Ritu Mann-Nüttel

2. SARS-CoV-2 infection is increasingly recognized to produce long-lasting physiological disturbances that extend beyond the acute phase. The gut microbiome has emerged as a potential contributor to post-infection outcomes, yet the longitudinal progression of microbial disruption following infection remains poorly defined. Here, we used a mouse model of SARS-CoV-2 infection to characterize gut microbiome dynamics at 7 (late acute phase), 14 (early recovery), and 21 (post-COVID condition, PCC) days post-infection (dpi). Viral RNA was detected in the lungs through 21 dpi. Longitudinal microbiome profiling revealed a two-phase restructuring marked by early shifts in Bacillota and Bacteroidota abundance, followed by pronounced post-acute dysbiosis characterized by reduced diversity, expansion of Bacillota, and near-complete loss of Bacteroidota. Functional pathway predictions showed progressive metabolic remodeling, including disruptions in nucleotide turnover, fermentation, and vitamin-related pathways. Together, these findings demonstrate that SARS-CoV-2 infection drives progressive and sustained alterations in gut microbial composition and function after the transition from acute infection through recovery into PCC. 3. Data summary: The authors confirm all supporting data, code and protocols have been provided within the article or through supplementary data files. Any other information can be acquired by contacting the first author via email.

Introduction: Protease activated receptor (PAR2) is a prominent sensor of environmental and microbial proteases and may serve as an important interface between the host epithelium and mucosal microbes. However, whether PAR2 helps shape microbial community structure and function at barrier surfaces remains unclear. To address this, we examined how PAR2 deficiency or activation affects microbial composition and metabolic potential across the gut lumen, airway lumen, and lung tissue in the context of exposure to protease-rich house dust mite allergen (HDM) exposure. Methods: Wild type and PAR2 deficient littermates of both sexes received a single intranasal challenge with phosphate buffered saline, HDM extract, or a selective PAR2 agonist. Microbial communities from feces, bronchoalveolar lavage fluid (BALF), and lung tissue were profiled using 16S rRNA gene sequencing and PICRUSt2 based functional inference to assess compartment specific taxonomic and metabolic responses. Results: Alpha and beta diversity remained stable across all experimental groups, but distinct conditions resulted in compartment specific remodeling of the microbial population. At baseline, PAR2 deficiency altered multiple genera in the gut and lung and shifted predicted pathways linked to amino acid, lipid, and sulfur metabolism. HDM induced broad taxonomic and functional changes in the gut and lung tissue, including shifts in coenzyme A biosynthesis, reductive TCA activity, lysine fermentation, and nucleotide biosynthesis, while producing only limited taxonomic changes in BALF. PAR2 signaling accounted for a substantial portion of HDM driven remodeling, and direct PAR2 activation reproduced many compartment specific effects, including mucin derived sugar degradation in the gut and suppression of nucleotide biosynthesis in the lung. Sex moderately modified microbial and metabolic responses, with males and females exhibiting divergent, condition dependent functional biases across gut and lung. Conclusion: These findings identify PAR2 as a mucosal niche modifying receptor whose activation or loss reshapes microbial composition and metabolic potential along the gut-lung axis.

Postpartum depression (PPD) is a mood disorder that affects the ability of mothers to engage with and care for their infants. Stress exposure is known to be a major predisposing factor for PPD, while immune factors such as T regulatory cells (Tregs) are also hypothesized to influence the development of the disorder. Here we assessed limited nesting (LN) in mice, with or without depletion of Tregs through anti‐CD25 antibody treatment, as a potential model to investigate the relationship between stress and the immune system in PPD. Dams and their pups were exposed to LN from post‐natal day 3–10 and maternal behaviour was evaluated over this period followed by assessment of maternal self‐care using the splash test. Gene expression in selected brain regions and the peripheral lymphocyte profile were also assessed. LN exposure led to a significant increase in aggressive behaviour towards the pups and altered grooming in the splash test. These effects on behaviour were associated with brain region specific changes in expression of several genes related to depression and maternal behaviour and with increased levels of Tregs in the periphery. When LN was combined with anti‐CD25 antibody treatment, there were further deficits in nursing behaviour and changes in the brain circuitry related to lactation and stress. Our study indicates that LN in mice may be a useful model for studying neuroimmune relationships in certain aspects of PPD. Our data also suggest that post‐partum regulatory immune changes may mitigate effects of stress on brain circuitry associated with maternal behaviour, lactation and stress.

