Nature Aging

Dietary restriction extends lifespan across model organisms, but the plasma molecular changes mediating this effect remain incompletely characterized. We present a longitudinal multiomic analysis of 2,234 plasma samples from 960 Diversity Outbred mice subjected to intermittent fasting or caloric restriction and followed to natural death. Using mass spectrometry, we quantified 1,512 metabolites, lipids, and proteins and mapped their associations with diet, age and longevity. DR-induced molecular changes scale with caloric intake and modulate inflammatory, lipid catabolism, and oxidative stress pathways. Aging showed a biphasic signature with sharp acceleration beyond 85% of lifespan, demarcating terminal decline. Mediation and survival modeling both identified superoxide dismutase (SODE) and vascular cell adhesion molecule (VCAM1) as top lifespan predictors. Genetic analysis revealed 9,599 QTL, nine of which coincided with previously identified lifespan QTLs, and were largely related to immune regulation. These findings provide a rich multiomic and genetic resource for the aging research community.

Aging is a multifaceted process that occurs on the background of and is significantly driven by transcriptional changes. Aging-related transcriptional changes may include reduced transcription of maintenance, repair and DNA methylation genes, de-differentiation, or increased transcription of transposons. Unbiased detection of these changes and full understanding of their physiological effects requires single-cell resolution. We studied single-nuclei transcriptomes of a model microcrustacean Daphnia magna sampled from 3 age- and reproduction status groups: young, old reproductively senescent, and old, regaining reproductive function late in life. We detected 17 cell clusters, some identifiable as ovary or fat body-, midgut-, epithelium-, and neural tissue-related, some escaping unambiguous identification. We detect significant changes of cell type abundance with age and with reproductive "rejuvenation" in ovary- and gut-related clusters. We also detect several patterns of functional transcriptional differences between treatment groups with nearly all cell types, with changes between old reproductive and old non-reproductive Daphnia often reversing age-related changes.

Biological aging clocks are typically evaluated through competitive benchmarking, implicitly assuming that a single metric can sufficiently capture the complexities of aging1-6. Here, we tested an alternative hypothesis: that distinct clock types capture orthogonal dimensions of aging and therefore yield greater value when integrated. Using the Framingham Heart Study, we compared the immune-aging metric, IMM-AGE, with established DNA methylation clocks and found that integrated models consistently outperformed single-clock approaches. To investigate the basis of this complementarity, we derived IMMAGE-Epi, a 22-CpG methylation surrogate of IMM-AGE which exhibited minimal overlap with canonical epigenetic clock CpGs, suggesting that immune aging is associated with a distinct methylomic feature and pathway space rather than representing a reformulation of existing clock architectures. Together, our findings support an emerging multidimensional model of biological aging in which integrating orthogonal biological clocks may offer greater translational utility than competitive single-clock optimization.

Alzheimers disease (AD) is characterized not only by tau and amyloid-{beta} aggregation but also by systemic disruptions in circadian rhythms, metabolism, and gut-brain communication that exacerbate neuroinflammation and neurodegeneration. While glial cells play central roles in inflammatory signaling and proteostasis, the contribution of the gut microbiome to glia-driven AD pathology remains poorly understood. Here, we used Drosophila models with glial-specific expressions of human tau and amyloid-associated transgenes to investigate how microbiome integrity influences disease progression. AD models exhibited significant shifts in gut microbial composition, particularly in Lactobacillus and Acetobacter species, suggesting an adaptive microbial response to pathological stress. Strikingly, microbiome depletion (axenic condition) markedly worsened behavioral and physiological outcomes, including disrupted sleep-circadian rhythms, impaired memory, and reduced locomotor function. These deficits were accompanied by amplified neuroinflammatory signaling (Upd-Dome-Hop-Stat92e axis), increased apoptotic gene expression, lipid dysregulation, and altered synaptic markers. Moreover, microbiome loss induced energy stress marked by elevated phospho-AMPK (p-AMPK), yet failed to restore proteostasis, as evidenced by accumulation of ubiquitinated proteins and the autophagy adaptor Ref2p, indicating impaired autophagic flux. This dysfunction correlated with increased tau, phospho-tau, and A{beta}42 accumulation. Together, our findings demonstrate that microbiome depletion exacerbates glial-mediated inflammation, disrupts circadian and metabolic homeostasis, impairs, and accelerates cognitive and motor decline. This work highlights a previously underappreciated role of the gut microbiome in restraining glial dysfunction and mitigating AD-like pathology, positioning microbial homeostasis as a critical modulator of neurodegenerative disease progression.

