Pathogen-specific CD4⁺ T cells expand and contract during infection, generating memory clones that shape subsequent immune responses. How distinct tissue environments influence differentiation and clonal selection of pol...Pathogen-specific CD4⁺ T cells expand and contract during infection, generating memory clones that shape subsequent immune responses. How distinct tissue environments influence differentiation and clonal selection of polyclonal T cells remains unclear. Here we develop Tracking Recently Activated Cell Kinetics (TRACK) mice, a dual-recombinase fate-mapping system enabling the spatial and temporal labeling of recently activated CD4⁺ T cells. Using TRACK mice during influenza infection, we observed organ-specific transcriptional differentiation and clonal selection in lung, mediastinal lymph nodes (medLNs) and spleen. During the effector phase, spleen-derived CD4⁺ T cells adopted a stem-like migratory phenotype, whereas medLN-activated cells differentiated into T follicular helper cells. T cell receptor sequencing showed low clonal overlap between tissues during the effector response, consistent with distinct antigenic landscapes. During memory formation, overlap increased between lung- and medLN-derived cells, while splenic clones retained a distinct repertoire. These findings define tissue-dependent mechanisms that shape CD4⁺ T cell fate and clonal architecture.
Liu W, Ping J, Deng L
… +14 more, Wang K, Xu J, Peng N, Yang M, Tang H, Liu Z, Wang W, Li T, Xie J, Han Y, Dong Z, Hu W, Liu Z, Wu N
Nat Immunol
· 2026 May · PMID 41781710
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Neutrophil extracellular traps (NETs) constitute a vital antimicrobial defense mechanism of neutrophils, contributing to various physio-pathological processes; however, the role of plasma membrane asymmetry in this proce...Neutrophil extracellular traps (NETs) constitute a vital antimicrobial defense mechanism of neutrophils, contributing to various physio-pathological processes; however, the role of plasma membrane asymmetry in this process remains unknown. Here we identify Xk-related protein 8 (XKR8), a plasma membrane phospholipid scramblase, as a pivotal regulator of NETs formation. Upon NETs induction, XKR8 is cleaved by caspase-3, thereby disrupting plasma membrane lipid asymmetry via phospholipid scrambling. Mutation of the caspase-3 cleavage site in XKR8 impairs NET formation. Inhibition of calcium signals before lipid scrambling abrogates NET formation, whereas blockade after scrambling does not. Cleaved XKR8 reorients plasma membrane lipids, altering membrane lipid tension and promoting Ca signals through mechanosensitive channels. XKR8-deficient mice exhibit compromised NET formation and impaired control of Candida albicans pulmonary infection, showing that XKR8 is indispensable for neutrophil-driven immune responses in vivo. These findings define caspase-3-XKR8plasma membrane phospholipid scrambling as a central mechanism controlling NET formation and underscore its critical role in neutrophil-dependent antifungal immunity.
Natural killer (NK) cells expressing inhibitory receptors that recognize self human leukocyte antigen (HLA) class I molecules gain enhanced functionality-a process influenced by genetic polymorphism that dictates the str...Natural killer (NK) cells expressing inhibitory receptors that recognize self human leukocyte antigen (HLA) class I molecules gain enhanced functionality-a process influenced by genetic polymorphism that dictates the strength of interactions between inhibitory receptors and their HLA ligands. Inhibitory CD94/NKG2A binds HLA-E loaded with epitopes derived from polymorphic HLA class I signal peptides (SPs). We generated a metric, called SP score, that quantifies the overall strength of CD94/NKG2A-HLA-E interactions based on a person's SP genotype. SP scores correlated positively with NKG2ACD56 NK cell response to HLA class I-negative cells, indicating that CD94/NKG2A-HLA-E interaction strength promotes NK cell education. Concordantly, higher SP scores associated with lower risk of nasopharyngeal carcinoma and ulcerative colitis. Thus, the SP score may serve as a genetic tool to guide clinical NK cell intervention strategies, including therapeutic NKG2A blockade.
Prevention and regulation of excessive inflammation is a key target to protect against inflammatory pathologies such as autoimmunity and allergy. In a mouse model of acute lung protease hypersensitivity, we assessed the...Prevention and regulation of excessive inflammation is a key target to protect against inflammatory pathologies such as autoimmunity and allergy. In a mouse model of acute lung protease hypersensitivity, we assessed the efficacy of immunological cross-regulation to mitigate pathogenic inflammation. We show that induction of a type 1 response using Toll-like receptor ligands or a bacterial lysate efficiently blocks acute eosinophilia and type 2 responses evoked by the cysteine protease papain. Upon rechallenge with papain weeks later, mice displayed enhanced type 2 responses and eosinophilia, whereas this response was absent if the initial inflammation was cross-regulated. Memory of the initial event was stored in adventitial stromal cells expressing CCL11. Accessibility of the Ccl11 locus was increased by papain exposure in an interleukin-4- and interleukin-13-dependent manner and blocked by interferon gamma. Our results show how the nature of an initial inflammation is memorized by tissue-resident cells and shapes subsequent inflammatory responses.
