclear exclusion), GSK-3β (suppressing glycogen synthesis inhibition), BAD (promoting survival), and TSC2 (activating mTORC1) — thereby coordinating cell survival, glucose metabolism, protein synthesis, and proliferation. The tumour suppressor PTEN counteracts PI3K by dephosphorylating PIP3. Reduced PI3K/AKT activity in C. elegans and other organisms extends lifespan through FOXO activation, but in humans the pathway is hyperactivated in many cancers and in insulin-resistant states, representing a complex, context-dependent role in ageing.

PINK1 (PTEN-induced kinase 1) is a mitochondrial serine/threonine kinase that serves as a sensor of mitochondrial damage. In healthy mitochondria with an intact membrane potential, PINK1 is imported into the inner membrane and rapidly cleaved by PARL and degraded. When the membrane potential collapses, import fails and PINK1 instead accumulates on the outer mitochondrial membrane, where it dimerizes and autophosphorylates. Active PINK1 phosphorylates ubiquitin and the E3 ligase Parkin at conserved Ser65 residues, recruiting and activating Parkin to drive ubiquitination of outer-membrane proteins and selective autophagy of the damaged mitochondrion (mitophagy). Loss-of-function mutations in PINK1 cause autosomal recessive early-onset Parkinson disease, and impaired PINK1-Parkin signaling has been implicated in age-associated mitochondrial dysfunction.

Protein carbonylation is an irreversible, oxidative post-translational modification in which carbonyl groups (aldehydes or ketones) are introduced into protein side chains, most often at proline, arginine, lysine, and threonine residues, either by direct metal-catalysed oxidation or by Michael addition of reactive lipid electrophiles such as 4-HNE. Carbonylated proteins are structurally altered, tend to form aggregates, and are poor proteasomal substrates, making their accumulation a marker of proteostatic stress. Carbonyl content rises progressively with biological age across species and is elevated in tissues affected by Alzheimer's disease, Parkinson's disease, and chronic obstructive pulmonary disease, establishing it as a widely used biomarker of cumulative oxidative damage.

Protein crosslinks are covalent bonds that join two protein molecules or different segments of the same protein. They can form enzymatically, as with collagen maturation, or non-enzymatically through oxidation and glycation by sugars and reactive aldehydes. Pathological crosslinks accumulate in long-lived structural proteins like collagen, elastin, and crystallins, stiffening tissues. This contributes to vascular rigidity, skin ageing, cataracts, and reduced organ elasticity.

Proteostasis, short for protein homeostasis, is the integrated network that controls protein synthesis, folding, trafficking, and degradation to keep the proteome functional. Key players include ribosomes, molecular chaperones, the ubiquitin-proteasome system, and autophagy-lysosome pathways. Maintaining proteostasis is essential for cellular function; its progressive failure with age underlies neurodegenerative diseases such as Alzheimer's and Parkinson's and is recognized as a hallmark of aging.

Pyroptosis is a highly inflammatory form of programmed cell death executed primarily by gasdermin family proteins, especially gasdermin D (GSDMD), which oligomerise to form pores in the plasma membrane after cleavage by inflammatory caspases (caspase-1, -4, -5 in humans; caspase-11 in mice). In the canonical pathway, caspase-1 directly cleaves both GSDMD and pro-IL-1β and pro-IL-18 into their mature secreted forms; in the non-canonical pathway, caspase-4/-5/-11 cleave GSDMD to form pores, while IL-1β and IL-18 maturation requires secondary NLRP3/caspase-1 activation triggered by potassium efflux through the GSDMD pores. Pyroptosis is triggered downstream of inflammasome complexes, including the NLRP3 inflammasome, in response to pathogen-associated molecular patterns, damaged-self signals and sterile stressors. In the context of ageing and age-related disease, dysregulated pyroptosis contributes to tissue inflammation in conditions including atherosclerosis, neurodegeneration and metabolic disease.

Reactive oxygen species are oxygen-containing molecules such as superoxide, hydrogen peroxide, and hydroxyl radicals produced by multiple cellular sources, including mitochondrial respiration, NADPH oxidases, peroxisomes, and the immune respiratory burst. At low levels they act as signalling molecules regulating immunity and metabolism, but excess ROS damages lipids, proteins, and DNA. Chronic ROS accumulation contributes to mitochondrial decline, cellular senescence, and age-related diseases including cardiovascular and neurodegenerative disorders.

