Stanford University School of Medicine, Stanford, California.
Arthritis Rheumatol. 2015 May;67(8):2129-40. doi: 10.1002/art.39179.
To examine the genome-wide distribution of hydroxymethylated cytosine (5hmC) in osteoarthritic (OA) and normal chondrocytes in order to investigate the effect on OA-specific gene expression.
Cartilage was obtained from OA patients undergoing total knee arthroplasty or from control patients undergoing anterior cruciate ligament reconstruction. Genome-wide sequencing of 5hmC-enriched DNA was performed in a small cohort of normal and OA chondrocytes to identify differentially hydroxymethylated regions (DhMRs) in OA chondrocytes. Data from the genome-wide sequencing of 5hmC-enriched DNA were intersected with global OA gene expression data to define subsets of genes and pathways potentially affected by increased 5hmC levels in OA chondrocytes.
A total of 70,591 DhMRs were identified in OA chondrocytes as compared to normal chondrocytes, 44,288 (63%) of which were increased in OA chondrocytes. The majority of DhMRs (66%) were gained in gene bodies. Increased DhMRs were observed in ∼50% of genes previously implicated in OA pathology including MMP3, LRP5, GDF5, and COL11A1. Furthermore, analyses of gene expression data revealed gene body gain of 5hmC appears to be preferentially associated with activated, but not repressed, genes in OA chondrocytes.
This study provides the first genome-wide profiling of 5hmC distribution in OA chondrocytes. We had previously reported a global increase in 5hmC levels in OA chondrocytes. Gain of 5hmC in the gene body is found to be characteristic of activated genes in OA chondrocytes, highlighting the influence of 5hmC as an epigenetic mark in OA. In addition, this study identifies multiple OA-associated genes that are potentially regulated either singularly by gain of DNA hydroxymethylation or in combination with loss of DNA methylation.
研究骨关节炎（OA）和正常软骨细胞中羟甲基化胞嘧啶（5hmC）的全基因组分布，以探讨其对 OA 特异性基因表达的影响。
从接受全膝关节置换术的 OA 患者或接受前交叉韧带重建术的对照患者中获取软骨。在一小部分正常和 OA 软骨细胞中进行富含 5hmC 的 DNA 全基因组测序，以鉴定 OA 软骨细胞中差异羟甲基化区域（DhMRs）。从富含 5hmC 的 DNA 的全基因组测序中获取的数据与全球 OA 基因表达数据相交，以定义潜在受 OA 软骨细胞中 5hmC 水平升高影响的基因和途径子集。
与正常软骨细胞相比，OA 软骨细胞中总共鉴定出 70591 个 DhMR，其中 44288 个（63%）在 OA 软骨细胞中增加。大多数 DhMR（66%）在基因体中获得。在以前与 OA 病理学相关的基因中，约有 50%观察到 DhMR 增加，包括 MMP3、LRP5、GDF5 和 COL11A1。此外，对基因表达数据的分析表明，OA 软骨细胞中 5hmC 基因体获得似乎与基因的激活而不是抑制更相关。
本研究首次对 OA 软骨细胞中 5hmC 分布进行了全基因组分析。我们之前曾报道过 OA 软骨细胞中 5hmC 水平的整体升高。在 OA 软骨细胞中发现基因体中 5hmC 的获得是激活基因的特征，突出了 5hmC 作为 OA 中的一种表观遗传标记的影响。此外，本研究还鉴定了多个可能单独受 DNA 羟甲基化增加或与 DNA 去甲基化相结合调节的 OA 相关基因。
