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Introduction. Colon cancer (RCC) clinically manifests itself in the late stages, therefore, early diagnosis presents significant difficulties. There are many types of microorganisms in the human colon that form symbiosis with intestinal cells to maintain normal function. Аim of the study was to determine the composition of the parietal microflora of the colon under conditions of a tumor process and to assess the possibility of using these data in the diagnosis of colon cancer. Material and methods. The main group included 63 patients operated on for cancer (adenocarcinoma) of the left half of the colon (descending, sigmoid, rectosigmoid regions) with I T1-2N0M0, II T3-4aN0M0, III T1-2N1M0 stages of the tumor process. Among them are 32 men and 31 women aged 20 to 75 years (57.7 ± 3.8 years). In all patients, before hospitalization, the tumor was confirmed by colonoscopy followed by histological examination. The group of clinical comparison in the amount of 25 people consisted of patients with chronic hemorrhoids without exacerbation, who underwent colonoscopy. Material from the main group, biopsies of tumor tissue and visually unchanged colon mucosa, were taken intraoperatively during tumor removal. In patients of the clinical comparison group, the material was taken during the colonoscopy process. The composition of the intestinal microbiota was determined by a bacteriological method. Results and discussion. As a result of comparing the colon microbiota of cancer patients and the clinical comparison group, statistically significant differences in the quantitative composition of Lactobacillus spp., Bifidobacterium spp., Bacteroides spp., Clostridium spp., Enterococcus spp., Escherichia coli (typical), Escherichia coli (lactose-negative), Enterobacteriaceae, Staphylococcus spp. (CNS), Candida spp. It was established for the first time that Bifidobacterium spp., Enterococcus spp. and the age of the patient can be further used in the diagnosis of a malignant process. Conclusion. The created additive model can be used as an additional screening criterion in the early diagnosis of colon cancer.

Human intestinal spirochetosis (HIS) is a possible cause of chronic diarrhoea and affects mainly men who have sex with men (MSM) and people living with HIV. Diagnosis is based on colon biopsy, where spirochetes can be observed on the luminal surface, especially with the Warthin-Starry stain or similar silver stains. We conducted a retrospective descriptive study of all HIS cases diagnosed in two sexually transmitted infections (STI) centres in Barcelona from 2009 until 2018. The medical histories were reviewed to gather epidemiological, clinical, and diagnostic variables. Six patients were diagnosed with HIS. All the individuals were MSM, with a median age of 31.5 years (interquartile range [IQR] 29.5;49.25) and half of them were living with HIV. Five patients reported condomless anal intercourse and 4 patients had practised oro-anal sex previously. Concomitantly, two of them had rectal gonorrhoea, one had rectal Chlamydia trachomatis and none of them had syphilis. The predominant clinical symptom was diarrhoea (5 patients). All cases were diagnosed by a Warthin-Starry stain on a colon biopsy specimen, and mild inflammatory changes were found in 5 cases. Five patients were treated with metronidazole and one with benzathine penicillin G. Treatment was successful in all the patients. HIS should be considered in patients with chronic diarrhoea who report risky sexual practices and/or concomitant STI. HIS may also be sexually transmitted according to the context.

Summary Colorectal poorly differentiated neuroendocrine carcinomas (NECs) are typically associated with poor outcomes. The mechanisms of their aggressiveness are still being investigated. Microsatellite instability (MSI) has recently been found in colorectal NECs showing aberrant methylation of the MLH1 gene and is associated with improved prognosis. We present a 76-year-old lady with an ascending colon tumour showing features of a pT3 N0 R0, large cell NEC (LCNEC) following right hemicolectomy. The adjacent mucosa showed a sessile serrated lesion (SSL) with low-grade dysplasia. Immunohistochemistry showed loss of expression for MLH1 and PMS2 in both the LCNEC and dysplastic SSL. Molecular analysis indicated the sporadic nature of the MLH1 mismatch repair (MMR) protein-deficient status. Our patient did not receive adjuvant therapy and she is alive and disease-free after 34 months follow-up. This finding, similar to early-stage MMR-deficient colorectal adenocarcinoma, is likely practice-changing and will be critical in guiding the appropriate treatment pathway for these patients. We propose that testing of MMR status become routine for early-stage colorectal NECs. Learning points: Colorectal poorly differentiated neuroendocrine carcinomas (NECs) are known to be aggressive and typically associated with poor outcomes. A subset of colorectal NECs can display microsatellite instability (MSI) with mismatch repair (MMR) protein-deficient status. MMR-deficient colorectal NECs have been found to have a better prognosis compared with MMR-proficient NECs. MMR status can be detected using immunohistochemistry. Immunohistochemistry for MMR status is routinely performed for colorectal adenocarcinomas. Immunohistochemical expression of MMR protein and MSI analysis should be performed routinely for early-stage colorectal NECs in order to identify a subgroup of MMR-deficient NECs which are associated with a significantly more favourable prognosis.