Regenerative medicine is the field developing therapies to repair, replace, or regenerate damaged cells, tissues, and organs. Approaches include stem cell transplantation, tissue engineering, gene therapy, organoids, biomaterial scaffolds, and cellular reprogramming. By restoring lost function rather than only managing symptoms, it aims to address age-related degeneration, organ failure, and chronic disease. It is closely intertwined with longevity science, where reversing cellular and tissue aging is a central therapeutic objective.

S6K1 (ribosomal protein S6 kinase 1, encoded by RPS6KB1) is a serine/threonine kinase and a primary downstream effector of mTORC1 that promotes protein synthesis by phosphorylating ribosomal protein S6 and eIF4B, thereby stimulating ribosome biogenesis and translational capacity. It operates within a negative-feedback loop that attenuates insulin receptor substrate signalling, linking anabolic drive to insulin resistance. In model organisms from yeast to mice, genetic reduction of S6K1 activity extends lifespan (in mice the Selman 2009 effect was female-specific, with no significant longevity benefit in males) and confers metabolic benefits, including improved insulin sensitivity and resistance to age-related adiposity; in humans, S6K1 hyperactivity is associated with obesity, type 2 diabetes, and accelerated cellular ageing, though direct longevity evidence in humans remains limited.

Senescence-associated β-galactosidase (SA-β-Gal) is an enzyme activity detectable at pH 6.0 that reflects the increased lysosomal content and elevated expression of lysosomal β-galactosidase (encoded by GLB1) found in senescent cells. First described in 1995 by Dimri and colleagues, it became the most widely used single histochemical marker for senescent cells in tissue sections and cell culture due to its relative ease of detection. SA-β-Gal activity is not exclusive to senescent cells — it can also appear under conditions of quiescence, overconfluence or lysosomal stress — so it is best used alongside complementary markers such as p21, p16^INK4a, SASP components and heterochromatin foci for reliable senescence identification.

S-adenosylmethionine (SAM) is the principal biological methyl-group donor, formed by the condensation of methionine with adenosine triphosphate (ATP) in a reaction catalysed by methionine adenosyltransferase. After donating its methyl group to substrates ranging from DNA and histones to neurotransmitters and phospholipids, SAM is converted to S-adenosylhomocysteine (SAH), which is then hydrolysed to homocysteine — a branch point between remethylation back to methionine and the transsulfuration pathway toward cysteine and glutathione. Intracellular SAM:SAH ratio serves as a cellular indicator of methylation capacity; declining SAM availability with age or methionine restriction is proposed to alter epigenetic programming and modulate longevity in several model organisms, though the net effects in mammals remain context-dependent.

The senescence-associated secretory phenotype, or SASP, is the complex mixture of cytokines, chemokines, growth factors, proteases and extracellular vesicles released by senescent cells. It is regulated by multiple pathways, prominently including NF-kB, with mTOR, cGAS-STING, p38 MAPK and C/EBPbeta also influencing SASP output in certain contexts. Depending on context, the SASP can recruit immune cells to clear damaged tissue or, when persistent, fuel chronic low-grade inflammation, fibrosis and paracrine senescence in neighbouring cells, making it a key mechanistic link between cellular senescence and age-related disease.

Senolytics are compounds that selectively induce cell death in senescent cells by exploiting context-specific survival vulnerabilities, including BCL-2 family proteins and PI3K/AKT signalling; specific compounds such as the FOXO4-DRI peptide additionally target the FOXO4-p53 interaction. The vulnerabilities targeted are heterogeneous and compound-specific. Studied candidates include the dasatinib plus quercetin combination, fisetin and navitoclax. In animal models, intermittent senolytic dosing improves physical function and extends healthspan, but human evidence is still limited to early-phase trials and clinical use outside studies is not established.

Senomorphics, also called senostatics, are compounds that suppress the harmful secretory activity of senescent cells without killing them. They typically target signalling pathways that drive the SASP, including NF-kB, mTOR, JAK/STAT and p38 MAPK. Examples studied preclinically include rapamycin, metformin, ruxolitinib and certain flavonoids. The aim is to reduce chronic inflammation and tissue damage from senescent cells while preserving any beneficial roles they may have in wound healing and tumour suppression.

