Longevity Papers

Kompot is a statistical framework for holistic comparison of multi-condition single-cell datasets, supporting both differential abundance and differential expression. Differential abundance captures changes in how cells populate the phenotypic manifold across conditions, while differential expression identifies condition-specific changes in gene regulation that may be localized to particular regions of that manifold. Kompot models the distribution of cells and gene expression as continuous functions over a low-dimensional representation of cell states, enabling single-cell resolution inference with calibrated uncertainty estimates. Applying Kompot to aging murine bone marrow, we identified a continuum of shifts in hematopoietic stem cell and mature cell states, transcriptional remodeling of monocytes independent of compositional changes, and divergent regulation of oxidative stress response genes across cell types. By capturing both global and cell-state specific effects of perturbation, Kompot reveals how aging reshapes cellular identity and regulatory programs across the hematopoietic landscape. This framework is broadly applicable to dissecting condition-specific effects in complex single-cell landscapes.

Post-translational modifications (PTMs) regulate protein homeostasis, but how aging impacts PTMs remains unclear. Here, we used mass spectrometry to reveal changes in hundreds of protein ubiquitylation, acetylation, and phosphorylation sites in the mouse aging brain. We show that aging has a major impact on protein ubiquitylation. 29% of the quantified ubiquitylation sites were affected independently of protein abundance, indicating altered PTM stoichiometry. Using iPSC-derived neurons, we estimated that 35% of ubiquitylation changes observed in the aged brain can be attributed to reduced proteasome activity. Finally, we tested whether protein ubiquitylation in the brain can be influenced by dietary intervention. We found that one cycle of dietary restriction and re-feeding modifies the brain ubiquitylome, rescuing some but exacerbating other ubiquitylation changes observed in old brains. Our findings reveal an age-dependent ubiquitylation signature modifiable by dietary intervention, providing insights into mechanisms of protein homeostasis impairment and highlighting potential biomarkers of brain aging.

Declines in cardiometabolic health among older individuals are so ubiquitous in Western, high-income countries that non-communicable diseases (NCDs) like type 2 diabetes, hypertension, and cardiovascular disease have been termed "diseases of aging". In contrast, research from non-industrial contexts has found low rates of cardiometabolic NCDs in old age, suggesting protective effects of lifestyle. To test if industrialization and urbanization generates or magnifies age-associated cardiometabolic health patterns, within-population analyses are needed. We worked with Turkana pastoralists of Kenya and Orang Asli mixed subsistence groups of Peninsular Malaysia-two groups that are transitioning from non-industrial to urban, market-integrated lifestyles. We find that rural, non-industrial environments produce minimal to modest age-dependent increases in body size, lipid, and blood pressure traits, and that urban environments significantly amplify age effects in repeatable ways across two distinct populations. However, we did not find that urban environments consistently accelerate biomarkers of more generalized functional capacity and biological aging, namely grip strength, walking speed, and epigenetic age. Together, these findings challenge the view that cardiometabolic "diseases of aging" are an intrinsic feature of aging, instead implicating urban lifestyle features as drivers of age-associated variation; however, these same lifestyle exposures may have heterogeneous effects on biological aging. These results underscore the urgency of understanding how rapid lifestyle changes shape aging trajectories, especially in populations undergoing industrial transitions.

The focus of aging research has shifted from increasing lifespan to enhancing healthspan to reduce the time spent living with disability. Despite significant efforts to develop biomarkers of aging, few studies have focused on biomarkers of healthspan. We developed a proteomics-based signature of healthspan [healthspan proteomic score (HPS)] using proteomic data from the Olink Explore 3072 assay in the UK Biobank Pharma Proteomics Project (53,018 individuals and 2,920 proteins). A lower HPS was associated with higher mortality risk and several age-related conditions, such as chronic obstructive pulmonary disease, diabetes, heart failure, cancer, myocardial infarction, dementia, and stroke. HPS showed superior predictive accuracy for these outcomes compared to other biological age measures. Proteins associated with HPS were enriched in hallmark pathways such as immune response, inflammation, cellular signaling, and metabolic regulation. The external validity was evaluated using the Essential Hypertension Epigenetics study with proteomic data also from the Olink Explore 3072 and complementary epigenetic data, making it a valuable tool for assessing healthspan and as a potential surrogate marker to complement existing proteomic and epigenetic biological age measures in geroscience-guided studies.