Fisher K, Garcia MA, Frattari GS
… +39 more, Naasz C, Zhuo J, Rosás-Umbert M, Dietz LL, Juhl AK, Falling Iversen E, Olesen R, Schleimann MH, Pahus MH, Johansen IS, Henderson M, Carrere L, Roseto I, Gao C, Yu XG, Fray EJ, Aydin B, Lubbeck D, Lai J, Simonetti FR, Danesh A, Miller I, Mendoza P, Niessl J, Gaebler C, Seaman MS, Kaufmann DE, Lehmann C, Gruell H, Klein F, Caskey M, Nussenzweig MC, Tolstrup M, Jones RB, Gunst JD, Siliciano JD, Lichterfeld M, Siliciano RF, Søgaard OS
Nat Immunol
· 2026 Apr · PMID 41776101
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Antiretroviral therapy (ART) interruption typically leads to rapid HIV-1 viral rebound in people with HIV-1. To develop an HIV-1 cure, insight into immunological mechanisms capable of preventing HIV-1 viral rebound is ur...Antiretroviral therapy (ART) interruption typically leads to rapid HIV-1 viral rebound in people with HIV-1. To develop an HIV-1 cure, insight into immunological mechanisms capable of preventing HIV-1 viral rebound is urgently needed. Here, we describe three exceptional post-intervention controllers (PICs) who maintained ART-free virological control for >6.5 years (ongoing), >7.5 years (ongoing) and 2.5 years following administration of broadly neutralizing antibodies. PICs had quantifiable genetically intact/inducible infectious proviral reservoirs that were increasingly clonal and located in nongenic/centromeric chromosomal regions, indicating immune-mediated selection. Potent autologous neutralizing antibodies and polyfunctional HIV-1-specific CD4 and CD8 T cell responses, pre-programmed for antigen response, were present before, and persisted during, ART interruption. In one PIC, viral rebound following 2.5 years of ART-free control was associated with accumulated viral mutations that resulted in escape from neutralizing antibody and T cell responses. Collectively, our findings support developing HIV-1 curative strategies aimed at enhancing pre-existing adaptive immune responses.
Li Z, Xu B, Sharma P
… +8 more, Guy C, Boada-Romero E, Verbist K, Guo A, Mari L, Poudel S, Yang M, Green DR
Nat Immunol
· 2026 Apr · PMID 41776100
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The clearance of dying cells by phagocytes (efferocytosis) is important for maintenance of tissue homeostasis and the active repression of inflammatory responses but can promote an immunosuppressive tumor microenvironmen...The clearance of dying cells by phagocytes (efferocytosis) is important for maintenance of tissue homeostasis and the active repression of inflammatory responses but can promote an immunosuppressive tumor microenvironment. Here we show that Notch signaling is suppressed actively during efferocytosis and that activation of this pathway by ectopic expression of the Notch intracellular domain in myeloid cells improves anticancer immunity in mice. Contact with dead cells or IgG-coated surfaces induces the activation of an integrin barrier that excludes Notch from the contact site to prevent it signaling. The formation of this active integrin barrier requires the Rubicon-VPS34 complex, which recruits phospholipase D (PLD) to regulate integrin activation. Ablation of Rubicon in the host or inhibition of PLD increases Notch activation during efferocytosis and improves anticancer immunity in a manner dependent on Notch signaling. These findings identify a regulatory mechanism that restricts Notch signaling during efferocytosis.
Langston PK, Vijaya Raghavan J, Benoist C
… +1 more, Mathis D
Nat Immunol
· 2026 Mar · PMID 41775886
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As the actuator of movement and a key regulator of organismal metabolism, skeletal muscle is a site at which inflammatory responses must be carefully calibrated to counteract stressors while preventing protracted functio...As the actuator of movement and a key regulator of organismal metabolism, skeletal muscle is a site at which inflammatory responses must be carefully calibrated to counteract stressors while preventing protracted functional impairments. Exercise, injury and aging are common forms of stress associated with inflammation; yet the specific inducers and sensors driving such inflammation remain poorly characterized. Multipronged assessment of acute and chronic endurance exercise models uncovered a role for muscle mesenchymal stromal cells in transducing exercise-induced mechanical stress into local inflammatory responses and that the mechanosensitive ion channel Piezo1 is the primary molecular sensor. Mechanosensing by stromal cells is also necessary for appropriately timed inflammatory and myogenic responses to acute muscle injury and is associated with age-related muscle inflammation. These findings highlight sensing of altered tissue stiffness by Piezo1 on muscle mesenchymal stromal cells as a fundamental mechanism of stress-induced immunomodulation in skeletal muscle.