The postmenopausal ovary is commonly viewed as a passive organ, and its biology and cell composition remain incompletely characterized. Here, we generated a single-nucleus atlas of the aging postmenopausal human ovary comprising 439,011 nuclei across 64 ovarian samples from 28 donors. We resolved 37 fine cell states, revealing extensive stromal, vascular, and immune heterogeneity in the postmenopausal ovary. Aging was associated with stromal stress-state expansion, vascular and immune depletion, and enrichment of steroidogenic programs consistent with ovarian androgenization. Several major age-associated compositional shifts were supported in an independent GTEx ovary bulk RNA-seq cohort. Notably, the number of live births broadly opposed age-associated transcriptional and compositional remodeling. Together, our findings show that the postmenopausal ovary remains an actively remodeled aging tissue and that reproductive history leaves durable molecular and cellular imprints on ovarian aging.

Genome instability and mutagenesis are hallmarks of aging, acting as drivers of some age-associated pathologies, including cancer1-3. Somatic cells engage multiple layers of protection against mutagenesis, including detoxification of genotoxic metabolites; repair of DNA damage; and elimination of cells which suffer excessive damage4-7. In this context, the intrinsic apoptotic pathway is engaged in response to activation of the DNA damage response (DDR) and is thought to play a major role in limiting accumulation of mutations, particularly in cells that act as an origin for cancer, such as somatic stem cells8,9. However, the dissection of the relative contribution of different protective mechanisms that restrict mutagenesis in such cells is confounded by the long time frame of experiments; relatively low mutation burden in non-malignant cells; and high variance across individuals due to differences in germ line and environment. Here we employ deep whole-genome sequencing (WGS) combined with extended time-course sampling from a range of experimental mouse models to study mutation acquisition in hematopoietic stem cells (HSCs) during aging. Having validated that murine HSCs recapitulate mutation acquisition patterns observed in aged human HSCs, we made the surprising discovery that apoptosis has a negligible role in restricting mutagenesis. Instead, we found that HSC dormancy inhibits mutagenesis during normal aging, with dormant HSCs from old mice demonstrating a mutation burden akin to their young counterparts. Importantly, breaking HSC dormancy via induction of sterile inflammation led to a dramatic acceleration in mutation rate, demonstrating that non-genotoxic environmental stimuli can modulate genome stability. These findings provide new insights into the correlation between inflammation and both aging and carcinogenesis.

The pace of ageing varies markedly among vertebrate species and individuals. However, the mechanisms underlying these differences in ageing rates remain unclear. Here, we show that the activity of the gut ceramidase Asah2 determines species- and strain-specific rates of vertebrate ageing. Comparative genomic analyses of vertebrate species and strains with different ageing rates reveal an association between low Asah2 activity and increased lifespan. Using the ultra-short-lived killifish Nothobranchius furzeri as a model, we demonstrate that knockout of Asah2 (asah2 KO) extends lifespan and attenuates systemic ageing phenotypes, including declines in locomotor activity, abnormal protein accumulation in the brain, and accumulation of senescent cells in the liver. asah2 KO elevates levels of ceramide species with long-chain fatty acids in the intestine, and supplementation with these ceramide species suppresses ageing phenotypes and extends lifespan in wild-type fish. asah2 KO and ceramide supplementation alter gut microbiota composition, and asah2 KO-derived microbiota transplantation attenuates ageing phenotypes, suggesting that reduced Asah2 activity prevents ageing through intestinal ceramide-mediated modulation of the microbiota. Given the evolutionary conservation of the Asah2 gene and its age-dependent upregulation in fish and humans, Asah2 and ceramides may act as ageing accelerators and decelerators, respectively, across animal species.

