bims-traimu Biomed News
on Trained immunity
Issue of 2025–10–05
fifteen papers selected by
Yantong Wan, Southern Medical University



  1. Exp Mol Med. 2025 Oct 01.
      The immune system has traditionally been divided into innate and adaptive branches, with immunological memory considered a hallmark of adaptive immunity. However, recent studies reveal that innate immune cells can also exhibit memory-like properties, known as trained immunity. This phenomenon involves the long-term functional reprogramming of innate immune cells following exposure to exogenous or endogenous stimuli, mediated by epigenetic and metabolic changes. Trained immunity enhances responses to subsequent unrelated challenges and serves as a protective mechanism against reinfection. Nonetheless, it may also contribute to the development of chronic inflammatory diseases such as autoimmune disorders, allergies and atherosclerosis. Whereas much of the research has focused on pathogen-associated molecular patterns as inducers of trained immunity, emerging evidence highlights that sterile inflammation, driven by damage-associated molecular patterns and lifestyle-associated molecular patterns, can similarly induce this immune adaptation. Here we examine the molecular mechanisms underlying damage-associated molecular pattern- and lifestyle-associated molecular pattern-induced trained immunity and their roles in chronic inflammation. This Review also discusses central trained immunity, characterized by the durable reprogramming of hematopoietic stem and progenitor cells, and its implications in disease progression. Finally, potential therapeutic strategies targeting metabolic and epigenetic pathways are considered. Understanding noninfectious stimuli-induced trained immunity offers new insights into chronic inflammatory disease management.
    DOI:  https://doi.org/10.1038/s12276-025-01542-w
  2. Immunol Res. 2025 Oct 01. 73(1): 139
      Sepsis, a life-threatening systemic infection, has long been recognized for its immediate risks, but its long-term consequences on health are increasingly evident, particularly in predisposing survivors to chronic cardiometabolic disorders (CMDs) such as atherosclerosis, insulin resistance, and dyslipidemia. Central to this process is trained immunity, where innate immune cells like monocytes, macrophages, and neutrophils undergo long-lasting epigenetic reprogramming after sepsis. This reprogramming, sustained by molecular pathways such as NF-κB, mTOR, and altered lipid metabolism, drives chronic inflammation, oxidative stress, and metabolic dysfunction, contributing to long-term cardiovascular diseases (CVDs) and metabolic disorders post-sepsis. This review explores the key mechanisms through which trained immunity bridges sepsis and CMDs, particularly focusing on epigenetic modifications such as histone acetylation, DNA methylation, and mitochondrial alterations. We discuss how trained immunity enhances immune cell activation, leading to persistent low-grade inflammation, lipid dysregulation, and impaired insulin sensitivity, all of which predispose sepsis survivors to CVDs. Additionally, we highlight potential therapeutic approaches targeting trained immunity, including statins, which reduce inflammation and immune reprogramming; metformin, which restores metabolic balance by activating AMPK and reducing oxidative stress; dimethyl fumarate (DMF), a potent Nrf2 activator that counteracts inflammation; and probiotics, which help restore gut microbiota balance and limit endotoxin-driven inflammation. These therapies offer promising strategies to mitigate long-term metabolic dysfunction and reduce the incidence of CMDs following sepsis. Understanding these mechanisms and developing targeted interventions may ultimately help prevent chronic cardiovascular and metabolic diseases in sepsis survivors and improve long-term outcomes.
    Keywords:  Cardiometabolic disorders; Epigenetic reprogramming; Inflammation; Sepsis; Trained immunity
    DOI:  https://doi.org/10.1007/s12026-025-09698-3
  3. Elife. 2025 Oct 02. pii: e106688. [Epub ahead of print]14
      The skin is frequently subjected to minor mechanical insults that may compromise its barrier integrity and permit the entry of pathogens. Therefore, the immune system of the skin needs to rapidly balance antimicrobial defense with tissue repair. To maintain homeostasis, the skin relies both on acute immune defenses and on mechanisms of innate memory or trained immunity. This enhanced inflammatory response to a second challenge has been well characterized in bone marrow cells, such as monocytes, monocyte-derived macrophages, and stem cells. Yet, the specific memory responses in skin-resident immune cells remain less understood. Importantly, the common skin colonizer Staphylococcus aureus has been identified as a potent inducer of trained immunity, triggering both metabolic and epigenetic changes at local sites such as the skin, and centrally in the bone marrow. This review explores the emerging understanding of trained immunity in the skin, that is how infection-driven cellular processes induce long-lasting immune adaptation and modulate skin barrier integrity.
