bims-imseme Biomed News
on Immunosenescence and T cell metabolism
Issue of 2025–10–26
twenty papers selected by
Pierpaolo Ginefra, Ludwig Institute for Cancer Research



  1. Clin Rev Allergy Immunol. 2025 Oct 25. 68(1): 95
      T cell metabolism constitutes a pivotal regulator of cellular states and disease progression. At the cellular level, the metabolic status of T cells directly governs their function and fate determination. Senescent T cells, for instance, exhibit fundamentally distinct metabolic signatures compared to effector T subsets, underscoring metabolic reprogramming as a critical mechanistic driver of T cell senescence. In pathological contexts, aberrant metabolic rewiring in T cells disrupts differentiation, function, and cellular survival, thereby contributing to disease onset and progression. Notably, the pathological accumulation of senescent T cells observed across chronic inflammatory and autoimmune diseases positions metabolism-driven T cell senescence as a key nexus linking metabolic dysregulation to clinical manifestations. Consequently, targeted modulation of T cell metabolism offers a dual therapeutic potential: direct intervention in cellular states (e.g., delaying senescent phenotypes) and synergistic amelioration of disease pathology through functional immune restoration. This Review summarizes the fundamental principles of T cell metabolic reprogramming, its causative role in propelling T cell senescence, and the dynamic interplay between metabolic dysfunction, T cell senescence, and disease pathogenesis. We specifically dissect these relationships in two immunologically divergent conditions-systemic lupus erythematosus (SLE, exemplifying hyperactive autoimmunity) and chronic infection (Chronic HIV infection, reflecting immune exhaustion)-to establish a mechanistic framework for developing metabolism-targeted immunotherapeutics that precisely restore T cell efficacy.
    Keywords:  Autoimmune disease; Chronic infection; Metabolic reprogram; Senescent T cell; T cell
    DOI:  https://doi.org/10.1007/s12016-025-09109-3
  2. Cancer Res. 2025 Oct 20.
      In recent years, accumulation of mitochondrial reactive oxygen species (ROS) has been shown to limit the proliferative capacity and intratumoral persistence of CD8+ T cells, but the molecular mechanisms by which ROS produce functional defects in exhausted CD8+ T cells remain incompletely understood. Using a series of elegant genetic tools, Rivadeneira and colleagues demonstrate that accumulation of mitochondrial reactive oxygen species (ROS) is sufficient to directly compromise telomere integrity. The authors induced singlet oxygen within specific subcellular compartments in T cells, achieving precise temporal and spatial control over ROS production. Genetically driven mitochondrial ROS accumulation reproduced hallmarks of intratumoral T cell dysfunction while also producing marked telomere fragility. Consistent with these findings, tumor-infiltrating CD8+ T cells from patients with melanoma and head and neck cancers exhibited substantial accumulation of DNA damage at telomeres compared with healthy donor or autologous peripheral T cells. Moreover, restricting ROS generation specifically to telomeres was sufficient to reproduce T cell dysfunction, while targeting the antioxidant enzyme GPX1 to telomeres reduced DNA damage and enhanced T cell effector functions, leading to improved tumor control. These findings reveal telomeres as key mediators of redox stress-driven T cell dysfunction and suggest that interventions aimed at protecting chromosome ends may represent a novel strategy to enhance antitumor immunity.
    DOI:  https://doi.org/10.1158/0008-5472.CAN-25-4716
  3. iScience. 2025 Oct 17. 28(10): 112772
      Glutamate is best known as an excitatory neurotransmitter. However, its roles in T cell immunity remain underrecognized. We investigated the interplay between glutamate receptors (GluRs) and T cell receptors (TCRs) during CD8+ T cell activation. Our findings reveal that GluR expression in CD8+ T lymphocytes strongly correlates with the activation of TCR-CD28 signaling, enhancing their antitumor effector responses. Conversely, pharmacologic antagonism of GluRs in activated CD8+ T cells disrupts the colocalization of GluR with TCRVβ8.1, reduces the phosphorylation of TCR-signaling intermediates, alters calcium flux, and impairs the metabolic switch to glycolysis essential for T cell activation. Moreover, these disruptions blunt clonal proliferation and compromise the tumor-cytolytic capacity of CD8+ T cells. Thus, the glutamatergic system-via the GluR-TCR signaling complex-plays a critical amplifier role in activating CD8+ T cells and eliciting their full antitumor activity. This mechanistic insight reveals a previously underappreciated axis in T cell biology and opens avenues for immunotherapy regimens targeting GluR-TCR interactions to augment T cell-mediated responses in cancer and potentially other immunopathologies.
