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Tolerance to innocuous antigens from the diet and the commensal microbiota is a fundamental process essential to health. Why tolerance is efficiently induced to substances arising from the hostile environment of the gut lumen is incompletely understood but may be related to how these antigens are encountered by the immune system. We observed that goblet cell associated antigen passages (GAPs), but not other pathways of luminal antigen capture, correlated with the acquisition of luminal substances by lamina propria (LP) antigen presenting cells (APCs) and with the sites of tolerance induction to luminal antigens. Strikingly this role extended beyond antigen delivery. The GAP function of goblet cells facilitated maintenance of pre-existing LP T regulatory cells (Tregs), imprinting LP-dendritic cells with tolerogenic properties, and facilitating LP macrophages to produce the immunomodulatory cytokine IL-10. Moreover, tolerance to dietary antigen was impaired in the absence of GAPs. Thus, by delivering luminal antigens, maintaining pre-existing LP Tregs, and imprinting tolerogenic properties on LP-APCs GAPs support tolerance to substances encountered in the hostile environment of the gut lumen.

The intestinal immune system samples luminal contents to induce adaptive immune responses that include tolerance in the steady state and protective immunity during infection. How luminal substances are delivered to the immune system has not been fully investigated. Goblet cells have an important role in this process by delivering luminal substances to the immune system through the formation of goblet cell-associated antigen passages (GAPs). Soluble antigens in the intestinal lumen are transported across the epithelium transcellularly through GAPs and delivered to dendritic cells for presentation to T cells and induction of immune responses. GAPs can be identified and quantified by using the ability of GAP-forming goblet cells to take up fluorescently labeled dextran. Here, we describe a method to visualize GAPs and other cells that have the capacity to take up luminal substances by intraluminal injection of fluorescent dextran in mice under anesthesia, tissue sectioning for slide preparation and imaging with fluorescence microscopy. In contrast to in vivo two-photon imaging previously used to identify GAPs, this technique is not limited by anatomical constraints and can be used to visualize GAP formation throughout the length of the intestine. In addition, this method can be combined with common immunohistochemistry protocols to visualize other cell types. This approach can be used to compare GAP formation following different treatments or changes to the luminal environment and to uncover how sampling of luminal substances is altered in pathophysiological conditions. This protocol requires 8 working hours over 2-3 d to be completed.

Purpose The study aimed to investigate associations between maternal vitamin D status during pregnancy and molar incisor hypomineralisation (MIH) and hypomineralised second primary molars (HSPM) among children. Methods The study had a longitudinal design using prospectively collected data from 176 mother and child pairs. Mothers were initially recruited in a randomised controlled trial to assess a pregnancy exercise programme. Along with the 7-year follow-up, we invited the children to a dental examination. The exposure variable was maternal serum 25-hydroxyvitamin D in gestational weeks 18–22 and 32–36, categorised as insufficient ( Results Among the children (7–9 years old), 32% and 22% had at least one tooth with MIH or HSPM, respectively. A significant association was found between insufficient maternal vitamin D measured in gestational weeks 18–22 and the number of affected teeth among those with MIH at 7–9 years (adjusted RR = 1.82, 95% CI 1.13–2.93). Conclusion Considering any limitations of the present study, it has been shown that insufficient maternal serum vitamin D at mid-pregnancy was associated with a higher number of affected teeth among the offspring with MIH at 7–9 years of age. Further prospective studies are needed to investigate whether this finding is replicable and to clarify the role of maternal vitamin D status during pregnancy and MIH, as well as HSPM, in children.

The study aimed to investigate associations between maternal vitamin D status during pregnancy and molar incisor hypomineralisation (MIH) and hypomineralised second primary molars (HSPM) among children.The study had a longitudinal design using prospectively collected data from 176 mother and child pairs. Mothers were initially recruited in a randomised controlled trial to assess a pregnancy exercise programme. Along with the 7-year follow-up, we invited the children to a dental examination. The exposure variable was maternal serum 25-hydroxyvitamin D in gestational weeks 18-22 and 32-36, categorised as insufficient ( 50 nmol/l) and sufficient (≥ 50 nmol/l). Negative binomial hurdle models were used to analyse potential associations between the exposure variables and MIH or HSPM. The models were adjusted for potential confounders.Among the children (7-9 years old), 32% and 22% had at least one tooth with MIH or HSPM, respectively. A significant association was found between insufficient maternal vitamin D measured in gestational weeks 18-22 and the number of affected teeth among those with MIH at 7-9 years (adjusted RR = 1.82, 95% CI 1.13-2.93).Considering any limitations of the present study, it has been shown that insufficient maternal serum vitamin D at mid-pregnancy was associated with a higher number of affected teeth among the offspring with MIH at 7-9 years of age. Further prospective studies are needed to investigate whether this finding is replicable and to clarify the role of maternal vitamin D status during pregnancy and MIH, as well as HSPM, in children.