    Keywords:  Dermis; S. aureus; immunology; inflammation; macrophages; skin; trained immunity
    DOI:  https://doi.org/10.7554/eLife.106688
  4. Placenta. 2025 Sep 22. pii: S0143-4004(25)00700-3. [Epub ahead of print]
      Trained immunity, defined as the epigenetic and metabolic reprogramming of innate immune cells that shapes their subsequent responses, has emerged as a key paradigm in reproductive immunology. In pregnancy, trained immunity can act as a "double-edged sword." Beneficial training of decidual NK cells and macrophages promotes vascular remodeling, tissue repair, and host defense, thereby supporting implantation and placental development. Conversely, dysregulated training triggered by hypoxia, metabolic stress, or infection may sustain chronic inflammation and contribute to preeclampsia, fetal growth restriction, and recurrent pregnancy loss. In this review, we summarize current evidence for both protective and pathogenic roles of trained immunity during pregnancy, highlight the underlying molecular mechanisms, and discuss key research gaps. Considering pregnancy complications from the perspective of trained immunity may provide new insights into pathogenesis and suggest opportunities for biomarker discovery and targeted interventions.
    Keywords:  Decidual NK cells; Epigenetic reprogramming; Gestational diabetes mellitus; Metabolic adaptation; Preeclampsia; Trained immunity
    DOI:  https://doi.org/10.1016/j.placenta.2025.09.015
  5. Cell Rep. 2025 Sep 25. pii: S2211-1247(25)00973-8. [Epub ahead of print]44(10): 116202
      We developed an in vitro methodology to study trained immunity using murine bone-marrow-derived macrophages stimulated with β-glucan and lipopolysaccharide (LPS). Longitudinal analysis of interleukin (IL)-6 and tumor necrosis factor (TNF) production demonstrates that trained macrophages secrete higher cytokine levels following primary stimulation with β-glucan compared to unstimulated macrophages (step 1). After a resting period, trained macrophages return to basal levels of cytokine production (step 2) but rapidly produce enhanced levels of IL-6 and TNF after secondary stimulation with LPS, compared to macrophages individually stimulated with either β-glucan (step 3) or LPS (step 4) alone. The combined cytokine production of macrophages after single stimulation with β-glucan (stimulus 1) and LPS (stimulus 2) is significantly lower than the cytokine levels produced by trained macrophages sequentially stimulated with both β-glucan and LPS (stimulus 1 + 2) (step 5). These results experimentally reproduce the distinctive functional stages that macrophages undergo during the training process.
    Keywords:  CP: Immunology; SAA3; T cell proliferation; mTOR; mouse strains; sample cryopreservation; trained immunity
    DOI:  https://doi.org/10.1016/j.celrep.2025.116202
  6. Nat Plants. 2025 Sep 30.
      Plants face constant microbial threats and have evolved highly effective immune systems characterized by inducible defence mechanisms. On recognizing microbial patterns and/or effectors, plants activate localized pattern-triggered immunity and/or effector-triggered immunity, which culminate in systemic acquired resistance-a broad-spectrum immune response that enhances protection throughout the plant. Systemic acquired resistance shares striking similarities with mammalian trained immunity, particularly in defence priming, which equips organisms with an enhanced capacity to respond to subsequent infections. This Review explores the cross-kingdom similarities between systemic acquired resistance and trained immunity, emphasizing their potential to transform agricultural practices and medical therapies. These insights present innovative opportunities for developing new plant-protection strategies, producing disease-resistant crops and optimizing vaccine approaches, while also highlighting critical knowledge gaps to inspire future research.
    DOI:  https://doi.org/10.1038/s41477-025-02119-1
  7. Immunology. 2025 Oct 01.
      Understanding the innate immune memory induced by adjuvants provides an opportunity to improve vaccine efficacy by inducing nonspecific secondary responses alongside the intended adaptive defence against the target antigen. To understand the consequences of adjuvant-induced immune training, we treated mice with commercially available Sigma Adjuvant System (SAS) and performed functional assays of bone marrow-derived innate immune cells, assessed its functional consequences in vivo, determined the resulting haematopoietic stem and progenitor cell (HSPC) phenotypes, and extensively analyzed the HSPC transcriptome. SAS induced temporal shifts in HSPC frequencies, alterations in the circulating blood profile, and lowered proinflammatory output by macrophages. SAS-induced training caused disparate outcomes in models of inflammation and acute infection. Further, SAS enhanced antibody responses after primary immunisation, that were profoundly altered upon a secondary dose. Integrated transcriptional analysis revealed shifts in HSPCs defined by altered transcription factor activity and lineage-specific shifts in metabolic, epigenetic, myeloid, and kinase genes, resulting in enhanced antimicrobial neutrophil responsiveness and revealing regulators of central training. Together, these results contribute to the understanding of the plasticity and limitations of innate immune training.
