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Case-control studies have shown that patients with Crohn's disease (CD) have a microbial composition different from healthy individuals. Although the causes of CD are unknown, epidemiologic studies suggest that diet is an important contributor to CD risk, potentially via modulation of bacterial composition and gut inflammation. We hypothesized that long-term dietary clusters (DCs) are associated with gut microbiome compositions and gut inflammation. Our objectives were to identify dietary patterns and assess whether they are associated with alterations in specific gut microbial compositions and subclinical levels of gut inflammation in a cohort of healthy first-degree relatives (FDRs) of patients with CD.As part of the Genetic, Environmental, Microbial (GEM) Project, we recruited a cohort of 2289 healthy FDRs of patients with CD. Individuals provided stool samples and answered a validated food frequency questionnaire reflecting their habitual diet during the year before sample collection. Unsupervised analysis identified 3 dietary and 3 microbial composition clusters.DC3, resembling the Mediterranean diet, was strongly associated with a defined microbial composition, with an increased abundance of fiber-degrading bacteria, such as Ruminococcus, as well as taxa such as Faecalibacterium. The DC3 diet was also significantly associated with lower levels of subclinical gut inflammation, defined by fecal calprotectin, compared with other dietary patterns. No significant associations were found between individual food items and fecal calprotectin, suggesting that long-term dietary patterns rather than individual food items contribute to subclinical gut inflammation. Additionally, mediation analysis demonstrated that DC3 had a direct effect on subclinical inflammation that was partially mediated by the microbiota.Overall, these results indicated that Mediterranean-like dietary patterns are associated with microbiome and lower intestinal inflammation. This study will help guide future dietary strategies that affect microbial composition and host gut inflammation to prevent diseases.

Inflammatory bowel disease (IBD) is a group of chronic digestive tract inflammatory conditions whose genetic etiology is still poorly understood. The incidence of IBD is particularly high among Ashkenazi Jews. Here, we identify 8 novel and plausible IBD-causing genes from the exomes of 4453 genetically identified Ashkenazi Jewish IBD cases (1734) and controls (2719). Various biological pathway analyses are performed, along with bulk and single-cell RNA sequencing, to demonstrate the likely physiological relatedness of the novel genes to IBD. Importantly, we demonstrate that the rare and high impact genetic architecture of Ashkenazi Jewish adult IBD displays significant overlap with very early onset-IBD genetics. Moreover, by performing biobank phenome-wide analyses, we find that IBD genes have pleiotropic effects that involve other immune responses. Finally, we show that polygenic risk score analyses based on genome-wide high impact variants have high power to predict IBD susceptibility.

Mutations in the tetratricopeptide repeat domain 7A (TTC7A) gene are a rare cause of congenital enteropathy that can result in significant morbidity. TTC7A deficiency leads to disruption of the intestinal epithelium. The histopathology of this condition has been partly described in case reports and clinical studies. This manuscript describes an in-depth investigation of the pediatric gastrointestinal pathology of the largest histologically examined cohort with confirmed TTC7A mutations reported to date and, for the first time, compared the findings to age- and sex-matched control patients with intestinal atresia not thought to be associated with TTC7A mutations. Hematoxylin and eosin-stained slides of endoscopically obtained mucosal biopsies and surgical resection specimens from seven patients with known TTC7A mutations were examined retrospectively. The microscopic findings were found to be on a spectrum from atresia-predominant to those with predominantly epithelial abnormalities. Several unique histopathologic characteristics were observed when compared to controls. These included neutrophilic colitis and prominent lamina propria eosinophilia throughout the gastrointestinal tract. Striking architectural abnormalities of the epithelium were observed in four of the seven patients. The five patients with intestinal atresia demonstrated hypertrophy and disorganization of the colonic muscularis mucosae accompanied by bland spindle cell nodules within the intestinal wall. The components of the latter were further elucidated using immunohistochemistry, and we subsequently hypothesize that they represent obliterated mucosa with remnants of the muscularis mucosae. Finally, atrophic gastritis was noted in four patients. In conclusion, the unique histopathologic characteristics of TTC7A mutation-associated enteropathy described herein more fully describe this novel disease entity in infants who present with congenital enteropathy or enterocolitis.

