Autoantibodies (autoAbs) are linked to mortality and Long COVID, yet their cellular origins remain unclear. We analyzed the INCOV cohort and identified 12 age- and sex-matched participants with varying autoAb abundance and integrated single-cell RNA-seq and ATAC-seq data from B cells, plasma proteomics, proteome-wide autoAb profiling, clinical data, and in vitro assays. AutoAb abundance inversely correlated with neutralizing IgG and declined as infection resolved, paralleling the contraction of atypical memory B cells (AtMs). In vitro, AtMs preferentially differentiated into autoAb-producing antibody-secreting cells upon TLR7/8 stimulation. CD11c+ AtMs (double-negative 2, DN2s) in autoAb-high individuals exhibited increased TLR7 signaling, oxidative stress, and isotype switching, regulated by transcription factors T-bet and XBP1. Integrated genetic and genomic analyses showed that DN2s had the strongest enrichment for autoimmune trait heritability and inferred regulatory effects of autoimmune risk variants among B cell subsets. These findings identify DN2s as key precursors of autoAb-producing cells during SARS-CoV-2 infection.
Mechanisms governing T cell responses to food or microbes have been characterized, but whether they also regulate gut autoimmunity is unknown. We compared ovalbumin (OVA)-specific T cell fates using mice fed OVA, or expressing secreted (s), cytosolic (c), or transmembrane (tm) epithelial OVA. At baseline and after reovirus infection, T cell responses were comparable. However, helminth infection induced T helper 2 (Th2) cell polarization in sOVA and tmOVA but not cOVA or OVA-fed mice. BATF3+ antigen-presenting cells (APCs) were indispensable for CD4+ T cell proliferation only in cOVA mice, yet they drove regulatory T (Treg) cell differentiation across all epithelial OVA models. In contrast, antigen presentation by RORγt+MHC class II+ APCs was exclusively required for Treg cell induction by dietary OVA. These distinct APC dependencies correlated with susceptibility to pathology elicited by dietary versus epithelial self-antigens. Thus, antigen origin and presentation context together shape T cell fate, aiding predictions of gut immune outcomes.
Tissue regeneration is viewed as a return to homeostasis, but whether the extracellular matrix (ECM) reverts during recovery from gut inflammation is unclear. Using temporal multi-omics, biomechanical profiling, and spatial fate mapping in colitis models, we showed that colonic ECM underwent lasting pathological reprogramming following inflammation, which we termed modified (mod)ECM. Characterized by collagen XVIII accumulation and immune-driven proteolysis, modECM redirected intestinal stem cells (ISCs) toward a wound-associated epithelial state with a pro-inflammatory transcriptional program. Ex vivo, modECM alone reshaped ISC fate by suppressing Wnt signaling and activating immune recruitment pathways. In vivo, modECM-rich zones sustained T cell infiltration and KRT14+ epithelial cell emergence from Lgr5+ progenitors. This aberrant epithelial program was mirrored in inflamed rectal biopsies from individuals with ulcerative colitis. Our findings redefine the ECM as a long-lived instructive compartment that encodes injury memory and promotes maladaptive regeneration, positioning it as a therapeutic target in chronic inflammatory diseases.
Naive CD4+ T cells interpret cytokine cues to commit to T helper lineages. Here, we examined the impact of cytokines on the Ets1-Fli1 locus, which encodes paralogous transcription factors essential for T cell effector responses. Epigenomic and chromatin interaction profiling in double-positive (DP) thymocytes defined a T cell super-enhancer and a CTCF-bound boundary. Chromatin tracing at single-allele resolution revealed concurrent multi-way interactions among Ets1, Fli1, and the super-enhancer coupled to transcription. Deleting the CTCF boundary decompacted the locus without altering Ets1 expression or T cell development, whereas deleting the super-enhancer drew Ets1 and Fli1 closer; promoter proximity increased Ets1-Fli1 co-expression. In CD4+ Th1 cells, cytokines increased multi-way interactions and repositioned the super-enhancer toward the geometric center, activating both paralogs. Super-enhancer deletion rendered Th1 cells structurally and transcriptionally DP like. Thus, cytokines can drive lineage-specific gene activation by repositioning a super-enhancer, providing a mechanistic framework for how noncoding variants at the Ets1-Fli1 locus contribute to CD4+ T cell-mediated immune disorders.