    Keywords:  haematopoiesis; macrophage; memory; transcriptomics; vaccination
    DOI:  https://doi.org/10.1111/imm.70047
  8. Immunology. 2025 Oct 02.
      Sepsis is a life-threatening condition characterised by a dysregulated host response to infection, resulting in systemic inflammation, immune dysfunction, and multi-organ failure. Kupffer cells (KCs), the largest population of tissue-resident macrophages in the body, are essential for pathogen clearance, endotoxin detoxification, and maintaining hepatic immune homeostasis during sepsis. However, sepsis induces substantial KC depletion, contributing to increased bacterial burden and mortality. In this study, we demonstrate that β-glucan treatment effectively protects against sepsis-induced KC loss and reduces circulating bacterial load. Mechanistically, β-glucan attenuates KC death by suppressing NLRP3 and gasdermin D (GSDMD)-mediated pyroptosis triggered by bacterial infections. Notably, we identify a previously unrecognised function of β-glucan in markedly enhancing KC self-renewal during sepsis through downregulation of the transcriptional repressors c-Maf and MafB, which are known to inhibit macrophage proliferation. This discovery reveals a novel mechanism of hepatic macrophage regeneration and supports β-glucan as a promising immunomodulatory therapy to preserve liver immune integrity, enhancing antibacterial defence, and reducing the risk of secondary infections in immunocompromised septic hosts.
    Keywords:  immune homeostasis; macrophage; sepsis
    DOI:  https://doi.org/10.1111/imm.70043
  9. Front Immunol. 2025 ;16 1588190
       Background: Measles-containing vaccines (MCV), by training innate immune cells, are hypothesized to prevent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and coronavirus disease 2019 (COVID-19).
    Methods: In this international, double-blind, placebo-controlled trial, we randomly assigned adults, 18 years and older, to receive MCV or saline. The primary outcome was polymerase chain reaction (PCR) confirmed symptomatic COVID-19, up to 60 days after intervention. Secondary outcomes were PCR-confirmed symptomatic COVID-19 and serologically confirmed SARS-CoV-2 infection, up to 150 days after intervention.
    Results: Of 3411 randomised participants, the modified intention-to-treat population included 1607 in the MCV and 1545 in the saline group. The estimated risk of symptomatic COVID-19 by 60 days was 1.5% in the MCV and 1.2% in the saline group (risk difference, 0.3 percentage points, 95% CI, -0.5 to 1.1; p=0.52). At 150 days, these percentages were 4.1% (65/1585) and 4.1% (64/1544) in the MCV and saline groups, respectively (risk difference, 0.04 percentage points, 95% CI, -1.4 to 1.3; p=0.95). Based on serology results available at 0 and 150 days, 10.6% (100/945) of participants in the MCV and 10.3% (98/951) in the saline group had infection with SARS-CoV-2 over the course of the trial (risk difference, 0.3 percentage points, 95% CI, -2.6 to 3.1; p=0.84). Three patients were hospitalised with COVID-19 disease in the MCV and one in the saline group.
    Conclusions: Administering MCVs to stimulate trained immunity did not prevent COVID-19 or SARS-CoV2 infection. Stimulating trained immunity might not be useful for preventing respiratory illness during future pandemics.
    Clinical trial registration: https://clinicaltrials.gov/, identifier NCT04333732.
    Keywords:  COVID-19; SARS-CoV-2; measles; measles containing vaccines; mumps; prevention; rubella; trained immunity
    DOI:  https://doi.org/10.3389/fimmu.2025.1588190
  10. Immun Inflamm Dis. 2025 Sep;13(9): e70272
       INTRODUCTION: Nucleotide-binding oligomerization domain 2 (NOD2) functions primarily as a cytoplasmic pattern recognition receptor (PRR) that detects muramyl dipeptide (MDP), a conserved bacterial cell wall component, thereby playing a pivotal role in pathogen surveillance. However, emerging evidence reveals that NOD2 exerts broad immunomodulatory effects beyond its canonical role as a PRR, though its effects can be contradictory, depending on genetic background, immunological microenvironment, and disease context. In this review, we integrate recent advances in understanding NOD2's functional plasticity and provide novel insights into its regulatory mechanisms in immune responses and mycobacterial infections.