    Video Abstract:
    Keywords:  immune response; immunology
    DOI:  https://doi.org/10.1016/j.isci.2025.112772
  4. Front Cell Dev Biol. 2025 ;13 1650677
      Metabolic Dysfunction-Associated Steatotic Liver Disease (MASLD) poses a disproportionately severe burden on the aging population, with a heightened risk of progression to advanced fibrosis and cancer. While immunosenescence and metabolic reprogramming are recognized as key drivers, this review proposes an age-dependent immunometabolic vicious cycle as a critical integrative framework underlying MASLD progression. We hypothesize that at the core of this cycle lies mitochondrial dysfunction and reactive oxygen species (ROS) accumulation, which may initiate a self-amplifying loop: triggering NLRP3 inflammasome activation in Kupffer cells, promoting a context-dependent dysfunction of adaptive immunity. This includes driving CD8+ T cells toward exhaustion in advanced disease and disrupting regulatory T cell (Treg) function, which may range from loss of suppressive capacity to a pro-fibrotic phenotypic switch. Together, these alterations in T cell immunity create a permissive environment for unchecked inflammation and fibrosis. This cycle is further reinforced by gut-liver axis dysfunction. Critically, this framework reveals that overcoming the therapeutic bottleneck in age-associated MASLD necessitates a paradigm shift toward combination therapies that simultaneously target multiple nodes of the cycle.
    Keywords:  combination therapy; immunosenescence; metabolic dysfunction-associated steatotic liver disease (MASLD); metabolic reprogramming; mitochondrial dysfunction; vicious cycle
    DOI:  https://doi.org/10.3389/fcell.2025.1650677
  5. Clin Immunol. 2025 Oct 18. pii: S1521-6616(25)00187-1. [Epub ahead of print]282 110612
      Transforming growth factor β (TGF-β) is recognized as an anti-inflammatory cytokine that negatively affects effector CD8 T cells. However, its impact is not confined to the effector CD8 T cell population; TGF-β also plays a role in suppressing naïve CD8 T cell activation, preserving stemness, and influencing the function and differentiation of memory CD8 T cells. Memory CD8 T cells are vital for eradicating pathogens that have previously infected the host. Both tissue-resident and central memory CD8 T cells have demonstrated a dependency on TGF-β for their differentiation. The mechanisms underlying many of these TGF-β effects remain unclear. This review summarizes the roles of TGF-β in various CD8 T cell subsets, with an emphasis on the memory T cell compartment, and discusses recent findings regarding its influence on memory CD8 T cell differentiation as well as open questions in the field.
    Keywords:  Dominant negative; Memory; Memory precursor effector; Short-lived effector; TGF-β signaling; Tissue-resident
    DOI:  https://doi.org/10.1016/j.clim.2025.110612
  6. Sci Immunol. 2025 Oct 24. 10(112): eads9456
      Immunotherapies targeting regulatory T (Treg) cells often trigger inflammation and autoimmunity. How Treg cells undergo functional reprogramming to reestablish immune homeostasis under these conditions remains unclear. Here, we demonstrate that mitochondrial and lysosomal signaling orchestrates Treg cell metabolic and functional fitness. Treg cell-specific loss of the mitochondrial protein Opa1 led to disrupted immune homeostasis and pronounced inflammation, and reduced the generation of Treg cells with high mitochondrial metabolic and suppressive function. Opa1 deletion triggered mitochondrial bioenergetic stress, associated with increased adenosine monophosphate-activated protein kinase (AMPK) signaling and transcription factor EB (TFEB) activation. Further, Treg cell-specific deletion of the lysosomal signaling protein Flcn partially phenocopied Opa1 deficiency-associated inflammation and aberrant TFEB activation, and these effects were rectified by TFEB codeletion. Flcn-deficient Treg cells were enriched in a terminal "metabolic quiescence reset" state and failed to accumulate in nonlymphoid tissues and suppress antitumor immunity. Our study demonstrates that organelle-directed metabolic and signaling processes and mitochondria-lysosome interplay control Treg cell differentiation and function.
