Single-cell analysis of the human immune system reveals sex-specific dynamics of immunosenescence

Single-cell analysis of the human immune system reveals sex-specific dynamics of immunosenescence

  • Aw, D., Silva, A. B. & Palmer, D. B. Immunosenescence: emerging challenges for an ageing population. Immunology 120, 435–446 (2007).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Peters, M. J. et al. The transcriptional landscape of age in human peripheral blood. Nat. Commun. 6, 8570 (2015).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Goronzy, J. J. & Weyand, C. M. Understanding immunosenescence to improve responses to vaccines. Nat. Immunol. 14, 428–436 (2013).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Huang, Z. et al. Effects of sex and aging on the immune cell landscape as assessed by single-cell transcriptomic analysis. Proc. Natl Acad. Sci. USA 118, e2023216118 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Luo, O. J. et al. Multidimensional single-cell analysis of human peripheral blood reveals characteristic features of the immune system landscape in aging and frailty. Nat. Aging 2, 348–364 (2022).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Mogilenko, D. A. et al. Comprehensive profiling of an aging immune system reveals clonal GZMK+ CD8+ T cells as conserved hallmark of inflammaging. Immunity 54, 99–115 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Terekhova, M. et al. Single-cell atlas of healthy human blood unveils age-related loss of NKG2C+GZMBCD8+ memory T cells and accumulation of type 2 memory T cells. Immunity 56, 2836–2854 (2023).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Carr, E. J. et al. The cellular composition of the human immune system is shaped by age and cohabitation. Nat. Immunol. 17, 461–468 (2016).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Gong, Q. et al. Multi-omic profiling reveals age-related immune dynamics in healthy adults. Nature 648, 696–706 (2025).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Alpert, A. et al. A clinically meaningful metric of immune age derived from high-dimensional longitudinal monitoring. Nat. Med. 25, 487–495 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Wertheimer, A. M. et al. Aging and cytomegalovirus infection differentially and jointly affect distinct circulating T cell subsets in humans. J. Immunol. 192, 2143–2155 (2014).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Zheng, Y. et al. A human circulating immune cell landscape in aging and COVID-19. Protein Cell 11, 740–770 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Wang, Y. et al. Integrating single-cell RNA and T cell/B cell receptor sequencing with mass cytometry reveals dynamic trajectories of human peripheral immune cells from birth to old age. Nat. Immunol. 26, 308–322 (2025).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Yousefzadeh, M. J. et al. An aged immune system drives senescence and ageing of solid organs. Nature 594, 100–105 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Widjaja, A. A. et al. Inhibition of IL-11 signalling extends mammalian healthspan and lifespan. Nature 632, 157–165 (2024).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Baht, G. S. et al. Exposure to a youthful circulaton rejuvenates bone repair through modulation of β-catenin. Nat. Commun. 6, 7131 (2015).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Conboy, I. M. et al. Rejuvenation of aged progenitor cells by exposure to a young systemic environment. Nature 433, 760–764 (2005).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Huang, Q. et al. A young blood environment decreases aging of senile mice kidneys. J. Gerontol. A Biol. Sci. Med. Sci. 73, 421–428 (2018).