Emerging data showed patients with chronic inflammatory disorders, including inflammatory bowel disease, are more likely to develop atherosclerotic cardiovascular diseases, heart failure, and atrial fibrillation. This article aims to review the evidence of those associations.PubMed was searched from inception to January 2022 using the keywords, including inflammatory bowel diseases, Crohn disease, ulcerative colitis, atherosclerotic cardiovascular disease, coronary artery disease, cardiovascular disease, atrial fibrillation, heart failure, and premature coronary artery disease. Relevant literature, including retrospective/prospective cohort studies, clinical trials, meta-analyses, and guidelines, were reviewed and summarized.Both ulcerative colitis and Crohn disease are associated with an increased risk of atherosclerotic cardiovascular diseases, cerebrovascular accidents, premature coronary artery disease, and atrial fibrillation. Ulcerative colitis is associated with an increased risk of heart failure. The increased atrial fibrillation occurred during inflammatory bowel disease flares and persistent activity but not during periods of remission. Hypotheses for the mechanism underlying the association of inflammatory bowel disease and atherosclerotic cardiovascular diseases include shared risk factors (ie, obesity, diabetes, smoking, diet) and pathophysiology (gut microbiome dysfunction) or adverse effects from inflammatory bowel disease itself or its treatment (ie, chronic inflammation, dyslipidemia, thrombocytosis, steroids).Inflammatory bowel disease is associated with an increased risk of atherosclerotic cardiovascular diseases, heart failure, and atrial fibrillation. A multidisciplinary team with gastroenterologists and cardiologists is needed to optimize the care for patients with inflammatory bowel disease and associated cardiac diseases.

Purpose: Receptor-interacting serine/threonine-protein kinase 1 (RIPK1) is an important regulator of necroptosis and inflammatory responses. We present the clinical features, genetic analysis and immune work-up of two patients with infantile-onset inflammatory bowel disease (IBD) resulting from novel RIPK1 mutations.Methods: Whole exome and Sanger sequencing was performed in two IBD patients. Mass cytometry time of flight (CyTOF) was conducted for in-depth immunophenotyping on one of the patient’s peripheral blood mononuclear cells, and compared to control subjects and patients with Crohn’s disease.Results: The patients presented with severe colitis and perianal fistulas in the first months of life, without severe/atypical infections. Genetic studies identified novel and pathogenic genetic variants in RIPK1. Using CyTOF unbiased clustering analysis, we identified peripheral immune dysregulation in one of these patients, characterized by an increase in IFNγ CD8+ T cells along with a decrease in monocytes, dendritic cells and B cells. Moreover, RIPK1-deficient patient’s immune cells exhibited decreased IL-6 production in response to LPS across multiple cell types including T cells, B cells and innate immune cells. Summary: Mutations in RIPK1 should be considered in very young patients presenting with colitis and perianal fistulas. Given RIPK1’s role in inflammasome activation, but also in epithelial cells, it is unclear whether IL1 blockade or allogeneic hematopoietic stem cell transplantation can suppress or cure the hyper-inflammatory response in these patients. Additional studies in humans are required to better define the role of RIPK1 in regulating intestinal immune responses, and how treatment can be optimized for patients with RIPK1 deficiency.

BACKGROUND Very early onset inflammatory bowel disease (VEOIBD) is defined as disease onset prior to age 6. VEOIBD is monogenic in >5% of cases; however, in the remaining cases, molecular basis of disease is unknown. We aimed to utilize bulk RNA-seq of blood to 1) define transcriptional signatures in established monogenic IBD and 2) to inform novel molecular diagnoses. METHODS We sequenced the transcriptomes of 115 whole blood samples, comprising patients with VEOIBD of a known monogenic cause (n=35), VEOIBD without a known monogenic cause (n=70), and healthy controls (n=10). We focused on genes whose normalized expression was at least 5 standard deviations away from the population mean in at least one sample. We comprehensively characterized clinical phenotypes, to assess concordance with known pathway and gene function, and compared to whole exome sequencing data where available. We interrogated Bayesian IBD networks to assess for enrichment of genes of interest. RESULTS First, we report on a novel transcriptional signature shared by two patients with VEOIBD secondary to X-linked agammaglobulinemia (pathogenic BTK mutations). The signature is defined by under-expression of CXCR5 and FCRL5 (Fig 1) and suggests reduced transcripts secondary to B-cell depletion or novel BTK-dependent mechanisms of gene transcription. Second, we report on three novel candidate VEOIBD genes identified through our approach: MSN, SLC39A4, and BTN3A2 (Fig 2). MSN expression was below threshold in one patient with VEOIBD complicated by fistulae, recurrent infections, and death from pneumonia at age 62. Review of his exome revealed a novel loss of function mutation in MSN. MSN encodes moesin, an actin cytoskeleton modulator, which regulates lymphocyte migration and adhesion. Mutations in MSN are associated with X-linked moesin-associated immunodeficiency, which was first reported in a patient with IBD this year. SLC39A4, which encodes an intestinal zinc transporter, was below threshold in two patients. Mutations in SLC39A4 are associated with acrodermatitis enteropathica, characterized by dermatitis and diarrhea. One patient has VEOIBD with dermatitis; the second has VEOIBD complicated by toxic megacolon and colectomy. Coding mutations in SLC39A4 have not been identified. Further molecular assessment of zinc transporter function is underway. Lastly, BTN3A2 expression was below threshold in two patients with infantile-onset IBD. BTN3A2 plays a role in T cell receptor interactions and NF-KB signaling. Bayesian IBD networks, built from independent cohorts, revealed BTN3A2 and SLC39A4 subnetworks to be enriched in predicted key driver genes of inflammation, further supporting these genes’ potential disease association. CONCLUSIONS Bulk RNA-seq in blood can be used as a diagnostic tool to aid in identifying novel molecular pathways and monogenic diagnoses in VEOIBD.