Sirtuins are a family of seven NAD+-dependent enzymes (SIRT1–SIRT7) that deacetylate or otherwise modify proteins involved in metabolism, DNA repair, mitochondrial function, and stress response. Their activity depends on cellular NAD+ availability, linking nutrient status to gene regulation. Sirtuins are implicated in caloric restriction's longevity effects, though direct lifespan extension by sirtuin activators in mammals remains debated. SIRT1, SIRT3, and SIRT6 receive the most aging-related research attention.

Stem cell exhaustion is the age-related decline in the number, function, and regenerative capacity of tissue-resident stem cells. Drivers include accumulated DNA damage, telomere attrition, epigenetic drift, mitochondrial dysfunction, and a deteriorating niche environment. Consequences include impaired wound healing, anemia, immunosenescence, sarcopenia, and reduced tissue homeostasis. Recognized as a hallmark of aging, it is a key target for regenerative and reprogramming-based interventions.

The stem cell niche is the spatially defined microenvironment — composed of neighbouring stromal cells, vascular elements, extracellular matrix, soluble factors, and biophysical cues such as stiffness and oxygen tension — that locally regulates stem cell quiescence, self-renewal, and differentiation. Landmark niches include the bone marrow endosteal and perivascular niches for haematopoietic stem cells, the intestinal crypt base for Lgr5-positive intestinal stem cells, and the bulge region of hair follicles for epidermal stem cells. With ageing, niche integrity deteriorates through ECM stiffening, loss of supporting stromal cells, inflammatory cytokine accumulation, and SASP from local senescent cells, impairing stem cell function even when the stem cells themselves retain intrinsic self-renewal potential — a distinction with therapeutic implications, since restoring niche signals can partially rejuvenate aged stem cell activity.

Telomerase is a ribonucleoprotein reverse transcriptase (TERT plus the TERC RNA template) that adds TTAGGG repeats to chromosome ends, counteracting replicative shortening. It is highly active in germline, stem, and most cancer cells but largely silenced in adult somatic tissues. In longevity research, telomerase reactivation has extended healthspan in mice, but it carries oncogenic risk because most human tumors depend on telomerase for unlimited proliferation.

Telomeres are repetitive TTAGGG DNA sequences capping the ends of linear chromosomes, protecting them from degradation, fusion, and erroneous repair. Each somatic cell division shortens telomeres because DNA polymerase cannot fully replicate chromosome ends. Critically short telomeres trigger senescence or apoptosis. Telomere attrition is one of the twelve hallmarks of aging and is associated with cardiovascular disease, immune decline, and reduced regenerative capacity.

Telomere attrition is the progressive shortening of the protective TTAGGG repeat sequences at chromosome ends with each cell division, due to the end-replication problem and oxidative damage. Once telomeres reach a critical length, cells enter replicative senescence or apoptosis via a DNA-damage response. Telomerase, which can extend telomeres, is largely silenced in adult somatic cells. Accelerated attrition is associated with premature ageing syndromes, cardiovascular disease and reduced healthspan.

TET1, TET2 and TET3 are Fe(II)- and alpha-ketoglutarate-dependent dioxygenases that catalyse stepwise oxidation of 5-methylcytosine (5mC) on DNA to 5-hydroxymethylcytosine (5hmC), then 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC). These oxidised bases can be excised by thymine DNA glycosylase and replaced via base excision repair, providing one route to active DNA demethylation. TET activity is sensitive to oxygen, vitamin C and TCA-cycle intermediates, linking the enzymes to cellular metabolism. Loss-of-function somatic mutations in TET2 are among the most frequent drivers of clonal haematopoiesis of indeterminate potential (CHIP), an age-associated expansion of mutant blood cell clones that is linked to increased risks of haematological malignancy, cardiovascular disease and all-cause mortality.