    Article 
    PubMed 

    Google Scholar
     

  • Katsimpardi, L. et al. Vascular and neurogenic rejuvenation of the aging mouse brain by young systemic factors. Science 344, 630–634 (2014).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Loffredo, F. S. et al. Growth differentiation factor 11 is a circulating factor that reverses age-related cardiac hypertrophy. Cell 153, 828–839 (2013).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Sinha, M. et al. Restoring systemic GDF11 levels reverses age-related dysfunction in mouse skeletal muscle. Science 344, 649–652 (2014).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Villeda, S. A. et al. The ageing systemic milieu negatively regulates neurogenesis and cognitive function. Nature 477, 90–94 (2011).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Villeda, S. A. et al. Young blood reverses age-related impairments in cognitive function and synaptic plasticity in mice. Nat. Med. 20, 659–663 (2014).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Sayed, N. et al. An inflammatory aging clock (iAge) based on deep learning tracks multimorbidity, immunosenescence, frailty and cardiovascular aging. Nat. Aging 1, 598–615 (2021).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Martínez de Toda, I., Maté, I., Vida, C., Cruces, J. & De la Fuente, M. Immune function parameters as markers of biological age and predictors of longevity. Aging 8, 3110–3119 (2016).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Tran Van Hoi, E. et al. Biomarkers of the ageing immune system and their association with frailty—A systematic review. Exp. Gerontol. 176, 112163 (2023).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Borgoni, S., Kudryashova, K. S., Burka, K. & de Magalhães, J. P. Targeting immune dysfunction in aging. Ageing Res. Rev. 70, 101410 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Furman, D. et al. Systems analysis of sex differences reveals an immunosuppressive role for testosterone in the response to influenza vaccination. Proc. Natl Acad. Sci. USA 111, 869–874 (2014).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Fischinger, S., Boudreau, C. M., Butler, A. L., Streeck, H. & Alter, G. Sex differences in vaccine-induced humoral immunity. Semin. Immunopathol. 41, 239–249 (2019).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Klein, S. L. & Flanagan, K. L. Sex differences in immune responses. Nat. Rev. Immunol. 16, 626–638 (2016).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Jacobson, D. L., Gange, S. J., Rose, N. R. & Graham, N. M. Epidemiology and estimated population burden of selected autoimmune diseases in the United States. Clin. Immunol. Immunopathol. 84, 223–243 (1997).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Márquez, E. J. et al. Sexual-dimorphism in human immune system aging. Nat. Commun. 11, 751 (2020).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Connolly, E. et al. Loss of immune cell identity with age inferred from large atlases of single cell transcriptomes. Aging Cell 23, e14306 (2024).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Teixeira, D. et al. Evaluation of lymphocyte levels in a random sample of 218 elderly individuals from São Paulo city. Rev. Bras. Hematol. Hemoter. 33, 367–371 (2011).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Hirokawa, K. et al. Slower immune system aging in women versus men in the Japanese population. Immun. Ageing 10, 19 (2013).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Abdullah, M. et al. Gender effect on in vitro lymphocyte subset levels of healthy individuals. Cell. Immunol. 272, 214–219 (2012).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Holdcroft, A. Gender bias in research: how does it affect evidence based medicine? J. R. Soc. Med. 100, 2–3 (2007).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Hägg, S. & Jylhävä, J. Sex differences in biological aging with a focus on human studies. eLife 10, e63425 (2021).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Yazar, S. et al. Single-cell eQTL mapping identifies cell type-specific genetic control of autoimmune disease. Science 376, eabf3041 (2022).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Sopena-Rios, M., Ripoll-Cladellas, A. & Melé, M. L’anàlisi a escala de cèl·lula única del sistema immunitari humà revela dinàmiques d’envelliment específiques segons el sexe biològic. Zenodo https://doi.org/10.5281/zenodo.19202768 (2026).

  • Mogilenko, D. A., Shchukina, I. & Artyomov, M. N. Immune ageing at single-cell resolution. Nat. Rev. Immunol. 22, 484–498 (2022).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Mittelbrunn, M. & Kroemer, G. Hallmarks of T cell aging. Nat. Immunol. 22, 687–698 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Hao, Y. et al. Integrated analysis of multimodal single-cell data. Cell 184, 3573–3587 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Satija, R., Farrell, J. A., Gennert, D., Schier, A. F. & Regev, A. Spatial reconstruction of single-cell gene expression data. Nat. Biotechnol. 33, 495–502 (2015).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Sansoni, P. et al. Lymphocyte subsets and natural killer cell activity in healthy old people and centenarians. Blood 82, 2767–2773 (1993).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Guo, C. et al. Single-cell transcriptomics reveal a unique memory-like NK cell subset that accumulates with ageing and correlates with disease severity in COVID-19. Genome Med. 14, 46 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Park, H.-J. et al. Transcriptomic analysis of human IL-7 receptor alpha low and high effector memory CD8+ T cells reveals an age-associated signature linked to influenza vaccine response in older adults. Aging Cell 18, e12960 (2019).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Dann, E., Henderson, N. C., Teichmann, S. A., Morgan, M. D. & Marioni, J. C. Differential abundance testing on single-cell data using k-nearest neighbor graphs. Nat. Biotechnol. 40, 245–253 (2022).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Alice, K., Marioni, J. C. & Morgan, M. D. Milo2.0 unlocks population genetic analyses of cell state abundance using a count-based mixed model. Preprint at bioRxiv https://doi.org/10.1101/2023.11.08.566176 (2023)

