The potential of dietary interventions as a therapy for IBDs is increasingly appreciated in clinical practice. A central role for Western diets as a rheostat for gut inflammation was demonstrated for IBD in the last years, and particular dietary patterns and food constituents have been linked to the development and course of IBD. Substantial progress in the understanding of nutritional immunology and genetic and epidemiological traits, and the emergence of clinical innovations has sparked a strong interest in dietary intervention, transforming nutritional support into a modifiable treatment option tailored to individuals which may act synergistically to pharmacological therapies. In this study, we review how Western diets act as a fuel for IBD and discuss nutritional concepts, exclusive enteral nutrition and solid food diets, with anti-inflammatory efficacy in IBD. We compare mutual strategies of efficacious solid food diets to deduce a healthy dietary pattern for patients with IBD and suggest incentives regulating our food environment and counselling of doctors and patients to disrupt Western dietary habits and to promote gut health globally.

Multi-omic and multimodal datasets with detailed clinical annotations offer significant potential to advance our understanding of inflammatory bowel diseases (IBD), refine diagnostics, and enable personalized therapeutic strategies. In this multi-cohort study, we performed an extensive multi-omic and multimodal analysis of 1,002 clinically annotated patients with IBD and non-IBD controls, incorporating whole-exome and RNA sequencing of normal and inflamed gut tissues, serum proteomics, and histopathological assessments from images of H&E-stained tissue sections. Transcriptomic profiles of normal and inflamed tissues revealed distinct site-specific inflammatory signatures in Crohn's disease (CD) and ulcerative colitis (UC). Leveraging serum proteomics, we developed an inflammatory protein severity signature that reflects underlying intestinal molecular inflammation. Furthermore, foundation model-based deep learning accurately predicted histologic disease activity scores from images of H&E-stained intestinal tissue sections, offering a robust tool for clinical evaluation. Our integrative analysis highlights the potential of combining multi-omics and advanced computational approaches to improve our understanding and management of IBD.

The potential of dietary interventions as a therapy for IBDs is increasingly appreciated in clinical practice. A central role for Western diets as a rheostat for gut inflammation was demonstrated for IBD in the last years, and particular dietary patterns and food constituents have been linked to the development and course of IBD. Substantial progress in the understanding of nutritional immunology and genetic and epidemiological traits, and the emergence of clinical innovations has sparked a strong interest in dietary intervention, transforming nutritional support into a modifiable treatment option tailored to individuals which may act synergistically to pharmacological therapies. In this study, we review how Western diets act as a fuel for IBD and discuss nutritional concepts, exclusive enteral nutrition and solid food diets, with anti-inflammatory efficacy in IBD. We compare mutual strategies of efficacious solid food diets to deduce a healthy dietary pattern for patients with IBD and suggest incentives regulating our food environment and counselling of doctors and patients to disrupt Western dietary habits and to promote gut health globally.

Metabolic dysfunction-associated steatotic liver disease (MASLD) is the most prevalent chronic liver disease worldwide, affecting one-third of the global population. Most patients exhibit simple steatosis, whereas up to 20% develop metabolic dysfunction-associated steatohepatitis (MASH), potentially culminating in liver cirrhosis and hepatocellular carcinoma. Diverse parallel mechanisms contribute to the development of MASH, which are fueled by hepatic lipotoxicity, intestinal dysbiosis, and pro-inflammatory diets shaping innate and adaptive immune responses. Moreover, adipose tissue is driving systemic inflammation in obesity, contributing to the inflammatory burden in obesity-related MASH. Polygenetic and multiomic risk scores identify distinct types of MASLD with dominant aggressive liver disease or extrahepatic cardiometabolic disease. Here, we review the complexity of multiple parallel inflammatory hits in MASH and delineate that most current MASH drugs exert pleiotropic metabolic and anti-inflammatory properties. These new therapies will change the clinical management of this disease in the near future.

