Biology subjects

Huehn, J.

Publications and source records attributed to Huehn, J..

8 recordsLinked to original sources

bioRxiv2026

Profiling of DNA-methylation signatures in human ILCs during homeostasis and allergic disease

The transcriptional programs of human ILCs are increasingly defined, but the DNA-methylation landscapes that stabilize their identity and function remain poorly understood. Here, we generated genome-wide DNA methylomes of human NK cells, ILC1, ILC2, and ILC3 from blood and lymphoid tissues. Subset-specific differentially methylated regions distinguished all populations and mapped to canonical regulators, including TBX21, GATA3, and RORC, as well as genes not previously linked to ILC biology, such as ERN1, DDX47, JAML, BTLA, and NRROS. Because ILC2 showed a particularly distinct methylation landscape and contribute to allergic inflammation, we tested whether selected ILC2-specific regions were functionally relevant. ILC2 marker regions were largely stable across tissues and during cytokine-driven expansion. CRISPR/Cas9-mediated deletion of the HPGDS or NRROS DMR revealed that these elements act as cis-regulatory sites controlling HPGDS/NRROS expression and promoting production of the type 2 cytokines IL-4, IL-5 and IL-13. Finally, methylome profiling of ILC2 from healthy, atopic, and asthmatic children identified disease-associated DMRs linked to PTGS2, QKI, and GIMAP4. These findings define stable epigenetic signatures of human ILC identity and uncover regulatory elements connecting ILC2 methylation to allergic disease.

immunology↗

bioRxiv2025

Probiotic-conditioned microbiota from preterm infants modulate immune response to pathogen challenge in a humanized mouse model

AbstractEarly-life host-microbe interactions critically shape immune development, lifelong homeostasis, and disease susceptibility. The PRIMAL trial (Priming Immunity at the Beginning of Life) demonstrated that multistrain probiotics shifted the gut microbiota of very preterm infants toward eubiosis without affecting sepsis incidence, yet the immunological consequences remained unresolved. To explore this, we colonized germ-free female mice with fecal samples from probiotic- or placebo-treated preterm infants from the PRIMAL trial. Microbiota composition was vertically transmitted and stable across generations. At steady-state, 3-week-old pups colonized with probiotic-conditioned microbiota exhibited markedly reduced populations of innate immune cells, particularly in the colon, with subtler effects in the small intestine and spleen, while adaptive immune subsets were less affected. Upon enteropathogenic Escherichia coli challenge at day 5, pups harboring probiotic-conditioned microbiota displayed reduced growth and impaired bacterial clearance, correlating with diminished numbers of key innate immune cell populations. These findings demonstrate that probiotic-driven shifts in human-derived microbial communities can attenuate immune cell development in mice and alter early-life infection outcomes. Our study underscores the complex, context-dependent effects of probiotics on the neonatal microbiota-immune axis and provides mechanistic insight into how interventions in preterm infants may influence susceptibility to infection.

immunology↗

bioRxiv2025

Secondary lymphoid organ endothelial cells prime alloreactive CD4+ T cells to trigger acute graft-versus-host disease

Donor CD4 T cell priming is a pivotal determinant of acute graft-versus-host disease (aGvHD) after allogeneic hematopoietic cell transplantation (allo-HCT). While professional hematopoietic antigen-presenting cells (APCs) have long been implicated in the pathogenesis of aGvHD, the contribution of non-hematopoietic APCs has remained unclear. Here, we show that naive alloreactive CD4 T cells initially localize and activate specifically within secondary lymphoid organs (SLOs) before infiltrating target tissues. Using genetic models to selectively ablate MHC class II on endothelial cells (ECs) or hematopoietic cells, we demonstrate that blood endothelial cells (BECs) in SLOs function as APCs, efficiently processing and presenting antigen to prime donor CD4 T cells. Deletion of MHC class II (MHCII) specifically in ECs substantially attenuates T cell activation and protects mice from lethal aGvHD, whereas selective deletion of MHCII in lymphatic ECs has no effect. Likewise, selective deletion of MHCII in hematopoietic cells also protects mice against aGvHD, suggesting that both cell types contribute to pathogenic allogeneic T cells activation after allo-HCT. Mechanistically, IL-12/IFN{gamma} signaling upregulates MHC class II expression on BECs. These findings identify BECs in SLOs as initiators of alloreactive CD4 T cell responses and highlight a potential target for preventing aGvHD. HighlightsO_LIBlood endothelial cells in secondary lymphoid organs prime naive CD4 T cells to trigger acute GvHD. C_LIO_LIT cell activation occurs exclusively in secondary lymphoid organs before tissue infiltration. C_LIO_LIExpression of MHC class II only on endothelial cells is sufficient to drive lethal GvHD, independent of other antigen presenting cells. C_LIO_LIRegulation of MHC class II expression in blood endothelial cells by IL-12/IFN{gamma} offers the potential for new therapeutic targets and corroborates findings for existing therapeutics. C_LI