    DOI:  https://doi.org/10.1126/sciimmunol.ads9456
  7. Front Immunol. 2025 ;16 1656776
      Cancer incidence is increasing, becoming a significant public health concern. Cancer arises from the uncontrolled division of cells that cannot be restrained by the anti-tumour response mounted by the immune system. Both tumour and immune cells require high levels of energy in the form of ATP and synthesis of macromolecules to support differentiation and proliferation. To support these metabolic demands, adaptations at the cell, tissue and systemic level are required. Here, we take a systemic perspective to summarise the energetic needs of the anti-tumour response and how metabolic overload and obesity affects these processes. We describe how immunotherapies that aim to reverse immune cell exhaustion have unexpected effects depending on the metabolic background of the patient and finally we propose the use of this knowledge to advance current cancer prevention and treatment strategies.
    Keywords:  T cells; cancer; immunotherapy; obesity; systemic immunometabolism
    DOI:  https://doi.org/10.3389/fimmu.2025.1656776
  8. Nat Metab. 2025 Oct 21.
      The gut microbiota and its metabolites critically regulate immune cell phenotype, function and energy metabolism. We screened a collection of gut microbiota-related metabolites to identify modulators of mitochondrial metabolism in T cells. Here we show that indole-3-propionic acid (IPA) stimulates mitochondrial respiration of CD4+ T cells by increasing fatty acid oxidation (FAO) and amino acid oxidation (AAO), while inhibiting glycolytic capacity. IPA also impacts CD4+ T cell behaviour by inhibiting their differentiation to type 1 and type 17 helper T cell phenotypes. Mechanistically, the metabolic and immune effects of IPA are mediated by peroxisome proliferator-activated receptor-β/δ. The administration of IPA rescues mitochondria respiration in mice with gut bacteria depletion or colitis by enhancing FAO and AAO in colonic CD4+ T cells. Adoptive transfer experiments show that IPA acts on CD4+ T cells to exert its protective effect against inflammation. Collectively, our study reveals that the anti-inflammatory effects of IPA are mediated by metabolic reprogramming of CD4+ T cells toward the enhancement of mitochondrial respiration.
    DOI:  https://doi.org/10.1038/s42255-025-01396-6
  9. Cell. 2025 Oct 17. pii: S0092-8674(25)01089-X. [Epub ahead of print]
      T cell-mediated tumor killing underlies immunotherapy success. Here, we used long-term in vivo imaging and high-resolution spatial transcriptomics of zebrafish endogenous melanoma, as well as multiplex imaging of human melanoma, to identify domains facilitating the immune response during immunotherapy. We identified cancer regions of antigen presentation and T cell engagement and retention (CRATERs) as pockets at the stroma-melanocyte boundaries of zebrafish and human melanoma. CRATERs are rich in antigen-recognition molecules, harboring the highest density of CD8+ T cells in tumors. In zebrafish, CD8+ T cells formed prolonged interactions with melanoma cells within CRATERs, characteristic of antigen recognition. Following immunostimulatory treatment, CRATERs expanded, becoming the major sites of activated CD8+ T cell accumulation and tumor killing. In humans, elevation in CRATER density in biopsies following immune checkpoint blockade (ICB) therapy correlated with a clinical response to therapy. CRATERs are structures that show active tumor killing and may be useful as a diagnostic indicator for immunotherapy success.
