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Representative H&E-stained sections of the small intestine illustrate villous blunting with normal and altered villi from the duodenum and ileum (×100, scale bar 100 μm). 

Representative H&E-stained sections of the small intestine illustrate villous blunting with normal and altered villi from the duodenum and ileum (×100, scale bar 100 μm). 

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Histomorphology remains a powerful routine evaluating intestinal inflammation in animal models. Emphasizing the focus of a given animal study, histopathology can overstate differences between established models. We aimed to systematize histopathological evaluation of intestinal inflammation in mouse models facilitating interstudy comparisons. Sampl...

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... interspersing in the epithelial cell layer of the crypt in terms of a cryptitis ( Figure 3A ) intensified to crypt abscesses where neu - trophils accumulate in the crypt lumen eventu- ally disrupting the crypt epithelium ( Figure 3B ). Erosions, i.e. the loss of surface epithelium with underlying inflammation where the epithe - lial defect reached the basement membrane presented itself mostly focal ( Figure 3C ). Scoring this feature especially depended upon the model used as indicated by the wide range of final score values ( Table 1 ). With a “first hit” from the outside erosion was even abundant at a value of 1 ( Table 2 ); erosion resulting from severe mucosal inflammation due to an inside event accompanied values of 4 ( Table 4 ). All changes reaching deeper than the surface epithelial cell layer were considered alterations in the overall mucosal architecture and graded from the presence of ulcerations, granulation tissue, irregular crypts or of crypt loss. Specifics like the ratio of villous length to crypt depth accounted for general anatomical differences along the whole small intestine ( Table 1 ). Ulcerations i.e. erosions exceeding to the sub- mucosa ( Figure 3D ) were occasionally covered by an exudate rich in iNOS + neutrophils ( Figure 3E ) or by granulocyte-fibrin eschar ( Figure 3F ). Connective tissue repair was the hallmark of granulation tissue underlying ulcerations ( Figure 3G ). It comprised new capillaries lined by CD31 + endothelial cells ( Figure 3H ), myofi - broblasts, iNOS + macrophages and neutrophils ( Figure 3I ) as well as lymphocytes and cell debris. Generally, crypt appearance throughout the intestine and the villous morphology within the small intestine defined a major level of mucosal architecture. Irregular crypts with vari- able diameters along the depth of single crypts or dilated crypts ( Figure 4A ), crypts that did not run parallel ( Figure 4B ), bifurcation at the base of the crypt ( Figure 4C , 4D ) that might extend to branched crypts ( Figure 4E ), to a mucosa com- pletely devoid of crypts ( Figure 4F , 4G ) or crypts herniated to the submucosa ( Figure 4H ) mar- ked mucosal histopathology. In the duodenum and jejunum, the villi are long with a villous-to- crypt length ratio on the order of 3:1 to 5:1, while in the ileum the villi are typically shorter ( Figure 5 ). Thus, progressive broadening and blunting of the villi up to complete loss of villous structures clearly indicated pathological chang- es. We found two degrees of villous blunting ( Figure 5 ) and villous atrophy sufficient to grade the severity. As for epithelial changes and the mucosal architecture, each model system had different key aspects regarding degree, quality, extent and depth that made overall generalization in terms of a single generalized scoring system using all criteria for each model not feasible. Our schemata propose maximum severity rated 4-5 from combined changes in all three catego- ries. Characteristic discontinuities in inflamma - tory cell infiltrates and intestinal architecture were best reflected by additive scores with a maximum of 6 or 8, relating to the well-estab- lished evaluation of DSS-induced colitis [11] . We methodically inspected widely used rele- vant murine IBD models according to the defined categories and criteria and suggested scoring schemata. Evaluating histomorphology from H&E stained sections grouped our models according to the initial step weakening the bar- rier rather than the exact nature of immune interactions in the whole processes of acute or chronic intestinal inflammation. “First hits” from the outside, the luminal side, induced his- topathological specifics that were comparable among each other but distinguishable from those models resulting from inside events, i.e. from imbalanced immune dispositions ( Table 2 , Supplementary Figure 1). Additionally, in line with representative tissue samples excised from the most affected organ, the most affected section should be ...
