Chandramouli Muralidharan, Enikő Zakar-Polyák, Anita Adami ...
· Advanced science (Weinheim, Baden-Wurttemberg, Germany)
· Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, Lund University, Lund, 221 84, Sweden.
· pubmed
Aging is the primary risk factor for most neurodegenerative diseases, yet the cell-type-specific progression of brain aging remains poorly understood. Here, human cell-type-specific transcriptomic aging clocks are developed using high-quality single-nucleus RNA sequencing data fr...
Aging is the primary risk factor for most neurodegenerative diseases, yet the cell-type-specific progression of brain aging remains poorly understood. Here, human cell-type-specific transcriptomic aging clocks are developed using high-quality single-nucleus RNA sequencing data from post mortem human prefrontal cortex tissue of 31 donors aged 18-94 years, encompassing 73,941 high-quality nuclei. Distinct transcriptomic changes are observed across major cell types, including upregulation of inflammatory response genes in microglia from older samples. Aging clocks trained on each major cell type accurately predict chronological age, capture biologically relevant pathways, and remain robust in independent single-nucleus RNA-sequencing datasets, underscoring their broad applicability. Notably, cell-type-specific age acceleration is identified in individuals with Alzheimer's disease and schizophrenia, suggesting altered aging trajectories in these conditions. These findings demonstrate the feasibility of cell-type-specific transcriptomic clocks to measure biological aging in the human brain and highlight potential mechanisms of selective vulnerability in neurodegenerative diseases.
Longevity Relevance Analysis
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The paper develops human cell-type-specific transcriptomic aging clocks that can measure biological aging in the brain. This research is relevant as it addresses the biological mechanisms of aging and their implications for neurodegenerative diseases, contributing to the understanding of aging processes rather than merely treating symptoms.
Aisin, S. I., Lidskii, B. V., Lidsky, P. V.
· evolutionary biology
· Department of Biomedical Sciences, College of Biomedicine, City University of Hong Kong, Tat Chee Ave, Kowloon, Hong Kong SAR
· biorxiv
The biological feasibility of human rejuvenation remains a subject of intense debate, yet answering this question is critical for guiding research strategies. Should aging research focus on reversing aging in older individuals, or on pausing its progression at earlier ages? We ad...
The biological feasibility of human rejuvenation remains a subject of intense debate, yet answering this question is critical for guiding research strategies. Should aging research focus on reversing aging in older individuals, or on pausing its progression at earlier ages? We address this question with evolutionary biology. Classic evolutionary theories of aging - damage accumulation, antagonistic pleiotropy, and the disposable soma - consider aging as a detrimental byproduct of evolution. From this perspective, rejuvenation should confer strong fitness advantages and therefore be expected to evolve in species experiencing substantial aging in the wild. Its rarity in nature should thus be interpreted as evidence of its mechanistic implausibility. Yet, rejuvenation does occur in a few species, and, paradoxically, it is typically induced by stress but not used under optimal conditions. Using mathematical modeling of lifespan plasticity in eusocial insects, we show that this pattern cannot be reconciled with classic theories of aging, revealing an internal contradiction between these theories and the observed avoidance of rejuvenation. By contrast, the pathogen control hypothesis - which interprets aging as an adaptive, programmed process -offers a consistent evolutionary framework for understanding and potentially achieving rejuvenation.
Longevity Relevance Analysis
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The paper claims that the avoidance of rejuvenation in species is inconsistent with classic evolutionary theories of aging and suggests a new framework for understanding rejuvenation. This research is relevant as it addresses fundamental questions about the mechanisms of aging and potential strategies for rejuvenation, which are central to longevity research.
Ge, Y., Zhang, F., Liu, Y. ...
· bioinformatics
· Nanyang Technological University
· biorxiv
Extracting coherent, biologically meaningful insights from vast, complex multi-omics data remains challenging. Currently, pathway enrichment analysis serves as a cornerstone for the functional interpretation of such data. However, conventional approaches often suffer from extensi...