Elucidating the socio-ecological factors that shape patterns of epigenetic modification in long-lived vertebrates is of broad interest to evolutionary biologists, geroscientists, and ecologists. However, aging research in wild populations is limited due to inability to measure cellular hallmarks of aging noninvasively. Here, we demonstrate that cellular DNA methylation (DNAm) profiles from fecal samples provide an accurate and reliable molecular clock in wild capuchin monkeys. Analysis of blood, feces, and urine samples from a closely related species shows that DNAm differentiates between species and different types of biological samples. We further find age-associated differences in DNAm relevant to cellular damage, inflammation, and senescence, consistent with hallmarks conserved across humans and other mammalian species, speaking to the comparative potential. By demonstrating that DNAm can be studied non-invasively in wild animals, our research opens new avenues in the study of modifiers of the pace of aging, and increases potential for cross-population and species comparisons.

Multiple studies in mice with genetically disrupted growth hormone (GH) signaling have demonstrated that such disruption results in reduced body size, robustly increased longevity (> 50% in some cases), and improvements across multiple health parameters. However, it remains unclear how generalizable these findings are across mammals. Evidence in rats is limited and inconsistent. These conflicting results highlight the need for further investigation into the role of GH signaling in longevity across species. To address this gap, we developed a novel GH-deficient rat model using CRISPR/Cas9 technology to introduce a 10 bp deletion in exon 3 of the gene encoding rat GH-releasing hormone (GHRH) yielding a non-functional GHRH product. Physiological characterization of GHRH knockout (KO) rats revealed that they were half the body weight of wild-type controls. Additionally, relative to controls, they displayed an increased percent body fat, enhanced insulin sensitivity, reduced circulating insulin-like growth factor I (IGF-I) concentration, and a decreased reliance on glucose oxidation for energy metabolism, as determined by indirect calorimetry. Analysis of the gut microbial community in adult GHRH-KO rats further revealed a less diverse male microbiome, but a more diverse female KO microbiome compared to controls. Collectively, these findings demonstrate that multiple aspects of the GH activity-deficient phenotype, well-documented in mice, are faithfully recapitulated in our rat model. Therefore, the GHRH-deficient rat model represents a valuable new tool for advancing our understanding of the role of GH signaling in aging processes.

The geroprotective effects of rapamycin in mitigating frailty and cognitive complications in the perioperative period remains unknown. Of 39 C57BL/6 mice tested, 19 were young (16 weeks), and 20 were old (80 weeks). The interventional group (10 old, 10 young) received daily oral rapamycin for 8 weeks pre-op compared to controls (10 old, 9 young). Sham laparotomy was performed at week 9. Perioperative frailty was assessed using a murine clinical frailty scale, preoperatively and at 1, 4 and 8 weeks postoperatively. Spatial memory was assessed using the Barnes maze preoperatively, and at weeks 1 and 4 post-op. Rapamycin treatment is associated with significantly less decline in postoperative clinical frailty(p < 0.05). Subgroup analysis revealed similar findings for old and young mice. The rapamycin group demonstrated improved cognitive performance at 1-week postoperatively (β 40.18, 95%C.I. 8.70-71.67, p = 0.012), but only in older mice (β 54.51, 95%C.I. 6.77-102.25, p = 0.025). In a pre-clinical animal model of anesthesia and surgery, rapamycin supplementation protected against surgery-induced frailty and short-term postoperative cognitive dysfunction.

Loss of Y chromosome (LOY) and clonal hematopoiesis of indeterminate potential (CHIP) are common age-related events associated with multiple adverse outcomes in the elderly. While LOY has been associated with higher risk of Alzheimer disease (AD), CHIP has been suggested to perform a protective role against AD. Moreover, the co-occurrence of CHIP and LOY is debated. We performed deep whole-exome sequencing of FACS-isolated CD4T lymphocytes, NK and myeloid cells from men with AD and controls exhibiting either LOY or retention of Y chromosome (ROY). We found 39 sequence variants in known (canonical) myeloid driver genes of clonal hematopoiesis (MD-CH) and known lymphoid driver genes (LD-CH), and maximally 14(35%) of these could co-exist with LOY within the same clone. We further describe 192 unknown drivers of clonal hematopoiesis (UD-CH), which were markedly enriched in AD-LOY individuals (odds ratio=4.8, Benjamini-Hochberg adjustedp=0.041), and over 20% of these variants were protein-truncating. In myeloid cells, the total burden of all detected drivers correlated with the percentage of LOY cells (Spearman{rho}=0.52, adjustedp=0.00041). In conclusion, our findings suggest that LOY acts as the primary driver of clonal hematopoiesis in AD by seeding myeloid clones. These clones may subsequently accumulate additional, often truncating, UD variants, while most canonical CHIP mutations arise independently of LOY. Our study delineates distinct yet partially overlapping clonal architectures for LOY and CHIP in late-onset AD and underscores LOY-driven myeloid expansion as a potential contributor to disease pathogenesis.