  • Zhao, J. et al. Detection of differentially abundant cell subpopulations in scRNA-seq data. Proc. Natl Acad. Sci. USA 118, e2100293118 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Burkhardt, D. B. et al. Quantifying the effect of experimental perturbations at single-cell resolution. Nat. Biotechnol. 39, 619–629 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Vojdani, A. et al. Natural killer cells and cytotoxic T cells: complementary partners against microorganisms and cancer. Microorganisms 12, 230 (2024).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Oelen, R. et al. Single-cell RNA-sequencing of peripheral blood mononuclear cells reveals widespread, context-specific gene expression regulation upon pathogenic exposure. Nat. Commun. 13, 3267 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Bleve, A. et al. Immunosenescence, inflammaging, and frailty: Role of myeloid cells in age-related diseases. Clin. Rev. Allergy Immunol. 64, 123–144 (2023).

    Article 
    PubMed 

    Google Scholar
     

  • Quin, C. et al. Monocyte-driven inflamm-aging reduces intestinal barrier function in females. Immun. Ageing 21, 65 (2024).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Strati, P. & Shanafelt, T. D. Monoclonal B-cell lymphocytosis and early-stage chronic lymphocytic leukemia: diagnosis, natural history, and risk stratification. Blood 126, 454–462 (2015).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Ghia, P. et al. Monoclonal CD5+ and CD5 B-lymphocyte expansions are frequent in the peripheral blood of the elderly. Blood 103, 2337–2342 (2004).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Molica, S. Sex differences in incidence and outcome of chronic lymphocytic leukemia patients. Leuk. Lymphoma 47, 1477–1480 (2006).

    Article 
    PubMed 

    Google Scholar
     

  • Rolla, S. et al. Th22 cells are expanded in multiple sclerosis and are resistant to IFN-β. J. Leukoc. Biol. 96, 1155–1164 (2014).

    Article 
    PubMed 

    Google Scholar
     

  • Thomson, Z. et al. Trimodal single-cell profiling reveals a novel pediatric CD8αα+ T cell subset and broad age-related molecular reprogramming across the T cell compartment. Nat. Immunol. 24, 1947–1959 (2023).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Zhang, H. et al. Aging-associated HELIOS deficiency in naive CD4+ T cells alters chromatin remodeling and promotes effector cell responses. Nat. Immunol. 24, 96–109 (2023).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Shen, X. et al. Nonlinear dynamics of multi-omics profiles during human aging. Nat. Aging 4, 1619–1634 (2024).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Lehallier, B. et al. Undulating changes in human plasma proteome profiles across the lifespan. Nat. Med. 25, 1843–1850 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Fehlmann, T. et al. Common diseases alter the physiological age-related blood microRNA profile. Nat. Commun. 11, 5958 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Sampathkumar, N. K. et al. Widespread sex dimorphism in aging and age-related diseases. Hum. Genet. 139, 333–356 (2020).

    Article 
    PubMed 

    Google Scholar
     

  • Piñero, J. et al. The DisGeNET knowledge platform for disease genomics: 2019 update. Nucleic Acids Res. 48, D845–D855 (2020).