    Keywords:  CD8+ T cells; cancer; immune response; immunotherapy; melanoma; zebrafish
    DOI:  https://doi.org/10.1016/j.cell.2025.09.021
  10. Sci Adv. 2025 Oct 24. 11(43): eadt3879
      Aging is characterized by disruptions in metabolic homeostasis, yet the mechanisms that regulate these metabolic changes remain poorly understood. We show that the serine/threonine-protein phosphatase 6 (PP6) regulatory subunit 3, SAPS3, is a critical regulator of metabolism during aging. SAPS3 deletion significantly extends lifespan in mice and counteracts age-related impairments in metabolic health. SAPS3 deficiency improves the effects of aging on the affective behaviors, cognition, and motor functions in aged mice. We find that SAPS3 expression is increased during aging to inhibit adenosine monophosphate-activated kinase (AMPK) activity. Deletion of SAPS3 leads to AMPK activation and reverses cellular senescence and aging-induced metabolic alterations. Using in vivo U-13C6-D-glucose tracing and metabolomic analysis, we find that SAPS3 deficiency restores metabolic homeostasis with increased glycolysis, tricarboxylic acid (TCA) cycle, and decreased fatty acid synthesis in aged mice. These findings highlight a critical role of the SAPS3/PP6 phosphatase complex in aging and suggest that strategies targeting SAPS3 may promote longevity and healthy aging.
    DOI:  https://doi.org/10.1126/sciadv.adt3879
  11. Nat Biomed Eng. 2025 Oct 21.
      Immune-based cell therapy offers a promising approach to cancer treatment. While autologous chimeric antigen receptor (CAR) T cells have shown success, production is time-consuming, costly and patient specific. Gamma-delta (γδ) T cells are promising for 'off-the-shelf' CAR T cell therapy. However, clinical translation of γδ CAR T cells is hampered by low frequency, resistance to genetic manipulation and advanced differentiation after expansion, limiting therapeutic feasibility. Here we demonstrate a method for in vitro activation and expansion of peripheral blood γδ T cells, facilitating high rates of gene editing and efficient CAR integration. Using artificial antigen-presenting cells, we produce minimally differentiated, highly functional γδ CAR T cells. By targeting a US Food and Drug Administration-approved CD19 CAR to the CCR5 locus, we generate CCR5-deficient γδ CD19 CAR T cells (γδ CCR5KI-CAR19), which demonstrated resistance to HIV-mediated depletion and robust antitumour responses against B cell lymphoma and leukaemia. γδ CCR5KI-CAR19 T cells enable the immunotherapy of HIV-associated B cell malignancies. These studies provide preclinical evidence supporting large-scale development of potent allogeneic γδ CAR T cells for diverse immunotherapies.
    DOI:  https://doi.org/10.1038/s41551-025-01527-0
  12. Cell Death Dis. 2025 Oct 21. 16(1): 741
      Declining mitochondrial function is an established feature of aging and contributes to most aging-related diseases through its impact on various pathologies such as chronic inflammation, fibrosis and cellular senescence. Our recent work suggests that benign prostatic hyperplasia, which is an aging-related disease frequently associated with inflammation, fibrosis and senescence, is characterized by a decline in mitochondrial function. Here, we utilize glycolytic restriction and pharmacologic inhibition of the mitochondrial electron transfer chain complex I to promote mitochondrial dysfunction and identify the cellular processes impacted by declining mitochondrial function in benign prostate stromal cells. Using this model, we show that mitochondrial dysfunction induced alterations in cell-cell and cell-matrix adhesion, elevated fibronectin expression, resistance to anoikis and stress-induced premature senescence (SIPS). We also showed that ablation of ZC3H4, a transcription termination factor implicated in anoikis-resistance and reduced in BPH relative to normal prostates, phenocopied various phenotypes in the human BHPrS1 prostate stromal cell line that resulted from inhibition of complex I. Furthermore, ZC3H4 ablation resulted in the elevation of mitochondrial superoxide (mtROS) and mitochondrial membrane potential, altered mitochondrial morphology and NAD+/NADH ratio, and reduced CI function in BHPrS1 cells. Thus, ZC3H4 loss promotes mitochondrial dysfunction to drive pathophysiologic changes in the stromal compartment that are features of the aging prostate.
