Abstract Introduction Systemic sclerosis (SSc, scleroderma) is a chronic autoimmune disease with high mortality, characterized by progressive fibrosis of the skin and internal organs. Skin involvement is among the earliest manifestations of disease, and changes in skin pathology can mirror systemic progression. While single-cell studies have revealed striking transcriptional diversity among dermal fibroblasts in SSc, the spatial organization and immune signals that govern their function remain unclear. Methods To address this, we performed high-resolution spatial transcriptomic profiling of clinically affected and unaffected skin from SSc donors alongside healthy controls. Results We identify known disease-associated fibroblast subsets, including COMP+ myofibroblasts, which localize within cell neighborhoods enriched in activated endothelial and immune cells. In contrast, LGR5+/PI16+ fibroblasts — abundant in healthy skin and previously shown to contain a T cell-inducible gene program — are significantly reduced in both clinically involved and uninvolved SSc skin and occupy distinct microenvironments from disease-associated cells. Conclusion Our findings provide a spatial framework for understanding fibroblast heterogeneity and identify potential therapeutic strategies aimed at reinforcing protective fibroblast programs to prevent or delay fibrosis in scleroderma. Funding Source R21AI185642 NIAID/NIH, National Scleroderma Foundation Topic Categories Immune Mechanisms of Human Disease (HUM)

Understanding the variability of immune cell composition and responsiveness in health is critical to define changes that predict and explain immune-associated diseases like autoimmunity and cancer. Here, we comprehensively phenotyped a cohort of 100 healthy adults aged 25 to 35 and 55 to 65 years who were longitudinally followed for 10 visits over 2 years. Using mass cytometry, we identified four stable immunotypes derived from cell populations that remained stable within, but differed between, individuals. We characterized these immunotypes using whole-blood RNA sequencing, Olink proteomic profiling, and whole-blood ex vivo stimulation. Although cytomegalovirus (CMV) seropositivity, age, and sex are known to influence the immune landscape, the four immunotypes were not solely determined by these factors. A CMV-dominant immunotype exhibited exaggerated traditional markers of CMV positivity but also features unrelated to CMV positivity, including lower numbers of B cells and B cell-related transcripts. Immunotype was strongly associated with response to ex vivo stimulation with lipopolysaccharide (LPS) but not serological response to influenza vaccination, suggesting that these immunotypes are most relevant in understanding variations in innate immune responsiveness among healthy individuals. Last, we identified an immunotype comprising young females with unusually high LPS responsiveness, mature neutrophil frequency, and increased inflammatory markers. Overall, our findings establish that healthy individuals can exhibit one of four shared immunotypes, defined by adaptive and innate cell populations, that are stable over time, influence the response to innate signals, associate with clinical markers of inflammation, and shed light on overall immune health.

Background: Eosinophilic esophagitis (EoE) is a chronic, type 2 inflammatory disease that is increasing in incidence and has substantial morbidity. Despite being clinically defined as a food allergy, the molecular details of food antigen presentation and recognition by the immune system are unknown. Objective: The objective of this study was to identify and characterize the molecular basis of milk antigen presentation and T cell recognition in a patient with EoE milk allergy. Methods: Milk-expanded TCR clonotypes were identified using ex vivo stimulation followed by single cell RNA with linked, paired TRA and TRB sequencing. HLA restriction and antigen specificity of TCRs were identified using a combination of lentiviral expression, HLA sequencing, antibody blockade, and a peptide library screen. Results: We isolated a β-casein specific TCR clonotype (eoeTCR-4) and determined its HLA restriction (HLA-DRB1*07:01) and cognate antigen (β-casein AA 59-78). EoeTCR-4 was not detected among a larger group of subjects and is likely private to EoE Subject 1. Conclusion: In conjunction with the parent manuscript, this companion article provides the first molecular identity of food antigen presentation and immune recognition in EoE. ### Competing Interest Statement JD, JMS, and DAH hold a patent on the use of functional T cell assays for the identification of EoE-causal foods. The remaining authors have no conflicts of interest to disclose.

