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Open AccessArticle

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

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Institute of Biochemistry, Biological Research Centre, 6726 Szeged, Hungary
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Department of Immunology and Biotechnology, University of Pécs, 7624 Pécs, Hungary
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Lymphoid Organogenesis Research Group, Szentágothai János Research Center, University of Pécs, 7624 Pécs, Hungary
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1st Department of Internal Medicine, Medical School, University of Pécs, 7624 Pécs, Hungary
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Department of Physiology, Anatomy and Neuroscience, University of Szeged, 6726 Szeged, Hungary
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Institute of Pediatrics and Pediatric Health Center, University of Szeged, 6720 Szeged, Hungary
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Seqomics Biotechnology Ltd., 6782 Mórahalom, Hungary
*
Author to whom correspondence should be addressed.
Biomolecules 2020, 10(7), 974; https://doi.org/10.3390/biom10070974
Received: 8 May 2020 / Revised: 9 June 2020 / Accepted: 27 June 2020 / Published: 29 June 2020
(This article belongs to the Section Molecular Biology)
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. View Full-Text
Keywords: inflammatory bowel disease (IBD); immune cell gene signature (ImSig); whole transcriptome analysis inflammatory bowel disease (IBD); immune cell gene signature (ImSig); whole transcriptome analysis
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Boros, É.; Prontvai, B.; Kellermayer, Z.; Balogh, P.; Sarlós, P.; Vincze, Á.; Varga, C.; Maróti, Z.; Bálint, B.; Nagy, I. Transcriptome Based Profiling of the Immune Cell Gene Signature in Rat Experimental Colitis and Human IBD Tissue Samples. Biomolecules 2020, 10, 974.

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