Background Endoscopic and histological remission are important goals to achieve in patients with ulcerative colitis (UC). We aimed to define deep remission by assessing cellular architecture, expression of molecular markers and their correlation with endoscopic scores by using ultra-high-magnification endocytoscopy and histological indices Methods We conducted a prospective study enrolling 29 UC patients (18 males, mean age 41y) referred at a tertiary academic centre for assessing endoscopic remission (ER). All patients underwent colonoscopies with 520-fold magnification endocytoscope. The inflammatory activity was scored using the Mayo Endoscopic Score (MES). ER was defined as MES 0. To assess the grade of inflammation using ECS we set an ECS score (ECSS), whose parameters were summarized in table 1. Biopsies were taken targeting either the worst affected area of inflammation or the most representive area of ER and scored according to Nancy Histopatological Index (NHI) and Robarts Histopatological Index (RHI). Histological remission (HR) is defined as NHI≤1, and RHI≤3 without neutrophils in the epithelium and lamina propria.The correlation between ECSS and MES and with histological scores were determined. Soluble analytes relevant to inflammation were measured in serum and mucosal culture supernatants using Procartaplex Luminex assays and studied by Partial Least Square Discriminant Analysis (PLS-DA) and logistic model. Mucosal RNA sequencing and gene enrichment analysis (GO, KEGG) were performed to define differentially expressed genes/pathways. Results ECSS correlated strongly with RHI (r=0.89 [95%CI 0.51–0.98] and NHI (r=0.86 [95%CI 0.42–0.98] but poorly with MES (r=0.28 [95%CI-0.27–0.70]). We identified that BDNF, MIP-1α and sVCAM-1 predicted HR. Mucosal biopsy cultures also identified sVCAM-1 associated with healed mucosa. RNA-seq analysis identified genes expressed in colonic biopsies that discriminated between healed and non-healed mucosa and overlapped gene expression shared between ECSS, RHI or NHI defined healing. Based on PLS-DA, for healing vs. non healing comparison as defined by RHI, Nancy, Mayo and ECCS we found 32, 83, 127 and 60 differentially genes respectively. These included genes relevant to TGF-b signaling, macrophage recruitment into tissues, neutrophil and plasma cell function and tumour suppressor genes (Fig.1) A number of those identified were shared by MES and ECSS defined healing as well as histological criteria defined healing. Conclusion ECS may sit between endoscopy and histology but closer to the latter and identifies gene expression markers and pathways that are also detected by histology. *OMN,LJ,AA equal authors

In the present manuscript a case of a 61 years old man with a form of unclear colitis is reported. The patient presented to our hospital with history of prolonged diarrhea and consequent profound dehydration after treatment with an immunotherapeutic cycle with Rituximab for a B cell lymphoma. An endoscopic pan-colonic examination was performed and some intestinal randomized biopsies were done as to confirm the clinic hypothesis of a colitis, as to define its etiopathogenesis. Histopathological picture of the colon biopsy fragments suggested a diffuse colitis with ischemic aspects. Herein the involvement of rituximab in determining pancolitis is discussed.

