In an era where the fountain of youth has long been the subject of humanity’s deepest aspirations, a groundbreaking study published in Nature Communications by Zong, Park, Tekin-Turhan, and colleagues advances our understanding of the cellular mechanisms underlying aging and longevity. This research delves into the epigenetic landscape of hematopoietic stem cells (HSCs) derived from male mice, highlighting the pivotal roles of two key factors—KDR and PU.1—in orchestrating the aging transcriptome as well as modulating responses to caloric restriction. These findings offer profound implications for aging biology, regenerative medicine, and the pursuit of interventions that might mimic or enhance the beneficial effects of dietary restriction.
Hematopoietic stem cells represent the molecular wellspring from which the entire blood system arises, responsible for lifelong production of diverse blood lineages. However, the function and regenerative potential of HSCs decline with age, impairing immune competence and tissue renewal. What epigenetic changes drive this deterioration? By employing high-resolution epigenetic profiling technologies, the authors unravel how age-associated modifications to DNA methylation and chromatin accessibility reshape the transcriptomic networks that define HSC functionality. This extensive profiling in male murine models is among the most detailed to date, offering novel insights with possible human translational relevance.
Central to this research are the transcriptional regulators KDR (kinase insert domain receptor, also recognized as VEGFR2) and PU.1 (SPI1), both known for their involvement in hematopoietic development but now highlighted for their regulatory influence over age-associated transcriptional trajectories. KDR, traditionally studied in endothelial cell biology and angiogenesis, emerges here as a significant modulator of the aged HSC epigenome. PU.1, a master regulator of myeloid and lymphoid differentiation, similarly assumes a critical role in governing how the aging HSC transcriptome adapts both intrinsically and in response to extrinsic stimuli such as caloric restriction.
Caloric restriction (CR) stands as one of the most robust phenotypic interventions shown to extend lifespan and delay age-related decline across multiple species. Yet, the molecular intermediaries through which CR impacts stem cell aging have remained elusive. This study meticulously documents how CR influences the epigenetic states mediated by KDR and PU.1, indicating that these factors serve as molecular conduits translating metabolic cues into enduring alterations of gene expression programs. These findings bridge a significant knowledge gap by unveiling mechanistic links between diet, epigenetics, and stem cell aging.
Cutting-edge single-cell multi-omics approaches were harnessed to dissect how aging reconfigures chromatin landscapes across individual HSCs, revealing heterogeneity in responses that would be masked in bulk analyses. The investigators observed that age precipitates a progressive shift toward a repressive chromatin state, constraining the accessibility of genes crucial for stem cell maintenance and lineage commitment. Intriguingly, CR was shown to counteract some of these alterations, sustaining a more ‘youthful’ epigenomic architecture, which correlated with improved hematopoietic function. KDR and PU.1 motif enrichments were enriched in genomic loci whose accessibility was preserved with CR, indicating their central role.
The study also pioneers a systems biology perspective by integrating epigenetic profiling data with transcriptomic outputs to map the gene regulatory networks (GRNs) underpinning HSC aging. This reveals that the interplay between KDR and PU.1 forms a novel regulatory axis critical to maintaining HSC identity and plasticity during aging. Perturbation of this axis in ex vivo cultures altered the expression of key aging-associated genes, highlighting potential therapeutic targets to ameliorate aging phenotypes or rejuvenate aged stem cells.
An unexpected yet compelling aspect of this research is the demonstration of sex-specific epigenetic responses. Although the primary focus was on male mice, these findings open avenues for comparative analyses in females, where hormonal and epigenetic landscapes differ substantially. Understanding gender-specific differences will be crucial for designing personalized anti-aging interventions and ensuring that therapeutic strategies based on epigenetic regulation are broadly efficacious.
