Longevity Papers

Epigenetic clocks are powerful biomarkers of biological aging, however, their performance varies across studies and contexts. Current limitations include siloed datasets, inconsistent validation methods, and the absence of a standardized framework for systematic comparison. Here, we introduce TranslAGE: a publicly available online resource that addresses this gap by harmonizing 179 human blood DNA methylation datasets and precalculating a suite of 41 epigenetic biomarker scores for each of the >42,000 total samples. Users can explore these data through interactive dashboards that evaluate four fundamental performance domains: Stability, Treatment response, Associations, and Risk, collectively forming the STAR framework. Stability quantifies robustness to multiple types of technical and biological noise. Treatment response measures biomarker sensitivity to aging interventions and environmental exposures. Associations capture cross-sectional relationships with age, demographics, disease, and other phenotypes, and Risk assesses predictive power for future functional decline, morbidity and mortality. The STAR framework unifies these test metrics into a single composite scoring system that enables researchers to identify, benchmark, and validate biomarkers best suited to their scientific or clinical applications. TranslAGE will be continually updated, with rapid scaling by adding datasets, biomarkers, or analyses. By providing harmonized datasets, precomputed biomarker scores, and interactive data tools, TranslAGE establishes the first standardized, reproducible framework for benchmarking epigenetic aging biomarkers across populations, and accelerates the translation toward clinical use.

Cellular senescence is a fundamental driver of ageing and age-related diseases, characterized by irreversible growth arrest and profound epigenetic alterations. While long non-coding RNAs (lncRNAs) have emerged as key regulators of senescence, their potential for senescent cell rejuvenation remains unexplored. Here, we identify the ageing-associated lncRNA PURPL as an epigenetic regulator that controls cellular rejuvenation through H3K9me3-mediated transcriptional silencing. CRISPRi-mediated PURPL depletion produces striking rejuvenation effects, resulting in restored youthful cell morphology, as well as suppression of senescence markers such as p21 and SA-β-gal. Conversely, PURPL overexpression accelerates cellular senescence, recapitulating the transcriptional and phenotypic hallmarks of ageing. Mechanistically, nuclear-localized PURPL regulates H3K9me3 deposition at 411 genomic loci including SERPINE1 (PAI-1) and EGR1, which are key senescence drivers. PURPL-mediated H3K9me3 loss at these loci derepresses their transcription, establishing a pro-senescence gene expression program. These findings reveal that PURPL is an epigenetic modulator of senescence and highlight its potential as a therapeutic target for age-related pathologies.

Hutchinson Gilford progeria syndrome (HGPS) is a fatal premature aging disorder caused by pathogenic farnesylated lamin A variants that disrupt nuclear architecture and DNA repair. Current therapies, including farnesyltransferase inhibitors, provide only modest survival benefits and lack molecular specificity, while mutation-specific genome-editing strategies cannot address atypical laminopathies. Here, we develop Farnesylation Amino acid Targeted Editing (FATE), a mutation-agnostic base-editing platform that selectively disrupts the LMNA farnesylation motif without affecting other farnesylated proteins. Using isogenic human pluripotent stem cell derived neuromuscular organoids (NMOs), we reveal muscle-specific progerin accumulation that sequesters 53BP1 and abolishes DNA damage foci formation. FATE eliminates perinuclear progerin, restores 53BP1 mobility, reconstitutes DNA repair foci, and normalizes heterochromatin architecture. Importantly, transient delivery of FATE mRNA conjugated with lipid nanoparticles to HGPS NMOs achieves efficient base editing and phenotypic rescue. These findings establish FATE as a mutation-independent therapeutic strategy targeting a fundamental pathogenic mechanism in HGPS and provide a proof-of-concept for RNA-based in situ genome editing in progeroid disease.

Aging imposes a significant socioeconomic and healthcare burden worldwide, while effective therapy is still lacking. Impaired brain drainage and excessive accumulation of metabolites and toxins such as advanced glycation end products (AGEs) are characteristics of aging that contribute to the development of neurological disorders. Recent discoveries have highlighted the role of meningeal lymphatic vessels (MLVs) in the clearance of toxic metabolites, cells, tumors, and viruses from the brain, positioning them as significant targets for the treatment of various brain diseases. In this study, we demonstrate that noninvasive 1275-nm photobiomodulation (PBM) effectively improves brain drainage and promotes lymphatic clearance of AGEs in a D-galactose-induced aging model (AM) in male mice, while being safe due to its minimal thermal effects. These improvements are associated with nitric oxide release-mediated dilation of MLVs. PBM can also effectively ameliorate redox imbalance, neuroinflammation, and neuronal damage, as well as improve spatial learning ability and short-term recognition memory in AM mice. These findings introduce a promising and easily accessible strategy for nonpharmacological phototherapy of meningeal brain drainage and neurological decline in individuals with aging and aging-related neurodegenerative diseases, offering high potential for rapid implementation into routine clinical practice.

Chaperone-mediated autophagy (CMA) declines in ageing and neurodegenerative diseases. Loss of CMA in neurons leads to neurodegeneration and behavioural changes in mice but the role of CMA in neuronal physiology is largely unknown. Here we show that CMA deficiency causes neuronal hyperactivity, increased seizure susceptibility and disrupted calcium homeostasis. Pre-synaptic neurotransmitter release and NMDA receptor-mediated transmission were enhanced in CMA-deficient females, whereas males exhibited elevated post-synaptic AMPA-receptor activity. Comparative quantitative proteomics revealed sexual dimorphism in the synaptic proteins degraded by CMA, with preferential remodelling of the pre-synaptic proteome in females and the post-synaptic proteome in males. We demonstrate that genetic or pharmacological CMA activation in old mice and an Alzheimer's disease mouse model restores synaptic protein levels, reduces neuronal hyperexcitability and seizure susceptibility, and normalizes neurotransmission. Our findings unveil a role for CMA in regulating neuronal excitability and highlight this pathway as a potential target for mitigating age-related neuronal decline.

