Introducing GATA3 as a prominent player in Crohn's disease

Sina Rezaei-Tavirani; Nastaran Asri; MohammadAli Emamhadi; Somayeh Jahani-Sherafat; Ali Seyed Salehi; Zahra Gholamrezaei; Elena Lak

Introducing GATA3 as a prominent player in Crohn's disease

Gastroenterol Hepatol Bed Bench. 2020 Winter;13(Suppl1):S53-S59.

Authors

Sina Rezaei-Tavirani¹, Nastaran Asri², MohammadAli Emamhadi³, Somayeh Jahani-Sherafat⁴, Ali Seyed Salehi⁵, Zahra Gholamrezaei², Elena Lak²

Affiliations

¹ Proteomics Research Center, Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
² Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
³ Forensic Medicine Department, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
⁴ Laser Application in Medical Sciences Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
⁵ Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran.

PMID: 33585004
PMCID: PMC7881413

Abstract

Aim: This study was aimed at gene assessment of Crohn's disease (CD) through protein-protein interaction (PPI) network analysis to find crucial genes.

Background: CD is a major subtype of inflammatory bowel diseases (IBD), which affects gastrointestinal tract. PPI network analysis is a suitable tool to clarify a critical gene as a drug target or diagnostic biomarker for these types of diseases.

Methods: Gene expression profile GSE126124 of 20 CD patients and 20 healthy controls was obtained from the Gene Expression Omnibus (GEO) database. RNA profile of peripheral blood mononuclear cells (PBMCs) and colon biopsy samples of the studied groups was investigated. Crucial genes were selected and analyzed via the PPI network by Cytoscape software. Gene ontology enrichment for the hubs, bottlenecks, and hub-bottlenecks was performed via CluGO plugin of Cytoscape software.

Results: Eighty-one differentially expressed genes (DEGs) among 250 initial DEGs were highlighted as significant by FC>2 and p-value ≤ 0.05, and 69 significant DEGs were used for PPI network construction. The network was characterized by poor connections, so 20 top neighbors were added to form a scale-free network. The main connected component included 39 query DEGs and 20 added first neighbors. Three clusters of biological processes associated with crucial genes were identified and discussed.

Conclusion: The results of this study indicated that GATA3 has a key role in CD pathogenesis and could be a possible drug target or diagnostic biomarker for Crohn's disease.

Keywords: Crohn’s disease; GATA3 transcription factor; Gene ontology; Genes.