    PubMed 
    PubMed Central 

    Google Scholar
     

  • Yasumizu, Y. et al. Single-cell transcriptome landscape of circulating CD4+ T cell populations in autoimmune diseases. Cell Genom. 4, 100473 (2024).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Künzli, M. & Masopust, D. CD4+ T cell memory. Nat. Immunol. 24, 903–914 (2023).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Raphael, I., Joern, R. R. & Forsthuber, T. G. Memory CD4+ T cells in immunity and autoimmune diseases. Cells 9, 531 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Davis, A. P. et al. The Comparative Toxicogenomics Database’s 10th year anniversary: update 2015. Nucleic Acids Res. 43, D914–D920 (2015).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Lee, J. S. et al. Age-associated alteration in naive and memory Th17 cell response in humans. Clin. Immunol. 140, 84–91 (2011).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Vitales-Noyola, M. et al. Levels of pathogenic Th17 and Th22 cells in patients with rheumatoid arthritis. J. Immunol. Res. 2022, 5398743 (2022).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Zhang, L. et al. Increased frequencies of Th22 cells as well as Th17 cells in the peripheral blood of patients with ankylosing spondylitis and rheumatoid arthritis. PLoS ONE 7, e31000 (2012).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Hu, Y. et al. Elevated profiles of Th22 cells and correlations with Th17 cells in patients with immune thrombocytopenia. Hum. Immunol. 73, 629–635 (2012).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Benham, H. et al. Th17 and Th22 cells in psoriatic arthritis and psoriasis. Arthritis Res. Ther. 15, R136 (2013).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Park, E. & Ciofani, M. Th17 cell pathogenicity in autoimmune disease. Exp. Mol. Med. 57, 1913–1927 (2025).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Zambrano-Zaragoza, J. F. et al. Th17 cells in autoimmune and infectious diseases. Int. J. Inflam. 2014, 651503 (2014).

    PubMed 
    PubMed Central 

    Google Scholar
     

  • Eyerich, S. et al. Th22 cells represent a distinct human T cell subset involved in epidermal immunity and remodeling. J. Clin. Invest. 119, 3573–3585 (2009).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Trifari, S., Kaplan, C. D., Tran, E. H., Crellin, N. K. & Spits, H. Identification of a human helper T cell population that has abundant production of interleukin 22 and is distinct from TH-17, TH1 and TH2 cells. Nat. Immunol. 10, 864–871 (2009).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Duhen, T., Geiger, R., Jarrossay, D., Lanzavecchia, A. & Sallusto, F. Production of interleukin 22 but not interleukin 17 by a subset of human skin-homing memory T cells. Nat. Immunol. 10, 857–863 (2009).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Seldin, M. F. The genetics of human autoimmune disease: a perspective on progress in the field and future directions. J. Autoimmun. 64, 1–12 (2015).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Sollis, E. et al. The NHGRI-EBI GWAS Catalog: knowledgebase and deposition resource. Nucleic Acids Res. 51, D977–D985 (2023).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Willems, L. M. et al. Frequency and impact of disease symptoms experienced by patients with systemic sclerosis from five European countries. Clin. Exp. Rheumatol. 32, 0088–0093 (2014).


    Google Scholar
     

  • Orlandi, M. et al. Towards a comprehensive approach to the management and prognosis of systemic sclerosis’s patients: the role of comorbidities in the SPRING-SIR registry. Eur. J. Intern. Med. 130, 130–136 (2024).