Teplizumab is approved for delay of diagnosis of type 1 diabetes and modulates new onset disease. Compared to EBV seronegative patients, those who were EBV seropositive prior to treatment had a more robust response to drug in two clinical trials. We compared the phenotypes, transcriptomes, and development of peripheral blood cells before and after teplizumab treatment. Higher number of Tregs and “partially exhausted” CD8+ T cells were found in EBV seropositive individuals at the baseline in the TN10 and AbATE trials. Single cell transcriptomics and functional assays identified downregulation of NFkB and other pathways after treatment in treated EBV seropositive patients. Among diabetes antigen specific CD8+ T cells, T cell receptor and mTOR signaling were also reduced. Impairments in function of adaptive immune cells were enhanced by teplizumab treatment in EBV seropositive individuals. Our data indicate that EBV can impair signaling pathways in immune cells, that broadly redirect cell differentiation Supported by grants DK057846 and AI66387 to KH. Research reported in this publication was supported by the National Institute of Allergy and Infectious Diseases of the National Institutes of Health under Award Number UM1AI109565. Translational and Interventional Immunology (TI)

Teplizumab is approved for delaying the diagnosis of type 1 diabetes by modulating progression of disease. Compared to EBV-seronegative patients, those who are EBV-seropositive prior to treatment have a more robust response to teplizumab in two clinical trials. Here we compare the phenotypes, transcriptomes and development of peripheral blood cells before and after teplizumab treatment in participants. Higher number of regulatory T cells and partially exhausted CD8+ T cells are found in EBV-seropositive individuals than in EBV-seronegative controls at the baseline in the TN10 and AbATE trials. Mechanistically, single cell transcriptomics and functional assays identify the downregulation of NFκB and T cell activation pathways after treatment in EBV-seropositive patients; among diabetes antigen-specific CD8+ T cells, T cell receptor and mTOR signaling are also reduced. In parallel, signaling impairment is greater in adaptive than innate immune cells following teplizumab treatment in EBV-seropositive individuals. Our data thus indicate that EBV can impair signaling pathways in immune cells to modulate their responses in the context of type 1 diabetes.

CD4 + CD25 hi CD127 lo/− FOXP3 + regulatory T cells (T regs ) play a key role in preventing autoimmunity. In autoimmune type 1 diabetes (T1D), adoptive transfer of autologous polyclonal T regs has been shown to be safe in adults in phase 1 clinical trials. We explored factors contributing to efficacy of autologous polyclonal expanded T regs (expT regs ) in a randomized phase 2 multi-center, double-blind, clinical trial (Sanford/Lisata Therapeutics T-Rex phase 2 trial, ClinicalTrials.gov NCT02691247). One hundred ten treated children and adolescents with new-onset T1D were randomized 1:1:1 to high-dose (20 × 10 6 cells/kilogram) or low-dose (1 × 10 6 cells/kilogram) treatments or to matching placebo. Cytometry as well as bulk and single-cell RNA sequencing were performed on selected expT regs and peripheral blood samples from participants. The single doses of expT regs were safe but did not prevent decline in residual β cell function over 1 year compared to placebo ( P = 0.94 low dose, P = 0.21 high dose), regardless of age or baseline C-peptide. ExpT regs were highly activated and suppressive in vitro. A transient increase of activated memory T regs was detectable 1 week after infusion in the high-dose cohort, suggesting effective transfer of expT regs . However, the in vitro fold expansion of expT regs varied across participants, even when accounting for age, and lower fold expansion and its associated gene signature were linked with better C-peptide preservation regardless of T reg dose. These results suggest that a single dose of polyclonal expT regs does not alter progression in T1D; instead, T reg quality may be an important factor.

