Frazee CS, Chen S, Berry CT
… +15 more, Lee CS, Banciella RA, Ngo L, Shon D, Herman PJ, Fischman JS, Leff CL, Chen A, Kuo Y, Shestov AA, Kelly AR, Valentic B, Milone MC, O'Connor RS, Ellebrecht CT
Nat Immunol
· 2026 Jul · PMID 42332264
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Chimeric antigen receptor (CAR) T cell therapy can result in impressive remissions in hematological malignancies, but relapse is common because a minority of infused cells acquire a long-lived, memory-like state. All US...Chimeric antigen receptor (CAR) T cell therapy can result in impressive remissions in hematological malignancies, but relapse is common because a minority of infused cells acquire a long-lived, memory-like state. All US Food and Drug Administration-approved CAR T cell products incorporate either 4-1BB or CD28 costimulatory domains, each conferring distinct phenotypic outcomes, but how these signals control early fate decisions is incompletely understood. Here we show that costimulatory domains control memory fate acquisition through asymmetric cell division. CD28 CAR T cells have higher CAR surface expression and enhanced surface proteome asymmetry after the first division, yet paradoxically they show muted transcriptional, epigenetic and metabolic divergence between daughter cells, correlating with reduced long-term persistence. Conversely, 4-1BB CAR T cells have less surface polarization but more pronounced transcriptional, metabolic and epigenetic divergence, yielding proximal effector-prone and distal persistence-prone daughters. Integrating surface proteomics, transcriptomics, metabolomics and chromatin accessibility, we show how costimulatory domains tune asymmetric cell division to shape CAR T cell fate, providing a mechanistic foundation for optimizing cellular immunotherapy.
Although people living in malaria-endemic areas experience repeated infections with Plasmodium, the role of regulatory T (T) cells in recurrent malaria remains poorly understood. During a primary infection with Plasmodiu...Although people living in malaria-endemic areas experience repeated infections with Plasmodium, the role of regulatory T (T) cells in recurrent malaria remains poorly understood. During a primary infection with Plasmodium, T cells suppress protective immunity by inhibiting germinal center (GC) reactions, thereby impeding the control of parasitemia. In contrast, memory T (mT) cells remaining after the clearance of initial Plasmodium infection acquire protective functions after recall. Longitudinal studies in humans and mice show that mT cells undergo antigen-driven expansion and inflammation-induced epigenetic reprogramming during reinfection to transition from FOXP3 immunosuppressive cells to BCL6 follicular T helper (T) cell-like effectors. These mT cell-derived T-like cells enhance GC responses and the generation of antibodies specific to Plasmodium, ultimately facilitating Plasmodium control. Precluding such mT-to-T cell differentiation abolished protection. Our findings reveal a previously unrecognized adaptive plasticity in canonical mT cells that enables a context-dependent functional switch from immunoregulatory to protective effectors during recurrent infections.
Peripherally induced regulatory T (pT) cells play an essential role in establishing immune tolerance to gut microbiota and food antigens. A subset of RORγt-expressing antigen-presenting cells, Thetis cell subset IV (TC I...Peripherally induced regulatory T (pT) cells play an essential role in establishing immune tolerance to gut microbiota and food antigens. A subset of RORγt-expressing antigen-presenting cells, Thetis cell subset IV (TC IV), plays an essential role in intestinal tolerance. However, the transcription factors governing the differentiation of this subset remain unclear. Here we show that Runx-CBFβ complexes regulate the development of specific TC subsets. Mice lacking CBFβ2 exhibited loss of TC II, III and IV, with loss of RORγt pT cells. Transgenic CBFβ2 expression by Cd11c-Cre restored TC IV and RORγt pT cell differentiation in CBFβ2-deficient mice. Conditional inactivation of Runx1 and Runx3 by Cd11c-Cre selectively impaired TC III and IV. Conversely Cd11c-Cre-driven transgenic Runx expression enhanced TC IV differentiation and thus RORγt pT cell induction. These findings establish a critical pathway for TC IV differentiation and provide new insights into therapeutic interventions to promote RORγt pT cell induction in autoimmune diseases.