Histopathological examination of tissue models is basic for the conclusion and reviewing of colon malignancy. In any case, the technique is subjective and prompts imperative intra/bury spectator distinction in the examination as it predominantly relies upon the graphical evaluation of histopathologists. Thus, a tried and true PC supported technique, which can naturally group harmful and ordinary colon tests are required; however, automating this strategy is demanding because of the nearness of exceptions. In this paper, a productive technique for identifying colon disease from biopsy tests which comprise of four imperative stages. DB-SCAN estimation to distinguish colon tumor from biopsy tests is presented in this paper. In the proposed approach, from the outset, the colon biopsy tests are preprocessed using DB-SCAN configuration to make a set of redundant localities in which groups or clusters are formed. At that point, the exceptions inside the bunched areas are created as a tree structure in light of the choice tree in which the anomalies are hubs, and the connection between hubs are delivered based on data about exceptions. At that point, entropy-based exception score calculation will be done on every hub of the tree. The Information picks up technique is utilized to figure the score for the exceptions. At long last, score based grouping is accomplished to order the ordinary or harmful cells. Experimental trials exhibit, the proposed strategy has better outcomes contrasted to existing strategies. It furthermore acclaims that the proposed procedure is adequate for the colon tumor identification process. The proposed strategy is executed on Matlab working platform and the investigations exhibit that the proposed technique has high accomplished high grouping precision contrasted and different strategies.

Background Crohn’s disease (CD) is characterized by a heterogeneous disease course and treatment response. There is a clinical need to identify CD patients at diagnosis who are at risk for developing a severe disease course. Patient stratification using state-of-the-art clinical, serological or genetic markers does not predict disease course sufficiently to facilitate clinical decision making. The current study aimed to investigate the additive predictive value of histopathological features at diagnosis to discriminate between patients with a long-term mild and severe disease course. Methods Diagnostic biopsies from treatment-naïve CD patients with mild or severe disease courses in the first 10 years after diagnosis (i.e. based on the number of quarterly flares) were reviewed by two senior gastrointestinal pathologists after developing a standardized form comprising 15 histopathological features related to acute and chronic inflammation. Multivariable logistic regression models were built to identify predictive features and compute receiver operating characteristics (ROC) curves. Model 1 included clinically relevant baseline characteristics (Montreal classification, smoking status and gender). Next, histopathological were added by applying two different model-building strategies (forward selection and purposeful selection algorithm)(Model 2). Prediction models were internally validated using bootstrapping to obtain optimism-corrected performance estimates. Results In total, 817 biopsies from 137 CD patients (64 mild disease course, 73 severe disease course) were included. Based on clinical baseline characteristics alone, disease course could only be moderately predicted (Model 1 Area under ROC (AUROC): 0.738 (optimism 0.018), 95%CI 0.65–0.83, sensitivity 83.6%, specificity 53.1%). When adding histopathological features, in colonic, but not ileal, biopsies a combination of (1) basal plasmacytosis, (2) severe lymphocyte and plasma cell infiltration in the lamina propria, (3) Paneth cell metaplasia and (4) absence of ulcers were identified and resulted in significantly better prediction of a severe disease course (Model 2 AUROC: 0.883 (optimism 0.033), 95%CI 0.82–0.94, sensitivity 80.4%, specificity 84.2%, model 2 vs. model 1 AUROC p = 0.001)[Figure 1]. Conclusion In this first study investigating the additive predictive value of multiple histopathological features in biopsies at CD diagnosis, we found that certain features of chronic inflammation in colonic biopsies contributed to prediction of a severe disease course, thereby presenting a novel approach to improve stratification and facilitate clinical decision making.

