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Coeliac disease (CeD) is an immune-mediated disorder triggered by the ingestion of gluten and an as yet unidentified environmental factor in genetically predisposed individuals. The disease involves a major autoimmune component that primarily damages the intestinal mucosa; although, it also has systemic involvement. The Th1 inflammatory response is one of the main events leading to mucosal damage; although, enterocytes and the innate immune response also participate in the pathological mechanism. In this study, we performed an analysis of the gene expression profile of the intestinal mucosa of patients with active disease and compared it with that of patients who do not suffer from gluten-related disorders but report dyspeptic symptoms. This analysis identified 1781 differentially expressed (DE) genes, of which 872 were downregulated and 909 upregulated. Gene Ontology and pathway analysis indicated that the innate and adaptive immune response, in particular the Th1 pathway, are important pathogenetic mechanisms of CeD, while the key cytokines are IL27, IL21, IL2, IL1b, TNF, CSF2 and IL7, as well as type I (IFNA1, IFNA2) and type II (IFNG) interferons. Finally, the comparison between the DE genes identified in this study and those identified in our previous study in the intestinal mucosa of patients with non-celiac gluten sensitivity (NCGS) revealed a high degree of molecular overlap. About 30% of the genes dysregulated in NCGS, most of which are long non-coding RNAs, are also altered in CeD suggesting that these diseases may have a common root (dysregulated long non-coding RNAs) from which they develop towards an inflammatory phenotype of variable degree in the case of CeD and NCGS respectively.

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Background:Celiac disease is an autoimmune enteropathy which can present with patchy mucosal lesions.Therefore,the diagnosis of the disease requires histological evaluation of multiple site biopsies.Aims:To analyze the pathological characteristics of multiple site small intestinal biopsies in adult patients with celiac disease and provide reference for early identification and diagnosis of celiac disease.Methods:The pathological data of 22 adult patients who were newly diagnosed as having celiac disease at the People's Hospital of Xinjiang Uygur Autonomous Region from August 2019 to April 2022 were collected retrospectively.All patients were positive for serum anti-tissue transglutaminase antibody IgA,and biopsies of duodenal bulb,descending part of the duodenum and terminal ileum were obtained under endoscopy.Histological examination was performed by experienced pathologists according to the modified Marsh grading system.Results:The most common pathological grade of duodenal bulb(50.0%)and descending part of the duodenum(45.5%)was Marsh Ⅲc,while those of terminal ileum was Marsh Ⅲa(63.6%).All of the bulb biopsies,95.5%of the descending part and 72.7%of the terminal ileum biopsies showed characteristic histological changes of celiac disease.Mucosal pathology was patchy in 7 patients,of which one patient was duodenal bulb and terminal ileum involved,and 6 were duodenum involved only.Fifteen patients had diffuse small intestinal mucosal pathology involving duodenal bulb,descending part and terminal ileum,of which 4 patients showed concordant histology(the same Marsh grade in duodenal bulb,descending part and terminal ileum)and 11 patients showed discordant histology.In 18 patients(81.8%),duodenum was the only affected site or duodenum showed more serious mucosal lesions compared with terminal ileum.Conclusions:Adult celiac disease may affect the whole small intestine,and the mucosal involvement may be patchy,which highlights the importance of taking small intestinal biopsies from multiple sites repeatedly in the diagnostic work-up of celiac disease.

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BACKGROUND: Low-grade intestinal T-cell lymphoma (LGITL) is the most common intestinal neoplasm in cats. Differentiating LGITL from lymphoplasmacytic enteritis (LPE) is challenging because clinical signs, laboratory results, diagnostic imaging findings, histology, immunohistochemistry, and clonality features may overlap. OBJECTIVES: To evaluate possible discriminatory clinical, laboratory and ultrasonographic features to differentiate LGITL from LPE. ANIMALS: Twenty-two cats diagnosed with LGITL and 22 cats with LPE based upon histology, immunohistochemistry, and lymphoid clonality. METHODS: Prospective, cohort study. Cats presented with clinical signs consistent with LGITL or LPE were enrolled prospectively. All data contributing to the diagnostic evaluation was recorded. RESULTS: A 3-variable model (P < .001) consisting of male sex (P = .01), duration of clinical signs (P = .01), and polyphagia (P = .03) and a 2-variable model (P < .001) including a rounded jejunal lymph node (P < .001) and ultrasonographic abdominal effusion (P = .04) were both helpful to differentiate LGITL from LPE. CONCLUSIONS AND CLINICAL IMPORTANCE: Most clinical signs and laboratory results are similar between cats diagnosed with LGITL and LPE. However, male sex, a longer duration of clinical signs and polyphagia might help clinicians distinguish LGITL from LPE. On ultrasonography, a rounded jejunal lymph node, and the presence of (albeit small volume) abdominal effusion tended to be more prevalent in cats with LGITL. However, a definitive diagnosis requires comprehensive histopathologic and phenotypic assessment.