Chronic inflammation and cellular stress are hallmarks of aging, obesity, and type 2 diabetes (T2D), but whether these programs can be modulated by lifestyle intervention in late life, particularly in the presence of established metabolic disease, remain unknown. We profiled circulating immune cells from older adults with obesity and T2D (ages 66-83 years; n = 9) before and after a 6-month lifestyle intervention combining caloric restriction with exercise training. Participants showed substantial weight loss ([~]7%) alongside improvements in glycemic control, insulin sensitivity, and physical performance. Longitudinal single-cell transcriptomic and epigenomic profiling identified two major changes. First, intervention was associated with downregulation of inflammatory and endoplasmic reticulum (ER) stress transcriptional programs, with the most pronounced effects observed in CD14+ monocytes. DDIT3 (CHOP) was transcriptionally and epigenetically downregulated and its inferred regulatory network encompassed multiple inflammatory mediators. Second, naive CD4+ T, naive Treg, and naive B cells exhibited an upregulation of naive cell identity genes, with naiveness scores increasing after intervention, which declines with age in an independent healthy adult cohort. Together, these findings suggest that lifestyle intervention is associated with coordinated remodeling of both innate and adaptive immune compartments in older adults, revealing substantial plasticity of the aging immune system especially targeting ER stress, inflammation, and naive lymphocyte identity programs.

AO_SCPLOWBSTRACTC_SCPLOWMetabolomic aging clocks estimate biological age by modeling metabolite concentrations, thereby capturing aging signals from healthspan and adverse outcomes. However, existing clocks generally assume homogeneous aging trajectories and yield only a single age acceleration metric, limiting their capacity to capture inter-individual metabolic heterogeneity and characterize nuanced individual-level representations. To address these limitations, we proposed MetFoundation, a metabolomic foundation model pre-trained on nuclear magnetic resonance (NMR) metabolomic profiles from over 430,000 participants in UK Biobank via self-supervised learning. This large-scale pre-training enables MetFoundation to learn a metabolomic representation space that captures the complex, non-linear structure of systemic metabolism as reflected in NMR data. Building on MetFoundation, we developed a mortality-informed metabolomic aging clock by fine-tuning an attached survival module, deriving age acceleration that demonstrates significant associations with multiple age-related diseases and factors. More importantly, we utilized embeddings generated by MetFoundation to identify metabolic subtypes, resulting in 13 distinct subtypes with differential susceptibility profiles for major age-related diseases, particularly dementia and diabetes. This finding empirically demonstrated profound metabolic heterogeneity across populations, persisting even at comparable levels of age acceleration. To enhance clinical applicability, we further employed contrastive learning to distill a lightweight model that approximates the learned metabolomic representation space using only routine blood test measurements as inputs. Both hold-out testing within UK Biobank and the external validation in China Health and Retirement Longitudinal Study replicated similar disease onset patterns across the identified subtypes, underscoring the robust generalizability of MetFoundation and the translational potential of the discovered metabolic subtypes.

Somatic copy-number alterations (CNAs) accumulate with age and contribute to age-related pathologies, but their systematic characterization at single-cell resolution has been limited by the throughput-resolution trade-off in single-cell whole-genome sequencing. Here, we developed ultra-CNA, a high-resolution single-cell analysis pipeline that extends CNA detection to 10-kb bin resolution and jointly profiles copy-number and single-nucleotide variation (SNV). Re-analyzing the Tasc-WGS dataset (Liu et al., 2022; previously analyzed at 200-kb resolution) of 32,526 lymphocytes from 16 healthy donors aged 0.7 to 79 years, we constructed a multi-dimensional CNA spectrum stratified by chromosomal context, copy-number state, size, and clonality. Small (<1 Mb), rare, predominantly loss-type CNAs accumulated progressively and stochastically with age. Sex-chromosome loss showed divergent kinetics: chromosome X loss cells in females accumulated at +0.10 percentage points per year, versus +0.03 for chromosome Y loss cells in males. Sex chromosome loss also had specific consequences for autosomal SNV burden: in younger donors, loss cells carried fewer autosomal SNVs than non-loss cells, whereas in older donors (>30 years), loss cells exceeded non-loss cells in both sexes. Female X-loss cells additionally exhibited elevated 45S rDNA copy number, supporting biologically distinct consequences of X loss and LOY. Clock-like SBS1 and SBS5 mutational signatures co-accumulated with age across both sexes. Applying KL-divergence non-negative matrix factorization to the channelized CNA spectra, we constructed an aging clock validated by leave-one-sample-out cross-validation. Applied to a matched esophageal cohort, the clock detected accelerated aging from normal squamous epithelium through Barretts esophagus to esophageal adenocarcinoma, with cancer-associated spectra additionally enriched for large, highly clonal events. Ultra-CNA thus provides a scalable framework for quantifying somatic genomic aging from blood and for detecting accelerated aging in cancer.