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... interspersing in the epithelial cell layer of the crypt in terms of a cryptitis ( Figure 3A ) intensified to crypt abscesses where neu - trophils accumulate in the crypt lumen eventu- ally disrupting the crypt epithelium ( Figure 3B ). Erosions, i.e. the loss of surface epithelium with underlying inflammation where the epithe - lial defect reached the basement membrane presented itself mostly focal ( Figure 3C ). Scoring this feature especially depended upon the model used as indicated by the wide range of final score values ( Table 1 ). With a “first hit” from the outside erosion was even abundant at a value of 1 ( Table 2 ); erosion resulting from severe mucosal inflammation due to an inside event accompanied values of 4 ( Table 4 ). All changes reaching deeper than the surface epithelial cell layer were considered alterations in the overall mucosal architecture and graded from the presence of ulcerations, granulation tissue, irregular crypts or of crypt loss. Specifics like the ratio of villous length to crypt depth accounted for general anatomical differences along the whole small intestine ( Table 1 ). Ulcerations i.e. erosions exceeding to the sub- mucosa ( Figure 3D ) were occasionally covered by an exudate rich in iNOS + neutrophils ( Figure 3E ) or by granulocyte-fibrin eschar ( Figure 3F ). Connective tissue repair was the hallmark of granulation tissue underlying ulcerations ( Figure 3G ). It comprised new capillaries lined by CD31 + endothelial cells ( Figure 3H ), myofi - broblasts, iNOS + macrophages and neutrophils ( Figure 3I ) as well as lymphocytes and cell debris. Generally, crypt appearance throughout the intestine and the villous morphology within the small intestine defined a major level of mucosal architecture. Irregular crypts with vari- able diameters along the depth of single crypts or dilated crypts ( Figure 4A ), crypts that did not run parallel ( Figure 4B ), bifurcation at the base of the crypt ( Figure 4C , 4D ) that might extend to branched crypts ( Figure 4E ), to a mucosa com- pletely devoid of crypts ( Figure 4F , 4G ) or crypts herniated to the submucosa ( Figure 4H ) mar- ked mucosal histopathology. In the duodenum and jejunum, the villi are long with a villous-to- crypt length ratio on the order of 3:1 to 5:1, while in the ileum the villi are typically shorter ( Figure 5 ). Thus, progressive broadening and blunting of the villi up to complete loss of villous structures clearly indicated pathological chang- es. We found two degrees of villous blunting ( Figure 5 ) and villous atrophy sufficient to grade the severity. As for epithelial changes and the mucosal architecture, each model system had different key aspects regarding degree, quality, extent and depth that made overall generalization in terms of a single generalized scoring system using all criteria for each model not feasible. Our schemata propose maximum severity rated 4-5 from combined changes in all three catego- ries. Characteristic discontinuities in inflamma - tory cell infiltrates and intestinal architecture were best reflected by additive scores with a maximum of 6 or 8, relating to the well-estab- lished evaluation of DSS-induced colitis [11] . We methodically inspected widely used rele- vant murine IBD models according to the defined categories and criteria and suggested scoring schemata. Evaluating histomorphology from H&E stained sections grouped our models according to the initial step weakening the bar- rier rather than the exact nature of immune interactions in the whole processes of acute or chronic intestinal inflammation. “First hits” from the outside, the luminal side, induced his- topathological specifics that were comparable among each other but distinguishable from those models resulting from inside events, i.e. from imbalanced immune dispositions ( Table 2 , Supplementary Figure 1). Additionally, in line with representative tissue samples excised from the most affected organ, the most affected section should be ...

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... After paraffin embedding, 5-μm-thick sections were cut and stained with H&E. Histological scoring was based on a previously described method (79). Briefly, H&E-stained cross sections of the descending colon tissue were scored microscopically in a blinded fashion on a scale from 0 to 4, based on the following histological criteria: 0, no change from normal tissue; 1, low level of inflammation with scattered infiltrating mononuclear cells (foci, 1 to 2); 2, moderate inflammation with multiple foci; 3, high level of inflammation with increased vascular density and marked wall thickening; and 4, maximal severity of inflammation with transmural leukocyte infiltration and loss of goblet cells. ...
... Next, quality-controlled samples were aligned to the human reference genome using the STAR aligner (78). Subsequently, featureCounts (79) was employed on the generated BAM files to produce a count table. This count table underwent further analysis using the DESeq2 (80) package in R. Additionally, KEGG pathway over-representation analysis was conducted separately for upregulated and downregulated genes, based on specific criteria (log2fold change <= -0.5 or >= 0.5 and a p-value less than 0.05), utilizing the clusterProfiler (81) package. ...
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... The pathological changes were assessed under an Olympus BX51 microscope (Olympus Life Science, Waltham, MA, USA). The intestinal histological inflammation score was determined as described by Erben et al. (2014) [43]. Briefly, the histopathological score evaluation included the sum of two scores: Score 1 (0-3 points), related to the inflammatory cell infiltration (mucosa; mucosa and submucosa; or transmural), and Score 2 (0-3 points), related to the intestinal architecture (focal erosions; erosions and focal ulcerations; or erosions with extended ulcerations). ...
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... The mounted sections were deparaffinized and stained with hematoxylin and eosin. The tissue sections were viewed and photographed at 20× and 100× using brightfield microscopy with a digital Keyence BZ-X microscope (Itaska, IL, USA) and scored with a previously designed scoring system for chemicalinduced colitis [35]. Briefly, a score of 1-3 is assigned based on the severity and extent of inflammatory cells within each tissue layer. ...
... Scoring system used for evaluation of colon histology. Reprinted/adapted with permission from Ref.[35]. Copyright 2014, IJCEP. ...
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... On day 8, mice were sacrificed and colons were collected for length measuring and H&E staining. The histological scoring scheme was based on the previous work (Table S5) [25]. ...
