Gene Network Analysis of Bone Marrow Mononuclear Cells Reveals Activation of Multiple Kinase Pathways in Human Systemic Lupus Erythematosus

Magdalene Nakou,George Bertsias,Ilias Stagakis,Dimitrios T Boumpas,Dimitrios Iliopoulos,George Goulielmos,Michael Centola,Maria Hatziapostolou,Ioannis Tassiulas,Iraklis Kritikos,Jacques Zimmer

doi:10.1371/journal.pone.0013351

Abstract

BackgroundGene profiling studies provide important information for key molecules relevant to a disease but are less informative of protein-protein interactions, post-translational modifications and regulation by targeted subcellular localization. Integration of genomic data and construction of functional gene networks may provide additional insights into complex diseases such as systemic lupus erythematosus (SLE).Methodology/Principal FindingsWe analyzed gene expression microarray data of bone marrow mononuclear cells (BMMCs) from 20 SLE patients (11 with active disease) and 10 controls. Gene networks were constructed using the bioinformatic tool Ingenuity Gene Network Analysis. In SLE patients, comparative analysis of BMMCs genes revealed a network with 19 central nodes as major gene regulators including ERK, JNK, and p38 MAP kinases, insulin, Ca2+ and STAT3. Comparison between active versus inactive SLE identified 30 central nodes associated with immune response, protein synthesis, and post-transcriptional modification. A high degree of identity between networks in active SLE and non-Hodgkin's lymphoma (NHL) patients was found, with overlapping central nodes including kinases (MAPK, ERK, JNK, PKC), transcription factors (NF-kappaB, STAT3), and insulin. In validation studies, western blot analysis in splenic B cells from 5-month-old NZB/NZW F1 lupus mice showed activation of STAT3, ITGB2, HSPB1, ERK, JNK, p38, and p32 kinases, and downregulation of FOXO3 and VDR compared to normal C57Bl/6 mice.Conclusions/SignificanceGene network analysis of lupus BMMCs identified central gene regulators implicated in disease pathogenesis which could represent targets of novel therapies in human SLE. The high similarity between active SLE and NHL networks provides a molecular basis for the reported association of the former with lymphoid malignancies.

Highlights

Gene profiling studies provide important information for key molecules relevant to a disease, they are less informative of protein-protein interactions, post-translational modifications and regulation by targeted subcellular localization
Expressed genes between systemic lupus erythematosus (SLE) patients and controls were organized into an interactome network using Ingenuity Pathway Analysis (IPA)
The differentially expressed genes derived from the microarray data constructed a gene network with 19 central nodes (Figure 1A)

Summary

Introduction

Gene profiling studies provide important information for key molecules relevant to a disease, they are less informative of protein-protein interactions, post-translational modifications and regulation by targeted subcellular localization. To identify the molecular mechanisms by which these genes lead to complex disease phenotypes, such as obesity, diabetes, osteoarthritis, multiple sclerosis, juvenile rheumatoid arthritis and other autoimmunse diseases [1,2,3,4], it is essential to integrate genomic data and construct functional gene networks that will be predictive of these diseases. By the use of microarrays in the peripheral blood or bone marrow, we and others have previously shown specific gene signatures that are involved in SLE and correlate with disease activity [5,6,7,8]. BM gene analysis differentiated SLE patients based on their disease activity and identified genes involved in apoptosis [5]. Integration of genomic data and construction of functional gene networks may provide additional insights into complex diseases such as systemic lupus erythematosus (SLE)

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Results

Conclusion