Cellular senescence, a hallmark of aging, leads to the accumulation of apoptosis-resistant cells that compromise tissue homeostasis. While senescent cells are known to influence neighboring cells through the senescence-associated secretory phenotype (SASP), the precise nature of the interactions between senescent and normal cells remains elusive. Here we show that progerin-induced senescent cells undergo apoptosis when co-cultured with normal cells. This elimination requires direct cell-cell contact and is mediated by the JNK and p38-MAPK pathways, leading to p53 upregulation and p21 downregulation in progerin-expressing cells. Furthermore, neighboring normal cells exert persistent mechanical compression on progerin-expressing cells prior to their elimination, consistent with mechanical cell competition. In contrast, p16-induced senescent cells resist elimination under the same co-culture conditions, maintaining high p21 levels. Our findings reveal a non-cell-autonomous mechanism for senescent cell clearance, providing new insights into the maintenance of tissue homeostasis during aging.

The mutation accumulation (MA) hypothesis posits that somatic mutations progressively escape selection and degrade tissue function during aging. Direct tests of this idea have been limited by the difficulty of predicting, at scale, the molecular consequences of individual somatic variants. Here I use AlphaGenome, a sequence-to-function deep learning model, to systematically score the predicted transcriptional impact of somatic mutations under a nested series of designs spanning individual variants, co-occurring variant bundles, and real mutation catalogues. First, I characterize the genome-wide effect-size baseline by scoring 4,000 random single-nucleotide variants (SNVs) in colon tissue, together with 1-Mb-window combined-effect tests. Second, I extend this baseline to gene-body resolution with a 60-cell x 4,000-SNV simulation and pseudobulk RNA-seq aggregation. Third, I analyze the real somatic mutation catalogue of Cagan et al. (Nature, 2022), scoring 54,158 substitutions and 9,799 indels from 54 mouse colonic crypts plus three human samples, together with region- and gene-level enrichment tests against GENCODE. Across all analyses, both random and real somatic variants, including single-nucleotide variants and indels, produce predicted expression changes whose distributions lie three to four orders of magnitude below the tissues endogenous aging transcriptional program. These results argue against a simple, direct mutation-accumulation explanation for the age-associated transcriptional signature of colonic epithelium and redirect attention to epigenetic and regulatory mechanisms.

Age-dependent changes in the major neuroglial junctional channel Connexin43 (Cx43) are poorly defined. We integrated public multi-organ and single-cell datasets with high-resolution morphological, biochemical, and functional analyses of human and mouse brains. We reveal a non-linear aging trajectory for Cx43, marked by an adaptational midlife elevation followed by a late-life decline. These molecular changes proceed in the absence of significant cell loss but are associated with extensive glial remodeling. Notably, while astrocytic gap junction coupling in the hippocampus remains largely preserved, aging induces a selective increase in hemichannel mediated dye uptake in both microglia and hippocampal astrocytes. In human cortical and hippocampal tissues, we confirm that aging drives a significant reduction in astrocytic Cx43 expression, alongside characteristic morphological simplification of cell structure and domain contraction. Together, our findings redefine the aging brain as a state of active, multi-level glial remodeling rather than a simple decline in connexin-mediated communication.

