Common and specific signatures of gene expression and protein-protein interactions in autoimmune diseases

Genes Immun. 2013 Mar;14(2):67-82. doi: 10.1038/gene.2012.55. Epub 2012 Nov 29.

Abstract

The aim of this study is to understand intracellular regulatory mechanisms in peripheral blood mononuclear cells (PBMCs), which are either common to many autoimmune diseases or specific to some of them. We incorporated large-scale data such as protein-protein interactions, gene expression and demographical information of hundreds of patients and healthy subjects, related to six autoimmune diseases with available large-scale gene expression measurements: multiple sclerosis (MS), systemic lupus erythematosus (SLE), juvenile rheumatoid arthritis (JRA), Crohn's disease (CD), ulcerative colitis (UC) and type 1 diabetes (T1D). These data were analyzed concurrently by statistical and systems biology approaches tailored for this purpose. We found that chemokines such as CXCL1-3, 5, 6 and the interleukin (IL) IL8 tend to be differentially expressed in PBMCs of patients with the analyzed autoimmune diseases. In addition, the anti-apoptotic gene BCL3, interferon-γ (IFNG), and the vitamin D receptor (VDR) gene physically interact with significantly many genes that tend to be differentially expressed in PBMCs of patients with the analyzed autoimmune diseases. In general, similar cellular processes tend to be differentially expressed in PBMC in the analyzed autoimmune diseases. Specifically, the cellular processes related to cell proliferation (for example, epidermal growth factor, platelet-derived growth factor, nuclear factor-κB, Wnt/β-catenin signaling, stress-activated protein kinase c-Jun NH2-terminal kinase), inflammatory response (for example, interleukins IL2 and IL6, the cytokine granulocyte-macrophage colony-stimulating factor and the B-cell receptor), general signaling cascades (for example, mitogen-activated protein kinase, extracellular signal-regulated kinase, p38 and TRK) and apoptosis are activated in most of the analyzed autoimmune diseases. However, our results suggest that in each of the analyzed diseases, apoptosis and chemotaxis are activated via different subsignaling pathways. Analyses of the expression levels of dozens of genes and the protein-protein interactions among them demonstrated that CD and UC have relatively similar gene expression signatures, whereas the gene expression signatures of T1D and JRA relatively differ from the signatures of the other autoimmune diseases. These diseases are the only ones activated via the Fcɛ pathway. The relevant genes and pathways reported in this study are discussed at length, and may be helpful in the diagnoses and understanding of autoimmunity and/or specific autoimmune diseases.

MeSH terms

  • Apoptosis
  • Arthritis, Juvenile / immunology
  • Arthritis, Juvenile / metabolism
  • Autoimmune Diseases / genetics*
  • Autoimmune Diseases / immunology*
  • Autoimmune Diseases / metabolism
  • B-Cell Lymphoma 3 Protein
  • Cell Proliferation
  • Chemokine CXCL1 / biosynthesis
  • Chemokine CXCL5 / biosynthesis
  • Chemokine CXCL6 / biosynthesis
  • Chemokines, CXC / biosynthesis
  • Colitis, Ulcerative / genetics
  • Colitis, Ulcerative / immunology
  • Colitis, Ulcerative / metabolism
  • Crohn Disease / genetics
  • Crohn Disease / immunology
  • Crohn Disease / metabolism
  • Diabetes Mellitus, Type 1 / genetics
  • Diabetes Mellitus, Type 1 / immunology
  • Diabetes Mellitus, Type 1 / metabolism
  • Gene Expression
  • Humans
  • Inflammation
  • Interferon-gamma / metabolism
  • Interleukin-8 / biosynthesis
  • Leukocytes, Mononuclear / immunology*
  • Leukocytes, Mononuclear / metabolism
  • Lupus Erythematosus, Systemic / genetics
  • Lupus Erythematosus, Systemic / immunology
  • Lupus Erythematosus, Systemic / metabolism
  • MAP Kinase Signaling System
  • Mitogen-Activated Protein Kinases / metabolism
  • Multiple Sclerosis / genetics
  • Multiple Sclerosis / immunology
  • Multiple Sclerosis / metabolism
  • Protein Interaction Maps*
  • Proto-Oncogene Proteins / metabolism
  • Receptors, Calcitriol / metabolism
  • Receptors, IgE / immunology*
  • Signal Transduction
  • Transcription Factors / metabolism
  • Transcriptome*

Substances

  • B-Cell Lymphoma 3 Protein
  • BCL3 protein, human
  • CXCL1 protein, human
  • CXCL3 protein, human
  • CXCL5 protein, human
  • CXCL6 protein, human
  • Chemokine CXCL1
  • Chemokine CXCL5
  • Chemokine CXCL6
  • Chemokines, CXC
  • Interleukin-8
  • Proto-Oncogene Proteins
  • Receptors, Calcitriol
  • Receptors, IgE
  • Transcription Factors
  • Interferon-gamma
  • Mitogen-Activated Protein Kinases