Longevity Papers

Mitochondrial epigenetic editing offers a potential strategy for modulating disease-causing mitochondrial genes while leaving the underlying DNA sequence unchanged. In this study, we present MEE, a mitochondrial epigenetic editor consisting of mitochondrion-targeted TALE modules fused to Dnmt3A and Dnmt3L methyltransferases. MEE efficiently directed site-specific 5mC methylation within cellular mitochondrial DNA with low detectable off-target activity under the tested conditions. MEE-mediated methylation at the C12191 (H) site exceeded 53% and was associated with an approximately 95% reduction in steady-state MT-ND5 mRNA levels in human cells. Notably, MEE increased methylation at the aging-associated C11168 (H) site by 11.76% in vivo, leading to reduced MT-ND4 expression in the targeted brain region and altered plasma levels of t-Tau and NFL in mice. These findings demonstrate that MEE provides a tool for precise epigenetic engineering of mitochondrial DNA, enabling experimental interrogation of specific 5mC modifications and exploration of the functional roles of mitochondrial DNA methylation in aging-associated diseases.

Aging tissues lose function in part because stem cells change in number and behavior, but how age-related changes in the stem cell niche drive these processes is not well understood. Using the fruit fly testis, we asked how aging of the niche microenvironment influences stem cell maintenance and competition. We show that levels of niche cell-derived bone morphogenetic protein (BMP) signals decline with age, leading to increased expression of the transcriptional corepressor Hairless in germline stem cells (GSCs). Elevated Hairless reduces the RNA binding protein Imp, causing loss of the stem cell factor Chinmo and triggering abnormal extracellular matrix accumulation, stem cell displacement, and niche deterioration. Overexpressing BMP signals in the niche, up-regulating Imp in GSCs, or depleting Hairless in GSCs ameliorate multiple aging-related defects. In contrast, GSC clones with low Imp or high Hairless outcompete their neighbors and take over the niche. These findings reveal how aging niche signals affect tissue decline and stem cell residence.

Despite the thousands of genes implicated in age-related phenotypes, effective interventions for aging remain elusive, due to the multifactorial nature of longevity and the interconnectedness of molecular components involved. Here we introduce a network medicine framework to map 2,358 longevity-associated genes onto the human interactome to identify drug-repurposing candidates capable of modulating specific hallmarks of aging. We find that genes associated with each hallmark form a connected subgraph, or hallmark module, allowing us to measure the network proximity of 6,442 compounds to each hallmark. We then introduce a transcription-based metric, pAGE, which evaluates whether drug-induced expression shifts reinforce or counteract known age-related expression changes within each hallmark module. By integrating network proximity and pAGE, we identify drug-repurposing candidates targeting specific hallmarks and provide a falsifiable framework to leverage genomic discoveries for accelerating drug repurposing in longevity. Our findings are interpretable, revealing molecular mechanisms through which drugs modulate hallmarks.

Vascular aging is characterized by endothelial senescence and vascular smooth muscle cell (VSMC) phenotypic switching, yet the role of endothelial extracellular vesicles (EVs) in these processes remains unclear. We show that EVs from non-senescent endothelial cells prevent PDGF-BB-induced VSMC dedifferentiation, preserving contractile markers and limiting migration. In endothelial cells, EVs protected against TNF-α-induced eNOS downregulation but failed to reverse inflammatory and mitochondrial features of senescence after short-term exposure, highlighting a context-dependent protective role.

Protein aggregates threaten cellular proteostasis and are linked to aging and disease. In metazoa, aggregate resolution relies on Hsp70-J-domain protein (JDP)-based disaggregases. Previous studies showed human class A and class B JDP assemblies enhance Hsp70-mediated disaggregation, but the underlying mechanism has remained unclear. Using J-domain mutants that impair Hsp70 binding while preserving mixed-class JDP interaction, we show that synergistic disaggregation is lost when either JDP partner cannot engage Hsp70. Size-resolved disaggregation assays further reveal that mixed-class JDP assemblies influence the processing of distinct luciferase aggregate populations, including aggregate species inefficiently handled by either JDP alone. Our findings support a model in which mixed-class JDP assemblies enhance Hsp70 disaggregation through expanded aggregate-processing capacity and multivalent Hsp70 recruitment by both JDP partners.