Neuroectoderm-derived tissues are highly metabolically active and exhibit minimal regenerative turnover, rendering them uniquely vulnerable to age-related stress while preserving undiluted degenerative signals. Yet aging dynamics in these tissues remain elusive in living primates. Here, we introduce an in vivo neuroectodermal aging clock and trace its trajectory in 66,602 human adults and six rhesus macaques across nine health and disease cohorts using an in situ optical biopsy. Through a digital histology atlas integrated with artificial intelligence, we resolve tissue representations of neuroectodermal aging within the human retina, predominantly localized to the metabolically active ganglion and bipolar cell populations and the photoreceptor complex, while demonstrating their evolutionary conservation across primate species. Neuroectodermal aging predicts health and longevity, scales across space and time, and captures preclinical aging signals within and beyond the neuroectodermal compartment. This framework is further validated in a diabetic population, where robust prognostic and dynamic sensitivity are preserved across physiological and perturbed states. Our work establishes a scalable framework for resolving neuroectodermal aging in living primates and linking tissue-level vulnerability to systemic health trajectories.

Nucleosomes control access to gene promoters. Histone H3 lysine 4 tri-methylation, catalyzed by 6 KMT2 complexes, correlates with accessible promoters and gene expression. The catalytic activity of KMT2 enzymes depends on an obligatory core complex with ASH2L being an essential subunit. We find that PROTAC induced depletion of ASH2L reduces H3K4me3, deregulates gene expression and prevents proliferation. Upon prolonged ASH2L loss, cells develop a senescent phenotype, a process linked to aging and disease. Competing the PROTAC reactivates ASH2L, reestablishes H3K4me3 at promoters and reverts gene expression changes. Cells reenter the cell cycle and resume proliferation, thereby reverting senescence. Structure-function studies demonstrate that these molecular and cellular consequences are primarily due to the loss of ASH2L functions associated with KMT2 complexes. Together, these findings indicate that stress inflicted by the loss of KMT2 catalytic activities promotes a reversible senescence phenotype, suggesting that the functions of KMT2 complexes are implicated in aging. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=127 SRC="FIGDIR/small/722411v1_ufig1.gif" ALT="Figure 1"> View larger version (30K): org.highwire.dtl.DTLVardef@10ace2forg.highwire.dtl.DTLVardef@667c81org.highwire.dtl.DTLVardef@78039dorg.highwire.dtl.DTLVardef@13563be_HPS_FORMAT_FIGEXP M_FIG C_FIG

Aging is the primary driver of chronic disease and mortality, requiring comprehensive frameworks for quantification of aging and nomination of longevity interventions. We developed mAge (multimodal age), a biological aging framework that integrates plasma proteomics, wearables, and mortality hazard to predict biological age, intrinsic capacity, and mortality risk. By combining proteomic and wearable data in UK Biobank samples, mAge exceeds unimodal baseline age prediction to 0.87 test R{superscript 2} and 2.3 years mean error, and reduces unimodal baseline mortality prediction error by 21%. We further constructed organ-and cell type-specific biological clocks that quantify aging across 49 distinct subsystems, revealing that cardiac, immune, and intracellular protein signatures benefit most from wearable integration. By mapping data to FDA-approved drug targets, we identified interventions, such as GLP-1 receptor agonists, gabapentin, and ACE inhibitors, that are associated with lower overall and subsystem-specific proteomic age and mortality risk or are associated with longer time-to-death and later age-at-death in longitudinal and deceased cohorts. mAge establishes a scalable framework for nominating and validating personalized longevity interventions, bridging continuous digital monitoring with molecular aging diagnostics.

Epigenome-wide association studies implicate DNA methylation in the development and progression of Alzheimers disease (AD). Although recent studies show that the epigenetics of non-neuronal cell types contribute to disease risk, the role of the methylome in individual glial cell types (i.e., astrocytes, oligodendrocytes) in biological aging and AD pathogenesis is unclear. In this study, we examined archived DNA methylation data across 13 cohorts and performed cell type deconvolution in silico to identify novel epigenetic signatures associated with aging and AD in glial cells. We observed pronounced age-associated methylation in astrocytes within the prefrontal cortex, whereas oligodendrocytes of the entorhinal cortex show the most differential methylation with AD status. Astrocytes, along with neurons, within the prefrontal cortex, emerge as key players in Braak stage-associated methylation, exhibiting strong concordance with previously reported associations at the brain tissue level. Age-associated changes in oligodendrocytes exhibit strong directional correlation with, and amplification of age-related effects with AD that affect neurodevelopmental processes, while AD-related methylation changes at age-associated sites in astrocytes diverge from those representative of normative aging processes. Our study expands on previous findings and reveals glial-specific methylation patterns associated with epigenetic aging and AD.

