To build the atlas, the team, led by researchers including Laura P. M. H. de Rooij and Abdel Rahman Abdel Fattah, mined 34 publicly available single-cell and single-nucleus RNA-sequencing studies, retaining only samples from healthy, non-diseased human tissue so that the map reflects normal aging rather than pathology. After rigorous quality control, removal of contaminating clusters and correction for technical differences between cell and nucleus sequencing, the final compendium contained 375,829 endothelial cells from 290 donors spanning adipose tissue, brain, breast, heart, intestine, kidney, liver, lung, muscle, ovary, skin and uterus.

One of the atlas’s central achievements is a gene-level description of the vascular tree that holds true across organs. The researchers identified robust pan-arterial markers such as SULF1, FBLN5 and ARL15; pan-capillary markers including RGCC, CA4, BTNL9 and RBP7; pan-venous markers such as SELP, ACKR1, VCAM1 and IL1R1; and conserved lymphatic markers including PROX1 and MMRN1. Pseudotime analysis showed that endothelial cells change gradually along the artery-to-capillary-to-vein axis in most tissues, supporting the idea that vascular hierarchy is organized, at least in part, by a transcriptional program shared across the body. Capillary endothelial cells proved the most tissue-specialized, consistent with their role in mediating organ-specific exchange functions.

With this framework in place, the team stratified donors into young and aged subgroups based on the tissue-specific median age and compared gene expression using pseudobulk differential expression analysis, cross-tissue meta-analysis and repeated subsampling to guard against statistical artifacts. Aged endothelial cells consistently showed enrichment of inflammatory and immunoregulatory genes, including senescence-associated secretory phenotype factors and tumor necrosis factor alpha signaling — a molecular echo of the inflammaging process long associated with aging tissues. In parallel, angiogenesis-related genes such as APLNR, COL4A1, ID3 and PLVAP, along with capillary markers like RGCC and CLEC14A, were reliably downregulated. Gene sets for oxidative phosphorylation, cell proliferation and MYC targets were also reduced, pointing to metabolic and proliferative decline.

These patterns were not confined to one organ. A congruent set of 287 age-enriched and 135 age-depleted genes emerged when the team compared two different age-stratification strategies, and repeating the analysis with absolute age cutoffs of 50 and 60 years produced similar results. The researchers describe this reproducible pattern as a pan-endothelial aging signature, although they caution that the analysis is observational and that causality between the transcriptional shifts and vascular dysfunction remains to be established experimentally.

Individual vessel types aged in distinct ways. Aged arterial cells showed enrichment of coagulation-associated signatures, while aged venous cells were characterized by extracellular matrix and cytoskeleton genes including DMD, TMOD1, RND1 and CNTNAP3. Most strikingly, angiogenic gene expression declined most strongly in aged veins — a notable finding because venous endothelial cells are the origin of angiogenic sprouting, the process by which new blood vessels form. Downregulated genes in aged veins included ANGPT2, ID3, EDN1, LAMA4 and PLVAP, many of which support vessel formation and stabilization. The authors suggest that this coordinated loss could contribute to impaired vascular regeneration and the capillary rarefaction seen in aging, though they emphasize this remains a hypothesis.

The atlas also uncovered widespread age-related remodeling of the extracellular matrix and glycocalyx, the sugar-rich layer coating endothelial cells. Liver, lung, skin and adipose endothelial cells showed the most prominent shifts, including increased expression of GALNT family genes and sialyltransferases involved in O-glycosylation. In the liver, these changes mirrored the well-described pseudo-capillarization of the aged sinusoidal endothelium, lending external validity to the atlas findings. The team also inferred transcription factor activity and found increased activity of the mechanoregulators YAP1, WWTR1 (TAZ) and TEAD family members in aged endothelial cells across tissues, with the pattern especially pronounced in skin.

To verify these mechanosignaling findings independently, the researchers performed MERFISH spatial transcriptomics on human skin, identifying 1,878 endothelial cells among 13,623 detected cells and confirming the atlas’s expression patterns. In a separate spatial dataset of 13 skin samples from donors aged 33 to 77, the endothelium showed the strongest positive correlation between YAP activity and age of all cell types, followed by pericytes. Immunofluorescence staining of skin sections then revealed a subtle but statistically significant increase in nuclear YAP localization in the endothelial compartment of aged tissue, indicating functional activation of this mechanical signaling pathway. The authors note it is not yet clear whether this activation is compensatory or pathogenic.

A major contribution of the study is a new, endothelial-specific senescence signature. Canonical senescence markers behaved unexpectedly: CDKN1A, which encodes p21, was broadly expressed across endothelial populations, while CDKN2A, encoding p16, was nearly absent, and the proportions of cells positive for either marker did not markedly differ between young and aged donors. To find more reliable indicators, the team induced senescence in laboratory-grown human umbilical vein endothelial cells through doxorubicin treatment and repeated passaging, confirmed senescence using beta-galactosidase activity and p21 staining, and intersected the resulting gene list with genes enriched in CDKN1A-positive cells from the atlas. This yielded a conserved set of candidates including MAFF, ADAMTS1, ADAMTS4, JUN, SRGN, KLF2 and UGCG. The signature correlated strongly with established senescence gene sets such as SenMayo and CellAge, and was validated in induced pluripotent stem cell-derived brain-like endothelial cells and in mouse models of accelerated vascular aging based on progerin expression. Notably, MAFF overexpression in young endothelial cells was sufficient to induce hallmark senescence phenotypes, including increased p21 expression and elevated senescence-associated beta-galactosidase activity, supporting its functional relevance.

The authors are candid about the limitations of their work. Age distributions were uneven across tissues, individuals aged 80 and older were underrepresented, and unreported confounders such as medication, lifestyle and comorbidities could not be controlled. The study was not powered to detect sex differences in vascular aging, and CDKN1A may not be fully specific to senescent endothelial cells — elevated p21 can also reflect transient activation during vascular remodeling rather than terminal growth arrest. Even so, by restricting the analysis to healthy tissue and cross-validating findings across datasets, model systems and species, the atlas provides a baseline reference of healthy endothelial aging against which disease-associated vascular dysfunction can be measured. The data are freely explorable through an interactive web tool, and the authors suggest the resource could inform future efforts to screen for and treat age-related vascular diseases, particularly as senolytic and senomorphic therapies show variable, context-dependent outcomes in early research.

Subject of Research: A single-cell transcriptomic atlas of human endothelial cell aging across 12 tissues

Article Title: Uncovering the transcriptional hallmarks of endothelial cell aging via integrated single-cell analysis

Article References: Dobner, S., Kleissl, L., Tóth, F., Paxton, R. L., Yordanova, I., Brazdilova, K., Vanluyten, C., Aizenshtadt, A., Tóth, H., Burton, J., Kopf, A., Belyaeva, V., Ferencevic, K., Al-Nuaimi, D. A., Lichtenstein, M. A., Winter, G. E., Rendeiro, A. F., Bock, C., Kalucka, J., … de Rooij, L. P. M. H. (2026). Uncovering the transcriptional hallmarks of endothelial cell aging via integrated single-cell analysis. Nature Aging. https://doi.org/10.1038/s43587-026-01247-3

Image Credits: AI Generated

DOI: 10.1038/s43587-026-01247-3

Keywords: endothelial cells, single-cell RNA sequencing, vascular aging, cellular senescence, angiogenesis, inflammaging, extracellular matrix, mechanotransduction, YAP, p21, CDKN1A, cell atlas