Boros, Éva and Prontvai, Bence and Kellermayer, Zoltán and Balogh, Péter and Sarlós, Patrícia and Vincze, Áron and Varga, Csaba and Bálint, Balázs and Nagy, István (2020) Transcriptome Based Profiling of the Immune Cell Gene Signature in Rat Experimental Colitis and Human IBD Tissue Samples. BIOMOLECULES, 10 (7). ISSN 2218-273X
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Abstract
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.
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| Additional Information: | Institute of Biochemistry, Biological Research Centre, Szeged, 6726, Hungary Department of Immunology and Biotechnology, University of Pécs, Pécs, 7624, Hungary Lymphoid Organogenesis Research Group, Szentágothai János Research Center, University of Pécs, Pécs, 7624, Hungary 1st Department of Internal Medicine, Medical School, University of Pécs, Pécs, 7624, Hungary Department of Physiology, Anatomy and Neuroscience, University of Szeged, Szeged, 6726, Hungary Institute of Pediatrics and Pediatric Health Center, University of Szeged, Szeged, 6720, Hungary Seqomics Biotechnology Ltd., Mórahalom, 6782, Hungary Export Date: 22 November 2020 Correspondence Address: Nagy, I.; Institute of Biochemistry, Biological Research Centre, Seqomics Biotechnology Ltd.Hungary; email: nagyi@baygen.hu Chemicals/CAS: alpha4 integrin, 355485-74-4; CD18 antigen, 172592-43-7; chemokine receptor CXCR4, 188900-71-2; endothelial leukocyte adhesion molecule 1, 128875-25-2; fucosyltransferase, 56626-18-7; gelatinase A, 146480-35-5; intercellular adhesion molecule 1, 126547-89-5; interleukin 8, 114308-91-7; L selectin, 126880-86-2; macrophage elastase; matrix metalloproteinase 14; trinitrobenzenesulfonic acid, 16655-63-3, 2508-19-2; tumor necrosis factor alpha induced protein 3; ubiquitin carboxyl terminal hydrolase 7; ubiquitin carboxyl terminal hydrolase CYLD Funding details: European Social Fund, ESF, NTP-NFTÖ-19-B-0076, A2-ELMH-12-0082 Funding details: European Commission, EC Funding details: GINOP-2.3.2-15-2016-00039 Funding text 1: Funding: This work was funded, in part, by a grant from the National Research, Development and Innovation Office (grant number GINOP-2.3.2-15-2016-00039). Éva Boros was funded by the European Union and the State of Hungary, co-financed by the European Social Fund in the framework of the ‘National Excellence Program’ (grant number A2-ELMH-12-0082) and supported by NTP-NFTÖ-19-B (grant number NTP-NFTÖ-19-B-0076). |
| Uncontrolled Keywords: | inflammatory bowel disease (IBD); immune cell gene signature (ImSig); whole transcriptome analysis; |
| Subjects: | R Medicine / orvostudomány > R1 Medicine (General) / orvostudomány általában > R850-854 Experimental medicine / kisérleti orvostudomány R Medicine / orvostudomány > RC Internal medicine / belgyógyászat |
| SWORD Depositor: | MTMT SWORD |
| Depositing User: | MTMT SWORD |
| Date Deposited: | 30 Nov 2020 10:54 |
| Last Modified: | 30 Nov 2020 10:54 |
| URI: | http://real.mtak.hu/id/eprint/117557 |
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