Longevity Papers

The bone marrow vascular niche is a highly specialized network essential for governing the maintenance, differentiation, and mobilization of tissue-resident stem cells, notably hematopoietic stem cells. With ageing, the spatial organization and functional integrity of this vasculature undergo significant decline. While prior studies have characterized broad vessel types into arterioles, sinusoids, and transitional capillaries, the molecular heterogeneity and spatial structural remodeling of the bone marrow endothelium during ageing remain poorly defined. Through a multi-modal analysis of murine tibial bone marrow across the lifespan, we demonstrate that vascular remodeling is a spatially heterogeneous process characterized by profound sex-specific differences. Structurally, ageing precipitated significant bone marrow adiposity and a contraction of the microvascular network, changes that were markedly more pronounced in females. At the single-cell level, we identified sinusoidal endothelial cells (SECs) as a uniquely vulnerable population exhibiting age-related molecular deterioration. These alterations were driven by a specific bioenergetic collapse, marked by the downregulation of mitochondrial genes and critical HSC-retention factors. Our results reveal that vascular ageing is not a uniform decline but a subtype-specific mosaic of failure. The selective dysfunction and bioenergetic collapse of SECs emerge as a central driver of niche degradation, identifying this population as a key therapeutic target to combat age-related hematopoietic dysfunction.

Age-varying DNA methylation sites reflect increasing interindividual epigenetic divergence during aging, offering insights into health heterogeneity and potential for personalized interventions. Leveraging longitudinal DNA methylation data (3 waves over 5 years) from 135 relatively healthy Chinese older adults in the Rugao Longitudinal Ageing Study, we systematically characterized dynamic DNA methylation changes with age via mixed-effects modeling, identifying 125,353 age-associated (i.e., sites showing significant shifts in average methylation levels with age) and 3145 age-varying CpG sites (i.e., sites showing significant interindividual variability in methylation trajectories with age). Functional analysis revealed distinct enrichment profiles: age-associated CpG sites were enriched in nervous system development, cell signaling, and disease-related pathways, whereas age-varying CpG sites were enriched in cell adhesion, synaptic organization, and organ morphogenesis pathways. Notably, both categories showed significant enrichment in nervous system-related pathways, such as regulation of nervous system development and neuronal cell body. Established epigenetic clocks (e.g., HannumAge) were significantly enriched for age-associated CpG sites but not for age-varying sites. Furthermore, we quantified the pace of aging across eight major organ systems and identified 925 significant associations between organ-specific pace of aging and longitudinal methylation change rates at age-varying CpG sites. Pathway enrichment analysis revealed organ system-relevant biological functions-CpG sites associated with a given organ system were often enriched in pathways relevant to that system's function-with additional evidence of cross-system enrichment. Together, our findings elucidate the role of methylation variability in multi-organ systems aging and its potential for revealing mechanisms of aging heterogeneity and guiding precision monitoring and interventions.

Aging includes both continuous gradual decline from microscopic mechanisms together with major deficit onset events such as morbidity, disability and ultimately death. These deficit events are stochastic, obscuring the connection between aging mechanisms and overall health. We propose a framework for modelling both the gradual effects of aging together with health deficit onset events, as reflected in the frailty index (FI) - a quantitative measure of overall age-related health. We model damage and repair dynamics of the FI from individual health transitions within two large longitudinal studies of aging health, the Health and Retirement Study (HRS) and the English Longitudinal Study of Ageing (ELSA), which together included N=47592 individuals. We find that both damage resistance (robustness) and damage recovery (resilience) rates decline smoothly with both increasing age and with increasing FI, for both sexes. This leads to two distinct dynamical states: a robust and resilient young state of stable good health (low FI) and an older state that drifts towards poor health (high FI). These two health states are separated by a sharp transition near age 75. Since FI accumulation risk accelerates dramatically across this tipping point, ages 70-80 are crucial for understanding and managing late-life decline in health.