    Article 
    PubMed 

    Google Scholar
     

  • Cook, M. B. et al. Sex disparities in cancer incidence by period and age. Cancer Epidemiol. Biomarkers Prev. 18, 1174–1182 (2009).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Haroon, M. Dr. & Aamer, M. Elderly onset of rheumatoid arthritis is more common in males, and requires maintenance of low-dose corticosteroids along with the combination of disease modifying anti rheumatic agents. Semin. Arthritis Rheum. 51, e10 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Zheng, Y., Liu, Q., Goronzy, J. J. & Weyand, C. M. Immune aging—A mechanism in autoimmune disease. Semin. Immunol. 69, 101814 (2023).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Vadasz, Z., Haj, T., Kessel, A. & Toubi, E. Age-related autoimmunity. BMC Med. 11, 94 (2013).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Bao, M., Yang, Y., Jun, H.-S. & Yoon, J.-W. Molecular mechanisms for gender differences in susceptibility to T cell-mediated autoimmune diabetes in nonobese diabetic mice. J. Immunol. 168, 5369–5375 (2002).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Gilmore, W., Weiner, L. P. & Correale, J. Effect of estradiol on cytokine secretion by proteolipid protein-specific T cell clones isolated from multiple sclerosis patients and normal control subjects. J. Immunol. 158, 446–451 (1997).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Baecher-Allan, C., Kaskow, B. J. & Weiner, H. L. Multiple sclerosis: mechanisms and immunotherapy. Neuron 97, 742–768 (2018).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Kebir, H. et al. Preferential recruitment of interferon-γ-expressing TH17 cells in multiple sclerosis. Ann. Neurol. 66, 390–402 (2009).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Chen, L. et al. Associations between biological ageing and the risk of, genetic susceptibility to, and life expectancy associated with rheumatoid arthritis: a secondary analysis of two observational studies. Lancet Healthy Longev. 5, e45–e55 (2024).

    Article 
    PubMed 

    Google Scholar
     

  • Puche-Larrubia, M. Á et al. Differences between early vs. late-onset of psoriatic arthritis: data from the RESPONDIA and REGISPONSER registries. Joint Bone Spine 90, 105563 (2023).

    Article 
    PubMed 

    Google Scholar
     

  • Urowitz, M. B., Ibañez, D., Jerome, D. & Gladman, D. D. The effect of menopause on disease activity in systemic lupus erythematosus. J. Rheumatol. 33, 2192–2198 (2006).

    PubMed 

    Google Scholar
     

  • Jiménez-Gracia, L. et al. Interpretable inflammation landscape of circulating immune cells. Nat. Med. 32, 633–644 (2026).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Rana, A. K., Li, Y., Dang, Q. & Yang, F. Monocytes in rheumatoid arthritis: circulating precursors of macrophages and osteoclasts and, their heterogeneity and plasticity role in RA pathogenesis. Int. Immunopharmacol. 65, 348–359 (2018).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Janossy, G. et al. Rheumatoid arthritis: a disease of T-lymphocyte/macrophage immunoregulation. Lancet 2, 839–842 (1981).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Anderson, A. et al. Monocytosis is a biomarker of severity in inflammatory bowel disease: analysis of a 6-year prospective natural history registry. Inflamm. Bowel Dis. 28, 70–78 (2022).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Thiesen, S. et al. CD14hiHLA-DRdim macrophages, with a resemblance to classical blood monocytes, dominate inflamed mucosa in Crohn’s disease. J. Leukoc. Biol. 95, 531–541 (2014).

    Article 
    PubMed 

    Google Scholar
     

  • Ramos-Leví, A. M. & Marazuela, M. Pathogenesis of thyroid autoimmune disease: the role of cellular mechanisms. Endocrinol. Nutr. 63, 421–429 (2016).

    Article 
    PubMed 

    Google Scholar
     

  • Cook, M. B., McGlynn, K. A., Devesa, S. S., Freedman, N. D. & Anderson, W. F. Sex disparities in cancer mortality and survival. Cancer Epidemiol. Biomarkers Prev. 20, 1629–1637 (2011).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Cartwright, R. A., Gurney, K. A. & Moorman, A. V. Sex ratios and the risks of haematological malignancies. Br. J. Haematol. 118, 1071–1077 (2002).