Background: Although the connection between aging and neurodegenerative pathologies like Alzheimer\'s disease (AD) has long been recognized, the underlying pathological mechanisms remain largely unknown. Senescent brain cells build up in the brains of AD patients and a causal link has been established between senescence and AD-related tauopathy. Methods: To investigate the role of cellular senescence in tau-mediated neuropathology, we crossed the Terc knockout (Terc-/-) senescent mouse model with the P301S tauopathy model (PS19 line). Using brain sections and protein extracts, we employed Western blot and immunostaining analyses to investigate the expression of tau-related neuropathological features within a senescent context. Results: We found that the brains of 6- and 9-month-old Terc-/- mice exhibit significant telomere attrition and signs of cellular senescence. Introducing a senescent phenotype in a tauopathy mouse model resulted in increased tau phosphorylation at key residues, particularly in the hippocampus. Over time, this was associated with enhanced tau truncation and aggregation. These pathological changes were accompanied by exacerbated astrocyte and microglial activation, as well as selective neuronal loss in vulnerable brain regions. Conclusions: Overall, our findings place senescence as a key upstream regulator of tau pathology, suggesting that targeting senescent cells and their detrimental effects may offer promising therapeutic strategies for AD and other related tauopathies.

Age-related decline in intrinsic capacity (IC), defined as the sum of an individual's physical and mental capacities, is a cornerstone for promoting healthy aging by prioritizing maintenance of function over disease treatment. However, assessing IC is resource-intensive, and the molecular and cellular bases of its decline are poorly understood. Here we used the INSPIRE-T cohort (1,014 individuals aged 20-102 years) to construct the IC clock, a DNA methylation-based predictor of IC, trained on the clinical evaluation of cognition, locomotion, psychological well-being, sensory abilities and vitality. In the Framingham Heart Study, DNA methylation IC outperforms first-generation and second-generation epigenetic clocks in predicting all-cause mortality, and it is strongly associated with changes in molecular and cellular immune and inflammatory biomarkers, functional and clinical endpoints, health risk factors and lifestyle choices. These findings establish the IC clock as a validated tool bridging molecular readouts of aging and clinical assessments of IC.

Intervertebral disc degeneration (IVDD) is a common pathology involving various degenerative diseases of the spine, with nucleus pulposus cell (NPC) senescence playing an important role in its pathogenesis. Transcriptional and epigenetic processes have been increasingly implicated in aging and longevity. E74-like factor 1 (ELF1) is a member of the erythroblast transformation specific family of proteins, which induce gene transcription by binding to gene promoters or enhancer sequences. However, the role of ELF1 in age-related diseases is unclear, with no reports of its involvement in NPC senescence or IVDD. ELF1 expression levels were assessed in human NP samples from IVDD patients, IVDD animal models, and naturally aged NP samples. Adeno-associated virus 5 (AAV5) vector-mediated Elf1 overexpressing mice and Elf1 knockout (KO) mice were used to investigate its role in NPC senescence and IVDD in vivo. The m6A methylase METTL3 and reading protein YTHDF2 were identified as downstream effectors of ELF1 using proteomic sequencing, RNA sequencing, ChIP-seq, promoter prediction, and binding analyses. MepRIP-qPCR, RNA pulldown, and double luciferase point mutation experiments revealed that METTL3 and YTHDF2 can recognize the m6A site on E2F3 mRNA, a key cell cycle gene. Finally, virtual screening techniques and various experiments were used to identify small molecule targets for ELF1 inhibition. ELF1 was found to drive m6A modification changes during NPC aging. The small molecule mycophenolate mofetil (MMF) could successfully target and inhibit ELF1 expression. In senescent NPCs, ELF1 can bind to the METTL3 and YTHDF2 gene promoter regions. Overexpressing METTL3 increased the E2F3 mRNA m6A modification abundance, while YTHDF2 was recruited to recognize this m6A site. This can accelerate the E2F3 mRNA degradation rate and ultimately lead to the onset of G1/S cell cycle arrest in NPC. For the first time, the transcription factor ELF1 has been identified as a novel regulator of NPC senescence and IVDD, which involves the ELF1-METTL3/YTHDF2-m6A-E2F3 axis. MMF, a small molecule designed to inhibit ELF1 and delay NPC senescence, was screened for the first time. This can potentially lead to new epigenetic therapeutic strategies for drug discovery and development for the clinical treatment of IVDD.