Background Vitamin D insufficiency is common in pregnant women worldwide. Regular prenatal exercise is considered beneficial for maternal and fetal health. There is a knowledge gap regarding the impact of prenatal exercise on maternal vitamin D levels. The objective of this study was to investigate whether a prenatal exercise program influenced serum levels of total, free and bioavailable 25-hydroxyvitamin D (25(OH)D) and related parameters. This is a post hoc analysis of a randomized controlled trial with gestational diabetes as the primary outcome. Methods Healthy, pregnant women from two Norwegian cities (Trondheim and Stavanger) were randomly assigned to a 12-week moderate-intensity exercise program (Borg perceived rating scale 13–14) or standard prenatal care. The intervention group (n = 429) underwent exercise at least three times weekly; one supervised group training and two home based sessions. The controls (n = 426) received standard prenatal care, and exercising was not denied. Training diaries and group training was used to promote compliance and evaluate adherence. Serum levels of 25(OH)D, parathyroid hormone, calcium, phosphate, magnesium and vitamin D-binding protein were measured before (18–22 weeks′ gestation) and after the intervention (32–36 weeks′ gestation). Free and bioavailable 25(OH)D concentrations were calculated. Regression analysis of covariance (ANCOVA) was applied to assess the effect of the training regime on each substance with pre-intervention levels as covariates. In a second model, we also adjusted for study site and sampling month. Intention-to-treat principle was used. Results A total of 724 women completed the study. No between-group difference in serum 25(OH)D and related parameters was identified by ANCOVA using baseline serum levels as covariates. The second model revealed a between-group difference in levels of 25(OH)D (1.9, 95% CI 0.0 to 3.8 nmol/L; p = 0.048), free 25(OH)D (0.55, 95% CI 0.10 to 0.99 pmol/L; p = 0.017) and bioavailable 25(OH)D (0.15 95% CI 0.01 to 0.29 nmol/L; p = 0.036). No serious adverse events related to regular exercise were seen. Conclusion This study, a post hoc analysis, indicates that exercise may affect vitamin D status positively, and emphasizes that women with uncomplicated pregnancies should be encouraged to perform regular exercise. Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.

Our current knowledge of the different immune cells in neuroblastoma is based on in vitro and in vivo studies mainly focusing on a single cell type. Different studies have conveyed conflicting results and despite the use of anti-GD2 immunotherapy in the clinic, a comprehensive immune cell overview at the single-cell level is still missing and understanding the complete composition of immune cells neuroblastoma will be crucial for the development of novel immunotherapeutics against the disease. In this study, we performed single-cell RNA-sequencing on human neuroblastoma coupled with multiplex immunohistochemistry and survival analysis to provide a complete cellular and molecular immune cell landscape of human neuroblastoma. Further, we contrasted the neuroblastoma data with single-cell RNA-sequencing data from normal fetal adrenal gland to characterize cell-state changes from normal tissue to neuroblastoma. Our analysis revealed 27 immune cell subtypes including distinct subpopulations of myeloid, NK, B and T cells that were associated with a survival benefit. Multiple subtypes of B and NK cells, not seen in neuroblastoma before, were identified. We propose the presence of tertiary lymphoid structures and showed that Active NK cells correlated with improved survival. In contrast to adult cancers, we detected no difference in cytotoxicity and exhaustion score for cytotoxic T cells, nor Treg activity. However, we demonstrated an increase in inflammatory monocyte signature score from normal to tumor derived myeloid cells. Finally, we performed receptor-ligand interaction analysis between tumor, stroma and immune cells, where we highlight several interactions that we suggest for future studies of how to exploit immune cells as a therapeutic option in neuroblastoma. Our findings significantly broaden the understanding of the immune composition in neuroblastoma and provides a resource for the development of novel immunotherapeutics. Citation Format: Bronte Manouk Verhoeven, Shenglin Mei, Thale K. Olsen, Karin K. Gustafsson, Anders Valind, Axel Lindström, David G. Nord, Shahrzad S. Fard, Catharina Hagerling, Peter V. Kharchenko, Per Kogner, John I. Johnsen, Ninib Baryawno. The immune cell atlas of human neuroblastoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 6215.