    Article 
    PubMed 

    Google Scholar
     

  • Yu, X. et al. Shared genetic architecture between autoimmune disorders and B-cell acute lymphoblastic leukemia: insights from large-scale genome-wide cross-trait analysis. BMC Med. 22, 161 (2024).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • vom Steeg, L. G. & Klein, S. L. SeXX matters in infectious disease pathogenesis. PLoS Pathog. 12, e1005374 (2016).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Shen, L. P. et al. Epidemiological changes in hepatitis B prevalence in an entire population after 20 years of the universal HBV vaccination programme. Epidemiol. Infect. 139, 1159–1165 (2011).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Baig, S. Gender disparity in infections of Hepatitis B virus. J. Coll. Physicians Surg. Pak. 19, 598–600 (2009).

    PubMed 

    Google Scholar
     

  • Rizzo, G. E. M., Cabibbo, G. & Craxì, A. Hepatitis B virus-associated hepatocellular carcinoma. Viruses 14, 986 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Kulik, L. & El-Serag, H. B. Epidemiology and management of hepatocellular carcinoma. Gastroenterology 156, 477–491 (2019).

    Article 
    PubMed 

    Google Scholar
     

  • Rankin, L. C. & Artis, D. Beyond host defense: emerging functions of the immune system in regulating complex tissue physiology. Cell 173, 554–567 (2018).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Coppé, J.-P., Desprez, P.-Y., Krtolica, A. & Campisi, J. The senescence-associated secretory phenotype: the dark side of tumor suppression. Annu. Rev. Pathol. 5, 99–118 (2010).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Coppé, J.-P. et al. Senescence-associated secretory phenotypes reveal cell-nonautonomous functions of oncogenic RAS and the p53 tumor suppressor. PLoS Biol. 6, 2853–2868 (2008).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Rodriguez-Garcia, M., Patel, M. V., Shen, Z. & Wira, C. R. The impact of aging on innate and adaptive immunity in the human female genital tract. Aging Cell 20, e13361 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • White, H. D. et al. CD3+ CD8+ CTL activity within the human female reproductive tract: influence of stage of the menstrual cycle and menopause. J. Immunol. 158, 3017–3027 (1997).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Rodriguez-Garcia, M., Fortier, J. M., Barr, F. D. & Wira, C. R. Aging impacts CD103+ CD8+ T cell presence and induction by dendritic cells in the genital tract. Aging Cell 17, e12733 (2018).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Rodriguez-Garcia, M., Shen, Z., Fortier, J. M. & Wira, C. R. Differential cytotoxic function of resident and non-resident CD8+ T cells in the human female reproductive tract before and after menopause. Front. Immunol. 11, 1096 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Shchukina, I. et al. Enhanced epigenetic profiling of classical human monocytes reveals a specific signature of healthy aging in the DNA methylome. Nat. Aging 1, 124–141 (2021).

    Article 
    PubMed 

    Google Scholar
     

  • Geiger, H., de Haan, G. & Florian, M. C. The ageing haematopoietic stem cell compartment. Nat. Rev. Immunol. 13, 376–389 (2013).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • De Maeyer, R. P. H. et al. Age-associated inflammatory monocytes are increased in menopausal females and reversed by hormone replacement therapy. Aging Cell 24, e70249 (2025).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Cuomo, A. S. E. et al. Impact of rare and common genetic variation on cell type-specific gene expression. Preprint at medRxiv https://doi.org/10.1101/2025.03.20.25324352 (2025).

  • Andreu-Sánchez, S. et al. Antibody signatures against viruses and microbiome reflect past and chronic exposures and associate with aging and inflammation. iScience 27, 109981 (2024).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Ramirez, J. M. et al. The molecular impact of cigarette smoking resembles aging across tissues. Genome Med. 17, 66 (2025).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Sánchez-Valle, J. & Valencia, A. Molecular bases of comorbidities: present and future perspectives. Trends Genet. 39, 773–786 (2023).