Background Intercellular communication is essential for growing and differentiating in multicellular organisms by transducing the signal from cell to cell. Despite its importance, the molecular background is less discovered due to the lack of data. This gap has started to be addressed with the appearance of single-cell omics approaches providing an insight among others into the gene expression of individual cells. Methods We have developed a method to predict and compare cell-cell signalling interactions using single-cell RNAseq data from colon biopsies. Transcriptomic data alone is not capable of connecting the cells, a reliable network resource is needed to mediate the signal via protein-protein interactions between the source and target cells. Here we used OmniPath - a resource providing not only intra- and intercellular interactions but also annotations of proteins involved in the interplay of cells - to reconstruct signalling networks. We examined intercellular communication among five cell-types (regulatory T cell, macrophage, dendritic cell, goblet cell and myofibroblast) in healthy colon and during Ulcerative Colitis. Results Our analysis shows that there are significant differences in the type of cell-cell communication (ligand-receptor connections, adherens junctions, etc.) between the healthy and Ulcerative Colitis (UC) conditions, and these differences lead to altered downstream effects in the signal receiving cell. In both conditions, the ligand-receptor and adhesion connections were overrepresented, however cell junctions were less abundant in UC. Regarding the communication among the five cell-types, in healthy condition, cells are tightly connected to dendritic cells while in diseased condition to regulatory T cells. Focusing on ligand-receptor interactions between myofibroblasts and regulatory T cells, our pipeline identified the MAPK, Toll-like receptor (TLR) 2/6 and TLR 7/8 pathways enriched downstream in healthy conditions. In contrast, TLR3 and TLR4 pathways were affected by the myofibroblast in Ulcerative Colitis. Conclusion We found key intercellular mechanisms leading to well-defined differential pathway activation profiles. We showed that in uninflamed UC condition myofibroblasts disrupt the anti-inflammatory effect of regulatory T cells. Our pipeline is able to predict and analyse cell-cell interactions and their downstream effects and to highlight the differences in healthy and diseased states.

Background Oncostatin M (OSM) may play an important role in Inflammatory Bowel Disease (IBD) pathogenesis. Specifically, both OSM and its receptor are upregulated in inflamed colonic regions of IBD patients, and high OSM expression has been associated with failure to respond to anti-TNF therapy. Our aim was to investigate the effect of OSM in fibrotic factors and chemokine expression on primary colonic subepithelial myofibroblasts (SEMFs) from healthy individuals (HI). Methods Primary SEMFs were isolated from endoscopically-obtained colonic biopsies from HI. SEMFs were stimulated with 1, 10, or 100ng/ml OSM for 6 hours, with or without pre-stimulation with 5ng/ml IL-1α plus 50ng/ml TNF-α for 24h. Total RNA was collected and mRNA transcripts for collagen type I, type III, fibronectin, and the chemokines CCL2, CXCL9, CXCL10 and CXCL11 were measured by reverse transcription quantitative PCR. Results Unstimulated SEMFs had a basal expression of collagen type I, III, fibronectin, CCL2, CXCL9, CXCL10 and CXCL11. OSM stimulation augmented chemokine mRNA expression in a dose-dependent manner (Table 1) but had no effect on fibrotic factors expression. Pre-stimulation of myofibroblasts with TNF-α and IL-1α resulted in augmented expression of collagens I and III and fibronectin, in addition to further increases in chemokine expression in response to subsequent stimulation by OSM (Table 2). Conclusion Our results show that stimulation with OSM induces fibrotic and chemokine responses by SEMFs. Our findings further support the hypothesis that SEMFs may play a key role in regulating chronic intestinal inflammation and response to biological therapy.

Background The histologic assessment of inflammatory bowel disease (IBD) relies on qualitative grading methods. Although widely accepted, these instruments are time consuming, require specialized training, and suffer from inter-rater disagreement. For these reasons there is a need for more consistent and less biased methods to assess IBD histology. Methods The algorithm was initially developed using hematoxylin and eosin (H&E) stained whole slide images of colon biopsies (238 ulcerative colitis [UC], 30 Crohn’s Disease [CD], and 28 endoscopically normal adjacent [ENA]). The first two stages implement convolutional neural networks (CNN) which segment 11 key anatomical features (Figure 1). The third stage extracts the features and models them for prediction. Results The first stage of the algorithm was validated on an independent test dataset by calculating the intersection-over-union (IoU) for the ground truth and prediction masks, resulting in a value of 0.97. A preliminary validation for stage 2 was performed by randomly selecting 30 unique biopsy sections from the test dataset and applying a 150um x 150um counting frame. An expert gastrointestinal pathologist confirmed correct cell identification by the algorithm for three of the primary inflammatory cell types: plasma cells, eosinophils, and neutrophils which resulted in a sensitivity/specificity of 0.76/0.99, 0.78/1.00, and 1.00/0.98 respectively. The final stage predicts RHI grades which could be directly compared to pathologist reads (Figure 2, 3, and 4). Conclusion This is the first study to demonstrate the value of machine learning to assess histologic activity in IBD. These methods lay the foundations for future work, and we believe stages 1 and 2 can be explored independently to statistically characterize the histologic changes of IBD, enabling the improvement of preexisting grading systems.