Given the scarcity of data on diabetes prevalence and associated risk factors among women in rural Nepal, we aimed to examine this, using glycated hemoglobin (HbA1c) as a diagnostic tool. A cross-sectional survey addressing reproductive health and non-communicable diseases was conducted in 2012–2013 among non-pregnant, married women in Bolde, a rural district of Nepal. HbA1c ≥ 6.5% (48 mmol/mol) was used as diagnostic criterion for diabetes, a cut-off of 7.0% (53 mmol/mol) was used to increase the specificity. HbA1c was measured in 757 women (17–86 years). The prevalence of diabetes and prediabetes was 13.5% and 38.5%, respectively. When using 7.0% as a cut-off, the prevalence of diabetes was 5.8%. Aging, intake of instant noodles and milk and vegetarian food (ns) were associated with increased risk for diabetes. Waist circumference was higher among women with diabetes, although not significant. The women were uneducated (87.6%), and only 12% had heard about diabetes. In conclusion, we observed a higher prevalence of diabetes and prediabetes than anticipated among rural, Nepalese women. The increased risk was mainly attributed to dietary factors. In contrast to most previous studies in Nepal, we used HbA1c as diagnostic criterion.

Along with rich health-related metadata, medical images have been acquired for over 40,000 male and female UK Biobank participants, aged 44–82, since 2014. Phenotypes derived from these images, such as measurements of body composition from MRI, can reveal new links between genetics, cardiovascular disease, and metabolic conditions. In this work, six measurements of body composition and adipose tissues were automatically estimated by image-based, deep regression with ResNet50 neural networks from neck-to-knee body MRI. Despite the potential for high speed and accuracy, these networks produce no output segmentations that could indicate the reliability of individual measurements. The presented experiments therefore examine uncertainty quantification with mean-variance regression and ensembling to estimate individual measurement errors and thereby identify potential outliers, anomalies, and other failure cases automatically. In 10-fold cross-validation on data of about 8500 subjects, mean-variance regression and ensembling showed complementary benefits, reducing the mean absolute error across all predictions by 12%. Both improved the calibration of uncertainties and their ability to identify high prediction errors. With intra-class correlation coefficients (ICC) above 0.97, all targets except the liver fat content yielded relative measurement errors below 5%. Testing on another 1000 subjects showed consistent performance, and the method was finally deployed for inference to 30,000 subjects with missing reference values. The results indicate that deep regression ensembles could ultimately provide automated, uncertainty-aware measurements of body composition for more than 120,000 UK Biobank neck-to-knee body MRI that are to be acquired within the coming years.

Precarious manhood beliefs portray manhood, relative to womanhood, as a social status that is hard to earn, easy to lose, and proven via public action. Here, we present cross-cultural data on a brief measure of precarious manhood beliefs (the Precarious Manhood Beliefs scale [PMB]) that covaries meaningfully with other cross-culturally validated gender ideologies and with country-level indices of gender equality and human development. Using data from university samples in 62 countries across 13 world regions (N = 33,417), we demonstrate: (1) the psychometric isomorphism of the PMB (i.e., its comparability in meaning and statistical properties across the individual and country levels); (2) the PMB’s distinctness from, and associations with, ambivalent sexism and ambivalence toward men; and (3) associations of the PMB with nation-level gender equality and human development. Findings are discussed in terms of their statistical and theoretical implications for understanding widely-held beliefs about the precariousness of the male gender role. © The Author(s) 2021.