Primary biliary cholangitis (PBC) is a chronic autoimmune liver disease, characterized by progressive destruction of small intrahepatic bile ducts and portal inflammation. Treatment options are limited, with reliance on liver transplantation in advanced cases. The adaptive immune response is implicated in disease pathogenesis by the presence of anti-mitochondrial antibodies targeting the E2 subunit of the pyruvate dehydrogenase complex (PDC-E2) in 90-95 % of patients and T cells infiltrating the portal tracts. Here, we examined T cell responses to peptides derived from PDC-E2, with a focus on CD4 T cell responses restricted to HLA Class II DRB4*01:01, an allele found in 62 % of PBC patients, to uncover PDC-E2 epitopes that could be used for engineered regulatory T cell (Treg; EngTreg) therapy. Using an activation-induced marker assay and single cell RNA-sequencing, we found clonal expansion of CD4 T cells reactive to PDC-E2 epitopes among both T conventional (Tconv) and Tregs. Those T cell receptor (TCR) repertoires were non-overlapping and private and included TCRs specific for a novel PDC-E2 epitope restricted to DRB4*01:01. CD4 Tconv cells reactive to the PDC-E2 novel epitope showed phenotypic heterogeneity skewed towards T follicular helper cells. Using a TCR specific for this novel PDC-E2 epitope, we created an EngTreg that suppressed PDC-E2-specific polyclonal CD4 Tconv cells from PBC patients. This study advances knowledge of PDC-E2-specific T cell responses and introduces a novel PDC-E2 epitope recognized by both Tconv and Tregs. Generation of EngTreg specific for this epitope provides therapeutic potential for PBC.

The thymus is an important site for the establishment and maintenance of an appropriate immune response through positive and negative selection of developing T cells. Cortical and medullary thymic epithelial cells (TECs), termed cTECs and mTECs, respectively, interact with developing thymocytes to mediate this selection process. Developing thymocytes also support the maturation and proliferation of mTECs by secreting transforming growth factor-beta (TGF-β) superfamily cytokines. Our lab has previously shown that deletion of TGF-β signaling in TECs enhanced negative selection and functional maturation of thymocytes, and increased the production of regulatory T cells. To investigate whether the proto-oncogene product Ski (Sloan-Kettering Institute), a negative regulator of TGF-β signaling, is associated with thymocyte development in homeostatic condition and inflammatory conditions, we generated mice that deleted Ski specifically in TECs (Foxn1Cre Ski fl/fl mice). We found that the mTEC population was decreased as predicted, however we did not find any differences in thymocyte development between the Foxn1Cre Skifl/fl mice and control mice. We also found that CD4 T cells purified from Ski deleted mice showed a defect in proliferation, and Th1 and Th17 differentiation in vitro, while regulatory T cell differentiation was normal. Lastly, we found that these mice were significantly protected from developing experimental autoimmune encephalomyelitis (EAE) disease compared to the control mice. Overall, our findings suggest that Ski signaling in TECs regulates peripheral T cell self-reactivity responses and further study may provide evidence for targeting Ski in T cell driven autoimmune diseases such as multiple sclerosis. Supported by grants from NIH grant R01-AI136475 (to SZ) and AAI Intersect fellowship (to HC)

Type 1 diabetes (T1D) is an autoimmune disease marked by immune destruction of insulin-producing β-cells of the pancreas. In an effort to halt disease progression, autologous polyclonal expanded regulatory T cells (expTregs) were adoptively transferred into adolescents with recent-onset T1D (Sanford/Lisata Therapeutics Trex Phase 2 clinical trial, NCT02691247). Overall, expTreg therapy (1–24×10 6cells/kg) did not preserve residual β-cell function, as measured by change in insulin C-peptide AUC-mean over 2 years compared to placebo (p=0.39) regardless of dose (p=0.27). Consistent with a more activated phenotype, expTregs expressed more CD25, CD38, HLA-DR, and CXCR3 than endogenous Tregs by flow cytometry, and bulk-RNAseq revealed 2377 genes (related to metabolism, cell cycle, and immune response) up-regulated in expTregs compared to endogenous Tregs. In subjects from the high-dose group (>10×10 6cells/kg), there was a transient increase of total Tregs one week after infusion (p=0.003), which had an activated memory phenotype, consistent with infused expTreg accounting for this difference. However, the increase in the activation of Tregs post-treatment was associated with poorer outcome (p=0.03), and the extent of expansion of the expTregs ex vivo (range 24.3–643-fold) negatively correlated with C-peptide change (p=0.01) in treated subjects regardless of Treg dose. Yet, neither purity nor suppressive function correlated with outcome, suggesting differences in endogenous Treg qualities leading to increased expansion may influence outcome. These results suggest that expTreg quantity alone does not influence outcome; instead, both endogenous and expTreg quality may be important factors modulating T1D progression.