Extracting coherent, biologically meaningful insights from vast, complex multi-omics data remains challenging. Currently, pathway enrichment analysis serves as a cornerstone for the functional interpretation of such data. However, conventional approaches often suffer from extensive functional redundancy caused by shared molecular components and overlapping pathway definitions across databases. This redundancy can obscure key biological signals and compromise the interpretability of pathway enrichment results. Here, we present MAPA (Functional Module Identification and Annotation for Pathway Analysis Results Using Large Language Models [LLM]), an open-source computational framework that resolves redundancy and enhances pathway analysis result interpretation. MAPA computes functional similarity between pathways using LLM-based text embeddings, enabling comparison across different databases. It constructs pathway similarity networks and identifies functional modules via community detection algorithms. Crucially, MAPA employs LLMs for automated functional annotation, integrating Retrieval-Augmented Generation (RAG) to generate comprehensive and real-time biological summaries and reduce hallucinations. Benchmarking demonstrated MAPA\'s superior performance: the biotext embedding similarity showed a large effect size (Cliff\'s {delta} = 0.96) compared with the Jaccard index ({delta} = 0.73), and module identification achieved high accuracy (Adjusted Rand Index [ARI] = 0.95) versus existing methods (ARI = 0.23-0.33). Human expert evaluation confirmed that MAPA\'s annotations match expert-quality interpretations. Finally, a multi-omics aging case study illustrates that MAPA uncovers coherent functional modules and generates insights extending beyond conventional pathway analyses. Collectively, MAPA represents a significant advance in redundancy-aware pathway analysis, transforming pathway enrichment results from fragmented lists into biologically coherent narratives. By leveraging the capabilities of LLMs, MAPA offers researchers a robust, scalable tool for deriving deep mechanistic insights from complex and vast multi-omics datasets, marking a new direction for AI-driven bioinformatics.
Longevity Relevance Analysis
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MAPA enhances pathway analysis by resolving redundancy and providing deep biological interpretations of multi-omics data. The paper is relevant as it addresses complex biological insights that could contribute to understanding the mechanisms of aging and potentially inform strategies for lifespan extension.
Daniel L Vera, Patrick T Griffin, David Leigh ...
· The journals of gerontology. Series A, Biological sciences and medical sciences
· VoLo Foundation, Palm Beach, FL 33410 USA.
· pubmed
Biological age refers to a person's overall health in aging, as distinct from their chronological age. Diverse measures of biological age, referred to as "clocks", have been developed in recent years and enable risk assessments, and an estimation of the efficacy of longevity inte...
Biological age refers to a person's overall health in aging, as distinct from their chronological age. Diverse measures of biological age, referred to as "clocks", have been developed in recent years and enable risk assessments, and an estimation of the efficacy of longevity interventions in animals and humans. While most clocks are trained to predict chronological age, clocks have been developed to predict more complex composite biological age outcomes, at least in humans. These composite outcomes can be made up of a combination of phenotypic data, chronological age, and disease or mortality risk. Here, we develop the first such composite biological age measure for mice: the mouse phenotypic age model (Mouse PhenoAge). This outcome is based on frailty measures, complete blood counts, and mortality risk in a longitudinally assessed cohort of male and female C57BL/6 mice. We then develop clocks to predict Mouse PhenoAge, based on multi-omic models using metabolomic and DNA methylation data. Our models accurately predict Mouse PhenoAge, and residuals of the models are associated with remaining lifespan, even for mice of the same chronological age. These methods offer novel ways to accurately predict mortality in laboratory mice thus reducing the need for lengthy and costly survival studies.
Longevity Relevance Analysis
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The paper claims to develop a composite biological age measure for mice that predicts mortality risk based on multi-omic data. This research is relevant as it addresses biological aging mechanisms and offers a novel approach to assess longevity interventions in a model organism, potentially advancing our understanding of aging and lifespan extension.
Homann, J., Korologou-Linden, R., Viallon, V. ...
· neurology
· Institute of Epidemiology and Social Medicine, University of Muenster, Muenster, Germany; Ageing and Epidemiology Unit (AGE), School of Public Health, Imperial
· medrxiv
Background: Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disorder with a largely unknown duration and pathophysiology of the pre-diagnostic phase, especially for the common non-monogenic form. Methods: We leveraged the European Prospective Investigation into C...
Background: Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disorder with a largely unknown duration and pathophysiology of the pre-diagnostic phase, especially for the common non-monogenic form. Methods: We leveraged the European Prospective Investigation into Cancer and Nutrition (EPIC) cohort with up to 30 years of follow-up to identify incident ALS cases across five European countries. Pre-diagnostic plasma samples from initially healthy participants underwent high-throughput proteomic profiling (7,285 protein markers, SomaScan). Cox proportional hazards models based on 4,567 participants (including 172 incident ALS cases) were used to identify protein biomarkers associated with future ALS diagnosis. Top results were indirectly validated in two independent case-control studies of prevalent ALS (n=417 ALS, 852 controls). Functional annotation included cross-disease comparisons, gene set and tissue enrichment testing, organ-specific proteomic clocks, and the application of large-language models (LLM). Findings: Five proteins (SECTM1, CA3, THAP4, KLHL41, SLC26A7) were identified as significant pre-diagnostic ALS biomarkers (FDR=0.05), detectable approximately two decades before diagnosis. Of these, all except SECTM1 were indirectly validated in independent cohorts of prevalent ALS cases, supporting their clinical significance. Additionally, 22 nominally significant (p<0.05) pre-diagnostic biomarkers were FDR-significant in prevalent ALS with consistent effect directions. Cross-disease comparisons with pre-diagnostic Parkinson and Alzheimer disease suggested a largely specific pre-diagnostic ALS biomarker signature. Gene ontology and tissue enrichment highlighted early involvement of immune, muscle, metabolic, and digestive processes. Furthermore, analyses of proteomic clocks revealed accelerated aging in brain-cognition, immune, and muscle tissues before clinical diagnosis. Druggability and LLM analyses revealed possible therapeutic targets and novel strategies, emphasizing translational relevance. Interpretation: Our study provides first evidence of ultra-early molecular changes in common ALS up to two decades prior to clinical onset, mainly affecting immune, muscle, metabolic, digestive, and cognitive systems. Our study nominates several compelling candidates for risk stratification studies and novel therapeutic targets for early intervention.
