Longevity Papers

Allosteric regulation enables proteins to couple local structural changes to distal functional outcomes, yet the underlying mechanisms often remain difficult to fully decipher. Using yeast SIR2, an NAD ⁺ -dependent deacetylase, as a model system, this study systematically elucidates how cofactor binding reshapes its conformational dynamics and internal communication network. Through multiple 3-μs molecular dynamics simulations combined with a graph-based deep learning model (Neural Relational Inference), we identify a highly reproducible characteristic response across independent replicates: the β1-α2 loop near the active site undergoes pronounced rigidification, whereas several distal structural modules exhibit concomitant increases in flexibility, together forming a "core-locking with peripheral-release" dynamic mode. Further signal-pathway analysis reveals that the local and distal conformational changes are not independent; instead, they are interconnected through newly identified "relay-type" residues such as Pro214 and Thr224. These residues act as bridges, converting the previously β1-α2-centered centralized network into a relay-style network coordinated by multiple nodes, thereby establishing a continuous and directionally coherent allosteric cascade. Beyond mechanistic insights, we also identify a distal cavity spatially overlapping with key relay residues, whose physicochemical properties meet the criteria of druggable pockets. This structural convergence suggests that future small-molecule allosteric activators may exploit this intrinsic communication pathway to mimic or amplify the regulatory effects of the cofactor NAD ⁺. Given that NAD⁺ levels decline with aging, this cavity provides a rational target for designing longevity-promoting allosteric activators.

Heat hormesis describes the beneficial adaptations resulting from transient exposure to mild heat stress, which enhances stress resilience and promotes healthy aging. While heat hormesis is widely observed, much remains to be learned about its molecular basis. This study bridges a critical knowledge gap through a comprehensive multiomic analysis, providing key insights into the transcriptomic and chromatin accessibility landscapes throughout a heat hormesis regimen in Caenorhabditis elegans. We uncover highly dynamic, dose-dependent molecular responses to heat stress and reveal that while most initial molecular changes induced by mild stress revert to baseline, key differences emerge in response to subsequent heat shock challenge that likely contribute to physiological benefits. We further demonstrate that heat hormesis extends life span specifically in wild-type animals, but not in germline-less mutants, likely due to transient disruption of germline activities during mild heat exposure, which appears sufficient to trigger pro-longevity mechanisms. This finding points to tissue-specific responses in mediating the physiological outcomes of heat hormesis. Importantly, we identify several highly conserved regulators of heat hormesis that likely orchestrate gene expression to enhance stress resilience. Among these regulators, some (MARS-1/MARS1, SNPC-4/SNAPc, FOS-1/c-Fos) are broadly required for heat-hormesis-induced benefits, whereas others (ELT-2/GATA4, DPY-27/SMC4) are uniquely important in specific genetic backgrounds. This study advances our understanding of stress resilience mechanisms, points to multiple new avenues for future investigations, and provides a molecular framework for promoting healthy aging through strategic mid-life stress management.

Ageing is traditionally conceived as a continuous process of progressive physiological decline. Recent evidence across multiple species challenges this view, suggesting ageing may proceed through distinct phases. Here we present a rigorous statistical framework to test and refine the two-phase ageing model using longitudinal survival data from Drosophila melanogaster. We analyzed 1,159 individually tracked female flies from the Smurf assay, which identifies a transition from a non-Smurf state to a Smurf state characterized by increased intestinal permeability that precedes death. Using non-parametric hazard rate estimation followed by mechanistic modelling, we reveal three key findings. First, the Smurf transition rate follows a Gompertz-Makeham law, increasing exponentially with age. Second, contrary to previous constant-rate assumptions, newly transitioned Smurf flies exhibit remarkably high mortality - approximately 40% die within 24 hours - followed by an exponential decline in death rate. Third, we identified a subtle but statistically significant negative dependence between time spent non-Smurf and subsequent Smurf lifespan, though this relationship varies: flies transitioning before 200 hours show minimal dependence and higher early mortality. Our best-fit model captures the bimodal nature of mortality curves using simple, biologically interpretable functions. Validation using data from two mouse strains confirms the broader applicability of this framework. These results establish a quantitative foundation for the two-phase ageing paradigm and highlight a critical period of vulnerability immediately following the physiological transition to frailty.