Regulatory T cells (Tregs) suppress the activation and subsequent effector functions of CD4 effector T cells (Teffs). However, molecular mechanisms that enforce Treg-mediated suppression in CD4 Teff are unclear. We found that Tregs suppressed activation-induced global protein synthesis in CD4 Teffs prior to cell division. We analyzed genome-wide changes in the transcriptome and translatome of activated CD4 Teffs. We show that mRNAs encoding for the protein synthesis machinery are regulated at the level of translation in activated CD4 Teffs by Tregs. Tregs suppressed global protein synthesis of CD4 Teffs by specifically inhibiting mRNAs of the translation machinery at the level of mTORC1-mediated translation control through concerted action of immunosuppressive cytokines IL-10 and TGFβ. Lastly, we found that the therapeutic targeting of protein synthesis with the RNA helicase eIF4A inhibitor rocaglamide A can alleviate inflammatory CD4 Teff activation caused by acute Treg depletion in vivo. These data show that peripheral tolerance is enforced by Tregs through mRNA translational control in CD4 Teffs.

Variation in the preservation of β cell function in clinical trials in type 1 diabetes (T1D) has emphasized the need to define biomarkers to predict treatment response. The T1DAL trial targeted T cells with alefacept (LFA-3–Ig) and demonstrated C-peptide preservation in approximately 30% of new-onset T1D individuals. We analyzed islet antigen–reactive (IAR) CD4+ T cells in PBMC samples collected prior to treatment from alefacept- and placebo-treated individuals using flow cytometry and single-cell RNA sequencing. IAR CD4+ T cells at baseline had heterogeneous phenotypes. Transcript profiles formed phenotypic clusters of cells along a trajectory based on increasing maturation and activation, and T cell receptor (TCR) chains showed clonal expansion. Notably, the frequency of IAR CD4+ T cells with a memory phenotype and a unique transcript profile (cluster 3) were inversely correlated with C-peptide preservation in alefacept-treated, but not placebo-treated, individuals. Cluster 3 cells had a proinflammatory phenotype characterized by expression of the transcription factor BHLHE40 and the cytokines GM-CSF and TNF-α, and shared TCR chains with effector memory–like clusters. Our results suggest IAR CD4+ T cells as a potential baseline biomarker of response to therapies targeting the CD2 pathway and warrant investigation for other T cell–related therapies.

SUMMARYIncreased protein synthesis is a hallmark of lymphocyte activation. Regulatory T cells (Tregs) suppress the activation and subsequent effector functions of CD4 effector T cells (Teffs). However, molecular mechanisms that enforce Treg-mediated suppression in CD4 Teff are not fully clear. Control of CD4 Teff activation by Tregs has largely been defined at the transcriptional level, which does not reflect changes in post-transcriptional control. We found that Tregs suppressed activation-induced global protein synthesis in CD4 Teffs prior to cell division. We analyzed genome-wide changes in the transcriptome and translatome of activated CD4 Teffs using two independent approaches. We show that mRNAs encoding for the protein synthesis machinery are regulated at the level of translation in activated Teffs. Strikingly, Tregs suppressed global protein synthesis of CD4 Teffs by specifically inhibiting mRNAs of the translation machinery at the level of mTORC1-mediated translation control. Lastly, we found that the RNA helicase eIF4A inhibitor rocaglamide A (RocA) can suppress CD4 Teff activation in vitro to alleviate inflammatory CD4 Teff activation caused by acute Treg depletion in vivo. These data provide evidence that peripheral tolerance is enforced by Tregs through mRNA translational control in CD4 Teffs. Therefore, therapeutic targeting of the protein synthesis machinery can be expected to mitigate inflammatory responses invoked by Treg loss of function.