    Article 
    PubMed 

    Google Scholar
     

  • Levine, M. E. et al. An epigenetic biomarker of aging for lifespan and healthspan. Aging 10, 573–591 (2018).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Lu, A. T. et al. DNA methylation GrimAge strongly predicts lifespan and healthspan. Aging 11, 303–327 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Zhang, Z. et al. Deciphering the role of immune cell composition in epigenetic age acceleration: insights from cell-type deconvolution applied to human blood epigenetic clocks. Aging Cell 23, e14071 (2024).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Bonder, M. J. et al. scEpiAge: an age predictor highlighting single-cell ageing heterogeneity in mouse blood. Nat. Commun. 15, 7567 (2024).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Deltourbe, L. G. et al. Steroid hormone levels vary with sex, aging, lifestyle, and genetics. Sci. Adv. 11, eadu6094 (2025).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Kunz, S. et al. Age- and sex-adjusted reference intervals for steroid hormones measured by liquid chromatography–tandem mass spectrometry using a widely available kit. Endocr. Connect. 13, e230225 (2023).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Aitchison, J. The statistical analysis of compositional data. J. R. Stat. Soc. Series B Stat. Methodol. 44, 139–160 (1982).

    Article 

    Google Scholar
     

  • Kolde, R. pheatmap: Pretty Heatmaps. R package version 1.0.13. https://doi.org/10.32614/cran.package.pheatmap (2010).

  • Korsunsky, I. et al. Fast, sensitive and accurate integration of single-cell data with Harmony. Nat. Methods 16, 1289–1296 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Benjamini, Y. & Hochberg, Y. Multiple hypotheses testing with weights. Scand. J. Stat. 24, 407–418 (1997).

    Article 

    Google Scholar
     

  • Hoffman, G. E. et al. Efficient differential expression analysis of large-scale single cell transcriptomics data using dreamlet. Preprint at bioRxiv https://doi.org/10.21203/rs.3.rs-2705625/v1 (2024).

  • Aquino, Y. et al. Dissecting human population variation in single-cell responses to SARS-CoV-2. Nature 621, 120–128 (2023).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Oliva, M. et al. The impact of sex on gene expression across human tissues. Science 369, eaba3066 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Baydar Ovek, D. et al. JASPAR: an open-access database of transcription factor binding profiles. Nucleic Acids Res. 54, D184–D193 (2026).


    Google Scholar
     

  • Ashburner, M. et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet. 25, 25–29 (2000).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Yu, G., Wang, L.-G., Han, Y. & He, Q.-Y. clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS 16, 284–287 (2012).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Sayols, S. rrvgo: a Bioconductor package for interpreting lists of Gene Ontology terms. MicroPubl Biol 2023 https://doi.org/10.17912/micropub.biology.000811 (2023).

  • Pinero, J. et al. DISGENET: accelerating data-driven discovery in disease genomics and therapeutic development. Preprint at bioRxiv https://disgenet.com/About?section=gdaStatistics (2026).

  • Borcherding, N. et al. Mapping the immune environment in clear cell renal carcinoma by single-cell genomics. Commun. Biol. 4, 122 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Aibar, S. et al. SCENIC: single-cell regulatory network inference and clustering. Nat. Methods 14, 1083–1086 (2017).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Sergushichev, A., Sukhov, V. & Sergushichev A. Fast gene set enrichment analysis. Preprint at bioRxiv http://biorxiv.org/content/early/2016/06/20/060012 (2019).

  • Perng, Y.-C. & Lenschow, D. J. ISG15 in antiviral immunity and beyond. Nat. Rev. Microbiol. 16, 423–439 (2018).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Der, S. D., Zhou, A., Williams, B. R. & Silverman, R. H. Identification of genes differentially regulated by interferon α, β, or γ using oligonucleotide arrays. Proc. Natl Acad. Sci. USA 95, 15623–15628 (1998).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Sopena-Rios, M. et al. Single-cell atlas of the human immune system reveals sex-specific dynamics of immunosenescence. Zenodo https://zenodo.org/records/19097052 (2024).