immunology↗

bioRxiv2024

Different CMV-specific effector T cell subtypes are associated with age, CMV serostatus, and increased systolic blood pressure

Cytomegalovirus (CMV) infection is one of the most common infections in humans, and CMV antigens are the major drivers of repetitive T-cell stimulation as a part of a well-adapted immune response in immunocompetent individuals. With higher age, the recurrent clonal expansion of CMV-specific T cells results in high frequencies of CMV-specific effector T cells. CMV seropositivity has also been linked to arterial stiffness and an increased risk of developing cardiovascular diseases (CVD). The RESIST Senior Individuals (SI) cohort is a population-based cohort with focus on the elderly, established to shed light on the age-related changes of the immune system and the accompanied reduced capability to fight infectious diseases. Here we investigated the frequency and phenotype of CMVpp65-specific CD8+ T cells in the circulation of individuals of different age groups by means of MHC-I tetramer staining and their associations with age and associated factors such as serostatus and blood pressure. In the SI cohort, the frequency of CMV-specific T cells within the CD8+ T cell fraction was increased with age, as previously reported. We add to previous knowledge by showing that this frequency is associated with the total percentage and absolute counts of CD8+ and CD4+CD8+ double-positive T cells within leukocytes. Systolic blood pressure (SBP) and history of CVD correlated with the frequency of CMV-specific CD8+ T cells. Focusing on CMV-specific T cell subtypes, we show here that the frequencies of TEM and CD27-expressing TEMRA cells were associated with higher age. TEM and CD27- TEMRA cell frequencies were increased in donors with high CMV-IgG titers. Furthermore, SBP significantly correlated with CMV-specific effector CD8+ T cells, which was mostly reflected by CD27- TEMRA cells. In conclusion, different effector T-cell subtypes were associated with age, serostatus and SBP, suggesting that it is not age per se that renders elderly CMV-positive individuals susceptible to CVD, but the immune response to CMV. Our study suggests that detailed immunophenotyping may identify individuals whose immune systems are strongly influenced by the response to CMV, leading to health consequences and impairing healthy aging.

immunology↗

bioRxiv2024

CREB determines the expression of ST2 in Tregs and mediates the balance between type 1 and type 2 immune responses

Regulatory T cells (Tregs) are gatekeepers of immune homeostasis and characterized by expression of Foxp3, which maintains Treg identity. Here we demonstrate that in mice with a Foxp3-specific knockout of CREB, enhanced numbers of Tregs are found in vivo in spleen, lung and colon. These Tregs display a reduced Foxp3 expression, but enhanced expression of the IL-33 receptor (ST-2), IL-10, IL-13, and CREM. CREB deficient Tregs were highly suppressive in vitro and prevented disease activity in CD4 T cell mediated transfer colitis in an IL-10 dependent way. Mechanistically CREB fulfils dual roles in Tregs. First it downregulates Foxp3 expression, however in cooperation with CREM, CREB expression in Tregs alters chromatin accessibility to the ST-2 region and thereby influences T cell specific immune responses mediated by IL-10. Brief summary: Mice with a Foxp3-specific knockout of CREB display enhanced expression of IL-13, IL-10, ST-2 and CREM, which prevents gut inflammation GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=140 SRC="FIGDIR/small/601312v2_ufig1.gif" ALT="Figure 1"> View larger version (22K): org.highwire.dtl.DTLVardef@a2d341org.highwire.dtl.DTLVardef@1db6852org.highwire.dtl.DTLVardef@19e024borg.highwire.dtl.DTLVardef@a8c84d_HPS_FORMAT_FIGEXP M_FIG C_FIG Created by Biorender

immunology↗

bioRxiv2023

DNA methylation profiling identifies TBKBP1 as potent amplifier of cytotoxic activity in CMV-specific human CD8+ T cells