Aims Labour market marginalisation (LMM), i.e. severe problems in finding and keeping a job, is common among young adults with attention-deficit/hyperactivity disorder (ADHD). This study aimed to disentangle the extent of LMM as well as the heterogeneity in patterns of LMM among young adults with ADHD and what characterises those belonging to these distinct trajectories of LMM. Methods This population-based register study investigated all 6287 young adults, aged 22–29 years, who had their first primary or secondary diagnosis of ADHD in Sweden between 2006 and 2011. Group-based trajectory (GBT) models were used to estimate trajectories of LMM, conceptualised as both unemployment and work disability, 3 years before and 5 years after the year of an incident diagnosis of ADHD. Odds ratios (ORs) with 95% confidence intervals (CIs) for the association between individual characteristics and the trajectory groups of LMM were estimated by multinomial logistic regression. Results Six distinct trajectories of LMM were found: ‘increasing high’ (21% belonged to this trajectory group) with high levels of LMM throughout the study period, ‘rapidly increasing’ (19%), ‘moderately increasing’ (21%), ‘constant low’ (12%) with low levels of LMM throughout the study period, ‘moderately decreasing’ (14%) and finally ‘fluctuating’ (13%), following a reversed u-shaped curve. Individuals with the following characteristics had an increased probability of belonging to trajectory groups of increasing LMM: low educational level (moderately increasing: OR: 1.4; CI: 1.2–1.8, rapidly increasing: OR: 1.7; CI: 1.3–2.1, increasing high: OR: 2.9; CI: 2.3–3.6), single parents (moderately increasing: OR: 1.6; CI: 1.1–2.4, rapidly increasing: OR: 2.0; CI: 1.3–3.0), those born outside the European Union/the Nordic countries (rapidly increasing: OR: 1.7; CI: 1.1–2.5, increasing high: OR: 2.1; CI: 1.4–3.1), persons living in small cities/villages (moderately increasing: OR: 2.4; CI: 1.9–3.0, rapidly increasing: OR: 2.1; CI: 1.6–2.7, increasing high: OR: 2.6; CI: 2.0–3.3) and those with comorbid mental disorders, most pronounced regarding schizophrenia/psychoses (rapidly increasing: OR: 6.7; CI: 2.9–19.5, increasing high: OR: 12.8; CI: 5.5–37.0), autism spectrum disorders (rapidly increasing: OR: 4.6; CI: 3.1–7.1, increasing high: OR: 9.6; CI: 6.5–14.6), anxiety/stress-related disorders (moderately increasing: OR: 1.3; CI: 1.1–1.7, rapidly increasing: OR: 2.0; CI: 1.6–2.5, increasing high: OR: 1.8; CI: 1.5–2.3) and depression/bipolar disorder (moderately increasing: OR: 1.3; CI: 1.0–1.6, rapidly increasing: OR: 1.7; CI: 1.4–2.2, increasing high: OR: 1.5; CI: 1.2–1.9). Conclusions About 61% of young adults were characterised by increasing LMM after a diagnosis of ADHD. To avoid marginalisation, attention should especially be given to young adults diagnosed with ADHD with a low educational level, that are single parents and who are living outside big cities. Also, young adults with comorbid mental disorders should be monitored for LMM early in working life.

Accurate 3D object detection (3DOD) is crucial for safe navigation of complex environments by autonomous robots. Regressing accurate 3D bounding boxes in cluttered environments based on sparse LiDAR data is however a highly challenging problem. We address this task by exploring recent advances in conditional energy-based models (EBMs) for probabilistic regression. While methods employing EBMs for regression have demonstrated impressive performance on 2D object detection in images, these techniques are not directly applicable to 3D bounding boxes. In this work, we therefore design a differentiable pooling operator for 3D bounding boxes, serving as the core module of our EBM network. We further integrate this general approach into the state-of-the-art 3D object detector SA-SSD. On the KITTI dataset, our proposed approach consistently outperforms the SA-SSD baseline across all 3DOD metrics, demonstrating the potential of EBM-based regression for highly accurate 3DOD. Code is available at https://github.com/fregu856/ebms_3dod., Code is available at https://github.com/fregu856/ebms_3dod

This paper is directed towards the problem of learning nonlinear ARX models based on observed input-output data. In particular, our interest is in learning a conditional distribution of the current output based on a finite window of past inputs and outputs. To achieve this, we consider the use of so-called energy-based models, which have been developed in allied fields for learning unknown distributions based on data. This energy-based model relies on a general function to describe the distribution, and here we consider a deep neural network for this purpose. The primary benefit of this approach is that it is capable of learning both simple and highly complex noise models, which we demonstrate on simulated and experimental data.