Mice missing the complex I subunit Ndufs4 of the electron transport chain are widely used as a leading animal model of Leigh syndrome, a pediatric neurodegenerative disorder that leads to premature death. More broadly, this animal model has enabled a better understanding of the pathophysiology of mitochondrial disease and mitochondrial dysfunction in sporadic disorders. Intriguingly, longevity interventions are very effective at treating symptoms of disease in this model. Herein, we introduce the model and its notable features that may help provide insights in longevity research. We performed a retrospective analysis of historical data from our laboratories over the past 10 years regarding the use of this animal model in aging studies, the manifestation and progression of mitochondrial disease, and factors that influence their premature death. We observed a correlation between weight and lifespan in female animals and a sex-independent correlation between the onset of clasping, a typical neurodegenerative symptom, and overall survival. We observed a sexual dimorphism in lifespan with female mice being more resilient despite a similar age of onset of disease symptoms. Lastly, we report increased lifespan and delayed onset of disease symptoms following treatment with 17-alpha-estradiol, a non-feminizing estrogen which can extend lifespan in genetically heterogeneous mice. This analysis serves as a useful guide for researchers utilizing this animal in the discovery of effective interventions for longevity and to prevent the onset of disease. It suggests there may be unprecedented underlying sex-specific differences in patients with Leigh syndrome and further strengthens the connection between normative aging and mitochondrial dysfunction.

As the prevalence of age-related diseases rises, understanding and modulating the aging process is becoming a priority. Transcriptomic aging clocks (TACs) hold great promise for this endeavor, yet most are hampered by platform or tissue specificity and limited accessibility. Here, we introduce Pasta, a robust and broadly applicable TAC based on a novel age-shift learning strategy. Pasta accurately predicts relative age from bulk, single-cell, and microarray data, capturing senescent and stem-like cellular states through signatures enriched in p53 and DNA damage response pathways. Its predictions correlate with tumor grade and patient survival, underscoring clinical relevance. Applied to the CMAP L1000 dataset, Pasta identified known and novel age-modulatory compounds and genetic perturbations, and highlighted mitochondrial translation and mRNA splicing as key determinants of the cellular propensity for aging and rejuvenation, respectively. Supporting Pasta\'s predictive power, we validated pralatrexate as a potent senescence inducer and piperlongumine as a rejuvenating agent. Strikingly, chemotherapy drugs were highly enriched among pro-aging hits. Taken together, Pasta represents a powerful and generalizable tool for aging research and therapeutic discovery, distributed as an easy-to-use R package on GitHub.

Debate regarding the premature aging of knee joints in acquired immune deficiency syndrome (AIDS) patients has remained contentious, with conjectures pointing towards its correlation with distinct antiviral regimes. Protease inhibitors (PIs) stand as a prominent class of antiviral agents frequently utilized in AIDS management and have been significantly linked to premature senescence. This study aimed to investigate whether PI-containing regimens would accelerate osteoarthritis (OA) development and explore the molecular mechanisms underlying this association. A retrospective cohort of 151 HIV-infected individuals, categorized into PI and non-PI groups, was established. Patients in PI group exhibited lower KOOS and a higher prevalence of radiological knee OA than those in non-PI group. Additionally, 25 anti-HIV drugs were screened and among all antiviral drugs, lopinavir had the most detrimental impact on cartilage anabolism, accelerating cartilage senescence and promoting mouse OA development. Mechanistically, lopinavir accelerated cellular senescence by inhibiting Zmpste24 and interfering nuclear membrane stability, which leads to decreased binding between nuclear membrane-binding protein Usp7 and Mdm2 and activates Usp7/Mdm2/p53 pathway. Zmpste24 overexpression reduces OA severity in mice. These findings suggest that PI-containing regimens accelerate cartilage senescence and OA development through Zmpste24 inhibition, which provides new insights into the selection of HIV regimens.

Hippocampal adult neural stem cells (NSCs) contribute to neurogenesis and astrogliogenesis throughout life. They play multifaceted roles in hippocampal function, including memory processing, stress regulation, and cognitive flexibility. Located in unique neurogenic niches like the subgranular zone of the hippocampal dentate gyrus, NSCs exhibit notable heterogeneity and can be classified into quiescent, activated, and intermediate transitioning states. This diversity, while instrumental to their adaptability and function, presents challenges in molecular classification and functional interrogation. Here, we discuss current limitations and compare NSC transcriptional profiles from publicly available single-cell RNA sequencing datasets. We address discrepancies in NSC classification between studies, identify conserved gene expression profiles, and propose new markers that could serve as standardized references. Furthermore, we explore how pseudotime inference analyses provide insights into the temporal dynamics of NSCs and their progression toward neural progenitors, further aiming to optimize their classification. We also examine cellular changes in NSCs during aging and explore the potential of these cells to undergo senescence. Our work helps to resolve inconsistencies in current cell-type annotations in literature and proposes a framework to study and classify the different states of NSCs, thereby offering a better understanding of their dynamic roles in neurogenesis, aging, and cellular senescence.