Longevity Relevance Analysis
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The study identifies pre-diagnostic biomarkers for ALS that indicate molecular changes up to two decades before clinical onset. This research is relevant as it explores early biological changes associated with a neurodegenerative disease, potentially contributing to understanding aging processes and identifying targets for early intervention.
Matthew A McLoughlin, Sruthi Cheloor Kovilakam, William G Dunn ...
· Nature genetics
· Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK.
· pubmed
The mechanisms through which mutations in splicing factor genes drive clonal hematopoiesis (CH) and myeloid malignancies, and their close association with advanced age, remain poorly understood. Here we show that telomere maintenance plays an important role in this phenomenon. Fi...
The mechanisms through which mutations in splicing factor genes drive clonal hematopoiesis (CH) and myeloid malignancies, and their close association with advanced age, remain poorly understood. Here we show that telomere maintenance plays an important role in this phenomenon. First, by studying 454,098 UK Biobank participants, we find that, unlike most CH subtypes, splicing-factor-mutant CH is more common in those with shorter genetically predicted telomeres, as is CH with mutations in PPM1D and the TERT gene promoter. We go on to show that telomere attrition becomes an instrument for clonal selection in advanced age, with splicing factor mutations 'rescuing' HSCs from critical telomere shortening. Our findings expose the lifelong influence of telomere maintenance on hematopoiesis and identify a potential shared mechanism through which different splicing factor mutations drive leukemogenesis. Understanding the mechanistic basis of these observations can open new therapeutic avenues against splicing-factor-mutant CH and hematological or other cancers.
Longevity Relevance Analysis
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Telomere attrition influences clonal selection in aging hematopoiesis and leukemogenesis through splicing factor mutations. The study addresses the role of telomere maintenance in the aging process and its implications for understanding the mechanisms of age-related diseases, which is central to longevity research.
Cheyenne Rechsteiner, Francesco Morandini, Sei Joong Kim ...
· Nature aging
· Department of Biology, University of Rochester, Rochester, NY, USA.
· pubmed
The comparative biology of aging leverages the remarkable diversity in aging rates and lifespans across species to uncover naturally evolved adaptations that promote longevity, disease resistance and injury resilience. The beauty of comparative biology is that it discovers adapta...
The comparative biology of aging leverages the remarkable diversity in aging rates and lifespans across species to uncover naturally evolved adaptations that promote longevity, disease resistance and injury resilience. The beauty of comparative biology is that it discovers adaptations that evolved outside of the protected laboratory environment, shaped by natural selection under real-world pressures. In this Review, we outline key approaches in comparative biology of aging studies, including the study of public mechanisms, which are shared between species, and private mechanisms, which are species-specific. Additionally, we present insights gained through high-throughput omics technologies-including genomics, transcriptomics, epigenomics, proteomics and metabolomics-and illustrate how these findings advance our understanding of how to ameliorate the hallmarks of aging, enhance cancer resistance and improve regeneration, with a focus on mammals. Finally, we offer practical guidance for designing and interpreting comparative studies aimed at understanding and translating longevity mechanisms.
Longevity Relevance Analysis
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The paper claims that understanding the comparative biology of aging can uncover adaptations that promote longevity and disease resistance. This research is relevant as it addresses the root causes of aging and seeks to identify mechanisms that could lead to lifespan extension and improved health in aging populations.
Fedichev, P., Gruber, J.
· systems biology
· GERO PTE. LTD., 133 Cecil Street 14-01 Keck Seng Tower, Singapore 069535
· biorxiv
Aging varies widely across species yet exhibits universal statistical regularities, such as Gompertzian mortality and scaling laws, challenging efforts to link microscopic mechanisms with macroscopic outcomes. We present a minimal phenomenological model that captures these patter...