The NLRP3 inflammasome has been implicated in a wide range of human diseases, including cardiovascular, metabolic, neurodegenerative (such as Alzheimer's disease), and other age-related conditions. This has positioned NLRP3 as a promising pharmacological target. Numerous studies have shown that complete NLRP3 ablation can prevent or mitigate these diseases. However, total elimination of NLRP3 is not a feasible therapeutic strategy for the millions of patients affected by these degenerative disorders. Consequently, drug development efforts have focused on partial inhibition of NLRP3 using compounds that reduce its expression or activity. Paradoxically, although many studies have used

Reproductive systems are highly sensitive to diet, yet the long-term reproductive consequences of overnutrition are poorly defined. Glucose supplementation shortens Caenorhabditis elegans lifespan, and here we find that it also hastens age-related reproductive decline, evidenced by a greater oocyte deterioration and lower fertility with age. 20-mM glucose enrichment still shortens the lifespan of daf-2(e1370) mutants with reduced insulin-like signaling, but unexpectedly, we do not detect detrimental impacts on their reproductive aging phenotypes. Using auxin-induced tissue-selective degradation, we show that DAF-2/insulin-like receptor signaling in C. elegans intestine and body wall musculature is required for glucose enrichment to impair reproductive function of aged worms, and DAF-2 degradation in either tissue protects against glucose-induced reproductive aging. We also observe that disrupting lipid homeostasis via RNAi against the lipl-4 lipase can impair daf-2(e1370) reproductive function under glucose enrichment. Therefore, insulin-like signaling in metabolically active somatic tissues could represent a key link between overnutrition and reproductive aging.

Somatic mutations accumulate with age and can cause cell death, but their quantitative contribution to limiting human lifespan remains unclear. We developed an incremental modeling framework that progressively incorporates factors contributing to aging into a model of population survival dynamics, which we used to estimate lifespan limits if all aging hallmarks were eliminated except somatic mutations. Our analysis reveals fundamental asymmetry across organs: post-mitotic cells such as neurons and cardiomyocytes act as critical longevity bottlenecks, with somatic mutations reducing median lifespan from a theoretical non-aging baseline of 1759 years to 156 years. In contrast, proliferating tissues like liver maintain functionality for thousands of years through cellular replacement, effectively neutralizing mutation-driven decline. Multi-organ integration predicts median lifespans of 146-194 years-approximately twice current human longevity. This substantial yet incomplete reduction indicates that somatic mutations significantly drive aging but cannot alone account for observed mortality, implying comparable contributions from other hallmarks.

Inflammaging represents a hallmark of biological aging, yet the causal inflammatory mediators driving multi-dimensional epigenetic aging and their effector genes remain poorly characterized at the genetic level. We developed a four-tier analytical framework integrating causal screening, multi-omics effector gene mapping, spatial transcriptomics, and drug target evaluation. Two-sample Mendelian randomization (MR) of 91 circulating inflammatory proteins against six aging phenotypes identified IL-12B, IFNG, and IL-2 as the most robust pro-aging mediators with consistent effects across independent outcomes. Using multi-omics summary-based MR (SMR) as the core analytical engine, we integrated four-layer whole-blood molecular QTL resources eQTL (eQTLGen, n = 31,684), sQTL (GTEx, n = 755), pQTL (INTERVAL + SCALLOP, n = 34,232), and mQTL (McRae et al., n = 1,980) - with GWAS summary statistics for four epigenetic age acceleration measures. At a stringent threshold (P_SMR < 1×10⁻¹²), seven high-confidence effector genes were identified: NHLRC1, TPMT, SELP, and RIPPLY3 for IEAA; ZNF373A and PLDN for HannumAA; and EDARADD for PhenoAA. The chromosome 6p21 NHLRC1-TPMT locus, overwhelmingly driven by methylation QTL signals (-log₁₀P = 26.06), emerged as the dominant genetic node of epigenetic aging. Spatial projection via gsMap onto a mouse E16.5 embryo atlas (121,767 cells) revealed preferential enrichment in smooth muscle and lung, with EDARADD showing marked specificity in mucosal epithelium. Cross-database drug target mining classified TPMT and SELP as repurposable known targets and NHLRC1 as a high-priority novel druggable candidate. This study provides multi-omics convergent causal evidence for inflammation-driven epigenetic aging and delivers genetically anchored targets for precision anti-aging intervention.

Aging is characterized by progressive physiological decline and age-related pathologies, yet the molecular determinants underlying lineage- and species-specific aging traits remain poorly understood. Although protein-coding regulators have dominated aging research, the contribution of long non-coding RNAs (lncRNAs), particularly primate-specific lncRNAs, has not been systematically explored. Here, through evolutionary screening and cross-species aging-associated analyses, we identified a set of primate-specific lncRNAs (including LINC01021, CTC-575 l10.1, CTA-150C2.13, and RP11-305F18.1, etc.) associated with human aging, and we functionally characterized LINC01021 as a representative candidate to assess their causal involvement. In human cells, LINC01021 promotes cellular senescence, whereas its silencing attenuates senescence-associated phenotypes. Mechanistically, LINC01021 is predominantly located in the nucleus, where it facilitates DAZAP1-dependent destabilization of RBMX mRNA, leading to activation of the P53 pathway and induction of canonical senescence features. At the organismal level, ectopic expression of human LINC01021 in mice contributes to aging-like phenotypes, including increased frailty and impaired motor coordination. Together, these findings implicate primate-specific lncRNAs in lineage-restricted aging and highlight an evolutionarily recent regulatory layer that may modulate aging trajectories.