    DOI:  https://doi.org/10.1038/s41419-025-08027-8
  13. Cancer Immunol Res. 2025 Oct 23.
      Tumor-specific CD8+ T cells in blood appear to be important for and predictive of response to anti-PD-1 therapies. However, as most tumor antigens are unique to a given patient, identification of tumor-specific CD8+ T cells is not routinely feasible. Here, we characterized polyomavirus-specific CD8+ T cells from blood of 17 patients with virus-driven Merkel cell carcinoma (MCC). We identified a 98-gene signature, SPoTT (Signature of Peripheral Tumor-specific CD8+ T cells), that discriminated circulating tumor-specific CD8+ T cells from other T cells in immunotherapy-naïve patients. We observed profound transcriptomic differences among tumor-specific CD8+ T cells from blood versus from tumor. In validation cohorts of MCC, as well as neoantigen-driven cancers, SPoTT was able to identify viral oncoprotein- and neoantigen-specific CD8+ T cells with both sensitivity and specificity above 75%. We also tested a previously described 151-gene signature (NeoTCR_PBL) trained on neoantigen-specific CD8+ T cells and found it was able to recognize MCPyV-specific T cells with sensitivity of 66% and a specificity of 88%. These findings show that circulating tumor-specific CD8+ T cells share fundamental characteristics across diverse tumor antigen types. More broadly, insights into antitumor T cells gained from virus-driven cancers are also likely to be relevant in mutationally-driven cancers.
    DOI:  https://doi.org/10.1158/2326-6066.CIR-25-0082
  14. J Immunother Cancer. 2025 Oct 23. pii: e013025. [Epub ahead of print]13(10):
       BACKGROUND: Immune checkpoint blockade (ICB) therapy has demonstrated significant clinical potential in a variety of cancers; however, its efficacy in clear cell renal cell carcinoma (ccRCC) remains suboptimal. In ccRCC, an increased infiltration of CD8+ T cells does not necessarily correlate with improved prognosis, indicating the presence of unique immune evasion mechanisms within the tumor microenvironment (TME).
    METHODS: Tripartite motif-containing 28 (TRIM28) was identified as a potential therapeutic target through single-cell transcriptomics (GSE159115) and Geneformer-based perturbation screening. Functional validation was performed by constructing shTRIM28 and overexpression cell models to assess tumor proliferation, CD8+ T cell co-cultures, flow cytometry, and patient-derived xenograft models. Co-immunoprecipitation and GST pull-down assays were used to analyze the TRIM28-poly (ADP-ribose) polymerase 1 (PARP1) interaction. SUMOylation/ubiquitination studies elucidated the mechanism regulating PARP1 stability, and chromatin immunoprecipitation-quantitative PCR identified the transcriptional regulation of programmed death-ligand 1 (PD-L1). High-throughput screening was conducted with RNA-seq, liquid chromatography-tandem mass spectrometry, and metabolomics. Virtual screening identified the TRIM28 inhibitor Eltrombopag, which was tested in combination with anti-programmed cell death protein-1 (PD-1) therapy for in vivo efficacy and metabolic reprogramming.
    RESULTS: We identified TRIM28 as a central regulator of immune evasion in ccRCC. Using high-throughput gene knockout screening, we demonstrated that TRIM28 depletion reprograms malignant epithelial cells toward a less aggressive phenotype and significantly enhances tumor cell susceptibility to cytotoxic T lymphocyte killing. Mechanistically, TRIM28 promotes immune resistance through dual immunometabolic mechanisms: first, by stabilizing PARP1 and promoting its SUMOylation, which in turn amplifies PD-L1 expression via NAD+-SIRT1-p65 signaling; second, by depleting NAD+ in the TME, limiting NAD+ availability for CD8+ T cells and impairing their respiration and effector function. These findings provide a novel mechanistic framework for TRIM28-driven immune suppression, integrating tumor-intrinsic metabolic reprogramming with CD8+ T cell dysfunction. Notably, we identified Eltrombopag as a candidate TRIM28 inhibitor, which synergized with anti-PD-1 therapy to enhance antitumor immunity and overcome ICB resistance in murine models.
    CONCLUSIONS: This study reveals that TRIM28 is a key regulator of PD-L1 expression and T cell dysfunction in ccRCC through PARP1 stabilization and NAD+ metabolic reprogramming. Targeting TRIM28/PARP1/PDL1 with Eltrombopag reshapes the immunosuppressive TME and enhances checkpoint blockade efficacy, providing a novel combinatorial strategy for ccRCC immunotherapy.