Background The gut-associated lymphoid tissue (GALT) is a major reservoir of HIV-1 established early in acute HIV-1 infection (AHI). Sampling tissue from GALT can provide information about viral reservoirs and immune responses but may be complicated during AHI for reasons such as high viral replication, CD4 T cell depletion and immune activation. Risk of adverse events (AEs) associated with research sigmoid colon biopsies was assessed in participants with AHI in Bangkok, Thailand. Methods Between 2009 and 2016, 170 biopsies collected from the sigmoid colon were performed during AHI and at follow-up visits (median 24 weeks post AHI diagnosis). Adverse event incidence was evaluated, as well as the associations of procedure timing, repetition and clinical parameters with AE risk. Negative binomial regression models were used to calculate incidence rate ratios and 95% confidence intervals. Results Among 103 participants (median age of 27 years, 97.1% male, 96.1% men who have sex with men), 87 sigmoidoscopies were completed during AHI and 83 at a follow-up visit. Approximately 30 biopsies were obtained per procedure for assessment of colonic viral load and HIV-1 reservoir, immunohistochemistry or phenotypic assays. All 11 AEs were grade 1 (6.5%) and included abdominal discomfort (n = 5, 2.9%), mild rectal bleeding (n = 5, 2.9%) and difficulty passing stool (n = 1, 0.6%). Biopsy-related AE risk was not significantly associated with age, HIV-1 RNA, CD4 T cell count, or number and time of biopsy. Conclusions Complications of sigmoidoscopy with biopsy in participants with AHI were infrequent and mild. Longitudinal sampling of the sigmoid colon to evaluate the gut-associated HIV-1 reservoir can be safely performed as part of research studies.

Background: The clinical importance of microscopic colitis (MC) is increasing. This is explained by both the increasing incidence and the challenges posed by the disease. However, recent MC data also reveal a number of doubts and uncertainties. Summary: This review focuses on current knowledge of MC and highlights the various controversies and criticisms regarding the clinical data about definitions, subtypes, pathogenesis, diagnosis, and treatment of this condition. Key Messages: The diagnosis of MC is based on histology, which distinguishes 2 subtypes. However, transitional forms often cause misclassification, which calls into question the reality (specificity, meaning) of the distinction between the 2 forms. The location of the colon biopsy is not defined by international consensus. There is no credible, clear explanation for the incidence increase. The pathogenesis is unknown, probably multifactorial, but the importance of the immunological background is increasing. The natural history of the disease and the underlying cause of relapses are unclear. It is suggested that MC would be the prelude of IBD. Further data collection is needed to clarify these issues.

