Differentially expressed genes identified in the muscle of patients with polymyositis by microarray analysis

Objective To profile the differentially expressed genes in the muscle of polymyositis (PM) patients. Methods A mRNA microarray analysis was performed to profile mRNAs from 5 treatment-naive PM patients and 5 healthy controls. Gene Ontology and KEGG pathway analyses were applied to delineate the functional roles of the differentially expressed mRNAs. Quantitative real-time PCR analysis was conducted to validate the microarray data. The Student's t-test was used to analyze the statistical significance of the microarray results, and Benjamini-Hochberg FDR was used for multiple-test correction. Results Microarray analysis revealed that a total of 1 905 mRNAs (787 up-regulated and 1 118 down-regulated) were significantly differentially expressed in PM patients compared with the healthy controls (fold change>2, P<0.05). Six mRNAs were selected to analyze by quantitative RT-PCR to validate their expression levels and the results were consistent with that of the microarray analysis, and thus provide reliable validation for the microarray results. Gene ontology and KEGG pathway analysis for the differentially expressed mRNAs revealed that these genes were mainly involved in the biological process of infection and cytotoxic effect. In addition, there were some common signaling pathways that shared by PM and other autoimmune diseases. Conclusion There are differences in gene expressions between PM patients and healthy controls. The muscle damage in PM patients may be due to multi gene involvement and multi gene regulation. Key words: Polymyositis; Gene expresion; Microarray analytical procedures