    Keywords:  Immunosuppression; Immunotherapy; Kidney Cancer; T cell
    DOI:  https://doi.org/10.1136/jitc-2025-013025
  15. J Neurochem. 2025 Oct;169(10): e70265
      Myelinating Schwann cells depend on precise metabolic regulation to support axonal function and maintain peripheral nerve integrity. Peripheral Myelin Protein 2 (PMP2), a fatty acid-binding protein enriched in myelinating Schwann cells, has been implicated in lipid metabolism and mitochondrial energy production. Here, we examine the role of PMP2 in regulating Schwann cell bioenergetics and myelination. Using both immortalized and primary Schwann cells, we show that PMP2 overexpression enhances mitochondrial ATP production. We also reveal that PMP2 alters metabolic dependencies during high metabolic demand, reducing Schwann cell reliance on glutamine while promoting greater metabolic adaptability under substrate restriction. Finally, PMP2 overexpression significantly increases myelination in vitro, indicating that PMP2-driven metabolic modulation supports the energetic demands of myelination. These findings position PMP2 as a key regulator of Schwann cell metabolism and a potential therapeutic target for demyelinating neuropathies.
    Keywords:  ATP; PMP2; Schwann cell; seahorse
    DOI:  https://doi.org/10.1111/jnc.70265
  16. Aging Cell. 2025 Oct 21. e70278
      Aging and obesity are associated with pro-inflammatory changes in adipose tissue. Overlapping mechanisms, such as the infiltration of inflammatory macrophages and T cells into visceral adipose tissue, have been implicated in contributing to inflammation. However, a comparative analysis of both states is needed to identify distinct regulatory targets. Here, we performed single-cell RNA sequencing of stromal vascular fractions (SVF) isolated from gonadal white adipose tissue (gWAT) of young mice fed either a normal or a high-fat diet, and aged mice fed a normal diet. Our analysis revealed that physiological aging, compared to high-fat diet-induced obesity, was associated with an accumulation of phenotypically distinct CD8 T cells resembling virtual memory (VM) CD8 T cells. These cells expressed high levels of Cd44, Sell, Il7r, Il2rb, lacked Itga4, and exhibited elevated Fcgr2b expression which was associated with pseudotime differentiation trajectories. Flow cytometry confirmed an age-associated increase in Fcgr2b + CD49d- VM-like CD8 T cells in gWAT. Notably, these Fcgr2b-expressing cells exhibited a cytotoxic profile and expressed granzyme M. Functional analysis using recombinant granzyme M revealed its potential in inducing inflammation in mouse fibroblasts and macrophages. Together, our study has identified Fcgr2b + CD49d- VM-like CD8 T cells in the adipose tissue of aged mice with regulatory, cytotoxic, and inflammatory potential.
    Keywords:  CD8 T cells; adipose tissue; aging; memory T cells; obesity; single‐cell analysis
    DOI:  https://doi.org/10.1111/acel.70278
  17. Adv Sci (Weinh). 2025 Oct 23. e15121
      Immunotherapy remains ineffective in many solid tumors due to poor T-cell infiltration and a metabolically suppressive tumor microenvironment. A dual strategy combining low-level light (LLL) therapy with a nanoscale stimulator of interferon genes (STING) agonist formulation (nanoSTING@Mn) is presented to enhance immune activation and metabolic fitness for durable tumor immunity against T-cell lymphoma (EL4) model. NanoSTING@Mn, composed of ADU-S100 complexed with Mn2⁺ and encapsulated in biomimetic liposomes, potently activates the cGAS-STING pathway, induces a type I interferon response, and promotes lymphocyte infiltration. These monocytes polarize into M1 macrophages, suppressing regulatory T cells. Simultaneously, LLL photo-biomodulation reprograms mitochondrial metabolism in tumor-infiltrating CD8⁺ T and natural killer cells, restoring their durability and leading to complete local tumor eradication. This combination expands a distinct CD8⁺ T-cell subset with Tcf-1⁺ progenitor-exhausted features and elevated memory/effector gene expression, enhancing proliferation and cytotoxicity, as shown by single-cell RNA sequencing. Intranasal nanoSTING@Mn delivery mobilizes these LLL-revived T cells to the lung, where they differentiate into resident memory T cells and establish systemic antitumor immunity. Upon intravenous rechallenge, disseminated tumor cells are eliminated, preventing metastasis and ensuring long-term protection. This synergistic approach offers a scalable platform to boost immunotherapy efficacy and redefines immune-based metastasis prevention strategies.