Skeletal muscle metabolic and physical capacities are influenced by both genetics and load status and decline with age. Recent advances in sequencing have detailed cell types at unprecedented detail; yet these approaches do not scale to adequately model human muscle physiological heterogeneity. We produced a powerful resource for ageing studies, including consistent deep transcriptomic profiles of 1,675 human muscle biopsies (approx 28,000 genes per profile) and multiple single-cell spatial transcriptomic technologies. We present several novel models of tissue ageing. Five Quantitative network models (QNMs), built using >40 trillion calculations and 930 human muscle transcriptomes, modelled aging and the influence of load status. Additional differential expression (DE) signatures for atrophy, hypertrophy and cardio-respiratory adaptation were integrated with single-cell RNAseq and cell-specific bulk profiles to reveal cell-enriched modules and the topology of human skeletal aging. Rapamycin transcriptomes from cultured muscle and endothelial cells, along with in vivo signatures for insulin resistance and sex, were integrated into these analyses. We show that >3,000 genes are DE with muscle age (equally up and down); that a novel pre-frailty signature in elderly subjects has a remarkably strong overlap with the response of healthy muscle during experimental atrophy and that the hypertrophy signature in elderly muscle, but not young muscle, opposes the age-regulated transcriptome. We report that non-responders for hypertrophy or gains in cardio-respiratory capacity have highly distinct genome-level response to exercise. QNM revealed cell-specific processes in endothelial cells and fibroblasts, including novel interactions between insulin sensitivity, age and senescence. From two hundred and eighty-six hub genes consistent in both young and old muscle network models, 27% had known roles in muscle biology, while of the top 50 hub genes (45% protein coding), 80% were newly linked to human muscle biology, including ARHGAP4, CEP131 and IFITM10 and many short- and long- noncoding RNAs. Many genes demonstrated extreme changes in topology in old muscle, such as the neddylation and aging linked gene, DCUN1D5. GeoMX-based spatial muscle fibre-type profiling (57 regions), along with Xenium (8 regions) and Merscope (54 regions) single-cell spatial technologies located key aging, frailty and load-responsive genes to individual cell types and provided novel insight into the location of autocrine/paracrine secreted factors such as GDNF, while IL6 was located to rare endothelial cells. A machine-learning model ranked the factors most associated with the topological changes with age. This prioritised network features over DE signatures, highlighting positive correlating edges to down-regulated genes during atrophy, genes up-regulated by Rapamycin and both positive and negative correlating insulin sensitivity features, along with gene hub status, best explained muscle ageing. Genome level modelling produced an independently validated transcriptomic age clock and found it to be invariant to muscle load status in people >50y, while we revealed novel interactions between gene length and age. Release of an unprecedented level of consistently aligned genomic data, along with QNMs with >7,000 searchable modules, provides a powerful resource for the aging research communities

The molecular and cellular basis of aging and its associated functional decline remains poorly understood. Even free-living microorganisms age and, in yeast, replicative aging shares key hallmarks with human cellular senescence, including progressive cell enlargement. Recent work has shown that chemical and genetic manipulations that increase cell size promote the onset of senescence in both yeast and human cells, suggesting that cell enlargement can drive some of the physiological changes associated with aging. Here, we quantitatively determined how cell enlargement contributes to age-associated physiology in yeast by combining automated aging technologies with quantitative proteomics. We find that the majority of aging-associated proteome remodeling can be recapitulated by genetically enlarging young proliferating cells. These enlarged cells exhibit accelerated proteome aging and shortened replicative lifespans, while smaller cells are longer-lived. While cell enlargement is the predominant factor driving proteome remodeling during aging, we also identified a minority of aging-specific molecular markers whose expression influences lifespan. Together, our results demonstrate that cell enlargement is a major driver of aging-associated proteome remodeling and influences lifespan independently of established aging factors such as extrachromosomal rDNA circles.

Cortical myelination is critical for circuit function, plasticity, and long-term stability in the adult brain. With age and disease, the capacity to restore myelin after oligodendrocyte (OL) loss declines, and this failure is thought to reflect intrinsic limitations of OL precursor cells (OPCs) and a loss of permissive cues within the cortical environment. Here, using single-OL ablations and intravital imaging in mice, we show that as cortical remyelination efficiency declines, OPC motility declines, a phenomenon that can be mimicked by blocking CXCL12/CXCR4 signaling. Counter to prevailing notions, however, we find that even in aging, OPCs retain the capacity to generate new OLs and sheath axons, which can be rekindled by a graded demyelinating stimulus, inducing a more juvenile OPC motile state. This reveals an unrecognized remyelination potential in aging and identifies OPC dynamics as a key determinant of cortical remyelination, a property that could be targeted to improve myelin repair.