Background: Pulmonary neuroendocrine cells (PNECs) are rare airway sensory cells implicated in amplifying allergic inflammation, yet due to their scarcity, the contribution of PNECs to the metabolic programs and responses of the airway epithelium remains poorly defined. Using a newly developed PNEC-enriched human airway epithelial model (ePNEC), we investigated the influence of PNECs on neuroendocrine and immune-modulatory metabolite production in response to the common aeroallergen of the house dust mite (HDM). Methods: Human bronchial epithelial cells (HBECs) and ePNEC cultures were differentiated at the air–liquid interface. Global untargeted metabolomics was performed to quantify metabolite abundance at baseline and following stimulation with HDMs. Differential expression, overlap significance, metabolite class enrichment, and pathway analyses were used to define PNEC-specific metabolic programs. Results: Principal component analysis (PCA) demonstrated strong baseline separation between ePNECs and HBECs, with HDMs inducing additional within-cell-type shifts. ePNECs displayed broader and more pronounced metabolite changes than HBECs. Baseline differences were largely preserved following allergen exposure, with significant overlap in both up- and down-regulated metabolites. ePNECs exhibited enriched neurotransmitter-linked metabolites—including serotonin, L-noradrenaline, dopamine, and histamine—at baseline and after HDM exposure. Amino acid–centered metabolism dominated the dataset, with enhanced histidine and tryptophan pathway activity in ePNECs. Pathway analysis revealed significant enrichment of phenylalanine, tyrosine, tryptophan, glutathione, and arginine–proline metabolism in ePNECs, whereas HBECs showed no significant pathway-level enrichment after HDM exposure. Conclusions: Human ePNECs engage a distinct, neuroactive metabolic program that is amplified upon HDM exposure. These findings provide a metabolic framework for how PNECs shape epithelial and neuroimmune responses to inhaled allergens.

Background: Pulmonary neuroendocrine cells (PNEC) are rare airway epithelial cells that have recently gained attention as potential amplifiers of allergic asthma. However, studying PNEC function in humans has been challenging due to a lack of cell isolation methods, and little is known about human PNEC function in response to asthma‐relevant stimuli. Here we developed and characterized an in vitro human PNEC model and investigated the neuroendocrine response to extracts of the common aeroallergen house dust mite (HDM). Methods: PNEC‐enriched cultures were generated from human induced pluripotent stem cells (iPNEC) and primary bronchial epithelial cells (ePNEC). Characterized PNEC cultures were exposed to HDM extract, a volatile chemical odorant (Bergamot oil), or the bacterial membrane component, lipopolysaccharide (LPS), and neuroendocrine gene expression and neuropeptide release determined. Results: Both iPNEC and ePNEC models demonstrated similar baseline neuroendocrine characteristics and a stimuli‐specific modulation of gene expression. Most notably, exposure to HDM but not Bergamot oil or LPS, leads to dose‐dependent induction of the CGRP encoding gene, CALCB, and corresponding release of the neuropeptide. HDM‐induced CALCB expression and CGRP release could be inhibited by a protease‐activated receptor 1 (PAR1) antagonist or protease inhibitors and was mimicked by a PAR1 agonist. Conclusions: We have characterized a novel model of PNEC‐enriched human airway epithelium and utilized this model to demonstrate a previously unrecognized role for human PNEC in mediating a direct neuroendocrine response to aeroallergen exposure.