Vascular tissue-resident macrophages (VRMs) maintain immune balance in blood vessels, but their role in abdominal aortic aneurysm (AAA) development remains unclear. Here we demonstrated that a specific group of VRMs loca...Vascular tissue-resident macrophages (VRMs) maintain immune balance in blood vessels, but their role in abdominal aortic aneurysm (AAA) development remains unclear. Here we demonstrated that a specific group of VRMs located in the adventitia marked by expression of Lyve1, protected against AAA by secreting the extracellular matrix protein Sparcl1 (Sc1). Deletion of Sc1 in VRMs promoted dysfunctional lymphangiogenesis and led to the formation of tertiary lymphoid structures (TLSs), thereby accelerating AAA progression. Mechanistically, the calcium-binding domain of Sc1 acted as a trap for the growth factor FGF2, inhibiting FGF2-mediated dysfunctional lymphangiogenesis and expression of genes associated with TLS formation. A therapeutic peptide derived from Sc1 (Spa17) mitigated AAA progression in several AAA models. Our findings reveal that VRM-derived Sc1 has a protective role in AAA and identify a potential therapeutic approach.
TOX is a nuclear factor critical for thymic development of CD4 thymocytes, natural killer and innate lymphoid cells. In post-thymic antigen-specific CD8 T cells, TOX is highly expressed in settings of chronic antigen enc...TOX is a nuclear factor critical for thymic development of CD4 thymocytes, natural killer and innate lymphoid cells. In post-thymic antigen-specific CD8 T cells, TOX is highly expressed in settings of chronic antigen encounter such as cancer and chronic infection and required for the persistence of exhausted CD8 T cells. The role of TOX in CD4 T cells is less clear. Here, we show that TOX is critical for CD4 type 1 helper T (T1) cell differentiation. Gain-of-function and loss-of-function studies show that TOX induces T1 cell-associated molecular programs that drive T1 cell-like phenotypes and interferon-γ production. TOX expression in CD4 T cells from individuals with cancer was associated with increased cytotoxicity, antitumor immunity and improved responses to immunotherapy, as well as pathogenic responses in autoimmune and inflammatory diseases in mice and humans. Thus, TOX has opposing functions in CD4 versus CD8 T cells: while TOX is associated with CD8 T cell exhaustion and generally with poor responsiveness to immunotherapy, in CD4 T cells TOX drives T1 cell fate commitment and is associated with antitumor immunity and pathogenic autoimmune responses.
Vollmers AC, Wu SZ, Altieri A
… +28 more, McCartney EE, Bender H, Davidson CD, Lee WP, Zhang J, Hu C, Jeet S, Hall B, Irizarry-Caro RA, Guarnieri A, Santosa EK, Preston J, Uttarwar S, Vander Heiden JA, Chung Y, Ortiz W, Long M, Asuncion R, Yang YA, Jiang JX, Modrusan Z, Chintalacharuvu S, Moussion C, Krishnamurty AT, Fu W, Müller S, Buechler MB, Turley SJ
Nat Immunol
· 2026 Apr · PMID 41760904
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Fibroblast-macrophage crosstalk is well-established in vitro, and fibroblast-derived colony-stimulating factor 1 (CSF1) supports macrophages in select tissues. However, whether macrophages regulate fibroblasts in vivo re...Fibroblast-macrophage crosstalk is well-established in vitro, and fibroblast-derived colony-stimulating factor 1 (CSF1) supports macrophages in select tissues. However, whether macrophages regulate fibroblasts in vivo remains unknown. Leveraging genetic mouse models, single-cell multi-omics, flow cytometry and imaging, we show that fibroblast depletion or loss of fibroblast-derived growth factors impacts skin macrophage populations in the dermis and hypodermis. Conditional deletion of Csf1 in Dpt fibroblasts progressively decreases CD64 and CD11c macrophages, impairing skin wound healing. Reduced macrophage abundance disrupts fibroblast cell cycle regulation, metabolism and immune signaling, and increases fibroblast abundance, affirming a reciprocal relationship. In human systemic sclerosis (scleroderma), elevated fibroblast-derived CSF1 and increased macrophage abundance correlate with disease severity, implicating the CSF1-CSF1R axis in pathology. These findings provide in vivo evidence of macrophage regulation of fibroblasts, revealing a bidirectional interplay that advances understanding of tissue homeostasis and immune regulation in skin.