Regulatory T cells (T cells), characterized by FOXP3 expression, maintain immune homeostasis, but their function is impaired in autoimmune diseases such as rheumatoid arthritis (RA). Here we used single-cell RNA sequenci...Regulatory T cells (T cells), characterized by FOXP3 expression, maintain immune homeostasis, but their function is impaired in autoimmune diseases such as rheumatoid arthritis (RA). Here we used single-cell RNA sequencing to analyze T cells in synovial tissues from patients with RA. We identified two predominant T states, CD25CXCR6 T cells and dysfunctional CD25AREG T cells, both enriched in synovial tissues but not in blood. Cortisol, activated by fibroblasts, drove AREG expression and impaired suppressive function in CD25AREG T cells, and AREG promoted an inflammatory phenotype in synovial fibroblasts. By contrast, CD25CXCR6 T cells remained highly suppressive and were supported by membrane-bound tumor necrosis factor (TNF)-expressing macrophages. TNFR2 engagement prevented or reversed the dysfunctional T cell state. These two T cell subsets were also observed in juvenile idiopathic arthritis, indicating shared mechanisms across inflammatory arthritis. These findings define distinct pathways driving functional and dysfunctional T cell states in inflamed tissues and implicate potential therapeutic strategies.
Conventional influenza virus vaccines induce antibody responses of limited breadth. Whether mRNA-based influenza virus vaccines can induce a superior germinal center (GC) response in humans remains unclear. Here we asses...Conventional influenza virus vaccines induce antibody responses of limited breadth. Whether mRNA-based influenza virus vaccines can induce a superior germinal center (GC) response in humans remains unclear. Here we assessed B cell responses in an observational study of cohorts of healthy young adults receiving a licensed, split-virion or investigative mRNA-based quadrivalent seasonal influenza virus vaccine over two consecutive seasons. mRNA-based vaccines consistently elicited higher antibody titers and frequencies of memory B cells. In the draining lymph nodes, mRNA vaccination stimulated sustained GC reactions that persisted for at least 26 weeks after vaccination in 5 of 13 participants across the two seasons. Proteomic analysis of serum IgG repertoire showed that mRNA vaccination increased the number of vaccine-elicited serum IgG clonotypes and promoted intraclonal expansion within pre-existing clonotypes. B cell lineage analyses further indicated that expanded serum clonotypes map to GC B cell-associated sub-branches, consistent with ongoing GC-driven evolution underlying intraclonal expansion. This repertoire remodeling was accompanied by increased binding breadth against antigenically divergent influenza viruses. These findings reveal a key role for persistent GC responses in broadening the repertoire of vaccine-induced antibodies.
Naive B cells diversify via clonal expansion, immunoglobulin isotype switching, phenotypic variation and somatic hypermutation (SHM). Diversity in antigenic targets, functional classes and the production kinetics of anti...Naive B cells diversify via clonal expansion, immunoglobulin isotype switching, phenotypic variation and somatic hypermutation (SHM). Diversity in antigenic targets, functional classes and the production kinetics of antibodies affects immunity to malaria. Here we show that individual clones diversify over time during Plasmodium infection. During the first week, amid widespread bystander activation, isotype switching initiates soon after Myc upregulation and overlaps with clonal expansion, resulting in isotype variegation among clones. During the second week, expanded clones seeding germinal centers (GC) bifurcate into extrafollicular plasmablasts, exhibit isotype variegation and initiate SHM, indicating substantial intraclonal diversification. Over the following month, GC clones exhibit SHM at approximately four mutations per week. Antimalarial intervention does not impede SHM, instead exerting quantitative limits on GC size, plasma cell emergence, circulating antibody levels and protection against reinfection. Finally, contemporaneous B cell development relocates from bone marrow to spleen. Thus, multiple temporally overlapping mechanisms combine in vivo to diversify and safeguard humoral immune responses.