Hepatocyte polyploidization promotes liver homeostasis by enhancing resistance to cellular stress. Caspase-2, a proapoptotic protease, restricts polyploidization by deleting polyploid and aneuploid cells. While caspase-2 protects against diet-induced hepatic injury, it also acts as a tumor suppressor by controlling genomic instability and oxidative stress. To investigate these roles, we assessed hepatic ploidy dynamics, liver damage, and age-associated tumorigenesis in caspase-2-deficient and catalytically inactive mutant mice. We found that caspase-2 loss promotes early-onset hepatocyte hyperpolyploidy, accompanied by progressive liver inflammation, fibrosis, oxidative liver damage, ferroptosis, and higher incidence of spontaneous hepatocellular carcinoma in aged animals. Proteomic profiling revealed a pathogenic polyploidy-associated signature associated with caspase-2 deficiency and increased predisposition to liver disease and malignancy. These findings establish caspase-2 enzymatic activity as a critical regulator of hepatic genome stability and preventing age-related liver cancer that strongly argue against therapeutic caspase-2 inhibition as a strategy for managing liver injury or cancer risk.

Myocytes are exceptionally long-lived cells that must maintain proteome integrity over decades while adjusting for changes in functional output and metabolic demand. We used in vivo stable isotope labeling combined with mass spectrometry proteomics and correlated multi-isotope imaging mass spectrometry to quantify and visualize protein turnover across cardiac, fast-twitch, and slow-twitch skeletal muscles, creating a resource of hundreds of individual protein turnover rates from each tissue. We found that cardiac muscle has the highest rate of protein turnover, followed by slow-twitch skeletal muscle and then fast-twitch skeletal muscle, and that these different rates of protein turnover are driven by different levels of muscle use, rather than myosin isoform composition. We also identified protein age heterogeneity at the myofiber and sarcomere levels. These findings uncover fundamental principles of muscle protein maintenance and have broad implications for understanding cellular aging, muscle disease, and the design of therapeutic strategies targeting muscle protein turnover.

Alternative splicing is a key gene regulatory process that diversifies the proteome and controls gene dosage. Previous studies have detected aging-associated splicing changes across various tissues. However, their use of bulk RNA-seq obfuscates the impacted cell-types and may confound cell-type proportion changes with cell-intrinsic ones. We present a framework that first assembles and maps alternative splicing events in appropriate single cell RNA-seq data (scRNA-seq), then applies LeafletFA, a probabilistic model that discovers coordinated splicing programs (SPs) without requiring prior knowledge of cell types or clinical information, such as age. Applying this framework to over 200,000 cells from mouse and human Smart-seq2 multi-tissue atlases, we discovered global and cell type specific aging-associated SPs. In mice, integrating SPs with gene expression significantly improved age prediction in 46 of 76 tissue-cell types tested. We identified the RNA-binding protein \\textit{Snrnp70} as a key upstream mediator driving the shift from youthful to aged SPs. To test evolutionary conservation of these patterns, we employed transfer learning to map the murine splicing dictionary onto human transcriptomes. This revealed a conserved \"youth\" program (SP4) that is maintained in quiescent endothelial tissues but lost in high-turnover organs. We identified a conserved, age-dependent alternative 5\' splice site usage in the splicing factor \\textit{SRSF5} as a molecular marker of this program in both species. Our work establishes alternative splicing as a coordinated, evolutionarily conserved dimension of cellular aging and provides LeafletFA as an open-source tool for single-cell splicing analysis.