Macroautophagy/autophagy exerts multilayered protective functions in intestinal epithelial cells (IECs) while a loss-of-function genetic variant in ATG16L1 (autophagy related 16 like 1) is associated with risk for developing Crohn disease (CD). Westernization of diet, partly characterized by excess of long-chain fatty acids, contributes to CD, and a metabolic control of intestinal inflammation is emerging. Here, we report an unexpected inflammatory function for ATG16L1-mediated autophagy in Crohn-like metabolic enteritis of mice induced by polyunsaturated fatty acid (PUFA) excess in a western diet. Dietary PUFAs induce ATG16L1-mediated conventional autophagy in IECs, which is required for PUFA-induced chemokine production and metabolic enteritis. By transcriptomic and lipidomic profiling of IECs, we demonstrate that ATG16L1 is required for PUFA-induced inflammatory stress signaling specifically mediated by TLR2 (toll-like receptor 2) and the production of arachidonic acid metabolites. Our study identifies ATG16L1-mediated autophagy in IECs as an inflammatory hub driving metabolic enteritis, which challenges the perception of protective autophagy in the context of diet westernization.Abbreviations: AA: arachidonic acid; ATG16L1: autophagy related 16 like 1; CD: Crohn disease; CXCL1: C-X-C motif chemokine ligand 1; ER: endoplasmic reticulum; GFP: green fluorescent protein; GPX4: glutathione peroxidase 4; IBD: inflammatory bowel disease; IECs: intestinal epithelial cells; PTGS2/COX2: prostaglandin-endoperoxide synthase 2; PUFA: polyunsaturated fatty acid; SDA: stearidonic acid; TLR2: toll-like receptor 2; WT: wild-type.

BACKGROUND & AIMS:Molecular phenotyping of Crohn's disease (CD) trajectories after ileocolonic resection (ICR) enables the identification of evolving disease mechanisms and related biomarker discovery. Here, we aimed at identifying a pathogenic node with predictive value for endoscopic disease recurrence after ICR in CD. METHODS:We performed unbiased transcriptomics of the postoperative ileum, comparing patients with an endoscopic Rutgeerts score i0 vs those with ≥i2b (N = 36). A potential biomarker from this analysis was then validated at the protein level by quantitative confocal microscopy on tissue slides, and its value for predicting endoscopic recurrence at resection was assessed in 3 independent ICR cohorts (total N = 241). Functional implications and therapeutic potential were investigated in mouse enteritis models. RESULTS:Patients with endoscopic CD recurrence exhibited a transcriptional node characterized by reduced glutathione peroxidase 4 (GPX4) expression, which was confined to the intestinal epithelium. Reduced intestinal epithelial GPX4 expression was already observed at the time of ICR and predicted endoscopic recurrence in addition to established clinical risk factors in a patient-level meta-analysis. Intestinal epithelial GPX4 expression was a surrogate of its enzymatic activity, inversely correlated with a mucosal endoplasmic reticulum stress signature, but was unrelated to a GPX4 genetic variant associated with CD susceptibility, histologic severity of inflammation, or clinical risk factors for recurrence. In mice, reduced intestinal epithelial Gpx4 expression fueled endoplasmic reticulum stress and enabled severe enteritis, which was ameliorated by restoration of epithelial GPX4 expression with selenium supplementation. CONCLUSIONS:Collectively, our study identifies a druggable biomarker that improves the prediction of endoscopic CD recurrence, potentially guiding patient management and therapy in the future. One of the studied ICR cohorts was part of the REMIND (Groupe de Recherche sur les Maladies inflammatoires digestives) study, registered at ClinicalTrials.gov (NCT03458195).