Goblet cells (GCs) are specialized cells of the intestinal epithelium contributing critically to mucosal homeostasis. One of the functions of GCs is to produce and secrete MUC2, the mucin that forms the scaffold of the intestinal mucus layer coating the epithelium and separates the luminal pathogens and commensal microbiota from the host tissues. Although a variety of ion channels and transporters are thought to impact on MUC2 secretion, the specific cellular mechanisms that regulate GC function remain incompletely understood. Previously, we demonstrated that leucine-rich-repeat-containing protein 26 (LRRC26), a known regulatory subunit of the Ca2+-and voltage-activated K+channel (BK channel), localizes specifically to secretory cells within the intestinal tract. Here, utilizing a mouse model in which MUC2 is fluorescently tagged allowing visualization of single GCs in intact colonic crypts, we show that murine colonic GCs have functional LRRC26-associated BK channels. In the absence of LRRC26, BK channels are present in GCs, but are not activated at physiological conditions. In contrast, all tested MUC2-negative cells completely lacked BK channels. Moreover, LRRC26-associated BK channels underlie the BK channel contribution to the resting transepithelial current across mouse distal colonic mucosa. Genetic ablation of either LRRC26 or BK-pore forming α-subunit in mice results in a dramatically enhanced susceptibility to colitis induced by dextran sodium sulfate (DSS). These results demonstrate that normal potassium flux through LRRC26-associated BK channels in GCs has protective effects against colitis in mice.SignificanceA primary function of goblet cells (GCs) of the intestinal epithelium is to generate a protective mucus layer lining the intestinal lumen. GC dysfunction is linked to Inflammatory Bowel Disease (IBD). GC mucus secretion is thought to be dependent on contributions of an ensemble of anion and cation fluxes, although understanding remains limited. Here, it is shown in mouse colon that the Ca2+- and voltage-dependent BK-type K+channel, specifically in association with the LRRC26 regulatory subunit, plays a critical role in normal GC function, protecting mice against chemically-induced colitis. The results demonstrate that normal K+fluxes mediated by LRRC26-containing BK channels are required for normal GC function, potentially providing insights into the potential role of BK channels in IBD.

Allergic disorders, characterized by Th2 immune responses to environmental substances, are increasingly common in children in Western societies. Multiple studies indicate that breastfeeding, early complementary introduction of food allergens, and antibiotic avoidance in the first year of life reduces allergic outcomes in at-risk children. Why the benefit of these practices is restricted to early life is largely unknown. We identified a preweaning interval during which dietary antigens are assimilated by the colonic immune system. This interval is under maternal control via temporal changes in breast milk, coincides with an influx of naive T cells into the colon, and is followed by the development of a long-lived population of colonic peripherally derived Tregs (pTregs) that can be specific for dietary antigens encountered during this interval. Desynchronization of mothers and offspring produced durable deficits in these pTregs, impaired tolerance to dietary antigens introduced during and after this preweaning interval, and resulted in spontaneous Th2 responses. These effects could be rescued by pTregs from the periweaning colon or by Tregs generated in vitro using periweaning colonic antigen-presenting cells. These findings demonstrate that mothers and their offspring are synchronized for the development of a balanced immune system.

While deep neural networks have become the go-to approach in computer vision, the vast majority of these models fail to properly capture the uncertainty inherent in their predictions. Estimating this predictive uncertainty can be crucial, for example in automotive applications. In Bayesian deep learning, predictive uncertainty is commonly decomposed into the distinct types of aleatoric and epistemic uncertainty. The former can be estimated by letting a neural network output the parameters of a certain probability distribution. Epistemic uncertainty estimation is a more challenging problem, and while different scalable methods recently have emerged, no extensive comparison has been performed in a real-world setting. We therefore accept this task and propose a comprehensive evaluation framework for scalable epistemic uncertainty estimation methods in deep learning. Our proposed framework is specifically designed to test the robustness required in real-world computer vision applications. We also apply this framework to provide the first properly extensive and conclusive comparison of the two current state-of-the-art scalable methods: ensembling and MC-dropout. Our comparison demonstrates that ensembling consistently provides more reliable and practically useful uncertainty estimates. Code is available at https://github.com/fregu856/evaluating_bdl., Comment: CVPR Workshops 2020. Code is available at https://github.com/fregu856/evaluating_bdl

