Population-based comparative analysis of differentially expressed genes between Kashin–Beck disease grades I and II

Abstract

Objectives: To identify the differences and similarities of differentially expressed genes in peripheral blood mononuclear cells (PBMCs) between Kashin–Beck disease (KBD) grades I and II.

Method: In total, 100 patients with KBD and 100 healthy controls were selected from a KBD endemic area and divided into 100 pairs of KBD vs. controls (50 pairs of patients with KBD grade I and healthy controls, 50 pairs of patients with KBD grade II and healthy controls). RNA was isolated from KBD PBMCs and healthy control PBMCs. Microarray analysis was conducted to identify differentially expressed genes in the different stages of KBD. The microarray data obtained were further confirmed using quantitative real-time polymerase chain reaction (qRT-PCR).

Results: In total, eight differentially expressed genes in KBD grade I and 69 differentially expressed genes in KBD grade II were identified. Among these genes, six common genes were differentially expressed in both stages of the disease. The expression ratios of four common genes differed significantly between KBD grades I and II. Based on the expression ratios of the four genes, linear discriminant analysis (LDA) correctly classified the KBD grade (I or II) with 81% accuracy.

Conclusions: The similarities and differences of differentially expressed genes in PBMCs of patients with different stages of KBD may play an important role in the pathogenesis of the early phase of KBD. Additionally, six common genes may be considered blood-based genetic biomarkers for the detection and treatment of KBD.

Acknowledgements

This work was supported by the Key Scientific and Technological Innovation Special Projects of Shaanxi 13115 of China (2009ZDKG-79) and the National Natural Science Foundation of China (81472924). We thank the Disease Control Centre of Yong-shou and Lin-you counties for support and cooperation in the collection of venous blood from patients and controls. We also thank S Wang, S He, C Wu, C Li, J Zheng, P Wang, and Y Wen for help in the laboratory experiments.

Supporting Information

Additional Supporting Information may be found in the online version of this article.

Table S1. General information of the participants included in the analysis.

Table S2. Characteristics of the patients with KBD and controls used for quantitative RT-PCR analysis.

Table S3. List of 69 differentially expressed genes in patients with KBD grade II.

Table S4. Results of linear discriminant analysis (LDA) with the expression ratio of common differentially expressed genes.

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