The research, led by Georgia Kontogianni and Panagiotis Kouzis as co-first authors, with Georgios Kararigas and Themis Alissafi as co-senior authors, brings together teams from the Biomedical Research Foundation Academy of Athens, the National and Kapodistrian University of Athens, the University of Tirana, the University of Tours, the University of Crete, FORTH and the University of Nicosia. The group focused on regulatory T cells, or Tregs, the specialized CD4-positive lymphocyte population that acts as the immune system’s built-in restraint. Tregs patrol the periphery and suppress excessive activation of self-reactive lymphocytes, maintaining what immunologists call peripheral tolerance. Previous work had shown that Tregs are directly affected by checkpoint inhibitors, which target inhibitory signaling pathways that Tregs themselves rely upon, and that during immune-related adverse events these cells undergo extensive inflammatory and metabolic reprogramming, acquiring traits that echo the effector cells they are supposed to restrain. What remained unknown was whether this reprogramming follows the same trajectory in men and women.

The rationale for asking this question is grounded in decades of immunological observation. Women mount stronger humoral and cellular immune responses to infection and vaccination, are far more susceptible to many autoimmune diseases, including lupus, Hashimoto’s thyroiditis and multiple sclerosis, and show sex-dependent differences in Treg biology and inflammatory signaling. Estrogen, androgen and X-linked genetic factors all feed into immune gene regulation. If biological sex shapes the baseline behavior of Tregs, it seemed plausible that it would also dictate how those cells respond when checkpoint blockade or spontaneous autoimmunity pushes the immune system toward self-attack. Testing that idea at scale required a bioinformatics approach rather than a single-cohort experiment, because the relevant patient populations are scattered across clinical studies.

The team therefore performed a sex-based integrative transcriptomic analysis of bulk RNA sequencing datasets generated from peripheral blood Tregs. The datasets came from patients with advanced melanoma and additional solid tumors treated with anti-PD-1 immunotherapy, from individuals living with chronic autoimmune diseases, and from healthy controls. By separating the data into male and female cohorts, the researchers could run differential gene expression, pathway enrichment and network-level analyses independently for each sex, mapping the inflammatory, metabolic and tolerance-associated transcriptional programs that accompany each condition. This design allowed a direct comparison not only between disease and health, but between the sexes and between two distinct contexts of tolerance breakdown: drug-induced toxicity and spontaneous autoimmunity.

The results reveal a layered picture. During spontaneous autoimmune disease, female-derived Tregs exhibited markedly broader transcriptional remodeling than their male counterparts. The female cells showed extensive enrichment of biological processes spanning immune regulation, inflammatory signaling, metabolism and oxidative stress, suggesting that in women, loss of tolerance engages a wide swath of the Treg transcriptional machinery simultaneously. Male-derived Tregs, by contrast, displayed comparatively restricted remodeling, involving a narrower set of immune-related and metabolic pathways. In other words, the depth and breadth of the regulatory cell’s response to autoimmunity is not the same in both sexes, a finding that helps explain why autoimmune susceptibility and severity so often diverge between men and women.

Immune-related adverse events, however, told a different story. Checkpoint inhibitor-associated toxicity produced a distinct pattern of sex-dependent transcriptional organization in Tregs, one that did not simply mirror what the researchers observed in autoimmunity. Although the two conditions share many underlying biological processes, since both represent failures of peripheral tolerance, the degree, directionality and network-level organization of the transcriptional responses differed substantially between the sexes and between disease settings. The same cells, facing the same fundamental problem of lost tolerance, appear to solve or succumb to it along different molecular routes depending on both the sex of the patient and the inflammatory context in which tolerance was disrupted. This argues against a single, uniform program of Treg failure and in favor of disease-specific, sex-shaped trajectories of reprogramming.

The technical implication is significant for how immunologists interpret single-cell and bulk transcriptomic studies. If male and female Tregs organize their responses differently at the pathway and network level, then pooling the sexes, as many studies historically have done, may obscure biologically meaningful signals or generate misleading averages. The authors emphasize that biological sex does not impose one common regulatory program on Tregs; rather, it shapes disease-specific transcriptional trajectories according to the inflammatory environment. That distinction matters for biomarker development, because a transcriptional signature predictive of severe colitis in a male patient treated with anti-PD-1 therapy may not hold for a female patient, and vice versa. Incorporating sex as a biological variable from the earliest stages of study design, rather than as an afterthought in the analysis, emerges as a practical necessity for personalized immunology.

The clinical stakes are considerable. Immune-related adverse events remain a leading cause of treatment interruption and morbidity in oncology, and clinicians currently lack reliable tools to predict which patients will develop severe toxicities. If Treg reprogramming trajectories diverge by sex, sex-stratified biomarkers could improve risk stratification before and during checkpoint inhibitor therapy, potentially guiding earlier intervention with immunosuppression or closer monitoring. Beyond oncology, the findings offer a molecular framework for a long-standing epidemiological puzzle: why women dominate the incidence of many autoimmune diseases while men, once affected, sometimes follow different disease courses. The observation that female Tregs undergo broader remodeling during autoimmunity provides a transcriptional correlate of that epidemiology, and a starting point for mechanistic work into the hormonal and genetic drivers behind it.

For now, the study stands as a reminder that the immune system is not a one-size-fits-all machine. The researchers, supported in part by a European Research Council grant under Horizon 2020 and by the Hellenic Foundation for Research and Innovation, and conducted within the framework of the COST Action ENOTTA, have shown that the cells tasked with keeping immunity in check remodel themselves along paths dictated by both biology and context. As checkpoint inhibitors continue to expand across tumor types and treatment lines, understanding how sex shapes the fragile balance between tumor rejection and tissue destruction may prove essential to making these powerful therapies safer for everyone.

Subject of Research: Sex-dependent transcriptional reprogramming of regulatory T cells in immune-related adverse events and autoimmunity

Article Title: Biological sex defines regulatory T-cell reprogramming trajectories in immune-related adverse events and autoimmunity

Article References: Kontogianni, G., Kouzis, P., Gogas, H., Rumano, M., Mulleman, D., Verginis, P., Kararigas, G., & Alissafi, T. (2026). Biological sex defines regulatory T-cell reprogramming trajectories in immune-related adverse events and autoimmunity. Biology of Sex Differences. https://doi.org/10.1186/s13293-026-00980-z

Image Credits: AI Generated

DOI: 10.1186/s13293-026-00980-z

Keywords: regulatory T cells, immune checkpoint inhibitors, immune-related adverse events, autoimmunity, biological sex, peripheral tolerance, transcriptomics, anti-PD-1 therapy, sexual dimorphism, personalized immunology, Biological, defines