Aging varies widely across species yet exhibits universal statistical regularities, such as Gompertzian mortality and scaling laws, challenging efforts to link microscopic mechanisms with macroscopic outcomes. We present a minimal phenomenological model that captures these patterns by reducing complex physiology to three variables: a dynamic factor characterizing reversible physiological responses to stress, an entropic damage variable reflecting irreversible information loss, and a regulatory noise term. This framework reveals two fundamental aging regimes. In stable species, including humans, aging is driven by linear damage accumulation that gradually erodes resilience, producing a hyperbolic trajectory toward a maximum lifespan. In unstable species, such as mice and flies, intrinsic instability drives exponential divergence of biomarkers and mortality. Model predictions agree with DNA methylation dynamics, biomarker autocorrelation, and survival curves across taxa. Crucially, this regime-based view informs intervention strategies at three levels: (i) targeting dynamic hallmarks, (ii) reducing physiological noise, and (iii) slowing or reversing entropic damage - offering a roadmap from near-term healthspan gains to potential extension of human lifespan beyond current limits.
Longevity Relevance Analysis
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The paper proposes a minimal model that identifies two fundamental aging regimes and suggests intervention strategies to extend lifespan. This research is relevant as it addresses the root causes of aging and offers insights into potential interventions for lifespan extension.
Human aging does not follow a single trajectory. Epigenetic changes offer insight into the heterogeneity in aging by reflecting the combined influence of genetic, environmental, and lifestyle factors on the timing and progression of age-related changes beyond what chronological a...
Human aging does not follow a single trajectory. Epigenetic changes offer insight into the heterogeneity in aging by reflecting the combined influence of genetic, environmental, and lifestyle factors on the timing and progression of age-related changes beyond what chronological age alone can explain. Emerging research in cancer and aging highlights the importance of methylation variability as a marker of biological disruption. It also shows little overlap between CpGs differing in means versus variability. We investigated the role of DNA methylation in aging heterogeneity by performing epigenome-wide differential methylation and variance association analysis in blood samples from 1,445 Canadians aged 45 to 85. We identified 448 differentially methylated (DMRs) and 488 differentially variable regions associated with health decline across health deficit accumulation (i.e. the Frailty Index), cognitive, and physical function. We observed minimal overlap between these types of regions, with distinct gene coverage, highlighting a unique and potentially additional contribution of variability to age-related epigenetic changes. Gene ontology analyses of DMRs revealed enrichment in immune and inflammation-related pathways pointing to immune function as a key driver of aging heterogeneity. By integrating significant positions from both analyses, we constructed a composite epigenetic biomarker. Our biomarker outperformed control models built on differential methylation alone as well as established epigenetic biomarkers (e.g. GrimAge, PhenoAge) in predicting mortality and the onset of chronic obstructive pulmonary disease.
Longevity Relevance Analysis
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The paper claims that DNA methylation variability contributes uniquely to aging heterogeneity and can serve as a predictive biomarker for health decline. This research is relevant as it explores the epigenetic mechanisms underlying aging, potentially addressing root causes of age-related changes rather than merely treating symptoms.
Li, Y., Zhang, X., Li, X. ...
· neurology
· Beijing Normal University
· medrxiv
Background: Cognitive reserve (CR) explains individual resilience to age-related cognitive decline, yet its neurobiological basis remains elusive. Current CR proxies lack direct mechanistic links, necessitating a system-level approach integrating brain structure-function interact...
Background: Cognitive reserve (CR) explains individual resilience to age-related cognitive decline, yet its neurobiological basis remains elusive. Current CR proxies lack direct mechanistic links, necessitating a system-level approach integrating brain structure-function interactions. Methods: We developed a novel CR metric using structural MRI and resting-state fMRI from 1,280 older adults. A youth-derived structural-functional prediction model estimated maximal attainable brain function in elders. CR was quantified as the deviation between observed and predicted function. Cross-sectional and longitudinal analyses assessed CR's spatial distribution, cognitive associations, and pathological relevance in MCI/AD cohorts. Results: CR hubs localized to prefrontal, cingulate, and precuneus regions, organized within high-order networks. Higher CR predicted slower cognitive decline (r = -0.21, p < 0.001) and correlated with reduced A{beta} deposition (r = -0.63, p < 0.001). CR demonstrated domain-specific associations with memory, attention, and processing speed. MCI exhibited broader CR reductions than AD, particularly in frontotemporal regions, likely reflecting stage-specific neuroplastic dynamics: early MCI retains partial compensatory capacity but inefficient CR utilization under mounting pathological stress, whereas advanced AD transitions to irreversible structural damage that disrupts CR's adaptive "software" mechanisms. Conclusions: This study establishes CR as a dynamic neuroprotective framework, bridging functional resilience and structural integrity. CR's spatial specificity and inverse link to amyloid pathology highlight its potential as an early biomarker for resisting pathological aging.
Longevity Relevance Analysis
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The paper claims that cognitive reserve (CR) can be quantified through structural-functional interactions in the brain, serving as a neuroadaptive biomarker for resilience against cognitive decline in aging. This research is relevant as it explores mechanisms underlying cognitive resilience, which could inform strategies for mitigating age-related cognitive decline and improving longevity.