Transcriptome Based Profiling of the Immune Cell Gene Signature in Rat Experimental Colitis and Human IBD Tissue Samples

Abstract

<jats:p>Chronic intestinal inflammation is characteristic of Inflammatory Bowel Disease (IBD) that is associated with the exaggerated infiltration of immune cells. A complex interplay of inflammatory mediators and different cell types in the colon are responsible for the maintenance of tissue homeostasis and affect pathological conditions. Gene expression alteration of colon biopsies from IBD patients and an in vivo rat model of colitis were examined by RNA-Seq and QPCR, while we used in silico methods, such as Ingenuity Pathway Analysis (IPA) application and the Immune Gene Signature (ImSig) package of R, to interpret whole transcriptome data and estimate immune cell composition of colon tissues. Transcriptome profiling of in vivo colitis model revealed the most significant activation of signaling pathways responsible for leukocyte recruitment and diapedesis. We observed significant alteration of genes related to glycosylation or sensing of danger signals and pro- and anti-inflammatory cytokines and chemokines, as well as adhesion molecules. We observed the elevated expression of genes that implies the accumulation of monocytes, macrophages, neutrophils and B cells in the inflamed colon tissue. In contrast, the rate of T-cells slightly decreased in the inflamed regions. Interestingly, natural killer and plasma cells do not show enrichment upon colon inflammation. In general, whole transcriptome analysis of the in vivo experimental model of colitis with subsequent bioinformatics analysis provided a better understanding of the dynamic changes in the colon tissue of IBD patients.</jats:p>

ACE2 in the Gut: The Center of the 2019-nCoV Infected Pathology

“…Additionally, the alterations in the number of lymphocytes within one organ may affect that in plasma, which could possibly cause physiological changes in others, as both 2019-nCoV and IBD patients show immune dysregulation characterized by elevated levels of neutrophils and inflammation markers ( Boros et al, 2020 ; Mehta et al, 2020 ). Similar changes have been observed in other organ diseases, such as Streptococcus pneumoniae infection and tubular injury ( Adams et al, 2020 ).…”

Global alteration of colonic microRNAome landscape associated with inflammatory bowel disease

“…Colonic biopsies were obtained from 21 consenting patients with IBD [13 females and 8 males; median age 41 years, 25-74 years (for more details see ( 24 )] undergoing colonoscopy for diagnostic purposes approved by Hungarian Medical Research Council (ETT) Medical Research Council’s Committee of Scientific and Research Ethics (TUKEB) (license number 59-32-PTE2015/IBD) as described previously ( 29 ). Human colonic biopsies were obtained in accordance with the guidelines set out by the Medical Research Council of Hungary.…”

“…In this work, we performed miRNA-Seq analysis of an in vivo rat model of IBD that we interpreted together with our previous whole transcriptome analysis data ( 24 ) to get insight into the complex regulatory network of transcriptional factors, miRNAs and their target genes. As model, we used the chemical irritant 2,4,6-trinitrobenzene sulfonic acid (TNBS) as a well-established rat model of IBD induction, allowing the analysis of various pathogenic factors ( 25 ).…”

Current Progress and Future Perspectives on the Use of Bacillus clausii

“…Ulcerative colitis is another disorder characterized by chronic inflammation due to immune dysregulation [61,73,74]. Mouse models in which colitis is induced by treatment with dextran sodium sulfate, can be used to study the gut microbiota alterations involved in colitis [61].…”