Background & Aims Increased intestinal permeability has been associated with Crohn’s disease (CD), but it is not clear whether it is a cause or result of the disease. We performed a prospective study to determine whether increased intestinal permeability is associated with future development of CD. Methods We assessed the intestinal permeability, measured by the urinary fractional excretion of lactulose-to-mannitol ratio (LMR) at recruitment in 1420 asymptomatic first-degree relatives (6–35 years old) of patients with CD (collected from 2008 through 2015). Participants were then followed up for a diagnosis of CD from 2008 to 2017, with a median follow-up time of 7.8 years. We analyzed data from 50 participants who developed CD after a median of 2.7 years during the study period, along with 1370 individuals who remained asymptomatic until October 2017. We used the Cox proportional hazards model to evaluate time-related risk of CD based on the baseline LMR. Results An abnormal LMR (>0.03) was associated with a diagnosis of CD during the follow-up period (hazard ratio, 3.03; 95% CI, 1.64–5.63; P = 3.97 × 10–4). This association remained significant even when the test was performed more than 3 years before the diagnosis of CD (hazard ratio, 1.62; 95% CI, 1.051–2.50; P = .029). Conclusions Increased intestinal permeability is associated with later development of CD; these findings support a model in which altered intestinal barrier function contributes to pathogenesis. Abnormal gut barrier function might serve as a biomarker for risk of CD onset.

NK1.1+ T cells in the mouse thymus and bone marrow were compared because some marrow NK1.1+ T cells have been reported to be extrathymically derived. Almost all NK1.1+ T cells in the thymus were depleted in the CD1−/−, β2m−/−, and Jα281−/− mice as compared with wild-type mice. CD8+NK1.1+ T cells were not clearly detected, even in the wild-type mice. In bone marrow from the wild-type mice, CD8+NK1.1+ T cells were easily detected, about twice as numerous as CD4+NK1.1+ T cells, and were similar in number to CD4−CD8−NK1.1+ T cells. All three marrow NK1.1+ T cell subsets were reduced about 4-fold in CD1−/− mice. No reduction was observed in CD8+NK1.1+ T cells in the bone marrow of Jα281−/− mice, but marrow CD8+NK1.1+ T cells were markedly depleted in β2m−/− mice. All NK1.1+ T cell subsets in the marrow of wild-type mice produced high levels of IFN-γ, IL-4, and IL-10. Although the numbers of marrow CD4−CD8−NK1.1+ T cells in β2m−/− and Jα281−/− mice were similar to those in wild-type mice, these cells had a Th1-like pattern (high IFN-γ, and low IL-4 and IL-10). In conclusion, the large majority of NK1.1+ T cells in the bone marrow are CD1 dependent. Marrow NK1.1+ T cells include CD8+, Vα14-Jα281−, and β2m-independent subsets that are not clearly detected in the thymus.

It remains puzzling how immunodeficiency with hypo-responsive cells can be associated with increased immune cell activation to seemingly harmless substances such as allergens. Here, we have investigated skin pathology in the severe primary immunodeficiency Wiskott-Aldrich syndrome (WAS). Wildtype and WAS protein-deficient (WASp KO) mice were challenged with the allergen Der p 2 to induce eczema or infected with Leishmania major to induce robust skin inflammation. Der p 2 challenge of wildtype mice induced eczema with epidermal hyperplasia and egress of Langerhans cells from the skin. WASp KO mice had increased accumulation of mature DCs in the skin and, in contrast to wildtype cells, Der p 2 induced expansion of WASp KO CD8+ T cells that produced IFNγ. Similar to challenge with Der p 2 and unlike wildtype mice, WASp KO mice infected with L. major showed a skewed immune response with increased expansion of IFNγ-producing CD8+ T cells in the draining lymph node. Finally, we show that WASp KO DCs have increased capacity to cross-present exogenous antigen and activate CD8+ T cells. Our results imply that WASp deficiency in skin inflammation causes a breach in tolerance and skews the immune system to DC mediated CD8+ T cell responses at incorrect sites.

