Longevity Papers

Autophagy maintains cellular homeostasis through lysosomal degradation of cytoplasmic components, yet how prolonged autophagy activation reshapes organelle architecture remains poorly understood. Here we identify a previously unrecognized form of endoplasmic reticulum (ER) remodeling induced by chronic mTOR inhibition. This process triggers the formation of autolamellasomes: multilamellar, ER-derived structures that mediate bulk ER degradation. Unlike canonical ER-phagy, autolamellosome biogenesis requires the core autophagy machinery but is independent of known ER-phagy receptors. Cryo-ET, CLEM, and in vitro reconstitution reveal that they arise from autophagy-dependent assembly and compaction of fragmented ER into concentric stacks, which are then engulfed by lysosomes. Autolamellasomes occur at low levels constitutively, but accumulate in senescent cells and HGPS fibroblasts, linking sustained mTOR suppression to aging and ER/lysosomal homeostasis. This work clarifies the origin of intra-lysosomal membrane whorls and introduces a cell-free system for studying autophagy-driven membrane remodeling, connecting nutrient sensing, lipid catabolism, and aging.

Direct reprogramming of fibroblasts into induced cardiomyocytes (iCMs) offers a regenerative strategy for heart repair, but efficiency declines in adult and aged cells. Transcriptomic and epigenetic profiling identified cellular senescence as a major barrier limiting cardiac fibroblast (CF) plasticity and cardiogenic conversion. Postneonatal fibroblasts exhibited impaired activation of cardiac gene programs and persistent expression of fibrotic and inflammatory signatures. A loss-of-function screen identified Nr4a3 as a central repressor. Nr4a3 overexpression promoted senescence and suppressed iCM induction, whereas knockdown enhanced reprogramming in murine and human senescent CFs. Mechanistically, Nr4a3 depletion remodeled the chromatin landscape from a fibrotic and inflammatory state to a regenerative cardiac program. Blocking downstream Cxcl14 restored reprogramming in refractory fibroblasts. In vivo, Nr4a3 knockdown improved heart function following myocardial infarction. These findings established cellular senescence as a major barrier to cardiac reprogramming and identified Nr4a3 and its effectors as potential targets to enhance heart regeneration.

Cellular senescence, a hallmark of ageing, drives tissue dysfunction by promoting inflammation and fuelling disease. Yet, the dynamics of senescent cell accumulation across tissues and their cell type identity remain poorly understood. Here, we introduce the first, single-cell, protein-level approach, combining multiple senescence markers for the identification and quantification of senescent cells across multiple tissues in mice and in human PBMCs. Applying this method, we reveal widespread but heterogeneous changes in senescence marker expression across cell types and tissues. The cells we identify as senescent displayed transcriptomic senescence signatures, providing a direct molecular link between protein- and mRNA-level detection of senescence. Importantly, senescence accumulation was strongly coordinated within organs but showed little correlation across them, supporting the idea of a tissue specific progression of ageing. These findings refine our understanding of the tissue-specific dynamics of senescence accumulation with age, and provide a framework for evaluating diverse therapeutic interventions.

Telomerase, crucial for maintaining telomere integrity and genomic stability, is typically silenced in somatic cells with advancing age. In this study, we identify circHERC1 as a regulator of telomerase reverse transcriptase (TERT) transcription. Specifically, circHERC1 binds to the TERT promoter, facilitating the recruitment of RNA polymerase II and c-Fos, thereby activating TERT expression. Notably, circHERC1 expression exhibits a decline with age, which correlates with reduced telomerase activity. Restoration of circHERC1 expression enhances telomerase activity, promotes telomere elongation, and reverses aging-associated phenotypes. Furthermore, delivery of circHERC1 using adeno-associated virus vectors or extracellular vesicles effectively restores telomerase activity, preserves telomere integrity, and mitigates senescence. This intervention leads to improvements in cognitive function, physical performance, and a reduction in inflammation. These findings highlight the important role of circHERC1 in telomerase regulation and the aging process, positioning it as a potential therapeutic target for antiaging interventions.

Biological age (BA) and its residual relative to chronological age are popularly used to quantify individual aging. Although these residuals independently predict age-related health outcomes, conventional BA measures often lack robustness in heterogeneous populations, and their residuals are not directly derivable in clinical practice. To address these limitations, we introduce the Gompertz law-based residual (GOLD-R) framework, a method designed to directly estimate BA residuals and optimized for cross-sectional data. We demonstrated the applicability and robustness of GOLD-R across multiple data types and populations. First, training on DNA methylation data from the EWAS Data Hub, the framework outperformed established epigenetic clocks in predicting mortality in a pan-cancer dataset. Then, applied to UK Biobank proteomics data, GOLD-R generated organismal and organ-specific aging measures that proved more robust than conventional age-prediction approaches in forecasting incident diseases and mortality. Finally, extending the analysis to clinical biomarkers using the NHANES and HRS, we found that GOLD-R residuals, derived from clinical biomarkers, surpassed those from both epigenetic and phenotypic clocks in performance. In summary, our findings establish GOLD-R as a robust algorithm for biological age estimation, providing a practical tool for both research and clinical applications.

Circulating non-cellular factors, such as plasma proteins, contribute to various features of aging. To determine the impacts of endogenous circulating factors on human age-related bioenergetic decline, we treated primary human fibroblasts with serum samples representing the adult life-course. Our results demonstrate that the maximal mitochondrial bioenergetic capacity of fibroblasts treated with serum is negatively correlated with the chronological and epigenetic age of the serum donor. Using targeted proteomics, we identified plasma proteins associated with the bioenergetic effects of serum. We then utilized elastic net, a linear regression modeling technique, to derive a novel proteomic signature of age-related mitochondrial differences. MitoAge is a 25-protein signature of age-related mitochondrial health that predicts the systemic bioenergetic effects of circulating factors and is related to differences in physical function across human aging. Signatures that report on cellular hallmarks of aging, such as mitochondrial function, represent a new generation of mechanistically-informed biomarkers of biological aging.

Aging is a complex biological process marked by progressive physiological decline and increased disease vulnerability. Single-cell RNA sequencing offers unprecedented resolution for studying aging, yet isolating aging-related signatures remains challenging because gene expression is primarily shaped by other factors such as cell type, tissue, and sex. We present ACE (Aging Cell Embeddings), an explainable deep generative framework that disentangles aging-related gene expression changes from background biological variation. ACE employs two latent representations: one capturing aging-related signatures and another representing non-aging-related variation in the data. Through explainable AI, ACE identifies key genes and pathways associated with aging amid dominant non-aging-related variations. Applied to large-scale mouse, fly, and human datasets, ACE uncovers aging signatures both within specific tissue-cell-type contexts and across all tissues and cell types, enabling accurate prediction of biological age. Moreover, ACE identifies aging genes conserved across species, highlighting its ability to reveal shared biological mechanisms of aging. Experimental RNAi knockdowns in C. elegans validate ACE\'s findings, confirming its ability to prioritize novel aging genes affecting lifespan. ACE reveals key pathways involved in proteostasis, immune regulation, and extracellular matrix remodeling, and identifies Uba52 through the cross-species model as an important aging gene, whose knockdown in C. elegans significantly shortens lifespan. By providing interpretable and generalizable aging embeddings, ACE establishes a foundation for cross-species single-cell aging studies and translational geroscience.