Aging is a highly complex and heterogeneous process that progresses at different rates across individuals, making biological age (BA) a more accurate indicator of physiological decline than chronological age. While previous studies have built aging clocks using single-omics data, they often fail to capture the full molecular complexity of human aging. In this work, we leveraged the Human Phenotype Project, a large-scale cohort of 12,000 adults aged 30--70 years, with extensive longitudinal profiling that includes clinical, behavioral, environmental, and multi-omics datasets -- spanning transcriptomics, lipidomics, metabolomics, and the microbiome. By employing advanced machine learning frameworks capable of modeling nonlinear biological dynamics, we developed and rigorously validated a multi-omics aging clock that robustly predicts diverse health outcomes and future disease risk. Unsupervised clustering of the integrated molecular profiles from multi-omics uncovered distinct biological subtypes of aging, revealing striking heterogeneity in aging trajectories and pinpointing pathway-specific alterations associated with different aging patterns. These findings demonstrate the power of multi-omics integration to decode the molecular landscape of aging and lay the groundwork for personalized healthspan monitoring and precision strategies to prevent age-related diseases.

Cellular senescence is a stable state of cell-cycle arrest characterized by extensive remodeling of the secretome, known as the senescence-associated secretory phenotype (SASP). The SASP profoundly influences tissue microenvironments and contributes to chronic inflammation and age-related diseases. While previous studies have characterized the SASP using bottom-up proteomics, intact proteoforms' diversity and structural complexity remain poorly understood. In this study, we apply quantitative top-down mass spectrometry to profile the intact proteoform composition of the SASP in senescent human fibroblasts, alongside quiescent and proliferating controls. This approach enables direct identification of intact proteoforms with post-translational modifications (PTMs), sequence variants, and isoforms, offering deep insight into the proteomic landscape of senescence. We identify a rich repertoire of previously uncharacterized proteoforms, including variants of HMGA2 with N-terminal acetylation and multiple phosphorylation states (di-, tri-, and tetra-phosphorylated), implicating them as potential senescence biomarkers. Our findings underscore the functional complexity of the SASP and the value of proteoform-level resolution in understanding cellular senescence. This work establishes a robust top-down proteomics strategy for SASP analysis and highlights novel molecular targets for therapeutic strategies aimed at mitigating age-related pathologies.

The human somatic genome evolves throughout our lifespan, producing mosaic individuals comprising clones harboring different mutations across tissues. While clonal expansions in the hematopoietic system have been extensively characterized and reported to be nearly ubiquitous, clonal mosaicism (CM) has more recently also been described across multiple solid tissues. However, outstanding questions remain about the parameters and processes of human somatic evolution in non-cancerous solid human tissues, including when clones arise, how they evolve over time, and what mechanisms lead to their expansion. Questions of timing and clonal dynamics can be addressed through phylogenetic reconstruction, which serves as a \'temporal microscope\', while uncovering the mechanisms of expansion necessitates simultaneous phenotypic profiling. To address this gap, here we develop Single-cell Miniaturized Automated Reverse Transcription and Primary Template-directed Amplification (SMART-PTA) for joint single-cell whole-genome and whole-transcriptome sequencing for large scale and cost-efficient interrogation of solid tissue CM. We established a workflow that generates hundreds of matched single-cell whole genome and transcriptome libraries within a week. We profiled phenotypically normal esophagus tissue from four aged donors\' and used somatic variants to build high-resolution single-cell lineages from >2,700 cells with accompanying transcriptomic information, reconstructing >70 years of somatic evolution. T cell expansions identified from T cell receptor (TCR) sequences validated the clonal structure of the single-nucleotide variant (SNV)-based phylogenies and phylogenetic cross-correlation analysis showed that epithelial cells had higher degrees of shared ancestry by spatial location compared to immune cells. Mapping mutation signatures to the phylogenetic tree revealed the emergence of tobacco/alcohol exposure-related signatures later in life, consistent with the donors\' exposure histories. We identified variants in driver genes that were previously reported in the phenotypically normal esophagus, detecting clonal expansions harboring mutations in genes including TP53 and FAT1. We mapped the evolution of clones with both monoallelic as well as biallelic TP53 loss, including a clone associated with high expression of cell cycling genes and higher chromosome instability. Leveraging the matched transcriptome data, we uncovered cell type biases in mutant clones, with a higher proportion of TP53 or FAT1-mutant cells in an earlier basal epithelial cell state compared to wild-type cells. We further observed copy-neutral loss of heterozygosity (CNLOH) events on chromosome 9q that spanned the NOTCH1 locus in up to ~35% of epithelial cells. Mapping CNLOH events to the phylogenetic tree revealed a striking pattern in which CNLOH was separately acquired many times, reflecting convergent evolution. Cells with CNLOH events were biased towards the earlier basal epithelial state, suggestive of a selective advantage that leads to prevalent recurrence of chr9q CNLOH. Together, we demonstrate that SMART-PTA is an efficient, scalable approach for single-cell whole-genome and whole-transcriptome profiling to build phenotypically annotated single-cell phylogenies with enough throughput and power for application to normal tissue somatic evolution. Moreover, we reconstruct the evolutionary history of the esophageal epithelium at high scale and resolution, providing a window into the dynamics and processes that shape clonal expansions in phenotypically normal tissues throughout a lifespan.