Objective To assess the association between levels of vitamin D and urinary incontinence (UI) in pregnancy. Design A cross‐sectional study. Secondary analysis of a randomised controlled trial. Setting Two university hospitals in Norway. Population A total of 851 healthy, pregnant women >18 years in gestational weeks 18–22 with a singleton live fetus. Methods Data on UI were collected from a questionnaire at inclusion and serum analysis of 25‐hydroxy vitamin D (25(OH)D) was performed. Univariable and multivariable logistic regression analyses were applied to study associations between exposure and outcomes. Main outcome measures Prevalence of self‐reported UI, stress (SUI) and urge (UUI) or mixed UI. Results In total, 230/851 (27%) of the participants were vitamin D insufficient (25(OH)D

The Visual Object Tracking challenge VOT2020 is the eighth annual tracker benchmarking activity organized by the VOT initiative. Results of 58 trackers are presented; many are state-of-the-art trackers published at major computer vision conferences or in journals in the recent years. The VOT2020 challenge was composed of five sub-challenges focusing on different tracking domains: (i) VOT-ST2020 challenge focused on short-term tracking in RGB, (ii) VOT-RT2020 challenge focused on “real-time” short-term tracking in RGB, (iii) VOT-LT2020 focused on long-term tracking namely coping with target disappearance and reappearance, (iv) VOT-RGBT2020 challenge focused on short-term tracking in RGB and thermal imagery and (v) VOT-RGBD2020 challenge focused on long-term tracking in RGB and depth imagery. Only the VOT-ST2020 datasets were refreshed. A significant novelty is introduction of a new VOT short-term tracking evaluation methodology, and introduction of segmentation ground truth in the VOT-ST2020 challenge – bounding boxes will no longer be used in the VOT-ST challenges. A new VOT Python toolkit that implements all these novelites was introduced. Performance of the tested trackers typically by far exceeds standard baselines. The source code for most of the trackers is publicly available from the VOT page. The dataset, the evaluation kit and the results are publicly available at the challenge website (http://votchallenge.net).

While deep learning-based classification is generally tackled using standardized approaches, a wide variety of techniques are employed for regression. In computer vision, one particularly popular such technique is that of confidence-based regression, which entails predicting a confidence value for each input-target pair (x, y). While this approach has demonstrated impressive results, it requires important task-dependent design choices, and the predicted confidences lack a natural probabilistic meaning. We address these issues by proposing a general and conceptually simple regression method with a clear probabilistic interpretation. In our proposed approach, we create an energy-based model of the conditional target density p(y|x), using a deep neural network to predict the un-normalized density from (x, y). This model of p(y|x) is trained by directly minimizing the associated negative log-likelihood, approximated using Monte Carlo sampling. We perform comprehensive experiments on four computer vision regression tasks. Our approach outperforms direct regression, as well as other probabilistic and confidence-based methods. Notably, our model achieves a \(2.2\%\) AP improvement over Faster-RCNN for object detection on the COCO dataset, and sets a new state-of-the-art on visual tracking when applied for bounding box estimation. In contrast to confidence-based methods, our approach is also shown to be directly applicable to more general tasks such as age and head-pose estimation. Code is available at https://github.com/fregu856/ebms_regression.

Background Assessing risk of Crohn’s disease (CD) recurrence following ileocolic resection (ICR) is necessary to optimize medical management and prevent long-term complications. This study aimed to identify noninvasive markers that could predict postoperative disease activity. Methods Inclusion criteria were a diagnosis of CD, first ICR, interval colonoscopy, and whole transcriptome array meeting quality control standards. Demographic and clinical data were obtained from the electronic medical record. RNA extraction and human transcriptome microarray were performed on noninflamed ileal margins from operative specimens. Clinical data and random forest were analyzed in R. Principal components analysis, hierarchical clustering, and pathway enrichment were performed in Partek. Results Sixty-five patients completed the study, and 5 were excluded from analysis due to extreme variability on whole transcriptome analysis. Unsupervised hierarchical clustering revealed that patients with an i0 Rutgeerts score generally segregated from all others. In anti-TNF-naïve patients, unsupervised hierarchical clustering revealed complete segregation of patients with an i0 score. Reduced escalation in therapy and continued mucosal remission, consistent with indolent disease, were seen in the 4 years following surgery. Random forest identified 30 transcripts differentiating i0 patients from the other groups. Pathway enrichment highlighted toll-like receptor, NOD-like receptor, and TNF signaling. This transcriptome signature did not identify i0 anti-TNF-exposed patients. However, anti-TNF-exposed patients with indolent postoperative courses were found to have a transcriptome signature distinct from those with aggressive disease. Conclusions Anti-TNF-naïve and -exposed patients have unique expression profiles at the time of surgery, which may offer predictive value in assessing the risk of nonrecurrence.