Animal lifespan depends on coordinated gene expression networks that regulate metabolic adaptation, proteostasis, and stress resilience in response to environmental challenges. Histone variants are key regulators of chromatin dynamics, orchestrating nucleosome remodeling, DNA accessibility, and gene expression. While the role of histone H3.3 in aging and animal survival has been explored across model systems, the contribution of other replication-independent histone variants remains less well-defined. Here, we demonstrate that the evolutionarily conserved histone variant HTZ-1/H2A.Z is essential for organismal survival. In the nematode Caenorhabditis elegans, loss of HTZ-1/H2A.Z disrupts gene expression programs associated with longevity, including those activated in insulin/IGF-1 deficient daf-2 mutants and in mitochondrial Complex I deficient animals. Together, our findings show that HTZ-1/H2A.Z regulates gene expression programs that coordinate metabolic and proteostatic pathways, thereby fine-tuning stress responses and promoting lifespan in animals.

Mitochondrial stress activates nuclear transcriptional programs to restore homeostasis and promote longevity; yet, the nuclear effector that directly reshapes chromatin during stress remains unclear. Through a forward genetic screen in

Aging is a multifactorial process driven by interconnected hallmarks, including chronic inflammation, mitochondrial dysfunction, genomic and epigenetic alterations, and dysregulated intercellular communication. Extracellular vesicles (EVs), naturally derived nanoscale membrane vesicles capable of transporting diverse bioactive cargoes across tissues and biological barriers, have emerged as a highly promising platform for regenerative and anti-aging therapeutics. In this review, we systematically summarize the multifaceted anti-aging mechanisms of EVs, including suppression of the senescence-associated secretory phenotype (SASP), remodeling of the immune microenvironment, mitochondrial restoration and metabolic reprogramming, DNA damage repair, epigenetic modulation, recovery of proteostasis, activation of regenerative signaling pathways, and cross-organ communication-mediated rejuvenation. Beyond mechanistic insights, we integrate the targeting biology and cellular entry properties of EVs, encompassing natural tropism determinants, engineered targeting strategies, biodistribution profiles, receptor-ligand interactions, intracellular trafficking, and subcellular cargo release. Unlike previous reviews focusing on a single EV source or isolated pathways, we establish a comprehensive framework connecting molecular mechanisms with delivery engineering, tissue targeting, biosafety assessment, scalable manufacturing, and clinical translation. We address major technical bottlenecks limiting EV therapeutics-including EV heterogeneity, suboptimal delivery efficiency, endosomal degradation, and the lack of standardized quality-control frameworks-while highlighting emerging solutions such as bioengineered EVs, hybrid vesicle platforms, biomaterial-assisted delivery systems, and ultrasound-enhanced targeting technologies. By bridging fundamental biology, nanomedicine engineering, and clinical translation, this review provides a strategic roadmap for the development of next-generation precision anti-aging nanotherapeutics with systemic regulatory capacity, translational feasibility, and broad clinical potential.

Epigenetic mechanisms are considered adaptive regulators of gene expression, yet mechanisms driving aging-associated DNA methylation remain unclear. Prior work hinted that epigenetic aging might reflect a response to oxygen availability, with age‑differential methylation in immune cells enriched near binding sites for hypoxia‑responsive factors ARNT and REST. To test this hypothesis, we exposed adult (11 months) and old (23 months) mice to 1 month of intermittent hypoxia (IH) followed by normoxic recovery. IH induced epigenetic age acceleration in lungs, spleen, and heart in old mice only. This acceleration reversed upon return to normoxia. Reversible shifts were enriched at bivalent domains and PRC2 targets, indicating oxygen-sensitive chromatin remodeling. Human translational validation in young adults at high altitude (5260 m) confirmed rapid, conserved epigenetic aging. Our findings establish oxygen availability as a primary, conserved modulator of epigenetic aging across tissues and species, showing that oxygen fluctuations are a potent, reversible driver of epigenetic aging.

Senescent cell accumulation has been implicated in aging and fibrotic disease, which are both characterized by increased tissue stiffness. However, the direct connection between tissue mechanics and senescence induction remains disputed in the literature. Thus, this work investigates the influence of hydrogel stiffness and viscoelasticity in promoting fibroblast senescence directly and in combination with genotoxic stress. We show that while lung fibroblast YAP/TAZ signaling declines with senescence induction, senescent fibroblasts maintain their mechanosensing capabilities with increased YAP/TAZ nuclear localization on higher stiffness hydrogels. Most notably, we find a unique role for hydrogel viscoelasticity in senescence induction, with soft (2 kPa) viscoelastic substrates promoting both the onset and amplification of senescence, even in the absence of genotoxic stress. These changes are not associated with a decline in YAP/TAZ activity, but instead with a decline in nuclear DAPI intensity, suggesting a role of nuclear organization in driving this phenotype. Overall, this work highlights the influence of mechanics, and viscoelasticity in particular, on the induction of fibroblast senescence.

