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RNA‐Seq data analysis identifies the comprehensive profile of in vivo interferon‐β‐stimulated genes in multiple sclerosis
Author(s) -
Satoh Junichi,
Takitani Mika,
Miyoshi Junko,
Kino Yoshihiro
Publication year - 2016
Publication title -
clinical and experimental neuroimmunology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.297
H-Index - 15
ISSN - 1759-1961
DOI - 10.1111/cen3.12268
Subject(s) - transcriptome , gene , interferon , biology , multiple sclerosis , pseudogene , in vivo , population , rna , rna seq , immune system , computational biology , immunology , genome , genetics , gene expression , medicine , environmental health
Objectives Interferon‐beta ( IFN β) is the most widely used drug for reducing the disease activity of multiple sclerosis ( MS ), although a considerable population of MS patients are refractory to IFN β. To establish personalized therapy for MS , the molecular mechanism underlying the therapeutic effects of IFN β in MS should be thoroughly characterized by aid of next‐generation sequencing technology. Methods To elucidate a comprehensive profile of in vivo IFN β‐stimulated genes (ISGs) in MS patients, we analyzed a RNA sequencing ( RNA ‐Seq) dataset numbered SRP 045500, composed of the genome‐wide transcriptome of whole blood and purified populations of CD 4 + T cells, B cells, and monocytes isolated from MS patients at the time‐point before and 24 h after the first treatment with IFN β1a. Results We identified a set of 914 in vivo ISGs, containing a number of non‐coding RNAs and pseudogenes, along with differential spliced genes in the whole blood of MS patients. The set of 914 ISGs were relevant to the molecular pathways defined as “interferon signaling” and “proteasome,” and were closely associated with gene ontology terms of antiviral and immune responses. We also identified 640, 653 and 1018 ISGs from CD 4 + T cells, B cells, and monocytes of MS patients receiving IFN β treatment, respectively, and extracted 95 genes shared among the three cell types as the core set of ISGs. They included 78 genes that might serve as the most consistent blood biomarkers for assessment of the immediate early in vivo response to IFN β treatment in MS . Conclusions RNA ‐Seq data analysis promotes us to characterize the comprehensive profile of in vivo ISGs in MS patients receiving IFN β treatment.