The pathogenic mechanisms underlying pyoderma gangrenosum (PG) remain unclear. Here we report three patients with PG from two unrelated kindreds with homozygous R57C mutation of the linear deubiquitinase OTULIN. The pati...The pathogenic mechanisms underlying pyoderma gangrenosum (PG) remain unclear. Here we report three patients with PG from two unrelated kindreds with homozygous R57C mutation of the linear deubiquitinase OTULIN. The patients have isolated, pediatric-onset, OTULIN-related PG (ORP). In contrast to OTULIN-related autoinflammatory syndrome (ORAS), caused by mutations affecting the catalytic domain, R57C affects the PUB-interacting motif with distinct biochemical, immunological and clinical consequences. OTULIN-R57C is catalytically active but is unable to bind the linear ubiquitin assembly complex (LUBAC). Patient monocytes show heightened expression of IL1B, and OTULIN-R57C fails to suppress inflammasome activity. Patients have elevated levels of TNF, and their dermal fibroblasts show heightened susceptibility to TNF-dependent cell death. Homozygosity for OTULIN-R57C leads to accumulation of linear ubiquitin and LUBAC autoubiquitination in patients' dermal fibroblasts, consistent with pathogenic LUBAC activity. These findings identify a genetic etiology of isolated PG of childhood. We propose a multifactorial mechanism of ORP, including myeloid IL-1β production and TNF-driven death of skin-resident cells, suggesting that blockade of IL-1β or TNF are therapeutic options in PG.
We designed and preclinically tested two mRNA-lipid-nanoparticle-based vaccine candidates to protect against tuberculosis. BNT164a1 and BNT164b1 encode the same eight Mycobacterium tuberculosis antigens expressed across...We designed and preclinically tested two mRNA-lipid-nanoparticle-based vaccine candidates to protect against tuberculosis. BNT164a1 and BNT164b1 encode the same eight Mycobacterium tuberculosis antigens expressed across different infection stages: Ag85A, Hrp1, ESAT-6, RpfD, RpfA, HbhA, M72 and VapB47. BNT164a1 utilizes nucleoside-unmodified mRNA, whereas BNT164b1 utilizes N-methylpseudouridine-modified mRNA. Prime-boost immunization with BNT164 candidates elicited antibody and/or T cell responses against all antigens in three mouse strains (C57BL/6, BALB/c and HLA-A2.1/DR1 humanized mice). The candidates demonstrated favorable safety profiles in a rat toxicity study and significantly reduced bacterial burdens of two M. tuberculosis strains in murine aerosol challenge models. BNT164 protection was correlated with granuloma infiltration by CD8 T cells with memory precursor phenotypes. In conclusion, BNT164a1 and BNT164b1 were immunogenic, well tolerated and efficacious in preclinical models and have entered phase 1/2 clinical trials ( NCT05537038 , NCT05547464 ).
Chen G, Guo J, Heath J
… +27 more, Prestwood TR, Kwon WJ, Smith AR, Nguyen TT, Kathuria KR, Sola E, Sangare A, Mallajosyula V, Furuichi Fong R, Mohsin A, Chen L, Siva O, Padilla C, Tan M, Dekker CL, Grant P, Lu Y, Greenberg HB, Robinson WH, Blish C, Shen-Orr SS, Salehi A, Maecker HT, Khatri P, Utz PJ, Chien YH, Davis MM
Human vaccine responses vary widely, but the determinants remain incompletely defined. Here we analyzed 66 cytokines across four inactivated influenza vaccine (IIV) cohorts over five seasons (n = 581) and identified base...Human vaccine responses vary widely, but the determinants remain incompletely defined. Here we analyzed 66 cytokines across four inactivated influenza vaccine (IIV) cohorts over five seasons (n = 581) and identified baseline serum interleukin (IL)-18 and interferon (IFN)-β as correlates of day 28 antibody responses. To test causality, we evaluated 19 cytokines in human tonsil and spleen organoids and found that type I IFNs, IL-21 and IL-12, but not IL-18 or IFNγ, enhanced antibody production. The addition of IFNβ to IIV recapitulated key features of the live-vaccine cytokine program. IL-12 and IL-21 defined a parallel pathway independent of type I IFNs, with IL-12 inducing IL-21 in humans, unlike in mice. Delivery of IL-21 or IFNβ via mRNA lipid nanoparticles in vivo promoted long-lived plasma cell formation. Together, these findings define parallel pathways that regulate vaccine immunity. Our approach unites high-throughput organoid testing and human cohort studies, establishing a human-centric platform to identify adjuvant candidates.