Intestinal intraepithelial lymphocytes (IELs), including conventional CD8αβ T resident memory (Trm) cells and unconventional CD8αα T cells, promote tissue integrity. Here, we studied the G-protein coupled receptor signals regulating IEL positioning, homeostasis, and function. Deficiency in heterotrimeric G-protein subunit Gα13 or its effector Arhgef1 caused an intestine-specific loss of all types of CD8+ TCRαβ and TCRγδ IELs. Gα13-deficient IELs exhibited restricted intraepithelial movement and impaired maturation. Induction of intestinal CD8αβ+ Trm cells upon infection was intact in the absence of Gα13-signaling, but the cells had poor access to the villous niche and defective survival that could be rescued by increasing TGF-β or interleukin (IL)-15. In vivo CRISPR-Cas9 screening identified GPR132 as a Gα13-coupled receptor that regulates CD8αβ+ IEL homeostasis and migration to lysophosphatidylcholine. Mice bearing Gα13-deficient T cells suffered more severe colitis and increased colorectal tumor growth. The selective requirement for Gα13 signaling for IEL positioning and survival in the villous niche has implications for therapeutic intervention.
Canonical and noncanonical autophagic processes are integrated with innate and adaptive immunity and sterile or pathogen-induced inflammation. In canonical autophagy, double-membrane autophagosomes modified by ubiquitin-like ATG8 proteins in a process termed membrane atg8ylation sequester and eliminate intracellular targets such as invading microbes, defunct organelles, aggregates, and inflammatory molecules. Recently, a plethora of noncanonical processes that entail membrane atg8ylation of various intracellular organelles other than autophagosomes have been linked to immunity. This has led to confounding interpretations and conflation of diverse processes as autophagy. Here, we posit that these are divergent manifestations of a common ancestral homeostatic process of membrane atg8ylation and provide an overview of how they affect immunity and inflammation. These relationships are evident in model organisms and are reflected in human genetic predispositions to diseases with immune components. The membrane atg8ylation pathways affect acute and chronic inflammation, infections, autoimmunity, cancer, neurodegeneration, metabolic syndrome, diabetes, and other disorders.
Research that is done but never shared cannot make an impact. Science communication has many forms and audiences, from research colleagues to the general public. Here, investigators discuss the importance of engaging in the dissemination of science and research for personal engagement and societal progress.
UV radiation (UVR) drives high mutational burdens, yet precursor melanocytes accumulate these mutations without triggering immune clearance. Here, we investigated whether melanocyte-intrinsic transcriptional program(s) underlie immune tolerance to mutations resulting from UVR exposure. In primary human melanocytes, expression of PD-L1 (CD274) was dependent on microphthalmia-associated transcription factor (MITF), a crucial regulator of melanocyte development and an intermediate in the UV-tanning pathway. MITF directly activated PD-L1 transcription by binding a conserved upstream enhancer containing functional E-box elements. MITF determined both baseline melanocytic PD-L1 expression in healthy skin and its induction following UVR, independent of interferon signaling. Melanocyte-restricted Pd-l1 deletion in mice triggered CD8+ T cell infiltration and depigmentation after long-term UVB exposure, recapitulating features of human vitiligo. PD-L1-deficient human induced pluripotent stem cell (iPSC)-derived melanocytes underwent increased apoptosis and were more susceptible than PD-L1-intact melanocytes to gp100-specific CD8+ T cell killing. Thus, a melanocyte-intrinsic MITF-PD-L1 tolerance program protects melanocytes from autoimmune destruction, potentially facilitating early immune evasion during melanoma development and conversely underlying the responsiveness of melanoma to PD-1/PD-L1 blockade.
