Cheng Bolun, Wu Cuiyan, Wei Wenming, Niu Hui, Wen Yan, Li Cheng, Chen Ping, Chang Hong, Yang Zhengjun, Zhang Feng
Key Laboratory of Trace Elements and Endemic Diseases (Xi'an Jiaotong University), National Health and Family Planning Commission, Xi'an, China.
Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education, Xi'an, China.
Bone Joint Res. 2024 May 17;13(5):237-246. doi: 10.1302/2046-3758.135.BJR-2023-0271.R1.
To assess the alterations in cell-specific DNA methylation associated with chondroitin sulphate response using peripheral blood collected from Kashin-Beck disease (KBD) patients before initiation of chondroitin sulphate treatment.
Peripheral blood samples were collected from KBD patients at baseline of chondroitin sulphate treatment. Methylation profiles were generated using reduced representation bisulphite sequencing (RRBS) from peripheral blood. Differentially methylated regions (DMRs) were identified using MethylKit, while DMR-related genes were defined as those annotated to the gene body or 2.2-kilobase upstream regions of DMRs. Selected DMR-related genes were further validated by quantitative reverse transcriptase polymerase chain reaction (qRT-PCR) to assess expression levels. Tensor composition analysis was performed to identify cell-specific differential DNA methylation from bulk tissue.
This study revealed 21,060 hypermethylated and 44,472 hypomethylated DMRs, and 13,194 hypermethylated and 22,448 hypomethylated CpG islands for differential global methylation for chondroitin sulphate treatment response. A total of 12,666 DMR-related genes containing DMRs were identified in their promoter regions, such as (false discovery rate (FDR) = 2.11 × 10), (FDR = 7.05 × 10), and (FDR = 1.43 × 10). Additionally, and were hypermethylated in responders, while was hypomethylated in responders, all showing decreased gene expression. The patterns of cell-specific differential global methylation associated with chondroitin sulphate response were observed. Specifically, we found that DMRs located in and exhibited differential DNA methylation between responders and non-responders in granulocytes, monocytes, and B cells.
Our study identified cell-specific changes in DNA methylation associated with chondroitin sulphate response in KBD patients.
利用大骨节病（KBD）患者在开始硫酸软骨素治疗前采集的外周血，评估与硫酸软骨素反应相关的细胞特异性DNA甲基化变化。
在硫酸软骨素治疗基线时从KBD患者采集外周血样本。使用外周血的简化代表性亚硫酸氢盐测序（RRBS）生成甲基化图谱。使用MethylKit鉴定差异甲基化区域（DMR），而DMR相关基因定义为注释到DMR基因体或其2.2千碱基上游区域的基因。通过定量逆转录聚合酶链反应（qRT-PCR）进一步验证选定的DMR相关基因以评估表达水平。进行张量成分分析以从大块组织中鉴定细胞特异性差异DNA甲基化。
本研究揭示了21,060个高甲基化和44,472个低甲基化的DMR，以及13,194个高甲基化和22,448个低甲基化的CpG岛，用于硫酸软骨素治疗反应的差异全局甲基化。在其启动子区域共鉴定出12,666个含有DMR的DMR相关基因，如（错误发现率（FDR）=2.11×10）、（FDR = 7.05×10）和（FDR = 1.43×10）。此外，应答者中 和 高甲基化，而应答者中 低甲基化，均显示基因表达降低。观察到与硫酸软骨素反应相关的细胞特异性差异全局甲基化模式。具体而言，我们发现位于 和 的DMR在粒细胞、单核细胞和B细胞的应答者与非应答者之间表现出差异DNA甲基化。
我们的研究确定了KBD患者中与硫酸软骨素反应相关的DNA甲基化的细胞特异性变化。
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