Physical activity is among the most robust epidemiological correlates of reduced mortality and multi-morbidity, yet the molecular mechanisms through which exercise exerts these effects in humans remain incompletely resolved. This study combines causally-anchored multi-omic Mendelian Randomisation (MR) with graph-based deep learning for gene prioritisation in human exercise-ageing biology, using accelerometer-derived vigorous physical activity (VPA) in the UK Biobank as exposure. Combining multi-omic MR across five molecular layers, it asks whether causal inference and deep learning can recover exercise-responsive and potentially ageing-causal genes that were independently identified in prior studies. Enrichment for experimentally exercise-responsive genes was undetectable in the raw MR signal (p = 0.97) yet was recovered by the graph model (p = 0.007, reproducible across all initialisations); and the convergence between VPA MR-anchored and ageing-causal genes (significant on its own at 1.6-fold; p = 0.023) was likewise recovered by the graph model where p-value and effect-size ranking could not. The model further reproduced established acute exercise-responsive immune and lipid-metabolic programmes, supporting its recovery of genuine signal. Extending the prioritised genes to formal causal testing, systematic cis-MR with colocalisation across the eight convergent genes and four ageing outcomes identified cathepsin F (CTSF) as causally associated with exceptional longevity, with concordant positive estimates in the protein and LD-clumped expression arms and colocalisation support at the protein level. The contribution is therefore twofold: a model-free, like-for-like convergence between exercise-anchored and ageing-causal genes; and a graph-based method that recovers this convergence, together with exercise-responsive biology, beyond the reach of per-gene MR ranking.

It is necessary for naïve CD8 T cells to be actively maintained in a quiescent metabolic state in order to respond robustly to infection while avoiding inappropriate activation during homeostasis. With age this quiescent state is lost and the CD8 T cell response to infection decreases. The factors regulating metabolic quiescence of CD8 T cells and how this regulation is lost during aging are not completely understood. Herein, we identify the transcription factor AFF3 as a regulator of metabolic quiescence in naïve CD8 T cells. While naïve AFF3 deficient CD8 T cells are more metabolically active prior to infection, they have reduced accumulation in response to viral infection, and this is correlated with a poor capacity to engage glycolysis. During aging in both murine and human CD8 T cells, AFF3 expression is decreased. In mice, this is associated with a loss of metabolic quiescence and reduced capacity to accumulate following infection. Our data highlight the role of metabolic regulation in CD8 T cell quiescence and identifies a transcription factor that may be a target to reinvigorate CD8 T cell responses during aging.

DNA methylation changes predictably with age across taxa, but in most species, these patterns are confounded by genetic variation. As a result, age-predictive methylation models have mostly been developed in genetically heterogeneous, cross-fertilizing organisms, limiting inference about epigenetic aging per se. Disentangling epigenetic and genetic effects is therefore essential for understanding aging, adaptation, and evolution. Here, we exploit the mangrove rivulus (

Smoking injury extends beyond the epithelium and endothelium; we show that alveolar macrophage senescence is a central driver. Using single‑cell RNA sequencing of human bronchoalveolar lavage fluid integrated with macrophage models exposed to cigarette smoke extract (CSE), we profiled senescence at the cell‑type level. The results of functional assays (mitochondrial reactive oxygen species (mitoROS), DNA damage, Senescence-associated β-galactosidase, p16/p21, apoptosis, phagocytosis, senescence-associated secretory phenotype) confirmed the biology of these effects. Smokers' macrophages were enriched for senescence and the SASP. In vitro, CSE increased mitoROS and DNA damage signaling, impaired phagocytosis, and induced apoptosis. Multiple cohort analyses revealed the GTP Binding Protein Overexpressed In Skeletal Muscle (GEM) as a causal driver: GEM was elevated in smokers and correlated with CDKN1A, and its perturbation altered the phenotype. GEM increased mitoROS, suppressed SIRT3/SOD2, lowered adenosine triphosphate (ATP), and amplified p16/p21 and SASP. Pharmacologic SIRT3 activation reversed these defects. In addition, the results from the mouse smoking model strongly support the role of the GEM/SIRT3 pathway in mediating the effects of cigarette smoke on macrophage senescence. Upstream, CSE induced ATF3 to transactivate GEM, while IGF2BP2 stabilized GEM mRNA via m