Davidson S, Simone D, Jansen K
… +27 more, Cowan M, Machado C, Reekie I, Bhalla A, Borst R, Prada Medina C, Bull J, Wong ZY, Hill S, Garvilles M, Pledger S, Nisa PR, Schwingen NR, Windell D, Attar M, Disney C, Bodey AJ, Parmenter A, Byrne H, Ahmed S, Marathe S, Lee PD, Mahony C, Croft AP, Sansom S, Coles MC, Buckley CD
Nat Immunol
· 2026 Jul · PMID 42260300
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The cellular basis for site-specific inflammation remains unclear. In human fingers, proximal interphalangeal (PIP) joints are preferentially affected by inflammatory arthritis, whereas distal interphalangeal joints are...The cellular basis for site-specific inflammation remains unclear. In human fingers, proximal interphalangeal (PIP) joints are preferentially affected by inflammatory arthritis, whereas distal interphalangeal joints are spared, providing a model to investigate the predilection of inflammation to distinct sites. Here we combine single-cell RNA sequencing, imaging and X-ray tomography to examine cellular composition, spatial organization and structure of finger joints during fetal development. PIP joints had a larger synovial volume and were enriched for PI16 'universal' fibroblasts. These cells were located in perivascular regions and at developing tendon-ligament interfaces. PI16 fibroblasts exhibited both a shared inflammatory and cell-type-specific response to cytokine stimulation, suggesting that the combination of their spatial location and transcriptional responses promote inflammation. We suggest that differences in the stoichiometry of mesenchymal cells established in utero, including the key role of PI16 fibroblasts, is a general principle that drives inflammation susceptibility across tissues.
Szabo PA, Levitin HM, Nargund S
… +13 more, Connors TJ, Chen D, Jin J, Thapa P, Guyer R, Caron DP, Gray JI, Matsumoto R, Kubota M, Brusko M, Brusko TM, Farber DL, Sims PA
Nat Immunol
· 2026 Jul · PMID 42230957
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Early life is essential for establishing memory T cells, which rapidly populate mucosal sites during infancy, although these nascent memory T cells are less protective than their adult counterparts. Here we used single-c...Early life is essential for establishing memory T cells, which rapidly populate mucosal sites during infancy, although these nascent memory T cells are less protective than their adult counterparts. Here we used single-cell RNA sequencing of resting and CD3+CD28 antibody-stimulated T cells from lymphoid and mucosal tissues of infant (2-9 months) and adult (40-63 years) organ donors to investigate age-dependent mechanisms for functional regulation of human memory T cells. Infant CCL5 effector memory T cells exhibited reduced effector function compared to adults. Transcription factor network analysis identified HELIOS and KLF6 as regulators of memory T cell states in infant and adult tissues, respectively. Using single-nucleus RNA sequencing, assay for transposase-accessible chromatin sequencing and CRISPR-Cas9 knockout, we defined HELIOS (IKZF2) as a critical regulator of the infant-specific transcriptional program in CCL5 effector memory T cells and restricted effector function in SELLCCR7 naive and/or central memory T cells. Our findings reveal key mechanisms controlling T cell functional states in early life.