Longevity Papers

Environmental conditions experienced early in life have profound consequences for vertebrate health, yet the molecular pathways linking developmental stress to aging and reduced lifespan remain poorly understood. Through a novel highly accurate epigenetic clock, developed from RRBS-based blood DNA methylation profiles, we show that experimental lifespan-reducing early-life stress rapidly accelerates epigenetic age in zebra finch chicks (Taeniopygia guttata). Corticosterone-treated 29-day-old chicks share differentially methylated loci with non-treated aged birds and cluster with 6-month-old birds. The transcriptional repressor ZBTB16 emerges as an epigenetically top age-correlated gene and is strongest affected by corticosterone. Elevated developmental corticosterone causes rapid epigenetic remodelling of metabolic pathways well-established in aging and longevity. Our results demonstrate epigenetic rewiring of the aging trajectory through conserved stress-survival mechanisms immediately following elevated early-life stress exposure.

Cellular senescence is a central hallmark of aging, yet its measurement in humans remains invasive, low-throughput and tissue-specific, precluding population-scale study. We developed Methylation-associated Gene Expression (MaGE) predictors: whole-blood DNA methylation proxies of p14ARF, p16INK4A and p21CIP1 expression, plus a composite score, providing the first scalable measure of senescence-marker expression. Deployed across Generation Scotland (n=18,859), MaGE yielded 45 Bonferroni-significant associations spanning 18 incident diseases and all-cause mortality. The two strongest associations recapitulated the established tissue specificity of p21CIP1 and p16INK4A activation, with MaGE-p21 associating with incident alcoholic liver disease and MaGE-p16 with pulmonary fibrosis. In a separate study, MaGE tracked disease severity and treatment response in Crohn's disease. MaGE is a scalable, interpretable biomarker of senescence that enables its study at population scale and offers a route to patient stratification in senolytic trials.

Mitochondria and their biomacromolecular complexes-such as the electron transport chain (ETC), mitochondrial permeability transition pore (mPTP), and protein quality control systems-play pivotal roles in aging and age-related diseases. This review integrates recent insights into how structural and functional disruptions of these complexes drive cellular senescence and systemic decline. We outline the architecture of mitochondrial assemblies (e.g., oxidative phosphorylation (OXPHOS) complexes, mtDNA-protein interactions) essential for energy production and organelle stability. Age-related alterations in stoichiometry, conformational states (e.g., mPTP opening), and post-translational modifications (e.g., SIRT3-mediated acetylation) compromise mitochondrial integrity, fueling metabolic dysfunction and chronic inflammation ("inflammaging"). Therapeutic strategies include small-molecule stabilizers of ETC supercomplexes, peptide-based mPTP inhibitors, and CRISPR-mediated correction of mtDNA-protein mismatches. Tissue-specific models (e.g., Complex I in skin aging, Bcl-2 protein imbalance in ovarian aging) exemplify the clinical relevance. We also categorize nine age-associated diseases-neurodegenerative, cardiovascular, and cancer types-based on their dependence on distinct mitochondrial complexes, such as ATP synthase in cancer resistance and the TIM/TOM import machinery in Alzheimer's disease. By linking structural findings (e.g., cryo-EM studies) with therapeutic innovation, this review offers a framework for targeting mitochondrial complexes to mitigate aging and its related pathologies.

Aging paradoxically leads to both a decline in skeletal muscle mitochondrial function and a shift in muscle composition that favors fibers rich in mitochondria. Yet the biological rationale and mechanism underlying this phenomenon remain largely unknown. Here we show that synthesis of the mitochondrial membrane lipid, cardiolipin, causally links mitochondrial dysfunction to fiber-type adaptations in aging mouse and human skeletal muscle. By mimicking the aging decline of skeletal muscle cardiolipin levels in young mice using inducible tissue-specific cardiolipin synthase 1 (Crls1) deletion, we could reproduce key aging hallmarks, including the shift from glycolytic to oxidative fibers. This shift is mediated by mitochondria-to-nucleus signaling through the nuclear receptor, estrogen-related receptor γ, which promotes reactive oxygen species-sensitive glucose uptake and enhanced glycolytic rerouting to sustain antioxidant defenses. Restoring Crls1 expression in adult Crls1 knockout mice reestablishes cardiolipin levels, initiates reversal of muscle atrophy and fully rescues premature mortality. These findings reveal how changes in a mitochondrial membrane lipid cell autonomously orchestrate fiber-type adaptations in aging and myopathies.