Background Pulmonary neuroendocrine cells (PNEC) are rare airway epithelial cells that have recently gained attention as potential amplifiers of allergic asthma. However, studying PNEC function in humans has been challenging due to a lack of cell isolation methods and little is known about human PNEC function in response to asthma relevant stimuli. Here we developed and characterized an in vitro human PNEC model and investigated the neuroendocrine response to extracts of the common aeroallergen house dust-mite. (HDM). Methods PNEC enriched cultures were generated from human induced pluripotent stem cells (iPNEC) and primary bronchial epithelial cells (ePNEC). Characterized PNEC cultures were exposed to HDM extract, a volatile chemical odorant (Bergamot oil), or the bacterial membrane component, lipopolysaccharide (LPS) and neuroendocrine gene expression and neuropeptide release determined. Results Both iPNEC and ePNEC models demonstrated similar baseline neuroendocrine characteristics and a stimuli specific modulation of gene expression. Most notably, exposure to HDM but not Bergamot oil or LPS, lead to dose dependent induction of the CGRP encoding gene, CALCB, and corresponding release of the neuropeptide. HDM induced CALCB expression and CGRP release could be inhibited by a protease activated receptor 1 (PAR1) antagonist or protease inhibitors and was mimicked by a PAR1 agonist. Conclusions We have characterized a novel model of PNEC enriched human airway epithelium and utilized this model to demonstrate a previously unrecognized role for human PNEC in mediating a direct neuroendocrine response to aeroallergen exposure and highlighting CGRP production by these cells as a potential therapeutic target in allergic asthma.

The basic leucine zipper ATF-like transcription factor (BATF) plays a pivotal role in coordinating various aspects of lymphoid cell biology, yet essential functions in dendritic cells (DCs) have not been reported. Here we demonstrate that BATF deficiency leads to increased interferon (IFN) I production in Toll-like receptor 9 (TLR9)-activated plasmacytoid dendritic cells (pDCs), while BATF overexpression has an inhibitory effect. BATF-deficient mice exhibit elevated IFN I serum levels early in lymphocytic choriomeningitis virus (LCMV) infection. Through ATAC-Seq analysis, BATF emerges as a pioneer transcription factor, regulating approximately one third of the known transcription factors in pDCs. Integrated transcriptomics and ChIP-Seq approaches identified the transcriptional regulator DC-SCRIPT as a direct target of BATF that suppresses IFN I promoter activity by interacting with the interferon regulatory factor 7 (IRF7). Genome-wide association study (GWAS) analyses further implicate BATF in pDC-mediated human diseases. Our findings establish a novel negative feedback axis in IFN I regulation in pDCs during anti-viral immune responses orchestrated by BATF and DC-SCRIPT, with broader implications for pDC and IFN I-mediated autoimmunity.

Transcription factors (TFs) control gene expression by direct binding to regulatory regions of target genes but also by impacting chromatin landscapes and thereby modulating DNA accessibility for other TFs. To date, the global TF reservoir in plasmacytoid dendritic cells (pDCs), a cell type with the unique capacity to produce unmatched amounts of type I interferons, has not been fully characterized. To fill this gap, we have performed a comprehensive analysis in naïve and TLR9-activated pDCs in a time course study covering early timepoints after stimulation (2h, 6h, 12h) integrating gene expression (RNA-Seq), chromatin landscape (ATAC-Seq) and Gene Ontology studies. We found that 70% of all described TFs are expressed in pDCs for at least one stimulation time point and that activation predominantly “turned on” the chromatin regions associated with TF genes. We hereby define the complete set of TLR9-regulated TFs in pDCs. Further, this study identifies the AP-1 family of TFs as potentially important but so far less well characterized regulators of pDC function.

Multiple sclerosis (MS) is a chronic inflammatory disease of the central nervous system (CNS) leading to demyelination and axonal damage. It often affects young adults and can lead to neurological disability. Interferon β (IFNβ) preparations represent widely used treatment regimens for patients with relapsing-remitting MS (RRMS) with therapeutic efficacy in reducing disease progression and frequency of acute exacerbations. In mice, IFNβ therapy has been shown to ameliorate experimental autoimmune encephalomyelitis (EAE), an animal model of MS while genetic deletion of IFNβ or its receptor augments clinical severity of disease. However, the complex mechanism of action of IFNβ in CNS autoimmunity has not been fully elucidated. Here, we review our current understanding of the origin, phenotype, and function of microglia and CNS immigrating macrophages in the pathogenesis of MS and EAE. In addition, we highlight the emerging roles of microglia as IFNβ-producing cells and vice versa the impact of IFNβ on microglia in CNS autoimmunity. We finally discuss recent progress in unraveling the underlying molecular mechanisms of IFNβ-mediated effects in EAE.