The intestinal lamina propria (LP) contains antigen‐presenting cells with features of dendritic cells and macrophages, collectively referred to as mononuclear phagocytes (MNPs). Association of MNPs with the epithelium is thought to play an important role in multiple facets of intestinal immunity including imprinting MNPs with the ability to induce IgA production, inducing the expression of gut homing molecules on T cells, facilitating the capture of luminal antigens and microbes, and subsequent immune responses in the mesenteric lymph node (MLN). However, the factors promoting this process in the steady state are largely unknown, and in vivo models to test and confirm the importance of LP‐MNP association with the epithelium for these outcomes are unexplored. Evaluation of epithelial expression of chemoattractants in mice where MNP–epithelial associations were impaired suggested CCL20 as a candidate promoting epithelial association. Expression of CCR6, the only known receptor for CCL20, was required for MNPs to associate with the epithelium. LP‐MNPs from CCR6−/− mice did not display defects in acquiring antigen and stimulating T‐cell responses in ex vivo assays or in responses to antigen administered systemically. However, LP‐MNPs from CCR6‐deficient mice were impaired at acquiring luminal and epithelial antigens, inducing IgA production in B cells, inducing immune responses in the MLN, and capturing and trafficking luminal commensal bacteria to the MLN. These findings identify a crucial role for CCR6 in promoting LP‐MNPs to associate with the intestinal epithelium in the steady state to perform multiple functions promoting gut immune homeostasis.

Bacterial translocation is defined as the passage of live bacteria from the gut lumen to distant sites. Gut commensal bacteria translocation has been attributed to ‘leakiness’, or ‘barrier breach’ of the intestinal epithelium, allowing live bacteria to cross an inappropriately permeable barrier and disseminate to distant sites. Alternatively, studies suggest dendritic cells directly capture luminal commensal bacteria and transport them to distant sites in the steady-state by extending dendrites between epithelial cells into the lumen. Recently we identified translocation of commensal gut bacteria following antibiotics was associated with the formation of goblet cell associated antigen passages (GAPs) in the colon and dependent upon goblet cells (GCs). The translocation of native gut commensal bacteria resulted in low-level inflammatory responses and potentiated mucosal damage in response to concurrent epithelial injury. Here we extend these observations and demonstrate properties of colonic GAPs and observations supporting their priority in the translocation of colonic commensal bacteria.

Background Food-induced anaphylaxis (FIA) is an IgE-dependent immune response that can affect multiple organs and lead to life-threatening complications. The processes by which food allergens cross the mucosal surface and are delivered to the subepithelial immune compartment to promote the clinical manifestations associated with food-triggered anaphylaxis are largely unexplored. Objective We sought to define the processes involved in the translocation of food allergens across the mucosal epithelial surface to the subepithelial immune compartment in FIA. Methods Two-photon confocal and immunofluorescence microscopy was used to visualize and trace food allergen passage in a murine model of FIA. A human colon cancer cell line, RNA silencing, and pharmacologic approaches were used to identify the molecular regulation of intestinal epithelial allergen uptake and translocation. Human intestinal organoid transplants were used to demonstrate the conservation of these molecular processes in human tissues. Results Food allergens are sampled by using small intestine (SI) epithelial secretory cells (termed secretory antigen passages [SAPs]) that are localized to the SI villous and crypt region. SAPs channel food allergens to lamina propria mucosal mast cells through an IL-13–CD38–cyclic adenosine diphosphate ribose (cADPR)–dependent process. Blockade of IL-13-induced CD38/cADPR-dependent SAP antigen passaging in mice inhibited induction of clinical manifestations of FIA. IL-13–CD38–cADPR–dependent SAP sampling of food allergens was conserved in human intestinal organoids. Conclusion We identify that SAPs are a mechanism by which food allergens are channeled across the SI epithelium mediated by the IL-13/CD38/cADPR pathway, regulate the onset of FIA reactions, and are conserved in human intestine.