Neural stem cells (NSCs) in the mammalian brain decline rapidly with age, leading to impairment of hippocampal memory function in later life. However, the relationship between epigenetic remodeling and transcriptional regulation that compromises hippocampal NSC activity during the early stage of chronological aging remains unclear. Here, we performed single-cell RNA sequencing (scRNA-seq) and single-cell ATAC sequencing (scATAC-seq) on NSCs and newly generated neurons across different stages. Integrated data analysis revealed continuous alterations in the chromatin profile of hippocampal NSCs and their progeny from neonatal to mature adult stages, accompanied by consistent changes in transcriptional profiles. Further, decreased expression of Setd8, encoding the enzyme for histone H4 monomethylation at lysine 20 (H4K20me1), underlies age-related changes in mouse hippocampal NSCs. Notably, depletion of Setd8 elicits alterations in gene expression and epigenetic regulation that phenocopy age-related changes, and impairs NSC activity, leading to hippocampal memory deficits. Together, our study provides a global map of longitudinal chromatin and transcriptome changes during brain aging and identifies mechanistic insights into early-onset decline of NSC activity and hippocampal neurogenesis that precedes functional aging.

The incidence of spine-related pathologies is expected to increase in developed countries due to ongoing fundamental demographic shifts toward an older population. These changes present significant challenges to public health, as healthcare systems worldwide must confront the burden of musculoskeletal aging and its related consequences. Here, we synthesize current knowledge on the biologic mechanisms underlying musculoskeletal aging, focusing on the implications for the aging spine. The complexity of the aging process, characterized by a convoluted interplay between genetic, environmental, and lifestyle factors, necessitates a comprehensive understanding of the biologic processes and reliable methods of surveying biologic states to inform effective diagnostic, predictive, and prognostic strategies. Biomarkers emerge as invaluable tools in this domain, offering insights into the early detection, risk assessment, and targeted intervention for age-related musculoskeletal decline. This review highlights various biomarker types including diagnostic, predictive, and prognostic, and explores their distinct roles in enhancing our understanding of musculoskeletal aging. Navigating the interconnected landscape of cellular senescence, sarcopenia, osteoporosis, and frailty, this review underscores the critical importance of developing personalized care approaches for the aging population. By identifying and integrating functional biomarkers, researchers and clinicians can elucidate the underlying mechanisms and devise tailored strategies to alleviate the musculoskeletal decline associated with the aging process. We envision an "active surveillance" future where biomarkers of musculoskeletal aging are integrated into clinical practice, empowering clinicians to make proactive, data-driven decisions that improve spine health for older adults.

Age-associated neurodegenerative diseases (NDDs), including Alzheimer's disease, Parkinson's disease, and amyotrophic lateral sclerosis, are marked by progressive degeneration of the nervous system. Current diagnostic approaches, such as neuroimaging and cerebrospinal fluid biomarkers, are invasive, costly, and lack early diagnostic reliability. Recent studies highlight the potential of extracellular vesicles, particularly exosomes, derived from erythrocytes or red blood cells (RBCs), as emerging indicators of aging and age-associated diseases. Exosomes carry noncoding RNA, lipid, and protein molecules, and modulate cellular pathways at distant sites, providing neuroprotective and anti-inflammatory effects. In this study, we isolated RBC-derived exosomes of young and old mice. MicroRNA sequencing analysis revealed differential expression of several miRNA species between young and old mice. We report an upregulation of miR-125a-5p and a downregulation of miR-302a-5p in old mice that are potentially linked to neurodegenerative pathways. This study underscores the potential of RBC-derived exosomes as noninvasive biomarkers for NDDs.

The elderly are at increased risk of bone fracture and more often consume poor quality diets, such as high-fat diet (HFD). We hypothesized that HFD exacerbates the loss of bone fracture resistance in aging. Female and male 5-month and 22-month C57BL/6JN mice were fed moderate HFD (45%) or low-fat diet (10%) for 8 weeks. All HFD groups showed disrupted glucose metabolism. Aging and HFD lowered bone fracture toughness, while aging alone reduced bone strength. Raman Spectroscopy demonstrated that aging and HFD differently impact bone matrix. Aging altered matrix properties but the effect depended on sex. Both sexes had higher carbonate content and altered collagen structure (I1670/I1690) with age but males also had increased crystallinity. HFD decreased mineral maturity (i.e., crystallinity) as well as altered collagen structure in females but not males. Untargeted metabolomics revealed that cortical tissue metabolism was dysregulated with aging and HFD. Aging and HFD affected pathways related to cellular function and viability, or glucose regulation, respectively. In aging mice, HFD also impacted osteoclast and adipocyte abundance and osteocyte viability in both sexes. Together, these data demonstrate that HFD exacerbates the loss of bone matrix quality and fracture resistance in aging C57BL/6JN mice.