Moreover, the elucidation of the dynamic crosstalk between metabolism, epigenetics, and stem cell function exemplifies an integrative biological framework for aging. Metabolic states, modulated by nutritional interventions like CR, influence epigenetic enzymes such as DNA methyltransferases and histone-modifying complexes, which in turn regulate gene expression with lasting consequences on stem cell health. Unpacking this complexity underscores how lifestyle and cellular physiology are intertwined at the molecular level.
This research holds immense translational potential. Targeting the KDR–PU.1 regulatory axis could yield novel agents capable of mimicking caloric restriction’s beneficial effects without requiring drastic dietary changes. Such epigenetic therapeutics might restore youthful gene expression programs, enhance immune regeneration, and delay hematopoietic decline, ultimately improving health-span and resilience in aging populations. The identification of specific epigenetic markers governing stem cell aging also provides invaluable biomarkers for monitoring biological age and treatment efficacy.
The study’s methodology sets new standards for thoroughness and precision in aging research. Using state-of-the-art chromatin immunoprecipitation followed by sequencing (ChIP-seq), combined with assay for transposase-accessible chromatin using sequencing (ATAC-seq) and single-cell RNA sequencing (scRNA-seq), the authors assembled a comprehensive atlas of epigenomic and transcriptomic changes at unparalleled resolution. This multi-dimensional dataset will serve as a vital resource for researchers aiming to decipher aging mechanisms or develop rejuvenative strategies.
Furthermore, the role of PU.1 as a mediator of inflammatory signaling pathways links the aging hematopoietic system to age-related inflammation and immunosenescence, two phenomena at the heart of many chronic diseases. The modulation of PU.1 activity by caloric restriction highlights how environmental and metabolic cues can recalibrate immune cell function, potentially reducing the burden of inflammation-related pathology in the elderly.
While the study addresses important knowledge gaps, it also raises new questions about the reversibility of epigenetic aging marks and the long-term consequences of modulating KDR and PU.1 activities in vivo. Future research will need to explore whether these findings in mice translate to human HSCs, given species-specific nuances in gene regulation and metabolism. Additionally, investigations into the interplay between these factors and other aging hallmarks—such as telomere attrition, proteostasis, and cellular senescence—will complement and expand the current model.
The impact of this work extends beyond hematopoiesis. Since KDR and PU.1 are involved in broader cellular processes, their regulation could affect multiple tissues and organ systems undergoing age-dependent decline. Understanding how systemic factors like CR influence stem cell niches through epigenetic remodeling can pave the way for integrated anti-aging therapies targeting multiple cell types simultaneously.
In conclusion, Zong and colleagues have charted a new frontier in aging research by uncovering a complex epigenetic network with KDR and PU.1 at its core that governs hematopoietic stem cell aging and response to caloric restriction. Their findings not only deepen our comprehension of stem cell biology and aging but also illuminate promising pathways for developing interventions to prolong health-span and combat age-related diseases. As the quest to decode the molecular language of aging continues, this study stands as a milestone illustrating how epigenetics interfaces with metabolism to shape cellular destiny.
Subject of Research: Epigenetic regulation of hematopoietic stem cells aging and response to caloric restriction in male mice.
Article Title: Epigenetic profiling of hematopoietic stem cells from male mice identifies KDR and PU.1 as regulators of aging transcriptome and caloric restriction response.
Article References: Zong, L., Park, B., Tekin-Turhan, F. et al. Epigenetic profiling of hematopoietic stem cells from male mice identifies KDR and PU.1 as regulators of aging transcriptome and caloric restriction response. Nat Commun (2026). https://doi.org/10.1038/s41467-026-69718-0
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Tags: aging in male stem cellsaging transcriptome modulationcaloric restriction and stem cell functionchromatin accessibility in aged stem cellsDNA methylation changes in aging stem cellsepigenetic mechanisms in stem cell agingepigenetic profiling of hematopoietic stem cellskey regulators of hematopoietic stem cells agingmurine models in aging researchPU.1 transcription factor in agingregenerative medicine and agingrole of KDR in stem cell longevity