High endothelial cells (HECs) control lymphocyte homing for adaptive immunity. They are defined by plump morphology, reflecting endoplasmic reticulum (ER) and Golgi expansion, and are by display of sulfo-sialomucins of the peripheral node addressin (PNAd) critical for lymphocyte recruitment. How these features are linked was unclear. Here, we found that HEC genes for sulfoglycoprotein synthesis and organelle expansion are enriched in binding motifs for ER stress-response transcription factors XBP1 and CREB3L2. These factors bound and drove expression from conserved elements in sulfo- and fucosyl-transferase and transporter genes for PNAd synthesis. Endothelial-specific deletion of Xbp1, or pharmacologic inhibition of enzymes for XBP1 or CREB3L2 activation, impaired PNAd expression, flattened HECs, reduced lymphocyte recruitment, and prevented HEC induction during inflammation. Parallel programs were found in intestinal goblet cells, suggesting conserved mechanisms coupling organelle scaling with sulfoglycoprotein production. Thus, HECs employ adaptive ER programs to build the biosynthetic infrastructure driving their morphology and function.
Cutaneous inflammation involving neuroimmune interactions can be initiated by both neurons and immune cells, making it complicated to parse the mechanisms of neurogenic inflammation. Optogenetic activation of Trpv1-expressing nociceptors drives type-17 inflammation in the absence of other inflammatory triggers. We found that two rounds of nociceptor activation were required for Il23a expression and maximal expression of Il1b and Il6, key drivers of type-17 inflammation. The first round of nociceptor activation triggered transient type 2 dendritic cell (DC2) aggregation that required substance P-Mrgprb2-dependent mast cell activation and mast cell-derived chemokine CCL2. Spatial transcriptomic analysis revealed that DC aggregation allowed the second nociceptor stimulation to efficiently activate DCs via the neuropeptide calcitonin gene-related peptide α (CGRPα). Thus, early neurogenic inflammation is a two-step process: substance P induces Mrgprb2-dependent mast cell activation and formation of DC aggregates that allow for efficient subsequent CGRPα-mediated DC activation. These data reveal a multi-cell, dynamic mechanism underlying neurogenic inflammation.
Genetic associations point to a connection between lysosomal function and neurodegeneration. In this issue of Immunity, Balak et al. and Tejwani et al. show that genetically distinct lysosomal insults converge on a shared MITF/TFE-driven epigenetic program that underlies disease-associated microglial states, thereby connecting lysosomal dysfunction with transcriptional regulation in microglia.
Generating mice that express human antibodies is a lengthy and labor-intensive process. Knocking in human gene segments into mice has potential, but how large a gene segment can be knocked into a zygote? Nair et al. insert a 155-kb human VH locus directly into mouse zygotes by CRISPR-mediated homology-directed repair, generating functional humanized antibody mice in weeks rather than years.
Some regulatory T (Treg) cells differentiate at peripheral sites in response to antigens derived from innocuous sources. In this issue of Immunity, Chi et al. examine an extensive array of T cell receptors with specificity for self, microbial, or dietary antigens to define the rules governing peripheral Treg cell differentiation.
The metabolic mechanisms linking chronic TCR stimulation to T cell exhaustion remain incompletely understood. Mitra and colleagues show that sustained MEK signaling drives the bioenergetic demands of chronic activation to promote terminal exhaustion, whereas MEK inhibition maintains progenitor-like T cells.
