Galley Proof 30/08/2019; 13:49 File: hab–1-hab190393.tex; BOKCTP/ljl p. 1 Human Antibodies -1 (2019) 1–5 1 DOI 10.3233/HAB-190393 IOS Press Assessment the genes and molecular mechanisms of B cells activation through systems biology approaches Razieh Fatehi Department of Genetics and Molecular Biology, Isfahan University of Medical Sciences, Isfahan, Iran E-mail: razieh.fatehi@gmail.com Abstract. Two classes of T helper lymphocytes, Th1 and Th2 have different roles in B cell activation based on specific cytokines. To understand molecular mechanisms of B cell activation, the microarray dataset of B cells co-cultured with type 1 and 2 T helper, Be1 and Be2, were investigated. After quality assessment, using the GEO2R tool, the GSE84948 dataset was re-analyzed. Genes with adjusted p-value  0.05 were assumed as differentially expressed (DE). The protein-protein interaction (PPI) networks were constructed using CluePedia plugin of Cytoscape, and analyzed by NetworkAnalyzer tool and MCODE plugin. Using ClueGO plugin of Cytoscape software, gene ontology (GO) analysis was performed. The comparison of Be1 and Be2 cells with naive B cells revealed 8742 and 8748 DE genes, respectively. The topology analysis of PPI networks predicted central genes. Among these, Jak3, Actrt3, and Pik3cb genes were determined as crucial genes in Be1 network. Prkx, Smarca4, and Jak2 genes were defined crucial gene in Be2 PPI network. GO analysis with PPI networks genes resulted which most of the terms are related to immune system activation. In conclusion, we explored holistic methods for molecular assay of difference between B cell activation mechanisms with Th1 and Th2. Keywords: T-Lymphocytes, helper-Inducer, cytokines, microarray, protein interaction network, gene ontology 1. Introduction 1 Two major subtypes of T helper lymphocytes known 2 as type 1 and 2, (Th1) and (Th2), respectively [1]. Th1 3 cells response against intracellular parasites, whereas 4 Th2 cells cause to immune responses against extracel- 5 lular organisms. They secrete specific cytokines in re- 6 sponse to antigenic stimulation. Th1 cells produce in- 7 terleukin (IL)-2 and interferon (IFN)-g, while Th2 cells 8 produce IL-4, IL-5, IL-6, IL-10, and IL-13 [2,3]. Our 9 objective was to clear the difference of B cell activation 10 mechanisms into producing antibody secreting cells in 11 present Th1 or Th2. For this purpose, we used system 12 biology approaches to reach a comprehensive under- 13 standing of each process. We re-analyzed the microar- 14 ray expression profiling of activated B cells co-cultured 15 with Th1 and Th2. Be1 cells (B cells cultured with 16 Th1 cells) and Be2 cells (B cells cultured with Th2 17 cells) were compared with naive B cell. Beside func- 18 tional analysis, with protein-protein interaction (PPI) 19 network analysis, we identified novel genes related B 20 cell differentiation. 21 2. Methods 22 2.1. Microarray dataset analysis 23 The expression profile of GSE84948 microarray 24 dataset deposited by Rosenberg et al was extracted 25 from the Gene Expression Omnibus (GEO) NCBI 26 databases. The GSE84948 dataset which explores gene 27 expression profiles of B cells cultured with Th1 and 28 Th2 cells. The quality control assessment of microar- 29 ray data was calculated by unsupervised principle com- 30 ponent analysis (PCA) method using ggplot2 pack- 31 age of R software [4]. GEO2R web tool of GEO 32 was used to identify differentially expressed (DE) 33 ISSN 1093-2607/19/$35.00 c  2019 – IOS Press and the authors. All rights reserved uncorrected proof version