Background: Checkpoint inhibitor-induced colitis (CIC) is a severe side-effect of immune-checkpoint inhibitors (ICI). Its pathophysiology is poorly understood, impairing improvement of prevention and treatment strategies. CD4+ and CD8+ T cells and CD68+ macrophages are thought to be critical in colitis development. Studies suggest that CIC is histopathologically similar to inflammatory bowel disease (IBD) and acute graft-versus-host disease (aGVHD) colitis. However, the histopathology of these entities has not been directly compared. We aimed to improve knowledge on CIC by performing a direct immunohistochemical comparison of CIC, IBD and aGVHD. Methods: Archival formalin fixed paraffin-embedded colon biopsies obtained during routine diagnostic procedures from consecutive, eligible, treatment-naïve patients with CIC, IBD and aGVHD (all n=20) were studied. Biopsies from patients without histopathological abnormalities served as controls (n=20). Immunohistochemical staining was performed for CD4+ and CD8+ T cells and CD68+ macrophages. In each biopsy 3 mucosal areas with highest immune cell density were selected for cell counting. The number of cells/hotspot were classified as 0-10, 10-50, 50-100, 100-150 and >150. Next, the distribution of these cells was studied and compared between patient groups. We used descriptive statistics to depict and compare cell counts and infiltration patterns among patient groups. Results: In CIC higher CD4+ and CD8+ T cell density (100-150 cells/hotspot in most patients) was observed compared to IBD, aGVHD and controls (50-100 cells/hotspot in most patients in each group). In contrast to controls, some IBD (12%) and aGVHD (15%) patients had a CD4+ T cell count of 100-150 cells/hotspot and some IBD (20%) and aGVHD (21%) patients had a CD8+ T cell count of 100-150 cells/hotspot. CIC, IBD aGVHD and controls shared a similar CD68+ macrophage count (50-100 cells/hotspot in most patients in each group). During cell counting we noted that cells infiltrated the superficial (subepithelium) and deep (lamina propria and muscularis mucosae) layers of the mucosa with either a scattered or patchy distribution. We recognized 4 distribution patterns: A) superficial diffuse, deep scattered/patchy; B) superficial scattered/patchy, deep diffuse; C) superficial and deep diffuse; D) superficial and deep scattered/patchy. The most prevalent infiltration pattern of CD4+ T cells was D in CIC patients (74%), C in IBD patients (47%), B in aGVHD patients (54%) and A in control patients (83%). The most prevalent infiltration pattern of CD8+ T cells was D in CIC (45%), and A in IBD (85%), aGVHD (63%) and all control patients. In most patients, CD68+ macrophages occurred in pattern A (56% of CIC, 58% of IBD, 59% of aGVHD, 100% of controls). Conclusion: CIC has a distinct immunohistopathological pattern that shares key elements with both IBD and aGVHD.

Background: Checkpoint inhibitor-induced colitis (CIC) is a severe side-effect of immune-checkpoint inhibitors (ICI). Its pathophysiology is poorly understood, impairing improvement of prevention and treatment strategies. CD4+ and CD8+ T cells and CD68+ macrophages are thought to be critical in colitis development. Studies suggest that CIC is histopathologically similar to inflammatory bowel disease (IBD) and acute graft-versus-host disease (aGVHD) colitis. However, the histopathology of these entities has not been directly compared. We aimed to improve knowledge on CIC by performing a direct immunohistochemical comparison of CIC, IBD and aGVHD. Methods: Archival formalin fixed paraffin-embedded colon biopsies obtained during routine diagnostic procedures from consecutive, eligible, treatment-naïve patients with CIC, IBD and aGVHD (all n=20) were studied. Biopsies from patients without histopathological abnormalities served as controls (n=20). Immunohistochemical staining was performed for CD4+ and CD8+ T cells and CD68+ macrophages. In each biopsy 3 mucosal areas with highest immune cell density were selected for cell counting. The number of cells/hotspot were classified as 0-10, 10-50, 50-100, 100-150 and >150. Next, the distribution of these cells was studied and compared between patient groups. We used descriptive statistics to depict and compare cell counts and infiltration patterns among patient groups. Results: In CIC higher CD4+ and CD8+ T cell density (100-150 cells/hotspot in most patients) was observed compared to IBD, aGVHD and controls (50-100 cells/hotspot in most patients in each group). In contrast to controls, some IBD (12%) and aGVHD (15%) patients had a CD4+ T cell count of 100-150 cells/hotspot and some IBD (20%) and aGVHD (21%) patients had a CD8+ T cell count of 100-150 cells/hotspot. CIC, IBD aGVHD and controls shared a similar CD68+ macrophage count (50-100 cells/hotspot in most patients in each group). During cell counting we noted that cells infiltrated the superficial (subepithelium) and deep (lamina propria and muscularis mucosae) layers of the mucosa with either a scattered or patchy distribution. We recognized 4 distribution patterns: A) superficial diffuse, deep scattered/patchy; B) superficial scattered/patchy, deep diffuse; C) superficial and deep diffuse; D) superficial and deep scattered/patchy. The most prevalent infiltration pattern of CD4+ T cells was D in CIC patients (74%), C in IBD patients (47%), B in aGVHD patients (54%) and A in control patients (83%). The most prevalent infiltration pattern of CD8+ T cells was D in CIC (45%), and A in IBD (85%), aGVHD (63%) and all control patients. In most patients, CD68+ macrophages occurred in pattern A (56% of CIC, 58% of IBD, 59% of aGVHD, 100% of controls). Conclusion: CIC has a distinct immunohistopathological pattern that shares key elements with both IBD and aGVHD.