TFEB is a basic helix-loop-helix transcription factor that acts as a master regulator of autophagy and lysosomal biogenesis. It binds a conserved promoter motif called the CLEAR (Coordinated Lysosomal Expression and Regulation) element to drive coordinated transcription of genes encoding lysosomal hydrolases, lysosomal membrane proteins and core autophagy components such as ATG genes. Under nutrient-replete conditions, mTORC1 on the lysosomal surface phosphorylates TFEB at residues including Ser211, creating a 14-3-3 binding site that retains TFEB in the cytoplasm. Starvation, lysosomal stress or pharmacological inhibition of mTORC1 lead to dephosphorylation and nuclear translocation, where TFEB induces the CLEAR network. In aging models, sustained TFEB activity enhances clearance of damaged proteins and organelles and has been linked to improved proteostasis.

Transforming growth factor β (TGF-β) signaling is initiated when TGF-β ligands — including TGF-β1, TGF-β2, and TGF-β3 — bind to heteromeric serine/threonine kinase receptor complexes (TβRII/TβRI) that phosphorylate receptor-regulated SMADs (R-SMADs 2 and 3), which then partner with SMAD4 and translocate to the nucleus to modulate target gene expression. Beyond this canonical SMAD pathway, non-canonical branches engage MAPK, Rho-GTPase, and PI3K effectors. TGF-β is a contextually pleiotropic cytokine with anti-proliferative, immunomodulatory, pro-fibrotic, and pro-apoptotic functions; in the ageing context, elevated TGF-β1 is a component of the aged systemic milieu and has been implicated in suppressing neural progenitor activity and muscle stem cell function, as well as in driving fibrosis across multiple organs, making pathway antagonism an area of active therapeutic exploration.

The ubiquitin-proteasome system (UPS) is a major route for selective degradation of short-lived, misfolded, or regulatory proteins, complementary to autophagy-lysosomal degradation. Target proteins are tagged with ubiquitin chains via E1 activating, E2 conjugating, and E3 ligase enzymes, with the E3 ligase providing substrate specificity; K48-linked polyubiquitin chains are the canonical proteasome-targeting signal, while other linkages have non-degradative roles. Tagged proteins are then unfolded and degraded into short peptides inside the 26S proteasome. UPS activity declines with age, contributing to loss of proteostasis and neurodegeneration.

The unfolded protein response (UPR) is an adaptive signalling programme activated when misfolded or unfolded proteins accumulate in the endoplasmic reticulum (ER), engaging three parallel branches initiated by the sensors IRE1alpha, PERK, and ATF6. Collectively, these branches attenuate global cap-dependent translation via eIF2alpha phosphorylation, transcriptionally upregulate ER-resident chaperones and folding enzymes, and expand ER-associated protein degradation (ERAD) to clear aberrant proteins. When ER stress is resolved, the UPR is switched off and homeostasis is restored; when stress is chronic and irresolvable — a condition increasingly common with ageing — the UPR shifts its output to activate NF-kB-driven inflammation and CHOP-dependent apoptosis, coupling proteostatic failure to tissue degeneration.

Wnt signaling is a family of evolutionarily conserved intercellular communication pathways initiated by secreted Wnt glycolipoproteins binding to Frizzled receptors, with the canonical (β-catenin-dependent) branch being the most studied. In the absence of Wnt ligands, a destruction complex containing APC, Axin, GSK-3β and CK1 phosphorylates β-catenin, targeting it for proteasomal degradation; Wnt binding stabilises β-catenin, which then translocates to the nucleus to drive TCF/LEF target gene transcription. Wnt signaling is essential for stem cell self-renewal, tissue regeneration, and bone homeostasis, but its activity declines in aged tissues such as skeletal muscle, intestinal crypts, and the bone marrow niche, contributing to stem cell exhaustion; conversely, dysregulated Wnt activity is a driver of cancer and tissue fibrosis in other contexts.

The Yamanaka factors are four transcription factors, OCT4, SOX2, KLF4, and c-MYC (OSKM), identified by Shinya Yamanaka in 2006 as sufficient to reprogram differentiated somatic cells back into a pluripotent embryonic-like state. This work, recognized by the 2012 Nobel Prize in Physiology or Medicine (shared with John B. Gurdon for the discovery that mature cells can be reprogrammed to become pluripotent), demonstrated that cellular identity and aging are reversible. They are now central tools in regenerative medicine, disease modeling, and longevity research focused on epigenetic rejuvenation.