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Background Macrophages are key inflammatory immune cells that orchestrate the initiation and progression of autoimmune diseases. The characters of macrophage in diseases are determined by its phenotype in response to the local microenvironment. Ficolins have been confirmed as crucial contributors to autoimmune diseases, with Ficolin-2 being particularly elevated in patients with autoimmune diseases. However, whether Ficolin-A stimulates macrophage polarization is still poorly understood. Methods We investigated the transcriptomic expression profile of murine bone marrow-derived macrophages (BMDMs) stimulated with Ficolin-A using RNA-sequencing. To further confirm a distinct phenotype activated by Ficolin-A, quantitative RT-PCR and Luminex assay were performed in this study. Additionally, we assessed the activation of underlying cell signaling pathways triggered by Ficolin-A. Finally, the impact of Ficolin-A on macrophages were investigated in vivo through building Collagen-induced arthritis (CIA) and Dextran Sulfate Sodium Salt (DSS)-induced colitis mouse models with Fcna-/- mice. Results Ficolin-A activated macrophages into a pro-inflammatory phenotype distinct to LPS-, IFN-γ- and IFN-γ + LPS-induced phenotypes. The transcriptomic profile induced by Ficolin-A was primarily characterized by upregulation of interleukins, chemokines, iNOS, and Arginase 1, along with downregulation of CD86 and CD206, setting it apart from the M1 and M2 phenotypes. The activation effect of Ficolin-A on macrophages deteriorated the symptoms of CIA and DSS mouse models, and the deletion of Fcna significantly alleviated the severity of diseases in mice. Conclusion Our work used transcriptomic analysis by RNA-Seq to investigate the impact of Ficolin-A on macrophage polarization. Our findings demonstrate that Ficolin-A induces a novel pro-inflammatory phenotype distinct to the phenotypes activated by LPS, IFN-γ and IFN-γ + LPS on macrophages.
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... It was drained and embedded in paraffin and cut into sections (3 μm). The inflammation score with H&E staining was based on the method of Erben et al. (36). Briefly, the density of leukocytes in the lamina propria was classified as 1 (<10%), 2 (10-25%), 3 (26-50%), and 4 (>50%). ...
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Background Allergic Asthma is a disease presenting various endotypes and no current therapies act curative but alleviate disease symptoms. Dietary interventions are gaining increasing importance in regulating immune responses. Furthermore, short chain fatty acids (SFCA), as the main products of dietary fiber’s fermentation by the gut bacteria, ameliorate the pathogenesis and disease burden of different illnesses including asthma. Nevertheless, the connection and crosstalk between the gut and lung is poorly understood. Objective In this work, the role of high fiber diet on the development of allergic asthma at baseline and after exacerbation of disease induced by respiratory viruses was investigated. Methods Hereby, SCFA in serum of asthmatic and non-asthmatic pre-school children before and after airway disease symptoms were analyzed. Moreover, the effect of high fiber diet in vivo in a murine model of house dust mite extract (HDM) induced allergic asthma and in the end in isolated lung and spleen cells infected ex vivo with Rhinovirus was analyzed. Results In this study, a decrease of the SCFA 3-Hydroxybutyric acid in serum of asthmatic children after symptomatic episodes at convalescent visit as compared to asthmatic and control children at baseline visit was observed. In experimental asthma, in mice fed with high fiber diet, a reduced lung GATA3 + Th2 type mediated inflammation, mucus production and collagen deposition and expression of Fc epsilon receptor Ia (FcεRIa) in eosinophils was observed. By contrast, the CD8+ memory effector T cells were induced in the lungs of asthmatic mice fed with high fiber diet. Then, total lung cells from these asthmatic mice fed with either standard food or with fiber rich food were infected with RV ex vivo. Here, RV1b mRNA was found significantly reduced in the lung cells derived from fiber rich food fed mice as compared to those derived from standard food fed asthmatic mice. Looking for the mechanism, an increase in CD8+ T cells in RV infected spleen cells derived from fiber rich fed asthmatic mice, was observed. Conclusion Convalescent preschool asthmatic children after a symptomatic episode have less serum ß-Hydroxybutyric acid as compared to control and asthmatic children at baseline visit. Fiber rich diet associated with anti-inflammatory effects as well as anti-allergic effects by decreasing Type 2 and IgE mediated immune responses and inducing CD8+ memory effector T cells in a murine model of allergic asthma. Finally, ex vivo infection with Rhinovirus (RV) of total lung cells from asthmatic mice fed with fiber rich food led to a decreased RV load as compared to mice fed with standard food. Moreover, spleen cells derived from asthmatic mice fed with fiber rich food induced CD8+ T cells after ex vivo infection with RV. Clinical implications Dietary interventions with increased content in natural fibers like pectins would ameliorate asthma exacerbations. Moreover, respiratory infection in asthma downregulated SCFA in the gut contributing to asthma exacerbations.
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... A shorter colon length and increased colon weight are considered as hallmarks of experimental colitis [18,25]. Our results revealed a significant reduction in colon length in mice given 4% DSS compared to the mice given water whereas no change in colon length was observed in mice given 5% DSS ( Figure 2A). ...
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