Colitis occurs in mice and some patients deficient in the Wiskott-Aldrich Syndrome protein (WASP), a hematopoietic-specific molecule that regulates the actin cytoskeleton. This colitis is lymphocyte-dependent, but severe disease is observed in chimeric mice with WT T cells and WASP KO innate immune cells, generated by transfer of WT CD4+ T cells into WASP/RAG DKO mice. Given the immunomodulatory function of IL-10, coupled with our findings that mixed bone marrow chimeras are free of colitis, we investigated whether alterations in IL-10 play a role in our colitis model. We found reduced IL-10 transcript levels in mesenteric lymph nodes of chimeric mice. To tease out the cellular source of decreased IL-10 production, WASP/RAG DKO DCs were stimulated in vitro and observed to produce less IL-10. We then transferred IL-10GFP CD4+ cells and found a reduction in the IL-10-expressing proportion of T cells in WASP/RAG DKO compared to RAG KO mice. Lastly, exogenous administration of IL-10-Ig completely abrogated disease in chimeric mice. In summary, besides impaired Treg homeostasis and function, severe colitis in our chimeric mice is associated with reduced IL-10 production in MLNs and in vitro stimulated DCs. Taken together with prevention of disease with IL-10 treatment, colitis in this model may result from decreased IL-10 production by WASP KO innate immune cells.

Lymphocytes express both Wiskott-Aldrich syndrome protein (WASP) and N-WASP. WASP deficiency, the cause of WAS, generates more severe defects in T-cells than B cells, suggesting a strong compensatory role of N-WASP in B cells. Using knockout mouse models, this study shows that WASP knockout (WKO) reduces B cell spreading, B cell receptor (BCR) aggregation, tyrosine phosphorylation, Btk phosphorylation and F-actin accumulation at the B cell surface induced by membrane-associated antigen, and WASP/N-WASP double knockout nearly abolished these activities. However, in B cells with N-WASP conditional knockout (cNKO), B cell spreading and F-actin accumulation are enhanced, while the merge of BCR aggregates and attenuation of tyrosine and Btk phosphorylation are inhibited. Additionally, cNKO has a much stronger inhibitory effect on BCR endocytosis than WKO. In contrast to Btk-dependent activation of WASP, N-WASP phosphorylation is upregulated by Btk-deficiency but downregulated by SHIP KO. Furthermore, the phosphorylation of WASP and N-WASP is inversely regulated by each other. These results reveal that the combined function of WASP and N-WASP is required for the optimal activation of the BCR and its signaling attenuation, but these two proteins function distinctively: WASP and N-WASP play dominant roles in the initiation and attenuation of BCR activation respectively. Thus, the integrated action of WASP and N-WASP provide a critical regulatory mechanism for BCR activation.

Lymphocyte migration is at the heart of normal and pathological immune responses in the intestinal mucosa. We and others have shown that, in addition to activating lymphocytes, gut-associated dendritic cells (GALT-DC) can metabolize dietary vitamin A into all-trans retinoic acid (RA), which is required for inducing gut-tropic lymphocytes and IgA antibody-secreting cells (IgA-ASC). GALT-DC from mice deficient in the intracellular signaling adaptor MyD88, which lack most Toll-like receptor (TLR) signals, were significantly impaired in their capacity to induce gut-homing T cells and IgA-ASC and expressed low levels of retinal dehydrogenases (RALDH), which are critical enzymes for RA biosynthesis. MyD88-/- mice were also impaired in generating gut-tropic T cells upon immunization and exhibited low numbers of intestinal IgA-ASC. Pre-treatment of murine spleen-DC and human monocyte-derived DC with a TLR1/2 agonist was sufficient to induce RALDH and to confer these extra-intestinal DC with the capacity to induce gut-homing lymphocytes and IgA-ASC via a mechanism dependent on MyD88 and c-JNK/MAPK. Thus, MyD88-dependent TLR signals are both necessary and sufficient to educate DC with gut-specific imprinting properties.