Hematopoietic stem cell (HSC) transplantation offers a cure for a variety of blood disorders, predominantly affecting the elderly; however, its application, especially in this demographic, is limited by treatment toxicity. In response, we employ a murine transplantation model based on low-intensity conditioning protocols using antibody-mediated HSC depletion. While aging presents a significant barrier to effective HSC engraftment, optimizing HSC doses and non-genotoxic targeting methods greatly enhance the long-term multilineage activity of the transplanted cells. We demonstrate that young HSCs, once effectively engrafted in aged hosts, improve hematopoietic output and ameliorate age-compromised lymphopoiesis. This culminated in a strategy that robustly mitigates disease progression in a genetic model of myelodysplastic syndrome. These results suggest that non-genotoxic HSC transplantation could fundamentally change the clinical management of age-associated hematological disorders, offering a prophylactic tool to delay or even prevent their onset in elderly patients.

Biological aging and pressure overload-induced left ventricular cardiac hypertrophy (PO-CH) is marked by myocardial thickening, fibrosis, and functional decline, heightening the risk of heart failure. To advance therapeutic monitoring and intervention, we aimed to identify drug-responsive biomarkers with functional relevance to disease progression. Using rat models of biological aging (BA) and PO-CH, we evaluated the cardioprotective effects of Amalaki Rasayana (AR), a traditional nutraceutical, and its bioactive constituent gallic acid (GA), while concurrently profiling candidate serum biomarkers. Galectin-3 was present in full-length and oligomeric forms, with C-terminal (C-epitope) homo-oligomers closely associated with pathological remodeling. AR and GA significantly reduced these oligomers via cytoplasmic retention and phosphorylation-dependent downregulation of galectin-3 secretion, mitigating maladaptive cardiomyocyte signaling. Levels of atrial natriuretic peptide (ANP), cyclophilin A (PPIA), and albumin (ALB) showed consistent changes, reinforcing their utility as therapeutic response indicators. Findings were validated in sera from aged humans and patients responsive to clinical treatment, confirming translational potential. This study establishes a novel biomarker panel-galectin-3 C-epitope, ANP, PPIA, and ALB-for monitoring treatment efficacy and positions AR as a promising intervention in cardiac hypertrophy.

Information on individual age is a fundamental aspect in many ecological and evolutionary studies. However, accurate and non-lethal methods that can be applied to estimate the age of wild animals are often absent. Furthermore, since the process of ageing is accompanied by a physical decline and the deterioration of biological functions, the biological age often deviates from the chronological age. Epigenetic marks are widely suggested to be associated with this age-related physical decline, and especially changes in DNA methylation are suggested to be reliable age-predictive biomarkers. Here, we developed separate epigenetic clocks for ageing and development in a small passerine bird, the great tit (Parus major). The ageing clock was constructed and evaluated using erythrocyte DNA methylation data of 122 post-fledging individuals, and the developmental clock using 67 pre-fledging individuals from a wild population. Using a leave-one-out cross-validation approach, we were able to accurately predict the ages of individuals with median absolute deviations of 0.40 years for the ageing and 1.06 days for the development clock. Moreover, using existing data from a brood-size manipulation, we show that nestlings from reduced broods are estimated to be biologically older compared to control nestlings, while they are expected to have higher fitness. These epigenetic clocks provide further evidence that, as observed in mammals, changes in DNA methylation of certain CpG sites are highly correlated with chronological age in birds and this opens up new avenues for broad applications in behavioural and evolutionary ecology.

Aging is one of the most prominent risk factors for neurodegeneration, yet the molecular mechanisms underlying the deterioration of old neurons are mostly unknown. To efficiently study neurodegeneration in the context of aging, we transdifferentiated primary human fibroblasts from aged healthy donors directly into neurons, which retained their aging hallmarks, and we verified key findings in aged human and mouse brain tissue. Here we show that aged neurons are broadly depleted of RNA-binding proteins, especially spliceosome components. Intriguingly, splicing proteins-like the dementia- and ALS-associated protein TDP-43-mislocalize to the cytoplasm in aged neurons, which leads to widespread alternative splicing. Cytoplasmic spliceosome components are typically recruited to stress granules, but aged neurons suffer from chronic cellular stress that prevents this sequestration. We link chronic stress to the malfunctioning ubiquitylation machinery, poor HSP90α chaperone activity and the failure to respond to new stress events. Together, our data demonstrate that aging-linked deterioration of RNA biology is a key driver of poor resiliency in aged neurons.