Individuals with Down syndrome show cellular and clinical features of dysregulated aging of the immune system, including a shift from naïve to memory T cells and increased incidence of autoimmunity. However, a quantitative understanding of how various immune compartments change with age in Down syndrome remains lacking. Here, we performed deep immunophenotyping of a cohort of individuals with Down syndrome across the life span, selecting for autoimmunity-free individuals. We simultaneously interrogated age- and sex-matched healthy controls and people with type 1 diabetes as a representative autoimmune disease. We built an analytical software, IMPACD (Iterative Machine-assisted Permutational Analysis of Cytometry Data), that enabled us to rapidly identify many features of immune dysregulation in Down syndrome shared with other autoimmune diseases. We found quantitative and qualitative dysregulation of naïve CD4+ and CD8+ T cells in individuals with Down syndrome and identified interleukin-6 as a candidate driver of some of these changes, thus extending the consideration of immunopathologic cytokines in Down syndrome beyond interferons. We used immune cellular composition to generate three linear models of aging (immune clocks) trained on control participants. All three immune clocks demonstrated advanced immune aging in individuals with Down syndrome. One of these clocks, informed by Down syndrome–relevant biology, also showed advanced immune aging in individuals with type 1 diabetes. Orthologous RNA sequencing–derived immune clocks also demonstrated advanced immune aging in individuals with Down syndrome. Together, our findings demonstrate an approach to studying immune aging in Down syndrome that may have implications in other autoimmune diseases.

Therapeutics that inhibit IL-6 at different points in its signaling pathway are in clinical use, yet whether the immunological effects of these interventions differ based on their molecular target is unknown. We performed short-term interventions in individuals with type 1 diabetes using anti–IL-6 (siltuximab) or anti–IL-6 receptor (IL-6R; tocilizumab) therapies and investigated the impact of this in vivo blockade on T cell fate and function. Immune outcomes were influenced by the target of the therapeutic intervention (IL-6 versus IL-6R) and by peak drug concentration. Tocilizumab reduced ICOS expression on T follicular helper cell populations and T cell receptor–driven (TCR-driven) STAT3 phosphorylation. Siltuximab reversed resistance to Treg-mediated suppression and increased TCR-driven phosphorylated STAT3 and production of IL-10, IL-21, and IL-27 by T effectors. Together, these findings indicate that the context of IL-6 blockade in vivo drives distinct T cell–intrinsic changes that may influence therapeutic outcomes.

Cbl-b is a negative regulator of T cell activation, and in murine models, a lack of Cblb results in resistance of T effector (Teff) cells to T regulatory (Treg) cells, a feature of T cells in many autoimmune diseases. Here, we used trackable gene editing approaches to knock out CBLB in primary human CD4+ T cells. We found that CBLB-knockout (CBLB-KO) CD4+ T cells were hyperproliferative and produced excessive amounts of IL-2. CBLB-KO CD4+ T cells were resistant to Treg suppression in vitro, which was partially reversed by blockade of IL-2. RNA-sequencing and puromycin incorporation assays demonstrated that CBLB-KO CD4+ T cells can overcome Treg suppression on the transcriptional and translational levels, resulting in the overproduction of cytokines to drive the proliferation and activation of Teff cells. These findings highlight a potential mechanism of Teff resistance in human autoimmune disease and the power of gene editing primary T cells to explore disease mechanisms.