    Keywords:  cGAS–STING pathway; photo‐biomodulation; resident memory T cells; tumor microenvironment
    DOI:  https://doi.org/10.1002/advs.202515121
  18. Nat Aging. 2025 Oct 24.
      Age-related thymic involution increases vulnerability to cancers and infection in older adults, yet the driving mechanisms and its impact on peripheral T cells remain unclear. Using single-cell sequencing, we here analyzed 387,762 cells from human thymus and peripheral blood of young and aged individuals. Within thymus, we found aging reduced T-lineage potential in early thymic progenitors but increased innate lymphocyte lineage potential. Aged thymus were enriched in mature T cells with low SOX4 expression and inflammatory profiles but depleted of thymic epithelial cells and expression of tissue-restricted antigens. In the periphery, we identified transcriptional features of T cell aging and established a naive T cell-based model for immune age prediction. Furthermore, we identified CD38 as a marker of recent thymic emigrants. Finally, single-cell T cell receptor (TCR) repertoire sequencing identified shifts in TCR repertoire diversity within memory/effector T cells and expanded virus-specific T cells during aging. Collectively, our data offer insights into human thymic involution and peripheral T cell aging and could inform strategies to restore compromised T cell immunity.
    DOI:  https://doi.org/10.1038/s43587-025-00990-3
  19. Nat Biotechnol. 2025 Oct 21.
      Targeted epigenetic engineering of gene expression in cell therapies would allow programming of desirable phenotypes without many of the challenges and safety risks associated with double-strand break-based genetic editing approaches. Here, we develop an all-RNA platform for efficient, durable and multiplexed epigenetic programming in primary human T cells, stably turning endogenous genes off or on using CRISPRoff and CRISPRon epigenetic editors. We achieve epigenetic programming of diverse targeted genomic elements without the need for sustained expression of CRISPR systems. CRISPRoff-mediated gene silencing is maintained through numerous cell divisions, T cell stimulations and in vivo adoptive transfer, avoiding cytotoxicity or chromosomal abnormalities inherent to multiplexed Cas9-mediated genome editing. Lastly, we successfully combined genetic and epigenetic engineering using orthogonal CRISPR Cas12a-dCas9 systems for targeted chimeric antigen receptor (CAR) knock-in and CRISPRoff silencing of therapeutically relevant genes to improve preclinical CAR-T cell-mediated in vivo tumor control and survival.
    DOI:  https://doi.org/10.1038/s41587-025-02856-w
  20. Acta Biochim Biophys Sin (Shanghai). 2025 Oct 21.
      Gut inflammatory diseases, including inflammatory bowel disease (IBD), infectious enteritis, and other inflammatory conditions, are among the most common non-neoplastic intestinal disorders. Their pathogenesis is often driven by an imbalance between pro-inflammatory and anti-inflammatory signals, with immune cells playing pivotal roles in maintaining this equilibrium. Immune cells in the gut exhibit complex, multifaceted functions: they eliminate pathogens, promote tissue repair, and counteract tumors, but excessive immune activation can exacerbate tissue damage and disease progression. Notably, metabolic reprogramming in inflammatory contexts serves as a key regulator of immune cell function and phenotypic switching. This includes alterations in cellular energy metabolism ( e. g., macrophage polarization via disrupted glycolysis or fatty acid oxidation) and the modulation of immune responses by microenvironmental metabolites ( e. g., bile acid-mediated Th17/Treg balance). While alterations in immune cell function and composition within the inflammatory milieu are well-established, the significance of disease-associated metabolic reprogramming-specifically how metabolism regulates immune cell function-has garnered increasing attention. This review explores how cellular metabolic reprogramming, changes in the metabolic microenvironment, and gut dysbiosis collectively influence the differentiation, proliferation, and function of immune cells in various intestinal inflammatory diseases, as well as their impact on disease progression.
    Keywords:  immunometabolism; inflammation; intestinal disorder
    DOI:  https://doi.org/10.3724/abbs.2025192