Mitochondria play a pivotal role in energy production, signaling, and apoptosis. Yet, probing their functional state at the single-organelle level without invasive labels remains a major challenge. Here, we introduce a novel, label-free approach that leverages Atomic Force Microscopy (AFM) beyond its traditional imaging role, transforming it into a powerful tool for functional analysis of individual, isolated mitochondria. By immobilizing mouse liver mitochondria on polylysine-coated mica, we achieved nanoscale resolution of mitochondrial mechanical properties including height, height fluctuation power spectra, and Young\'s modulus, under different respiratory states. Strikingly, fluctuations in mitochondrial height fluctuations below 20 Hz showed robust correlation with the mitochondria membrane potential ({Delta}{psi}), a cornerstone of mitochondrial function. This relationship allows AFM to sensitively detect changes in the mitochondria bioenergetic status. Applying this method to mitochondria from liver-specific MTCH2 liver-conditional knockout mice, a model of mitochondrial malfunction, we confirmed AFM\'s diagnostic potential. The technique reliably distinguished malfunctional mitochondria, mirroring and adding new insights beyond conventional fluorescence assays. By bridging nanomechanics and mitochondrial bioenergetics, this approach paves the way for non-invasive, high-resolution diagnostics at the single-organelle level, holding promise to monitor the actual functional state of mitochondria in clinical settings.

The aging of mammalian ovary is accompanied by an increase in tissue fibrosis and heightened inflammation. Myeloid cells, including macrophages, monocytes, dendritic cells, and neutrophils, play pivotal roles in shaping the ovarian tissue microenvironment and regulating inflammatory responses. However, a comprehensive understanding of the roles of these cells in the ovarian aging process is lacking. To bridge this knowledge gap, we utilized single-cell RNA sequencing (scRNAseq) and flow cytometry analysis to functionally characterize CD45+ CD11b+ myeloid cell populations in young (3 months old) and aged (14-17 months old) murine ovaries. Our dataset unveiled the presence of five ovarian macrophage subsets, including a Cx3cr1lowCd81hi subset unique to the aged murine ovary. Most notably, our data revealed significant alterations in ANNEXIN and TGFβ signaling within aged ovarian myeloid cells, which suggest a novel mechanism contributing to the onset and progression of aging-associated inflammation and fibrosis in the ovarian tissue.

A major aging hallmark is the accumulation of cellular senescence burden. Over time, senescent cells contribute to tissue deterioration through chronic inflammation and fibrosis driven by the senescence-associated secretory phenotype (SASP). The human ovary is one of the first organs to age, and prominent age-related fibroinflammation within the ovarian microenvironment is consistent with the presence of senescent cells, but these cells have not been characterized in the human ovary. We thus established a doxorubicin-induced model of cellular senescence to establish a "senotype" (gene/protein signature of a senescence cell state) for ovarian senescent cells. Explants of human postmenopausal ovarian cortex and medulla were treated with doxorubicin for 24 h, followed by culture for up to 10 days in a doxorubicin-free medium. Tissue viability was confirmed by histology, lack of apoptosis, and continued glucose consumption by explants. Single nuclei sequencing and proteomics revealed an unbiased signature of ovarian senescence. We identified distinct senescence profiles for the cortex and medulla, driven predominantly by epithelial and stromal cells. Proteomics uncovered subregional differences in addition to 120 proteins common to the cortex and medulla SASP. Integration of transcriptomic and proteomic analyses revealed 26 shared markers, defining a senotype of doxorubicin-induced senescence unique to the postmenopausal ovary. A subset of these proteins: Lumican, SOD2, MYH9, and Periostin were mapped onto native tissue to reveal compartment-specific localization. This senotype will help determine the role of cellular senescence in ovarian aging, inform biomarker development to identify, and therapeutic applications to slow or reverse ovarian aging, senescence, and cancer.

Cellular epigenetic aging has become an important marker of healthy or unhealthy aging. The current study examined whether lifelong cumulative stressors across multiple domains were linked with epigenetic age acceleration (EAA; i.e., epigenetic age greater than chronological age) and whether psychological factors moderated this association. Dimensions of psychological well-being were hypothesized as protective factors, while neuroticism was posited as a vulnerability factor.