Extracellular vesicles (EVs) have been proposed to be mediators of the health-promoting effects of exercise throughout the body, but how EVs communicate these beneficial signals to recipient cells remains unknown. Here we interrogated these mechanisms using articular cartilage as a model. Network propagation of EV microRNA perturbations on a cartilage-specific network identified microRNA-29 as an exercise-responsive regulator of cellular aging. Consistent with this prediction, a 3-month aerobic exercise intervention in older adults increased microRNA-29 levels in EVs relative to baseline EVs. In vitro studies revealed that these exercise-primed EVs epigenetically de-repressed the KL gene, which encodes the longevity-associated protein α-Klotho, and restored a more youthful chondrocyte phenotype. EVs engineered to express microRNA-29 recapitulated these anabolic effects in a KL-dependent manner. Intra-articular administration of exercise-primed EVs into aged mice enhanced cartilage health, thereby confirming physiological and potentially translational relevance. These findings elucidate mechanisms by which exercise transduces beneficial signals in EVs to promote health in distal tissues through regulation of KL.

Aging is often characterized statically as molecular profiles, but how these profiles may affect the capacity of systems to respond to the external environment remains elusive. We perturbed young and aged mice via transient sleep deprivation and profiled transcriptomes from six organs immediately after stress and following recovery. The same perturbation induced complex temporal dynamics for each gene in an organ- and age- dependent manner. A shape parameter distinguished genes that recovered toward control expression from those that continued to drift away during recovery. Transcriptomic vector fields were inferred from these transitions using neural ordinary differential equations, revealing distinct stability regimes across organ systems. Interestingly, that of testis from the young mice contained a separatrix bounding the region within which perturbed state can return toward control. These findings establish transient perturbation and recovery as a framework for probing age-dependent transcriptomic stability and identifying boundaries that determine whether a perturbed system can return.

Currently, no generalizable tools exist for predicting the impact of interventions on aging using gene expression changes. Here, we build a model for predicting potential geroprotectors by deconstructing the aging transcriptome into coexpression modules and identifying those modulated by life span-extending interventions in

AMP-activated protein kinase (AMPK) is a key evolutionarily conserved sensor of energy homeostasis and plays a central role in metabolic health and disease. AMPK has also been implicated in ageing; however, most in vivo drug studies rely on the use of indirect activators, such as metformin, which have complex modes-of-action, therefore making conclusions on the specific role of AMPK more challenging. Here, we demonstrate that direct activation of AMPK with the compound 991 extends lifespan in Drosophila melanogaster, Caenorhabditis elegans and Schizosaccharomyces pombe. In mice, 991 treatment induces a pro-longevity proteomic profile, highlighting the potential for translation to mammals. Overall, our study provides important proof-of-principle for AMPK as a pharmacological target with longevity benefits.

The rapid fertility decline in women over 35 years of age has been attributed to decreasing oocyte quality. Aging oocytes accumulate DNA damage, chromosome segregation defects and altered epigenetic modifications. Critically, the molecular mechanisms underlying these changes remain poorly understood. Here we uncovered that in the mouse, the HIRA driven H3.3 histone replacement is attenuated during oocyte aging leading to the loss of chromatin homeostasis. The loss of HIRA function is caused by its SUMOylation resulting in the disruption of HIRA-UBN1-CABIN1 complex and its association with chromatin. We further show that preventing HIRA SUMOylation restores H3.3 incorporation and chromatin integrity in aged mouse oocytes leading to improved oocyte maturation and preimplantation development rates. Importantly, similar chromatin homeostasis defect is observed in aging human oocytes pointing towards a conserved process. Our findings provide novel insights into the molecular mechanisms underlying age-related oocyte quality decline and pave the way for clinical interventions.

Cellular senescence and chronic low-grade inflammation occupy a central, mechanistically coupled position among the hallmarks of aging. Natural killer (NK) cells decline in per-cell cytotoxicity with age, and lower NK cell cytotoxicity has been associated with higher cancer incidence and infection-related mortality in older adults. NK cells are also endogenous effectors of senescent-cell clearance, engaging stress-induced NKG2D and DNAM-1 ligands and depending on perforin-mediated cytolysis. These literatures meet at a hypothesis: that autologous cytokine-induced NK cells, manufactured from a patient's own peripheral blood mononuclear cells (PBMCs), might be developed as candidate cellular senolytics. Cytokine-induced killer (CIK) and cytokine-induced memory-like (CIML) manufacturing platforms are mature, with registry safety data across more than 2700 predominantly oncology patients and a first autologous NK cell trial in a non-cancer, aging-related indication (Alzheimer's disease). Yet no trial has tested such a product against a senescent-cell-burden or biological-age endpoint. This review maps the evidence across NK cell aging, NK cell-mediated senolysis, and autologous NK cell clinical experience; separates what is established in humans from what remains preclinical or hypothetical; and confronts three obstacles: the HLA-E/NKG2A evasion axis, the heterogeneity of senescent-cell surface phenotypes across tissue and inducing stimulus, and the physiological roles of senescent cells in wound healing, tissue remodeling, development, and tumor suppression that make indiscriminate clearance non-trivial. We conclude that the rationale is defensible but not yet trial-ready, and specify the precursor experiments (autologous NK cell cytotoxicity against autologous senescent cells from older donors, and a preclinical infusion model) that should gate any first-in-human program.

