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. 2016 Jun 3;11(6):e0156234.
doi: 10.1371/journal.pone.0156234. eCollection 2016.

Common Marker Genes Identified from Various Sample Types for Systemic Lupus Erythematosus

Peng-Fei Bing  1   2 , Wei Xia  1   2 , Lan Wang  1   2 , Yong-Hong Zhang  2 , Shu-Feng Lei  1   2 , Fei-Yan Deng  1   2
Affiliations

Common Marker Genes Identified from Various Sample Types for Systemic Lupus Erythematosus

Peng-Fei Bing et al. PLoS One. .

Abstract

Objective: Systemic lupus erythematosus (SLE) is a complex auto-immune disease. Gene expression studies have been conducted to identify SLE-related genes in various types of samples. It is unknown whether there are common marker genes significant for SLE but independent of sample types, which may have potentials for follow-up translational research. The aim of this study is to identify common marker genes across various sample types for SLE.

Methods: Based on four public microarray gene expression datasets for SLE covering three representative types of blood-born samples (monocyte; peripheral blood mononuclear cell, PBMC; whole blood), we utilized three statistics (fold-change, FC; t-test p value; false discovery rate adjusted p value) to scrutinize genes simultaneously regulated with SLE across various sample types. For common marker genes, we conducted the Gene Ontology enrichment analysis and Protein-Protein Interaction analysis to gain insights into their functions.

Results: We identified 10 common marker genes associated with SLE (IFI6, IFI27, IFI44L, OAS1, OAS2, EIF2AK2, PLSCR1, STAT1, RNASE2, and GSTO1). Significant up-regulation of IFI6, IFI27, and IFI44L with SLE was observed in all the studied sample types, though the FC was most striking in monocyte, compared with PBMC and whole blood (8.82-251.66 vs. 3.73-74.05 vs. 1.19-1.87). Eight of the above 10 genes, except RNASE2 and GSTO1, interact with each other and with known SLE susceptibility genes, participate in immune response, RNA and protein catabolism, and cell death.

Conclusion: Our data suggest that there exist common marker genes across various sample types for SLE. The 10 common marker genes, identified herein, deserve follow-up studies to dissert their potentials as diagnostic or therapeutic markers to predict SLE or treatment response.

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Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Fig 1
Fig 1. The Evidence View of Protein-Protein Interaction.
The PPI were analyzed using the STRING database 10. The predicted functional interaction network is shown in the evidence view where the different line colors represent different types of evidences for the association. The nodes inside the red polygon represent the common genes we identified in the present study.
Fig 2
Fig 2. Overview of Gene Expression for the Common Marker Genes in Various Immune Cell Subsets.
(A)The different bar colors represent different immune cell subsets. (B) The bar under the heatmap illustrates that the expression level increases gradually with the color changing from blue to red. The gene expression data was extracted from the ImmGen (available at http://www.immgen.org/). Two datasets were included in the ImmGen for the PLSCR1 gene. The Fig was processed on Dec 9, 2015.
See this image and copyright information in PMC

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