This study investigates the effects of N‑PEP‑12, a neuroprotective dietary supplement, on cognitive function, neuroplasticity, and neurogenesis in aged 129S1/SvImJ (S1) mice, which are known for age‑associated cognitive impairments. The primary objective was to determine whether N‑PEP‑12 could improve memory retention and enhance neural health by modulating hippocampal plasticity and neurogenesis. S1 mice were chronically treated with N‑PEP‑12 or a Vehicle to assess its impact on cognitive performance using cued fear conditioning (CFC) and object location memory (OLM) tests. Additionally, in vitro studies examined the effects of N‑PEP‑12 on neuroplasticity markers such as Neurofilament Light Chain (NF‑L) expression and vasopressin (AVP) promoter methylation, to elucidate the molecular mechanisms underlying cognitive enhancements. N‑PEP‑12 treatment significantly improved associative and contextual memory in the CFC and OLM tests respectively. In vitro assays revealed that N‑PEP‑12 increased NF‑L expression and decreased AVP promoter methylation, indicating enhanced neuroplasticity and neurogenesis. Furthermore, N‑PEP‑12 preserved blood‑brain barrier integrity under oxidative stress conditions, suggesting a protective role against vascular‑related cognitive decline. The findings suggest that N‑PEP‑12 promotes hippocampal health by enhancing neurogenesis and neuroplasticity, potentially mitigating age‑related cognitive decline. These results highlight N‑PEP‑12 as a promising agent for supporting healthy cognitive function in aging populations through the modulation of neurobiological pathways associated with learning and memory.

Telomeres are repetitive sequences of nucleotides at the end of chromosomes, whose evolution over time is intrinsically related to biological ageing. In most cells, with each cell division, telomeres shorten due to the so-called end replication problem, which can lead to replicative senescence and a variety of age-related diseases. On the other hand, in certain cells, the presence of the enzyme telomerase can lead to the lengthening of telomeres, which may delay or prevent the onset of such diseases but can also increase the risk of cancer. In this article, we propose a stochastic representation of this biological model, which takes into account multiple chromosomes per cell, the effect of telomerase, different cell types and the dependence of the distribution of telomere length on the dynamics of the process. We study theoretical properties of this model, including its long-term behaviour. In addition, we investigate numerically the impact of the model parameters on biologically relevant quantities, such as the Hayflick limit and the Malthusian parameter of the population of cells.

Elucidating the role of somatic mutations in cancer, healthy tissues, and aging depends on methods that can accurately characterize somatic mosaicism across different cell types, as well as assay their impact on cellular function. Current technologies to study cell-type-specific somatic mutations within tissues are low-throughput. We developed Duplex-Multiome, incorporating duplex consensus sequencing to accurately identify somatic single-nucleotide variants (sSNV) from the same nucleus simultaneously analyzed for single-nucleus ATAC-seq (snATAC-seq) and RNA-seq (snRNA-seq). By introducing strand-tagging into the construction of snATAC-seq libraries, duplex sequencing reduces sequencing error by >10,000-fold while eliminating artifactual mutational signatures. When applied to 98%/2% mixed cell lines, Duplex-Multiome identified sSNVs present in 2% of cells with 92% precision and accurately captured known sSNV mutational spectra, while revealing unexpected subclonal lineages. Duplex-Multiome of > 51,400 nuclei from postmortem brain tissue captured sSNV burdens and spectra across all major brain cell types and subtypes, including those difficult to assay by single-cell whole-genome sequencing (scWGS). This revealed for the first time that diverse neuronal and glial cell types show distinct rates and patterns of age-related mutation, while also directly discovering developmental cell lineage relationships. Duplex-Multiome identified clonal sSNVs occurring at increased rates in glia of certain aged brains, as well as clonal sSNVs that correlated with changes in expression of nearby genes, in both neurotypical and autism spectrum disorder (ASD) individuals, directly demonstrating that somatic mutagenesis can contribute to gene expression phenotypes. Duplex-Multiome can be easily adopted into the 10X Multiome protocol and will bridge somatic mosaicism to a wide range of phenotypic readouts across cell types and tissues.

Single-cell RNA sequencing (scRNA-seq) has significantly advanced our understanding of retinal aging, yet the specific molecular characteristics within cell populations remain incompletely defined. We profiled 223,612 single cells from 18 unfrozen human retinas obtained from 13 Chinese donors aged 34-92 years, providing an ethnically specific atlas across the adult lifespan. A sparsity-driven machine-learning (ML) pipeline (L1-regularized logistic regression, recursive feature elimination with cross-validation) identified age-discriminatory genes within each major retinal cell type, complemented by gene set scoring for cellular senescence and metabolic pathways. Using integrated differential expression and ML feature selection, we identified eleven major retinal cell populations and observed aging-associated shifts. ML classifiers achieved high accuracy (80-96%), particularly for microglia (96%), revealing mitochondria-centric aging signatures in rods and bipolar cells, proteostasis and retinoid metabolism in cones, and structural-RNA maintenance signatures in horizontal cells. This study delivers the first ML-derived, cell-type-specific aging gene signatures for the human retina in a Chinese cohort, offering a reference for population-tailored biomarker discovery.