Abstract Background Fecal calprotectin (CP) serves as a worldwide established biomarker used for the diagnosis and management of inflammatory bowel diseases (IBD). However, the biological function of CP in the human gut is still unknown and numerous studies obtained contradictory results. Calprotectin is mainly described to be present as a tetrameric protein complex (S100A8/S100A9)2, while the quaternary protein structure (configuration) of S100A8 and S100A9 in the human gut lumen remains enigmatic.1 In this study we resolved the fecal protein configurations of calprotectin and their biological functions in IBDs. Methods We defined biological functions of S100A8 and S100A9 dimers by antibody-mediated immunoprecipitation of S100A8 and S100A9 from stool obtained from IBD patients coupled with subsequent LC-MS/MS analysis. Next, we analysed human colonic organoids by single-cell RNA sequencing after S100A8 or S100A9 stimulation. Moreover, we orally exposed mice to recombinant human S100A8 and S100A9 protein during experimental gut inflammation and genetically inactivated S100a9 in toxic and genetic mouse models. To identify the protein configurations of S100A8 and S100A9 in the human gut lumen we examined stool samples from IBD patients using size-exclusion chromatography and LC-MS/MS analysis. Results We demonstrate pro-inflammatory actions for S100A8 and S100A9 dimers as oral administration of human S100A8 and S100A9 homodimers, but not CP, worsened experimental enteritis and colitis. In accordance, multi-omic phenotyping revealed that human S100A8 and S100A9 homodimers induce the NLRP1 inflammasome in intestinal epithelium. In turn, genetic deletion of S100a9 ameliorated experimental gut inflammation. S100A8 and S100A9 dimers were frequently detectable in stool from IBD patients from three independent IBD cohorts, but not in healthy individuals. More specifically, fecal S100A9 detection was associated with clinical and endoscopic disease activity in IBD patients with low fecal CP levels (≤150µg/g). Importantly, four fecal CP assays in clinical use were not able to detect S100A8 and S100A9 homodimers. Conclusion Our study is the first to reveal the presence of S100A8 and S100A9 dimers in stool from IBD patients. Moreover, we demonstrate a diagnostic gap for fecal CP assays in clinical use. We establish that fecal S100A9 detection is associated with endoscopic disease activity in IBD patients in which fecal CP fails to identify active disease. We reveal disease-modifying functions for S100A8 and S100A9 homodimers by inducing the NLRP1 inflammasome, while the same effects were not observable for calprotectin. Taken together, our findings may reflect a major advance in the IBD biomarker field. References Jukic, A., Bakiri, L., Wagner, E. F., Tilg, H. & Adolph, T. E. Calprotectin: from biomarker to biological function. Gut 70 , 1978-1988 (2021). https://doi.org/10.1136/gutjnl-2021-324855

Westernization of diet, partly characterized by long-chain fatty acid excess, perturbs intestinal immune responses in Crohn’s disease (CD). The cellular and molecular framework of lipid sensing in intestinal inflammation remains enigmatic. By small intestinal transcriptional profiling of CD, we identified increased transcriptional activity of retinoid X receptor alpha (RXRα) specifically in intestinal epithelial cells (IECs). Transcriptional RXRα activity was induced in IECs of mice by ω-3 and ω-6 polyunsaturated fatty acid (PUFA) excess in a Western diet. PUFA-induced RXRα activity in Paneth cells governed chronic transmural enteritis by enabling the expression of CXCL1. Oral exposure to isotretinoin ameliorated PUFA-induced metabolic enteritis in two mouse models, and isotretinoin therapy reduced the odds of developing CD in an analysis of electronic health care records from 170,597 patients. Collectively, we identify RXRα in Paneth cells as a metabolic stress sensor that enables enteritis, providing novel perspectives for the prevention and treatment of CD.