Adequate interpretation of colon biopsies forms a vital pillar in colon diseases. It aids in establishing the diagnosis of colitis, noting the severity and extent of inflammation and follow the course of the diseases. This review aims at classifying major forms of colitis also with approach to cases of colon biopsies.

Background Single-cell RNA sequencing (sc-RNAseq) provides high-resolution analysis of individual cells and cell clusters within complex tissues like the intestinal mucosa. No study to date has applied this novel technology to understand the complexity of intestinal inflammation in Crohn’s disease (CD) patients. Our aim is to identify the cellular subsets present in healthy and inflamed colon, and to describe how individual subsets are regulated in active CD. Methods Colon biopsies from a healthy control (HC) and two patients with endoscopically active colonic CD were collected and processed by enzymatic digestion and cell sorting to discard dead cells. Single-cell suspensions were processed by droplet-based protocol 10× chromium system followed by library preparation and sequencing. Sequencing data were aligned and quantified using Cell Ranger. Downstream analysis was performed using the R package Seurat. Results scRNA-seq analysis identified 14 transcriptionally different cell subsets in the healthy colon, including diverse types of T cells, plasma cells, mesenchymal cells, epithelial cells and myeloid populations, as well as a subset of MHCII+ CD20+ B cells. Overall, the number of transcriptionally differentiated cellular subsets was greater (16 and 17 subsets per sample) in the two CD colonic samples revealing higher cellular heterogeneity in active CD. In particular, in the HC we identified three T-cell subsets including a CD4+, CD8+ and a smaller subset of intraepithelial lymphocytes. In contrast, samples from CD patients presented four to six clearly differentiated T-cell clusters depending on the patient, with a marked enrichment of cytotoxicity genes (GZMA, GZMB, NKG7, CCL5 and AOAH) and T-regulatory genes (FOXP3, CTLA4, BATF and IL2RA). In addition, the HC sample presented three differentiated subsets of antibody-secreting plasma cells with predominant IgA and IgM production. In contrast, a clear expansion of IgG-producing plasma cells was observed in both CD patients. Moreover, the profiles of specific subsets significantly changed revealing transcriptional regulation within the individual subsets. Specifically, macrophages within the HC mucosa expressed the M2 markers CD163 and CD209 together with a whole signature of 163 additional genes, while in CD, they lost expression of these markers and upregulated CXCL8 and IL1B which were co-expressed with 268 additional genes common to macrophage populations in both CD patients. Conclusion We show that sc-RNAseq can be applied to study at a high cellular resolution human intestinal biopsies. Understanding the transcriptomic profile of the CD-related subsets will help dissect disease pathophysiology and provide knowledge for therapeutic targets.

Hirschsprung disease is one of the most important and difficult problems in pediatric surgery. The aim of our study was to determine the level of colon agangliosis in surgical treatment of Hirschsprung’s disease. During the histological examination of colon biopsy specimens, not only the presence and sufficient number of ganglia per unit area (more than 40 per square mm) was determined, but also their size, degree of maturity, and the presence of structural changes in the ganglionic cells.

Colon Cancer detection is an important task for the histopathologist as they have to analyze morphology of the images at different magnifications thereby leading to intra and inter observer variability. Thus an automation is needed to detect the colon cancer for all the magnifications. This paper focus on the colon cancer detection on the colon biopsy images at different magnifications. First the images are converted to its HSV color space and further processing are performed on the saturation component. Features are the coefficients obtained from Dual-tree and double-density 2-D wavelet transform. In the last phase classification is performed with the Random Forest classifier. The proposed system was evaluated on colon biopsy images collected from Aster Medcity at different magnifications 10X, 20X, 40X and combined magnifications where an accuracy of 85.4% is obtained for the combined magnifications.