Biological aging is heterogeneous across organ systems, yet whether CT-derived abdominal aging provides prognostic value beyond routine clinical data and whether organ decomposition adds beyond a unified estimate remains untested. We developed and evaluated organ-specific and ensemble biological age models from radiomic features across five abdominal organs in 68,675 CT scans from 32,883 subjects, evaluated on alignment with chronological age of healthy subjects (nested cross validation: MAE=3.68 years, R^2=0.90). In sequential analyses restricted to adults aged 20-60 years which is the stratum of strongest BAG-disease association, ensemble biological age gaps provided incremental prognostic value beyond demographic covariates for all-cause disease and mortality (Delta C-index=0.141, 0.051) and beyond routine blood biomarkers (Delta C-index=0.048), confirming CT-derived aging captures structural information beyond laboratory markers. Organ-specific biological age added incremental prognostic value beyond ensemble selectively for focal diseases: cardiovascular (aorta, Delta C-index=0.091) and hepato-pancreatic (pancreas, Delta C-index=0.096). These findings establish a hierarchical organization of CT-derived biological aging, positioning routine CT as a source that adds prognostic value to existing clinical biomarkers.

Muscle health varies continuously from optimal function to severe pathology, yet no unified genetic framework quantifies this spectrum objectively. Here we develop MyoScore, a transcriptomic scoring system derived from transcriptome-wide association studies of 27 muscle-related phenotypes in over one million participants. TWAS selects genes whose genetically regulated expression in skeletal muscle associates with muscle-related traits, providing the genetic anchoring of the scoring system, while MyoScore itself is computed from measured bulk RNA-seq expression in new samples. From 1,116 transcriptome-wide association study (TWAS)-significant genes, 417 are expressed in skeletal muscle and form the basis of the scoring system. These genes are organized into five dimensions of muscle biology (Strength, Mass, LeanMuscle, Youth and Resilience), each scored from 0 to 100. Across 1,722 human skeletal muscle transcriptomes from four independent cohorts, MyoScore defines a continuous four-stage muscle health spectrum, discriminates healthy from diseased muscle (area under the curve 0.751-0.873), and correlates with histopathological severity, quantitative MRI and clinical outcomes. Functional validation through iPSC-to-myotube differentiation supports predicted expression changes for novel MyoScore genes. UK Biobank analysis of blood biomarker proxies in 467,123 participants demonstrates concordant associations with muscle phenotypes, and two-sample Mendelian randomization using skeletal muscle cis-eQTL supports causal directionality for 78% of gene-outcome pairs tested. Single-cell validation across 475,584 cells from two independent muscle ageing atlases shows that pseudobulk MyoScore declines with age, with type II myofibre nuclei most affected. Together, MyoScore establishes the first genetically anchored, dimension-resolved quantification of human muscle health, enabling objective assessment, patient stratification and biomarker discovery across the full spectrum from optimal function to severe disease.

Tinnitus, the perception of sound without an external source, affects 10-15% of individuals, yet its neural mechanisms remain poorly understood. Building on evidence that chronological age predicts tinnitus risk beyond hearing loss, we tested the hypothesis that accelerated neural aging increases susceptibility to tinnitus by integrating cross-sectional resting-state MEG with longitudinal structural imaging data. In a large MEG dataset, spectral parametrization revealed that age-neural relationships were amplified in the tinnitus group compared to age-, sex- & hearing-matched controls. Complementing these findings, prospective analyses using data from the UK Biobank showed that among participants without tinnitus at baseline, stronger age-related declines in white-matter density predicted later tinnitus onset. Collectively, these converging functional and structural findings support accelerated brain aging as a key risk factor for tinnitus.