Abstract Background The rising incidence of Crohn’s disease (CD) is paralleled by a Westernization of diet including an increased consumption of long-chain polyunsaturated fatty acids (PUFA). Previous research demonstrated that PUFA consumption is positively correlated with clinical disease activity in CD patients1 and mice lacking antioxidant GPX4 in their intestinal epithelial cells develop CD like enteritis when fed a PUFA enriched Western diet2. In this study we investigated whether blocking PUFA signalling through the PUFA receptor RXRα could alleviate experimental enteritis and provide protection against CD development in a Western cohort. Methods We generated mice lacking GPX4 (Gpx4ΔPC) specifically in Paneth cells, fed them a PUFA enriched Western-style diet (PUFA-WD) to induce experimental enteritis and treated them with 9-cis retinoic acid, administered by oral gavage. MODE-K cells (murine IECs) were subjected to GPX4 and RXRα silencing using siRNA and then stimulated with PUFA, 9-cis retinoic acid or isotretinoin (which is partly metabolised to 9-cis retinoic acid3). Cytokine expression was measured using ELISA. Additionally, we conducted a retrospective analysis of electronic health records via TriNetX4 to evaluate how isotretinoin treatment in US acne patients influences the likelihood of CD development later in life. Results After one month of PUFA-WD feeding, Gpx4ΔPC mice developed CD-like enteritis which was significantly ameliorated when treated with 9-cis retinoic acid during the last 3 days of the experiment. In GPX4 deficient IECs, PUFA induced expression of the neutrophil attracting chemokine CXCL1 was suppressed by RXRα silencing and dose dependently reduced by treatment with the RXRα modulators 9-cis retinoic acid or isotretinoin. This indicates a competitive interaction between PUFA and these modulators for RXRα binding, leading to cytokine production. 85,338 acne patients treated with isotretinoin were compared to 85,259 age and sex matched isotretinoin-untreated acne patients. We analysed outcomes for diagnosis of inflammatory bowel disease within 1 year in these two cohorts. Isotretinoin therapy was significantly associated with protection from Crohn’s disease (OR 0,641, 95% CI (0.509, 0.806)), but not from ulcerative colitis (OR 0.981, 95% CI (0.789, 1.219)). Conclusion Our findings reveal that PUFA-induced cytokine production mediated by RXRα plays a key role in the development of diet-induced gut inflammation. This process can be mitigated through the use of RXRα modulators, including isotretinoin. Additionally, isotretinoin use is associated with a reduced risk of Crohn’s disease development in US acne patients. References 1.Schwärzler J, Mayr L, Vila AV, et al. PUFA-induced metabolic enteritis as a fuel for Crohn's disease. Gastroenterology. Jan 11 2022;doi:10.1053/j.gastro.2022.01.004 2.Mayr L, Grabherr F, Schwarzler J, et al. Dietary lipids fuel GPX4-restricted enteritis resembling Crohn's disease. Nat Commun. Apr 14 2020;11(1):1775. doi:10.1038/s41467-020-15646-6 3.Allenby G, Bocquel MT, Saunders M, et al. Retinoic acid receptors and retinoid X receptors: interactions with endogenous retinoic acids. Proc Natl Acad Sci U S A. Jan 1 1993;90(1):30-4. doi:10.1073/pnas.90.1.30 4.Palchuk MB, London JW, Perez-Rey D, et al. A global federated real-world data and analytics platform for research. JAMIA Open. Jul 2023;6(2):ooad035. doi:10.1093/jamiaopen/ooad035

Background & Aims Quantification of the human S100A8/S100A9 tetrameric protein complex in stool, referred to as fecal calprotectin, is an extensively validated biomarker supporting the diagnosis and management of gastrointestinal diseases. Here, we studied the quaternary protein structures (termed configuration) of S100A8 and S100A9 and their biological function in inflammatory bowel diseases (IBD). Methods We dissected fecal S100A8 and S100A9 configurations in patients with IBD by size-exclusion chromatography coupled with tandem mass spectrometry and systematically defined human S100A8 and S100A9 homodimer functions compared with the calprotectin heterotetramer (CP) in the intestine of mice and in human epithelium and T cells. Moreover, we report a protein interaction network of fecal S100A8 and S100A9 in IBD. Results Stool from patients with active IBD contained abundant S100A8 and S100A9 dimers besides CP. Fecal S100A9 detection associated with clinical and endoscopic disease activity in IBD patients with low CP concentration. Oral exposure to human recombinant S100A8 and S100A9 homodimers, but not to CP, worsened intestinal inflammation in toxic and genetic mouse models. Functional profiling revealed that human S100A8 and S100A9 homodimers enhanced activation of cluster of differentiation 4+ and 8+ T cells, which promoted experimental colitis. In turn, genetic inactivation of S100a9 protected against experimental enteritis and colitis, and pharmacologic inhibition of S100A9 ameliorated chronic colitis. Conclusions Collectively, this study links the detection of fecal S100A9 dimers with clinical and endoscopic disease activity in IBD and identifies inflammatory actions of S100A8 and S100A9 homodimers in the intestine. Our findings pave the way for novel diagnostic and therapeutic approaches in patients with inflammatory diseases of the intestine.