AIMS: Giardia duodenalis is a diarrheagenic parasite of the small intestine characterized by acute and chronic illnesses including irritable bowel syndrome. MUC5AC mucin in the stomach and MUC2 in the intestine are normally protective against pathogens. We hypothesized that Giardia is able to disrupt this barrier by several mechanisms that may contribute to both acute and chronic disease. METHODS: Muc2(-/-) (KO-inf) and C57BL/6 (WT-inf) mice were gavaged with Giardia trophozoites and euthanized on day 7. Tissues were collected for histological staining, qPCR, and analysis of bacterial translocation. Human colonic biopsies were exposed to Giardia trophozoites to quantify intracellular mucins. In vitro, Giardia trophozoites were incubated with or without a cysteine protease inhibitor, E64, then with a human mucus-producing cell line, LS174T, to assess intracellular mucin content and MUC2 transcription. Giardia’s secreted products were incubated with purified human MUC2 to assess proteolysis via western blot. RESULTS: KO-inf mice had a higher parasitic load compared to WT-inf mice and failed to gain weight over the period of infection. Compared to non-infected mice, WT-inf mice exhibited novel transcription of Muc5ac and decreased transcription of Muc2 in the jejunum. Both Muc2 and Muc5ac mRNA were increased in the colon. Of note, Muc5ac transcription was not induced in KO mice. WT-inf mice had larger colonic mucus granules but a thinner mucus layer, demonstrated by staining with periodic-acid Schiff/Alcian blue, wheat germ agglutinin, and with the use of microbiota markers using fluorescent in situ hybridization. Infected mice had increased aerobic and anaerobic bacterial translocation into the liver and spleen. In vitro, Giardia’s secreted products degraded human MUC2. This was attenuated by E64. Human biopsies exposed to Giardia had less intracellular mucus granule content. Giardia reduced intracellular mucin content in LS174T cells after 20, 40, and 60 minutes post-infection (also inhibited by E64), whereas it increased mucin content by 3 hours post-infection. In vitro, Giardia infection increased Muc2 transcription after 1 hour. CONCLUSIONS: In mice, Muc2 was protective against parasite accumulation and induced weight loss, but Giardia disrupted the mucosal barrier function by reducing the mucus layer and causing an alteration of mucin gene transcription, specifically an increase of Muc5ac and a decrease of Muc2 in the jejunum. Proteolysis of MUC2 could be a potential mechanism by which Giardia alters barrier function in vivo. Resultant loss of the mucus barrier was associated with increased bacterial translocation and may contribute to both acute and chronic disease. Mucin degradation and depletion were attenuated by a cysteine protease inhibitor, indicating a potential target to reduce Giardia-induced pathology. FUNDING AGENCIES: CAGNSERC CREATE Host-Parasite Interactions

Acute colitis is often diagnosed on multidetector row computed tomography (MDCT) because patients with this condition present with abdominal pain and a variety of nonspecific symptoms. Acute colitis has multiple causes with varying degrees of severity. Analysis of the extent of colonic involvement, presence of specific MDCT imaging features and associated signs should help radiologist narrow the diagnosis. Integrating the results of clinical examination and biological tests is mandatory, and in case of ambiguous or nonspecific MDCT findings, endoscopy and colon biopsy should always be considered for a definite diagnosis. The purpose of this review is to discuss and illustrate MDCT features that are helpful for characterizing acute colitis in adults and to provide an update in current MDCT features.

This paper presents the identification of colon histology images as normal and malicious ones for the determination of colon cancer. Such classification is very difficult as it takes into account numerous characteristics such as color, several biological interpretable factors. Also this process is subjective and may have some observational variations. In this paper the colon biopsy images are classified as normal and malicious ones based on the texture of the images for the Indian population. Various texture features such as GLCM, LBP, HOG, Gabor, GLRLM, Histogram are extracted from the images with different magnification factors such as 10X, 20X and 40X. Based on these features extracted at different magnification factor, they are trained using classifiers SVM with linear kernel, Naive Bayes and Perceptron. The system has been experimented on 24 normal and 35 malignant biopsy images of colon that were acquired fom Aster Medcity, Kochi. SVM and Perceptron is giving higher accuracy for magnification 10X and 20X.