The mammalian target of rapamycin (mTOR) pathway is a central regulator of cellular growth, metabolism, and homeostasis, integrating a wide array of intracellular and extracellular cues, including nutrient availability, growth factors, and cellular stress, to coordinate anabolic and catabolic processes such as protein, lipid, and nucleotide synthesis; autophagy; and proteasomal degradation. The dysregulation of this signaling hub has broad implications for health and disease. To commemorate the 50th anniversary of the discovery of rapamycin, we provide a comprehensive synthesis of five decades of mTOR research. This review traces the historical trajectory from the early characterization of the biological effects of rapamycin to the elucidation of its molecular target and downstream pathways. We integrate fundamental and emerging insights into the roles of mTOR across nearly all domains of cell biology and development, with a particular focus on the expanding landscape of therapeutic interventions targeting this pathway. Special emphasis is placed on the crosstalk between mTOR signaling and mitochondrial regulation, highlighting the mechanisms by which these two metabolic hubs co-regulate cellular adaptation, survival, and disease progression. The dynamic interplay between mTOR and mitochondrial networks governs key aspects of bioenergetics, redox balance, and cell fate decisions and is increasingly implicated in pathophysiological contexts ranging from cancer and aging to neurodegenerative and immune disorders.

Sarcopenia, a progressive skeletal muscle disorder marked by loss of mass and function, presents growing societal challenges due to limited therapeutic options. Here, we identify mitochondrial dysfunction and oxidative stress as central drivers of sarcopenia through integrated bioinformatics and clinical validation. To address this pathophysiology, we engineer a muscle-targeted nanocomposite (BP-PEG-MOTS-c, BM) combining mitochondrial-derived peptide MOTS-c with antioxidant black phosphorus nanosheets (BP). BM exhibits dual functionality: MOTS-c restores mitochondrial function, while BP synergistically amplifies ROS scavenging capacity. In cellular and murine models with age-related sarcopenia, BM treatment alleviates muscle dysfunction and muscle loss, concurrently normalizing mitochondrial function and reducing lipid peroxidation. Mechanistic profiling via RNA-seq reveals BM's activation of PI3K/AKT/Nrf2 and suppression of ROS/p38 MAPK signaling pathway, mediating antioxidant responses and maintenance of mitochondrial homeostasis. The nanocomposite demonstrats superior biocompatibility in toxicity assays, outperforming conventional delivery systems. Our findings establish that BM has been established as a promising mitochondrial redox modulator with translational potential for sarcopenia and related age-associated pathologies.

Although transcriptomic changes are known to occur with age, the extent to which these are conserved across tissues is unclear. Previous studies have identified little conservation in age-modulated genes in different tissues. Here, we sought to identify common transcriptional changes with age in humans (aged 20 to 70) across tissues using differential network analysis, assuming that differential expression analysis alone cannot detect all changes in the transcriptional landscape that occur in tissues with age. Our results demonstrate that differential connectivity analysis reveals significant transcriptional alterations that are not detected by differential expression analysis. Combining the two analyses, we identified gene sets modulated by age across all tissues that are highly enriched in terms related to "RNA splicing" and "RNA processing". The identified genes are also highly interconnected in protein-protein interaction networks. Co-expression module analyses demonstrated that other genes that show tissue-specific variations with age are enriched in pathways that combat the accumulation of aberrant RNAs and proteins, likely caused by defective splicing. Additionally, with convergent connectivity patterns, most tissues significantly reorganized their gene connectivity with age. Our results identified genes and processes whose age-associated transcriptional changes are conserved across tissues, demonstrating a central role for RNA splicing and processing genes and highlighting the importance of differential network analysis for understanding the ageing transcriptome.

Exposure to a younger system can induce organismal rejuvenation, yet whether all tissues can be rejuvenated and by what mechanisms remains understudied. We performed heterochronic and isochronic transplantation of subcutaneous white adipose tissue (WAT) between young and old mice and longitudinally tracked changes in biological age. Transplantation accelerated tissue aging, and the molecular age of grafts shifted toward that of the host. Most importantly, old WAT was rejuvenated in a young body. Epigenetic and transcriptomic clocks revealed a reduction of predicted age, accompanied by coordinated activation of canonical and previously unrecognized thermogenic pathways. Molecular rejuvenation was further supported by architectural changes toward a youthful state, including reduced lipid droplet size and decreased cellular heterogeneity. Mitochondrial abundance and morphology remained unchanged, while collagen deposition increased. These results demonstrate that WAT biological age is partially reversible and identify molecular and cellular features underlying its rejuvenation