Atg16l1 plays a critical role in autophagy, and Xbp1 is part of the endoplasmic reticulum (ER) homeostasis. Both, Atg16l1 and Xbp1 are known risk genes for inflammatory bowel disease (IBD). Previous studies have shown that dysfunctional Atg16l1 and Xbp1 are epithelial-derived drivers of small intestinal inflammation. Despite a clear link between Crohn’s disease and small intestinal adenocarcinoma, the molecular impact of autophagy and ER stress in this malignant transformation is not known. Using a model of impaired ribonucleotide excision repair (RER), a key homeostatic repair mechanism in highly proliferative cells, we investigated the impact of Atg16l1 on epithelial DNA damage responses and small intestinal carcinogenesis with and without functional ER homeostasis. We used conditional mouse models for deficient RER (Rnaseh2bΔIEC), bearing a co-deletion of disrupted autophagy (Atg16l1/Rnaseh2bΔIEC) or ER stress resolution (Xbp1/Rnaseh2bΔIEC), and triple-conditional knock-out mice for both, Xbp1 and Atg16l1 (Atg16l1/Xbp1/Rnaseh2bΔIEC). We assessed the degree of DNA damage and the incidence of small intestinal carcinoma. We report that defective epithelial RER induces autophagy, and that dysfunctional autophagy increases RER-induced DNA damage and causes the loss of RER-induced proliferative arrest but no spontaneous carcinogenesis in the gut. We demonstrate that dysfunctional Atg16l1 drastically increases the incidence of spontaneous intestinal adenocarcinomas in mice with defective epithelial RER and impaired ER homeostasis. We provide experimental evidence that the same epithelial mechanisms suppressing gut inflammation also critically protect from small intestinal carcinogenesis. Our findings set a molecular framework for the increased risk of intestinal carcinogenesis in patients with IBD, which links perturbations of ER homeostasis and autophagy defects with accumulating DNA damage.

Abstract Background The incidence of inflammatory bowel diseases (IBD) has increased drastically in recent years, which is mainly explained by environmental factors and changes in our diet. Recent studies indicated that a Western-style diet, characterized by an increased caloric intake and consumption of long-chain fatty acids such as polyunsaturated fatty acids (PUFAs), triggers inflammation in metabolic active tissues, termed metabolic inflammation. We recently demonstrated that ω-3 and ω-6 PUFAs fuel an inflammatory response in intestinal epithelial cells (IECs) with genetically reduced expression of the anti-oxidative enzyme glutathione peroxidase 4 (GPX4), and similarly a Western-style diet enriched with PUFAs triggered severe enteritis in mice with reduced GPX4 specifically in IECs (i.e., Gpx4+/-IEC mice). Here, we investigated if PUFAs similarly trigger an inflammatory response in IECs with chemically inhibited GPX4 activity. Methods Experiments were performed with an immortalised murine IEC line (MODE-K) cells. Cells were stimulated with the ω-3 PUFA stearidonic acid (50 µM), the ω-6 PUFA arachidonic acid (20 µM) or a respective control and the GPX4 inhibitor (1S,3R)-RSL3 (RSL3). Cell death, production of inflammatory cytokines, stress at the endoplasmic reticulum (ER) and activation of mitogen-activated protein kinases (MAPKs) were examined. Results Treatment with RSL3 induced cell death in IECs in a dose dependent manner. For further experiments, we worked with 20 nM RSL3, as this concentration already induced some amount of cell death but approximately 75% of cells were still viable. Stimulation with both ω-3 and ω-6 PUFAs triggered the production of interleukin 6 (IL-6) and chemokine (C-X-C motif) ligand 1 (CXCL1) in RSL3 co-treated IECs. Moreover, co-treating of RSL3 and PUFAs induced ER stress and activation of the ER stress sensor inositol-requiring enzyme 1 alpha (IRE1α), an inflammatory signalling hub, in IECs which was paralleled by the activation of MAPKs and especially the c-Jun N-terminal kinase (JNK) branch. Conclusion Our findings demonstrate that the chemical inhibition of GPX4 was sufficient to fuel inflammation in IECs in response to PUFAs, which we previously similarly observed in IECs with genetic depletion of Gpx4.