    METHODS: A literature search was conducted using the PubMed database with keywords including NOD2, signaling pathways, immune homeostasis, autophagy, trained immunity, and mycobacterial infection. Relevant information was extracted from the retrieved research articles and reviews and summarized.
    RESULTS: We delineated the MDP-dependent and -independent mechanisms of NOD2 activation and their downstream signaling cascades. We also elaborated on the classical immune responses orchestrated by NOD2, and its remarkably multifaceted noncanonical roles in regulating immune homeostasis by modulating autophagy, acting synergistically with toll-like receptor pathways to fine-tune inflammation, and balancing trained immunity and immune tolerance. Furthermore, we examined the multifaceted immunoregulatory functions of NOD2 in host defense against mycobacterial infections.
    CONCLUSIONS: We propose that further research is required to clarify the various roles of NOD2 across diverse genetic backgrounds, microenvironmental contexts, and disease paradigms. Such studies will provide critical mechanistic insights to inform the development of precision-based therapeutic strategies targeting NOD2.
    Keywords:  Crohn's disease; NOD2; immune homeostasis; mycobacterial infection; signaling pathways
    DOI:  https://doi.org/10.1002/iid3.70272
  11. bioRxiv. 2025 Sep 26. pii: 2025.09.24.676575. [Epub ahead of print]
      Understanding the consistency with which individual hosts respond to repeated pathogen exposures is crucial for accurately modeling pathogen transmission and eco-evolutionary dynamics. When hosts face repeated pathogen exposures, immune memory is expected to reduce the probability and/or severity of subsequent infections, yet it remains unclear whether individuals remain consistent in their level of response relative to others. We investigated this question in house finches ( Haemorhous mexicanus ) from two populations varying in history of endemism of the bacterial pathogen Mycoplasma gallisepticum (MG). Individuals were confirmed to be MG-naive at capture and then experimentally inoculated twice with MG, allowing recovery between inoculations. We then asked if host responses to the second inoculation were predicted by responses to initial inoculation, sex, or population of origin. Our results suggest that individuals were not consistent in their relative response levels; rather, a successful initial infection provided protection against a severe second infection, increasing both tolerance and resistance. While we found no population differences in response to the second inoculation, males showed higher susceptibility to the second inoculation than females. Investigating and accounting for individual variation in response to subsequent exposures may improve the precision and accuracy of transmission models for wildlife pathogens.
    DOI:  https://doi.org/10.1101/2025.09.24.676575
  12. Cell Host Microbe. 2025 Sep 30. pii: S1931-3128(25)00375-0. [Epub ahead of print]
      Cadaverine is a polyamine produced by the gut microbiota with links to health and disease, notably inflammatory bowel disease (IBD). Here, we show that cadaverine shapes monocyte-macrophage immunometabolism in a context- and concentration-dependent fashion to impact macrophage functionality. At baseline, cadaverine is taken up via L-lysine transporters and activates the thioredoxin system, while during inflammation, cadaverine signals through aconitate decarboxylase 1 (Acod1)-itaconate. Both pathways induce activation of transcription factor, nuclear factor erythroid 2-related factor 2 (Nrf2), which supports mitochondrial respiration and promotes immunoregulatory macrophage polarization. Conversely, under higher concentrations, cadaverine acts via histamine 4 receptor, leading to glycolysis-driven inflammation and pro-inflammatory functions in macrophages. Likewise, cadaverine exhibits paradoxical effects in experimental colitis, either protective or detrimental, evoking opposite fates on macrophages depending on levels dictated by Enterobacteriaceae. In IBD patients, elevated cadaverine correlated with higher flare risk. Our findings implicate cadaverine as a microbiota-derived metabolite manipulating macrophage energy metabolism with consequences in intestinal inflammation and implications for IBD pathogenesis.