Germinal centers (GCs) are specialized lymphoid structures in which activated B cells undergo clonal selection and B cell receptor (BCR) somatic hypermutation to generate high-affinity antibodies. Previous work has shown...Germinal centers (GCs) are specialized lymphoid structures in which activated B cells undergo clonal selection and B cell receptor (BCR) somatic hypermutation to generate high-affinity antibodies. Previous work has shown that T cells expressing choline acetyltransferase (ChAT), the enzyme that synthesizes acetylcholine (ACh), are linked to the production of high-affinity antibodies in the GC response. However, whether B cells in the GC also express ChAT, and the details of the interplay of cholinergic circuits within the GC, remain unclear. Here we show that Chat expressed by GC B cells contributes to the early accumulation of high-affinity GC B cells following antigen encounter. We identify key transcriptional regulators of Chat expression in GC B cells and demonstrate that ACh receptor (AChR) expression is dynamically coordinated during B cell activation. In vitro, we show that ACh binding to muscarinic AChRs limits plasma cell differentiation and dampens BCR signal transduction to fine-tune the threshold for affinity-based positive selection. Together, these findings reveal a previously unrecognized regulatory axis that operates early during GC selection and uses cholinergic signals to shape B cell fate decisions and humoral immunity.
Nat Immunol
· 2026 Mar · PMID 41735532
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Metabolic activity shapes cell fate but remains challenging to capture in vivo with high resolution. Here we performed longitudinal metabolic and phenotypic profiling of human antigen-specific CD8 T cells after yellow fe...Metabolic activity shapes cell fate but remains challenging to capture in vivo with high resolution. Here we performed longitudinal metabolic and phenotypic profiling of human antigen-specific CD8 T cells after yellow fever vaccination using flow cytometry and single-cell RNA sequencing. As assessed by protein translation rates, CD8 T cells upregulated glycolysis to fuel anabolic needs for proliferation but predominantly used oxidative phosphorylation for energy production during the acute phase (days 7-28) after vaccination. Simultaneously, CD8CD62LCD45RA central memory T cells were the most metabolically active subset, whereas CD8CD62LCD45RA effector T cells underwent metabolic shutdown. Weakly differentiated CD8CD62LCD45RACD95 naive-like memory T cells showed minimal activity, relied solely on oxidative phosphorylation and were preferentially maintained 26 years postvaccination, reinforcing the link between cellular quiescence and longevity. Our study highlights quiescence as a key feature for long-term immunological memory formation in humans.
McCaffrey EF, Delmastro AC, Fitzhugh I
… +31 more, Ranek JS, Douglas S, Peters JM, Fullaway CC, Bosse M, Liu CC, Gillen C, Greenwald NF, Anzick S, Martens C, Winfree S, Bai Y, Sowers C, Goldston M, Kong A, Boonrat P, Bigbee CL, Venugopalan R, Maiello P, Klein E, Rodgers MA, Scanga CA, Lin PL, Bendall SC, Kirschner DE, Fortune SM, Bryson BD, Butler JR, Mattila JT, Flynn JL, Angelo M
Despite being heavily infiltrated by immune cells, tuberculosis (TB) granulomas often subvert the host response to Mycobacterium tuberculosis (Mtb) infection and support bacterial persistence. Human TB granulomas are enr...Despite being heavily infiltrated by immune cells, tuberculosis (TB) granulomas often subvert the host response to Mycobacterium tuberculosis (Mtb) infection and support bacterial persistence. Human TB granulomas are enriched for immunosuppressive factors typically associated with tumor-immune evasion, raising the possibility that they promote tolerance to infection. Here we identify candidate drivers for establishing this tolerogenic niche and show that the magnitude of this response correlates with bacterial persistence. We conducted a multimodal spatial analysis of 52 granulomas from 16 nonhuman primates infected with low-dose Mtb for 9-12 weeks. Each granuloma's bacterial burden was quantified individually, enabling us to assess how granuloma spatial structure and function relate to infection control. We found that a universal feature of TB granulomas is partitioning of the myeloid core into two distinct metabolic environments, one of which is hypoxic. This hypoxic environment is associated with pathological immune cell states, dysfunctional cellular organization of the granuloma, and a near-complete blockade of lymphocyte infiltration that would be required for a successful host response. The extent of these hypoxia-associated features correlates with higher bacterial burden. We conclude that hypoxia correlates with immune cell state and organization within granulomas and might subvert immunity to TB.