Post-Acute Sequelae of SARS-CoV-2 infection (PASC), commonly known as Long COVID, represents a significant and complex health challenge with a wide range of symptoms affecting multiple organ systems. This review examines the emerging evidence suggesting a critical role of the gut and gut-brain axis in the pathophysiology of Long COVID. It explores how changes in the gut microbiome, disruption of gut barrier integrity, and the persistence of SARS-CoV-2 antigens within the gastrointestinal tract may contribute to the prolonged and varied symptoms seen in Long COVID, including chronic inflammation and neuropsychiatric disturbances. The review also summarizes key insights gained about Long COVID, highlighting its multifactorial nature, which involves immune dysregulation, microvascular damage, and autonomic nervous system dysfunction, with the gut playing a central role in these processes. While progress has been made in understanding these mechanisms, current evidence remains inconclusive. The challenges of establishing causality, standardizing research methodologies, and addressing individual variations in the microbiome are discussed, emphasizing the need for further longitudinal studies and more comprehensive approaches to enhance our understanding of these complex interactions. This review underscores the importance of personalized approaches in developing effective diagnostic and therapeutic strategies for Long COVID, while also acknowledging the significant gaps in our current understanding. Future research should aim to further unravel the complex interplay between the gut and Long COVID, ultimately improving outcomes for those affected by this condition.

Abstract Background Dietary constituents are believed to play a role in the development of Crohn’s disease (CD) (1). Recently we were able to demonstrate, that polyunsaturated fatty acids (PUFA), induce a CD like enteritis phenotype in genetically susceptible mice (2,3). Furthermore, we could show, that PUFA intake correlated negatively with disease course in CD patients (3). In this project we tried to untangle the role of Paneth cells (PC) in the development of PUFA induced enteritis. Methods scRNA sequencing was performed on cells isolated from mice lacking one allele of Gpx4 (GPX4+/-IEC) in their intestinal epithelial cells (IEC) after feeding them a PUFA enriched western style diet (PUFA-WD). Furthermore, mice lacking both alleles of Gpx4 in their PC (GPX4ΔPC) where fed a PUFA-WD for four weeks and enteritis was assessed based on a histological enteritis score and immunhistochemical stainings. Results scRNAseq of murine intestinal cells revealed an upregulation of IBD relevant pathways (such as JAK or TNFα) in Gpx4 deficient IECs and PC. GPX4ΔPC mice developed a CD like enteritis phenotype, characterized by a mucosal and submucosal infiltration of neutrophils, macrophages and other leucocytes, after only four weeks of PUFA enriched diet, indicating that GPX4 dependent intestinal inflammation is controlled by PC. Conclusion The upregulation of IBD relevant pathways in our model of dietary induced intestinal inflammation renders this model a valuable tool to investigate mechanistical understanding in the role of dietary components in IBD. Our results further link PC metabolism to the development of intestinal inflammation. References 1. Adolph TE, Meyer M, et al Nat Rev Gastroenterol Hepatol 2022 2. Mayr L, Grabherr F, et al Nat Com 2020 3. Schwaerzler J, Mayr L, et al Gastroenterology 2022

Adipose tissue is an immunologically active organ that controls host physiology, partly through the release of mediators termed adipokines. In obesity, adipocytes and infiltrating leukocytes produce adipokines, which include the hormones adiponectin and leptin and cytokines such as tumour necrosis factor and IL-1β. These adipokines orchestrate immune responses that are collectively referred to as metabolic inflammation. Consequently, metabolic inflammation characterizes metabolic disorders and promotes distinct disease aspects, such as insulin resistance, metabolic dysfunction-associated liver disease and cardiovascular complications. In this unifying concept, adipokines participate in the immunological cross-talk that occurs between metabolically active organs in metabolic diseases, highlighting the fundamental role of adipokines in obesity and their potential for therapeutic intervention. Here, we summarize how adipokines shape metabolic inflammation in mice and humans, focusing on their contribution to metabolic disorders in the setting of obesity and discussing their value as therapeutic targets.

