Gene Expression Profiling of the Response to Interferon Beta in Epstein-Barr-Transformed and Primary B Cells of Patients with Multiple Sclerosis

Abstract

The effects of interferon-beta (IFN-β), one of the key immunotherapies used in multiple sclerosis (MS), on peripheral blood leukocytes and T cells have been extensively studied. B cells are a less abundant leukocyte type, and accordingly less is known about the B cell-specific response to IFN-β. To identify gene expression changes and pathways induced by IFN-β in B cells, we studied the in vitro response of human Epstein Barr-transformed B cells (lymphoblast cell lines-LCLs), and validated our results in primary B cells. LCLs were derived from an MS patient repository. Whole genome expression analysis identified 115 genes that were more than two-fold differentially up-regulated following IFN-β exposure, with over 50 previously unrecognized as IFN-β response genes. Pathways analysis demonstrated that IFN-β affected LCLs in a similar manner to other cell types by activating known IFN-β canonical pathways. Additionally, IFN-β increased the expression of innate immune response genes, while down-regulating many B cell receptor pathway genes and genes involved in adaptive immune responses. Novel response genes identified herein, NEXN, DDX60L, IGFBP4, and HAPLN3, B cell receptor pathway genes, CD79B and SYK, and lymphocyte activation genes, LAG3 and IL27RA, were validated as IFN-β response genes in primary B cells. In this study new IFN-β response genes were identified in B cells, with possible implications to B cell-specific functions. The study's results emphasize the applicability of LCLs for studies of human B cell drug response. The usage of LCLs from patient-based repositories may facilitate future studies of drug response in MS and other immune-mediated disorders with a B cell component.

RNA‐Seq data analysis identifies the comprehensive profile of in vivo interferon‐β‐stimulated genes in multiple sclerosis

“…The present results also suggested the possibility that certain ISGs upregulated only in limited cell types are activated through cell type‐specific downstream signaling pathways after the immediate activation of common IFN signaling pathway. A recent microarray‐based gene expression study identified a panel of in vitro ISGs, such as NEXN, DDX60L, IGFBP4, HAPLN3, CD79B, SYK LAG3 and IL27RA in human Epstein–Barr virus‐transformed B cells . We identified NEXN, DDX60L, IGFBP4 and HAPLN3 as the set of in vivo ISGs in purified populations of B cells of IFNβ‐treated MS patients (Table S5).…”

DDX60L Is an Interferon-Stimulated Gene Product Restricting Hepatitis C Virus Replication in Cell Culture

“…It has yet only been part of some genome-wide siRNA screens on HIV host factors (59), nonalcoholic fatty liver disease (60), and childhood obesity (61) and was identified in a genome-wide association study as a biomarker for the antidepressant responses of selective serotonin reuptake inhibitors (62). DDX60L has also been recognized as an ISG product before in a study searching for genes induced by IFN-␤ in Epstein-Barr virus-infected multiple sclerosis patients (24). However, it was not included in two previous comprehensive functional analyses of potential effector proteins involved in the interferon response against HCV (6,15).…”

“…Previous studies have pointed to partially overlapping sets of genes mediating type I, type II, and type III IFN responses (6). In addition, DDX60L had been previously described as a type I IFN response gene, similar to DDX60 (24). Therefore, we were interested in whether DDX60L also significantly contributes to type I and type III IFN responses against HCV.…”

“…The most prominent ISG products among the DExD/H-box helicases family are the RIG-I-like helicases (RLH), which include RIG-I (DDX58) and melanoma differentiation-associated protein 5 (MDA5), two sensors of viral RNA molecules (21,22). In addition, DEAD box polypeptide 60 (DDX60) and its highly similar homolog DEAD box polypeptide 60-like (DDX60L) have recently been described to be ISG products as well (23,24). DDX60 and DDX60L are about 70% identical in their amino acid sequences, contain the same conserved DExD/H box domains, and likely have evolved from a gene duplication late in mammalian evolution (23).…”

Diverse Roles of DEAD/DEAH-Box Helicases in Innate Immunity and Diseases

“…DDX60L is likely to be highly specific in its antiviral functions, as it was unable to inhibit replication of hepatitis A virus, regardless of its similarity to HCV [71]. In addition, it is noteworthy to mention that DDX60L is also upregulated in IFN-β-treated EpsteinBarr-transformed B cells derived from multiple sclerosis patients [174].…”