Elsevier

Gene

Volume 553, Issue 2, 15 December 2014, Pages 166-169
Gene

Trans-omics pathway analysis suggests that eQTLs contribute to chondrocyte apoptosis of Kashin–Beck disease through regulating apoptosis pathway expression

https://doi.org/10.1016/j.gene.2014.10.018Get rights and content

Highlights

  • We conducted a trans-omics pathway analysis of KBD.

  • 4 KBD associated pathways were abnormally expressed in KBD articular cartilage.

  • eQTL contributed to KBD chondrocyte apoptosis through regulating apoptosis pathway.

  • Integrating pathway association and expression analysis performed well.

Abstract

Kashin–Beck disease (KBD) is a serious osteoarthropathia, mainly characterized by excessive chondrocyte necrosis and apoptosis. The molecular signaling pathways underlying KBD excessive chondrocyte apoptosis remain unclear, leading to a lack of effective medical interventions now. To clarify whether expression quantitative trait loci (eQTLs) contribute to excessive chondrocyte apoptosis of Kashin–Beck disease through regulating the expression of apoptosis pathways. We conducted a genome-wide eQTLs based pathway association analysis of KBD using Affymetrix Human SNP Array 6.0 in 1717 Chinese Han subjects. PLINK software was used for genome-wide association study (GWAS) of KBD. A modified gene set enrichment algorithm was applied for pathway association analysis based on GWAS results. The KBD-associated pathways were compared with abnormally expressed pathways in KBD articular cartilage, identified by microarray study of KBD. We identified 4 eQTLs pathways, which were not only significantly associated with KBD, but also abnormally expressed in KBD articular cartilage, including REACTOME_INTRINSIC_PATHWAY_FOR_APOPTOSIS (P = 0.008), MAHAJAN _RESPONSE_TO_IL1A_UP (P = 0.010), KEGG_PEROXISOME (P = 0.005) and MARKS_HDAC_TARGETS_UP (P = 0.006). Our results suggest that eQTLs contributed to KBD excessive chondrocyte apoptosis through regulating the expression of apoptosis related pathways. This study provides novel insight into the genetic susceptibility and therapeutic rationale of KBD.

Introduction

Kashin–Beck disease (KBD) is a chronic osteochondropathy (Moreno-Reyes et al., 1998, Stone, 2009), affecting more than 2.5 million people in China (Duan et al., 2010). The major clinical features of KBD include joint pain, joint deformities, continually aggravated osteoarthritis and growth retardation (Downey et al., 2009, Lu et al., 2011). Based on the severity of joint lesions, KBD is clinically classified into three grades (Duan et al., 2010). Comparing with grade I KBD patients, grade II and III KBD patients have serious multi-joint deformities and distinctive growth retardation, such as shortened phalanges and humeri, short stature and other features caused by impaired epiphyseal growth and ossification.

Excessive chondrocyte apoptosis is one of the primary pathological changes of KBD (Wang et al., 2006, Liu et al., 2010a). The molecular signaling pathways underlying KBD excessive chondrocyte apoptosis remain unclear, leading to a lack of effective medical interventions now. For instance, the prevalence of KBD in children reached 50.43% and 32.93% at KBD prevalent areas of Tibet and Shaanxi province of China (Wang et al., 2008). Recent studies demonstrated the involvement of genetic factors in the development of KBD (Lu et al., 2011, Xiong et al., 2010, Shi et al., 2011). Microarray studies of KBD observed significant abnormal expression of apoptosis-related genes, gene ontology and pathways in KBD articular cartilage (Wang et al., 2009, Zhang et al., 2011). It is interesting to clarify whether expression quantitative trait loci (eQTLs) contribute to excessive chondrocyte apoptosis of KBD through regulating the expression of apoptosis-related pathways.

Inspired by genome-wide pathway association analysis of complex diseases (Wang et al., 2007, Liu et al., 2010b), we conducted a genome-wide eQTL-based pathway association analysis of KBD in this study. The KBD-associated pathways were compared with abnormally expressed pathways in KBD articular cartilage, identified by microarray study of KBD.

Section snippets

eQTL-based pathway association analysis of KBD

To ensure the statistical power, extreme phenotype sampling was used here. 90 grade II or III KBD patients with extreme KBD phenotypes (including serious multiple-joint deformities and growth retardation) were recruited from Xi'an city of China (Table 1, Fig. 1). 1627 healthy subjects were collected from Xi'an city and Changsha city of China. All of study subjects underwent careful clinical and radiological examinations. KBD was diagnosed according to the KBD clinical diagnosis criteria of

Results

eQTL-based pathway association analysis identified 6 KBD-associated pathways with P values < 0.01 (Fig. 2), mainly involved in apoptosis, peroxisome and interleukin-1A mediated inflammation. Comparing with microarray pathway expression analysis results of KBD articular cartilage, we identified 4 eQTLs pathways, which were not only significantly associated with KBD, but also abnormally expressed in KBD articular cartilage, including REACTOME_INTRINSIC_PATHWAY_FOR_APOPTOSIS (P = 0.008), MAHAJAN

Discussion

Excessive chondrocyte apoptosis is one of major pathological changes of KBD (Wang et al., 2006, Wu et al., 2014). But little is known about the molecular mechanism underlying KBD excessive chondrocyte apoptosis. Wang et al. found that the percentage of apoptotic chondrocytes (33.60%) in KBD articular cartilage was much larger than that (1.33%) in healthy articular cartilage (Wang et al., 2006). Our result is consistent with that of previous study, supporting the key role of apoptosis in KBD

Acknowledgments

The study was supported by the National Natural Scientific Fund of China (81102086), the Science and Technology Research and Development Program of in Shaanxi Province of China (2013KJXX-51) and the Fundamental Research Funds for the Central Universities.

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