    Keywords:  IBD; cadaverine; cell energy metabolism; gut microbiota; macrophage; metabolite; microbiome; monocyte
    DOI:  https://doi.org/10.1016/j.chom.2025.09.009
  13. Research (Wash D C). 2025 ;8 0811
      Sepsis is a complex clinical syndrome marked by dysregulated immune responses, systemic inflammation, and subsequent organ dysfunction. Sepsis involves the interplay of multiple signaling pathways. Traditional sepsis treatment mainly depends on antibiotics and early directed therapy, with limited effectiveness. This article reviews major signaling pathways in sepsis, such as those related to nuclear factor κB (NF-κB), Janus kinase/signal transducer and activator of transcription (JAK/STAT), Toll-like receptors (TLRs), mitogen-activated protein kinase (MAPK), hypoxia-inducible factor 1α (HIF-1α), and nuclear factor-erythroid 2-related factor 2/Kelch-like ECH-associated protein 1 (Nrf2/Keap1). These molecules are pivotal in regulating immune activation, inflammation, and immune cell metabolism. Moreover, mitochondrial dysfunction and metabolic reprogramming substantially contribute to sepsis development, as they greatly affect energy production and immune cell function. Selectively inhibiting these pathways shows potential for effectively reducing hyperinflammation and preventing organ failure. We discussed how future research on these signaling pathways can translate into clinical applications and how personalized treatment strategies can handle the complexity and variability of sepsis. Given the dynamic nature of sepsis, treatment strategies should not solely rely on traditional single-target interventions. Instead, a dynamic and personalized multi-target modulatory approach is needed. While reducing side effects of single-target inhibition, inflammatory responses, immune balance, and metabolic disorders can be more precisely regulated. By precisely monitoring multiple sepsis-related signaling pathways and adjusting treatment regimens in real time, we aim to identify more effective intervention points in the complex dynamics of diseases, thus providing new hope for improving prognosis of septic patients.
    DOI:  https://doi.org/10.34133/research.0811
  14. Nat Genet. 2025 Oct 03.
      Reprogramming often yields heterogeneous cell fates, yet the underlying mechanisms remain poorly understood. To address this, we developed single-cell transcription factor sequencing (scTF-seq), a single-cell technique that induces barcoded, doxycycline-inducible TF overexpression and quantifies TF dose-dependent transcriptomic changes. Applied to mouse embryonic multipotent stromal cells, scTF-seq generated a gain-of-function atlas for 384 mouse TFs, identifying key regulators of lineage specification, cell cycle control and their interplay. Leveraging single-cell resolution, we uncovered how TF dose shapes reprogramming heterogeneity, revealing both dose-dependent and stochastic cell state transitions. We classified TFs into low-capacity and high-capacity groups, with the latter further subdivided by dose sensitivity. Combinatorial scTF-seq demonstrated that TF interactions can shift from synergistic to antagonistic depending on the relative dose. Altogether, scTF-seq enables the dissection of TF function, dose and cell fate control, providing a high-resolution framework to understand and predict reprogramming outcomes, advancing gene regulation research and the design of cell engineering strategies.
    DOI:  https://doi.org/10.1038/s41588-025-02343-7
  15. Comput Biol Chem. 2025 Sep 30. pii: S1476-9271(25)00363-9. [Epub ahead of print]120(Pt 2): 108702
      Gene regulatory networks (GRNs) govern gene expression and cellular identity, but accurately inferring their structure from high-dimensional single-cell RNA sequencing (scRNA-seq) data remains a major challenge. Here, we present EnsembleRegNet, a deep learning framework that infers transcription factor (TF)-target gene relationships by integrating an ensemble encoder-decoder and multilayer perceptron (MLP) architecture. EnsembleRegNet utilizes Hodges-Lehmann estimator (HLE)-based binarization, case-deletion analysis, motif enrichment using RcisTarget, and regulon activity scoring with AUCell to enhance both robustness and biological interpretability. Extensive evaluations across simulated and real scRNA-seq datasets demonstrate that EnsembleRegNet outperforms existing GRN inference methods, including SCENIC and SIGNET, in both clustering performance and regulatory accuracy. By uncovering cell-type-specific regulatory modules and enhancing interpretability, EnsembleRegNet offers a scalable and biologically grounded framework for exploring transcriptional regulation. Its demonstrated performance establishes a new benchmark for GRN inference and highlights its promise for applications in disease modeling, biomarker discovery, and cellular reprogramming.
    Keywords:  Cell clustering; Deep learning; Encoder-decoder; Ensemble; Gene regulatory network inference
    DOI:  https://doi.org/10.1016/j.compbiolchem.2025.108702