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BACKGROUND: Differentiation of low-grade intestinal T-cell lymphoma (LGITL) from lymphoplasmacytic enteritis (LPE) in cats is a diagnostic challenge for pathologists. OBJECTIVE: Characterize histologic, immunohistochemical, and molecular features of LGITL and LPE. ANIMALS: Forty-four client-owned cats, 22 diagnosed with LGITL and 22 with LPE. METHODS: Prospective, cohort study. Clinical suspicion of LGITL or LPE was based on persistent gastrointestinal signs, unresponsive to empirical treatments. All cats underwent a standardized diagnostic evaluation, including biopsy (preferentially full-thickness), and were diagnosed with LGITL or LPE after review of clinical, laboratory, sonographic, histologic, immunohistochemical, and clonality results. RESULTS: A monomorphic lymphocytic population (22/22, 100%) and in-depth mucosal infiltration (15/22, 68%) were hallmarks of LGITL. Epithelial patterns (nests and plaques) were significantly more frequent in LGITL (11/22, 50%) than in LPE (1/22, 5%) cases (P = .001). A CD3+ lymphocytic apical-to-basal gradient was observed in 9/22 (41%) of LGITL vs 1/22 (5%) of LPE cases (P = .004). Most LPE cases (17/18, 94%) featured marked fibrosis in the superficial part of the lamina propria. The Ki-67 20%- and 30%-thresholds discriminated between LGITL and LPE within both the epithelium (specificity >95%) and lamina propria (specificity >95%), respectively. All LGITL cases were CD3+ pSTAT3- and pSTAT5+. T-cell receptor gamma chain gene rearrangements indicated monoclonality in 86% of LGITL cases. Surprisingly, 70% of LPE cases featured monoclonality (40%) or monoclonality on a polyclonal background (30%). CONCLUSIONS AND CLINICAL IMPORTANCE: We identified new histologic, immunohistochemical, and clonality criteria to distinguish LGITL from LPE.

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BACKGROUND: In studies evaluating the microbiome, numerous factors can contribute to technical variability. These factors include DNA extraction methodology, sequencing protocols, and data analysis strategies. We sought to evaluate the impact these factors have on the results obtained when the sequence data are independently generated and analyzed by different laboratories. METHODS: To evaluate the effect of technical variability, we used human intestinal biopsy samples resected from individuals diagnosed with an inflammatory bowel disease (IBD), including Crohn's disease (n = 12) and ulcerative colitis (n = 10), and those without IBD (n = 10). Matched samples from each participant were sent to three laboratories and studied using independent protocols for DNA extraction, library preparation, targeted-amplicon sequencing of a 16S rRNA gene hypervariable region, and processing of sequence data. We looked at two measures of interest - Bray-Curtis PERMANOVA R 2 values and log2 fold-change estimates of the 25 most-abundant taxa - to assess variation in the results produced by each laboratory, as well the relative contribution to variation from the different extraction, sequencing, and analysis steps used to generate these measures. RESULTS: The R 2 values and estimated differential abundance associated with diagnosis were consistent across datasets that used different DNA extraction and sequencing protocols, and within datasets that pooled samples from multiple protocols; however, variability in bioinformatic processing of sequence data led to changes in R 2 values and inconsistencies in taxonomic assignment and abundance estimates. CONCLUSION: Although the contribution of DNA extraction and sequencing methods to variability were observable, we find that results can be robust to the various extraction and sequencing approaches used in our study. Differences in data processing methods have a larger impact on results, making comparison among studies less reliable and the combined analysis of bioinformatically processed samples nearly impossible. Our results highlight the importance of making raw sequence data available to facilitate combined and comparative analyses of published studies using common data processing protocols. Study methodologies should provide detailed data processing methods for validation, interpretability, reproducibility, and comparability.

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OBJECTIVES: Microscopic colitis (MC) is potentially induced by an inflammatory reaction to a luminal gut factor. The emerging pathogen Campylobacter concisus is associated with prolonged diarrhoea and subsequently increased risk of MC. We aimed to examine the prevalence of C. concisus in clinical samples from MC patients, analyse the subtypes collagenous colitis (CC) and lymphocytic colitis (LC), and characterise C. concisus isolates from MC patients by genomic sequencing. METHODS: Mucosal biopsies were collected by sigmoidoscopy in 55 MC patients (CC n = 34, LC n = 21). Saliva and faecal samples were also collected. A two-step cultivation method and PCR established C. concisus prevalence. Biopsy and faecal isolates were sequenced for genomic analysis. RESULTS: Cultivation revealed C. concisus in saliva 55/55, faeces 14/55 and biopsies 69/436, which was confirmed by PCR in faeces 28/55 and biopsies 215/430. Interestingly, biopsy prevalence was higher in CC patients than in LC patients both by cultivation (50/270 vs.19/166, p = .058) and by PCR (175/270 vs. 40/160, p < .0001). Long disease duration also affected biopsy prevalence both by cultivation 30/244 (<2 years) vs. 39/192 (>2 years) (p = .025) and by PCR 103/239 (<2 years) vs. 112/191 (>2 years) (p = .002). Genomic analysis on sixty biopsy and twenty faecal isolates revealed division into two clusters/genomospecies and a high presence of various, putative virulence genes (zot, exotoxin 9 and hcp). CONCLUSIONS: Campylobacter concisus was prevalent in MC patients. Interestingly, the biopsy prevalence differed in biopsies from CC and LC patients and with regard to disease duration. Further studies are needed to elucidate this possible association.

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