We have read with interest the recent article comparing different therapies in induction and maintenance of remission in Crohn’s disease (CD). Recently, Janus kinase (JAK) inhibitors have expanded the armamentarium to treat inflammatory bowel diseases (IBD), while patienttailored precision approaches are needed to further improve treatment. Rare gainoffunction variants affecting signal transducer and activator of transcription 1 (STAT1), a transcription factor activated by JAKs, have been linked with susceptibility to infection, immunodeficiency and immune dysregulation, 5 while some cases develop IBD. A 33yearold patient was referred to our tertiary care centre in poor condition. He presented a body mass index (BMI) of 12.9 kg/m, refractory fever up to 39.5°C and abdominal pain with watery diarrhoea 15 times per day for 3 months. He reported recurrent respiratory infections since childhood, which probably caused diffuse varicose bronchiectasis with mucus plugging diagnosed at the age of 23, requiring repeated antibiotic therapy, and a clinical history that was compatible with primary immunodeficiency as further detailed in the online supplemental file. At the age of 28, he reported the first episode of severe chronic diarrhoea and abdominal pain and was diagnosed with CD, as endoscopy indicated ileitis and pancolitis. Stool and mucosal biopsies were repeatedly tested for infections, but no pathogen was detected, and no other autoinflammatory disease was diagnosed. At admission, he presented elevated inflammatory parameters in the serum (C reactive protein, CRP 19.43 mg/dL) and stool (faecal calprotectin 2221.6 μg/g) (table 1). Pseudomonas aeruginosa and Mycobacterium chimaera were cultured from sputum, despite several antiinfective therapies before referral. Immunophenotyping documented adequate vaccination responses, but low abundance of lymphocytes (table 1). Colonoscopy revealed severe large discontinuous punchedout ulcers throughout the colon and ileitis, which appeared untypical for CD (figure 1A). Histology revealed a frank ulceration and dense discontinuous lymphocyte infiltration with lymphoid aggregates (figure 1B). Trio exome sequencing identified a heterozygous de novo missense variant c.1256C>G in the STAT1 gene (NM_007315.4), which was previously associated with a gainoffunction and described in two individuals from one family. 7 Indeed, peripheral blood mononuclear cells (PBMCs) from the patient exhibited increased phosphorylation of STAT1 (figure 1C), similar to T cells in the mucosa (online supplemental figure S1A) and bloodderived granulocytes and Thelper cells (online supplemental figure S1B). Moreover, increased activation and proliferation of T cells (online supplemental figure S1C, D) and expression of IFN-γ-induced and Th17related genes (figure 1D,E) were observed. In vitro, STAT1 signalling could be reduced by stimulation with JAK inhibitors (figure 1C–E and online supplemental figure S1B–D). We diagnosed primary immunodeficiency caused by STAT1 gainoffunction (STAT1 gainoffunction disease) and offered the patient tofacitinib therapy, despite risk of serious infection. We initiated tofacitinib 10 mg two times per day with reduction to 5 mg after 8 weeks, combined with antibiotic treatment for pulmonary infection and parenteral nutrition. After 2 weeks of treatment, the patient reported clinical remission and after 12 weeks his general appearance had substantially improved. He presented a BMI of 17.9 kg/m and reported no abdominal symptoms. Colonoscopy revealed mucosal healing with few small ulcers limited to the rectum (figure 1A), which was confirmed by histology (figure 1B) and a reduction in faecal calprotectin (300.6 μg/g) (table 1). Indeed, immunophenotyping indicated a reduction of STAT1 phosphorylation Letter

Summary: Inflammatory bowel diseases are characterized by the chronic relapsing inflammation of the gastrointestinal tract. While the molecular causality between endoplasmic reticulum (ER) stress and intestinal inflammation is widely accepted, the metabolic consequences of chronic ER stress on the pathophysiology of IBD remain unclear. By using in vitro, in vivo models, and patient datasets, we identified a distinct polarization of the mitochondrial one-carbon metabolism and a fine-tuning of the amino acid uptake in intestinal epithelial cells tailored to support GSH and NADPH metabolism upon ER stress. This metabolic phenotype strongly correlates with IBD severity and therapy response. Mechanistically, we uncover that both chronic ER stress and serine limitation disrupt cGAS-STING signaling, impairing the epithelial response against viral and bacterial infection and fueling experimental enteritis. Consequently, the antioxidant treatment restores STING function and virus control. Collectively, our data highlight the importance of serine metabolism to allow proper cGAS-STING signaling and innate immune responses upon gut inflammation.