Epigenetic mechanisms stabilize gene expression patterns during CD8+ T cell differentiation. However, although adoptive transfer of virus-specific T cells is clinically applied to reduce the risk of virus infection or reactivation in immunocompromised individuals, the DNA methylation pattern of virus-specific CD8+ T cells is largely unknown. Hence, we here performed whole-genome bisulfite sequencing of cytomegalovirus-specific human CD8+ T cells and found that they display a unique DNA methylation pattern consisting of 79 differentially methylated regions when compared to bulk memory CD8+ T cells. Among them was TBKBP1, coding for TBK-binding protein 1 that can interact with TANK-binding kinase 1 (TBK1) and mediate pro-inflammatory responses in innate immune cells downstream of intracellular virus sensing. Since TBKBP1 has not yet been reported in T cells, we aimed to unravel its role in virus-specific CD8+ T cells. TBKBP1 demethylation in terminal effector CD8+ T cells correlated with TBKBP1 expression and was stable upon long-term in vitro culture. TBKBP1 overexpression resulted in enhanced TBK1 phosphorylation upon stimulation of CD8+ T cells and significantly improved their virus neutralization capacity. Collectively, our data demonstrate that TBKBP1 modulates virus-specific CD8+ T cell responses and could be exploited as therapeutic target to improve adoptive T cell therapies.

immunology↗

bioRxiv2021

The thymic microenvironment gradually modulates the phenotype of thymus-homing peripheral conventional dendritic cells

Thymic conventional dendritic cells (t-DCs) are crucial for the development of T cells. A substantial fraction of t-DCs originates extrathymically and migrates to the thymus. Here, these cells contribute to key processes of central tolerance like the clonal deletion of self-reactive thymocytes and the generation of regulatory T (Treg) cells. So far, it is only incompletely understood which impact the thymic microenvironment has on thymus-homing conventional DCs (cDCs), which phenotypic changes occur after the entry of peripheral cDCs into the thymus and which functional properties these modulated cells acquire. In the present study, we mimicked the thymus-homing of peripheral cDCs by introducing ex vivo isolated splenic cDCs (sp-DCs) into re-aggregated thymic organ cultures (RTOCs). Already after two days of culture, the transcriptomic profile of sp-DCs was modulated and had acquired certain key signatures of t-DCs. The regulated genes included immunomodulatory cytokines and chemokines as well as co-stimulatory molecules. After four days of culture, sp-DCs appeared to have at least partially acquired the peculiar Treg cell-inducing capacity characteristic of t-DCs. Taken together, our findings indicate that peripheral cDCs possess a high degree of plasticity enabling them to quickly adapt to the thymus-specific microenvironment. We further provide indirect evidence that thymus-specific properties such as the efficient induction of Treg cells under homeostatic conditions can be partially transferred to thymus-homing peripheral cDC subsets.

immunology↗

bioRxiv2021

Postnatal lymph node expansion of stromal progenitors towards reticular and CD34+ stromal cell subsets is determined by distinct transcriptional programs

Gut-draining mesenteric lymph nodes (mLN) provide the framework and microenvironment to shape intestinal adaptive immune responses. We previously delineated transcriptional signatures in LN stromal cells (SC), pointing to tissue-specific variability in composition and immuno-modulatory function of SCs. Here, we dissect the tissue-specific epigenomic DNA accessibility and CpG methylation landscape of LN non-endothelial SCs and identify a microbiota-independent core epigenomic signature of LN SCs. By combined analysis of transcription factor (TF) binding sites together with the gene expression profiles of non-endothelial SCs, we delineated TFs poising skin-draining peripheral LN (pLN) SCs for pro-inflammatory responses. Furthermore, using scRNA-seq, we dissected the developmental trajectory of mLN SCs derived from postnatal to aged mice, identifying two distinct putative progenitors, namely CD34+ SC and fibroblastic reticular stromal cell (FRC) progenitors, which both feed the rapid postnatal LN expansion. Finally, we identified Irf3 as a key differentiation TF inferred from the epigenomic signature of mLN SCs that is dynamically expressed along the differentiation trajectories of FRCs, and validated Irf3 as a regulator of Cxcl9+ FRC differentiation. Together, our data constitute a comprehensive transcriptional and epigenomic map of mLN development and dissect location-specific, microbiota-independent properties of mLN non-endothelial SCs. As such, our findings represent a valuable resource to identify core transcriptional regulators that impinge on the developing mLN early in life, thereby shaping long-lasting intestinal adaptive immune responses.

immunology↗