Recruitment of regulatory T cells (Tregs) to tumors is a hallmark of cancer progression. Tumor-derived factors, such as the cytokine thymic stromal lymphopoietin (TSLP), can influence Treg function in tumors. In our study, we identified a subset of Tregs expressing the receptor for TSLP (TSLPR+ Tregs) that were increased in colorectal tumors in humans and mice and largely absent in adjacent normal colon. This Treg subset was also found in the peripheral blood of patients with colon cancer but not in the peripheral blood of healthy control subjects. Mechanistically, we found that this Treg subset coexpressed the interleukin-33 (IL-33) receptor [suppressor of tumorigenicity 2 (ST2)] and had high programmed cell death 1 (PD-1) and cytotoxic lymphocyte-associated antigen 4 (CTLA-4) expression, regulated in part by the transcription factor Mef2c. Treg-specific deletion of TSLPR, but not ST2, was associated with a reduction in tumor number and size with concomitant increase in TH1 cells in tumors in chemically induced mouse models of colorectal cancer. Therapeutic blockade of TSLP using TSLP-specific monoclonal antibodies effectively inhibited the progression of colorectal tumors in this mouse model. Collectively, these data suggest that TSLP controls the progression of colorectal cancer through regulation of tumor-specific Treg function and represents a potential therapeutic target that requires further investigation.

Key Points An IFN gene signature is present in the inflamed mucosa of individuals with EoE. This IFN signature is conserved between adults and children. IFN-γ is produced by circulating EoE T cells activated with EoE-causal allergens. Eosinophilic esophagitis (EoE) is an allergic inflammatory disease of the esophagus that occurs in both children and adults. Previous studies of affected tissue from pediatric cohorts have identified prominent signatures of eosinophilia and type 2 inflammation. However, the details of the immune response in adults with EoE are still being elucidated. To determine whether EoE in adults shares inflammatory profiles with those observed in children, we performed RNA sequencing of paired human esophageal biopsies and blood samples from adults with EoE or gastroesophageal reflux disease. Unbiased analysis of differentially expressed genes in tissue revealed a strong IFN signature that was significantly enriched in EoE patients as compared with patients with gastroesophageal reflux disease. Both type I and type II IFN–responsive genes were upregulated in adult biopsies, but not in blood. A similar increase in expression of IFN gene sets was observed in pediatric EoE biopsies as compared with non-EoE samples, and in public pediatric and adult RNA-sequencing data. Finally, we found that human peripheral CD4+ T cells from children with EoE produce IFN-γ upon activation with EoE-causal allergens. Together, this work identifies a conserved IFN signature in pediatric and adult EoE, highlighting a role for non–type 2 inflammatory networks in the disease process in humans.

Human islet antigen reactive CD4+ memory T cells (IAR T cells) play a key role in the pathogenesis of autoimmune type 1 diabetes (T1D). Using single-cell RNA sequencing (scRNA-Seq) to identify T cell receptors (TCRs) in IAR T cells, we have identified a class of TCRs that share TCRα chains between individuals (“public” chains). We isolated IAR T cells from blood of healthy, new-onset T1D and established T1D donors using multiplexed CD154 enrichment and identified paired TCRαβ sequences from 2767 individual cells. More than a quarter of cells shared TCR junctions between 2 or more cells (“expanded”), and 29/47 (~62%) of expanded TCRs tested showed specificity for islet antigen epitopes. Public TCRs sharing TCRα junctions were most prominent in new-onset T1D. Public TCR sequences were more germline like than expanded unique, or “private,” TCRs, and had shorter junction sequences, suggestive of fewer random nucleotide insertions. Public TCRα junctions were often paired with mismatched TCRβ junctions in TCRs; remarkably, a subset of these TCRs exhibited cross-reactivity toward distinct islet antigen peptides. Our findings demonstrate a prevalent population of IAR T cells with diverse specificities determined by TCRs with restricted TCRα junctions and germline-constrained antigen recognition properties. Since these “innate-like” TCRs differ from previously described immunodominant TCRβ chains in autoimmunity, they have implications for fundamental studies of disease mechanisms. Self-reactive restricted TCRα chains and their associated epitopes should be considered in fundamental and translational investigations of TCRs in T1D.