Aging drives chronic disease in part through senescent cells, including macrophages, which fuel inflammation. Senescent macrophages are functionally heterogeneous: canonical p16-high macrophages promote tumorigenesis or, in other contexts, disease tolerance, whereas we previously identified a distinct p21-high, p16-low senotype that drives metabolic dysfunction-associated steatotic liver disease (MASLD). The molecular basis of this senotype has remained undefined. Using genetic and multi-omic approaches, we show that a p53-p21-dependent program actively represses p16 and is required for senescent macrophage viability. We identify Cyclin D2 as a non-canonical downstream effector that redistributes from the nucleus to mitochondria and lipid droplets, where it partners with MIC60 to drive metabolic reprogramming and modulates AKT1-mTORC1 signaling that sustains the SASP. Cyclin D2-p21 double-positive macrophages accumulate with aging and MASLD in mice and in human liver cirrhosis, and can be selectively depleted by senolytic treatment. Together, these findings define a druggable p53-p21-Cyclin D2 axis that specifies macrophage senotype.

Despite the well-established importance of DHA in neural health, the mechanisms by which neural tissues respond to declining DHA availability and how this response contributes to aging remain poorly understood. Here, we show that chronic DHA deficiency triggers a neural-specific compensatory lipid-remodeling program with pathological consequences. DHA loss causes a neural-tissue-selective shift from DHA-containing phospholipids toward arachidonic and adrenic acid-containing omega-6 species, accompanied by an RPE-associated polyunsaturated fatty acid biosynthetic program. This remodeling expands the pool of oxidation-prone lipids, redirects lipid peroxidation toward omega-6-derived products, and increases oxidative damage. Dietary DHA restoration reversed lipid remodeling, oxidative stress, inflammation, and visual dysfunction, establishing DHA deficiency as a causal driver of these phenotypes in mice. We identified an APOE-dependent oxidized-lipid disposal pathway that transfers oxidized lipid cargo from the neural retina to subretinal microglia, limiting its retention within the neural retina and protecting against degeneration. However, with persistent lipid uptake, oxidized phospholipids accumulate in microglial lysosomes, with sustained galectin-3 activation. Galectin-3 deficiency preferentially protected against later-stage degeneration, indicating that prolonged lipid burden converts the initial clearance response into a pathogenic response. Physiologically aged retinas also showed a similar shift toward omega-6 lipid accumulation. These findings define an adaptive-to-maladaptive lipid-remodeling-microglia axis linking declining DHA availability to age-related neural dysfunction.

The functional decline of the hematopoietic system during aging affects organismal function and contributes to reduced healthspan. Quantifying hematopoietic aging holds great scientific and clinical relevance. Alterations in chromatin architecture are a well-established hallmark of aging that encode rich and informative signatures of the aging process, yet they remain largely unexplored as quantitative markers. Here, we present an interpretable deep learning approach based on convolutional neural networks, ChromAgeNet, that learns changes in the spatial features of chromatin architecture upon aging of hematopoietic stem cells (HSCs). We trained our algorithm on 3D microscope images of DAPI-stained HSC nuclei to discriminate between young and aged murine HSCs, achieving an AUROC of 0.77 ± 0.03. This approach outperforms classical machine learning models trained on handcrafted chromatin features from the same dataset. We then applied explainable artificial intelligence techniques, identifying chromatin entropy, peripheral heterochromatin, and chromatin condensates as predictive markers. As a proof of concept, we evaluated the potential of our model as a phenotypic screening tool for aged HSCs treated with epigenetic drugs to detect rejuvenation. Altogether, we demonstrate that changes in chromatin organization can be modeled via machine learning to predict age-associated chromatin states in the hematopoietic compartment. Our developed framework, ChromAgeNet, serves as an interpretable algorithm to unravel the intricate relationship between chromatin changes and stem cell aging, and advance high-throughput drug screening for rejuvenation therapies.