Single-cell transcriptomics identifies a convergent activation state of conventional dendritic cells (cDCs) shared by type 1 and type 2 cDCs (cDC1s and cDC2s). These activated DCs (actDCs) are characterized by co-expression of T cell-stimulating and inhibitory molecules. Here, we examined the functional contribution of actDCs to anti-tumor immunity by developing mouse models that leverage CCR7 expression to conditionally label or ablate actDCs. The capacity of cDCs to stimulate tumor-specific cytotoxic T lymphocytes (CTLs) was restricted to the actDC state. cDC1- and cDC2-derived actDCs supported CTL priming through cross-presentation and cross-dressing, respectively, with the latter occurring in a cancer type-dependent manner. actDCs were required for the activation of naive CTLs in tumor-draining lymph nodes and for sustaining effector CTL function within tumors. Consequently, ablation of actDCs impaired spontaneous tumor control and responses to immune checkpoint blockade or adoptive T cell therapy. Thus, the actDC state emerges as a critical determinant of cDC-mediated anti-tumor immunity.
The spleen harbors distinct macrophage subsets that support circulatory homeostasis and initiate immune responses, but the ontogeny and long-term dynamics of these populations remain incompletely understood. Here, we identified a transcriptionally and developmentally distinct CD163-expressing red pulp macrophage (CD163high RPM) population that arose from yolk sac progenitors and occupied a vascular-associated niche. Using fate-mapping models, we showed that CD163- RPMs were progressively replenished by monocytes during aging, whereas CD163high RPMs were mainly self-maintaining. During blood-stage malaria, CD163high RPMs were rapidly depleted, failed to recover despite parasite clearance, and were replaced by CD163- monocyte-derived RPMs. Single-cell RNA sequencing and genetic mouse models revealed that CD163 deficiency exacerbated structural disintegration of the marginal zone and selectively impaired marginal metallophilic macrophage (MMM) recovery, underscoring a CD163-dependent RPM-MMM crosstalk. This study reveals that the sustained loss of a specialized, yolk sac-derived CD163high RPM subset rewires splenic architecture and inter-macrophage crosstalk long after malaria resolution.
The meninges are a gateway for pathogenic T cells to enter the central nervous system (CNS). They possess a diverse repertoire of immune cells that orchestrate CNS inflammation and autoimmunity, yet the underlying mechanisms are poorly understood. Here, we report that group 2 innate lymphoid cells (ILC2s) accumulated in the dura as experimental autoimmune encephalomyelitis (EAE) progressed. Single-cell RNA sequencing and flow cytometry analyses revealed distinct features of ILC2s, including expression of MHC class II. ILC2s acted as antigen-presenting cells to activate and expand myelin-reactive T cells in an MHC class II-dependent manner. ILC2-mediated expansion of myelin-reactive T cells increased expression of cytokines IFN-γ and IL-17A. Genetic ablation of ILC2s or of H2-Ab1 in ILC2s alleviated neuroinflammation and CNS demyelination during EAE. These findings revealed a role of ILC2s in neuroinflammation via instructing myelin-reactive T cells, implying targeting ILC2s may be an avenue to restrict CNS inflammation and autoimmunity.
Interferon-stimulated gene 15 (ISG15) encodes a ubiquitin-like protein that regulates diverse cellular responses, including antiviral immunity, through its conjugation to proteins in a process known as ISGylation. Several pathogens, including SARS-CoV-2, subvert ISGylation by encoding deISGylating enzymes. However, the direct targets and physiological consequences of coronaviral deISGylation remain poorly defined. Here, we genetically ablated the deISGylating activity of the SARS-CoV-2-encoded papain-like protease (PLpro) and found that loss of deISGylation boosted innate immune activation, attenuated viral replication, and promoted viral clearance in human cells and mice. Metabolomics, ISGylome proteomics, and functional analyses revealed that PLpro deISGylation relieved metabolic restriction of virus infection by directly regulating the activity of key enzymes controlling glycolysis, the pentose phosphate pathway, and redox homeostasis. These findings provide fundamental insight into how reversible ISGylation regulates immunity and metabolic processes at the molecular level and highlight viral deISGylation as a major strategy to overcome host immunometabolic defenses.
