Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden.
Department of Clinical Chemistry and Transfusion Medicine, Institute of Biomedicine, Sahlgrenska University Hospital, 413 45, Gothenburg, Sweden.
Epigenetics Chromatin. 2019 Jan 7;12(1):4. doi: 10.1186/s13072-018-0252-7.
Chronic lymphocytic leukemia (CLL) has been a good model system to understand the functional role of 5-methylcytosine (5-mC) in cancer progression. More recently, an oxidized form of 5-mC, 5-hydroxymethylcytosine (5-hmC) has gained lot of attention as a regulatory epigenetic modification with prognostic and diagnostic implications for several cancers. However, there is no global study exploring the role of 5-hydroxymethylcytosine (5-hmC) levels in CLL. Herein, using mass spectrometry and hMeDIP-sequencing, we analysed the dynamics of 5-hmC during B cell maturation and CLL pathogenesis.
We show that naïve B-cells had higher levels of 5-hmC and 5-mC compared to non-class switched and class-switched memory B-cells. We found a significant decrease in global 5-mC levels in CLL patients (n = 15) compared to naïve and memory B cells, with no changes detected between the CLL prognostic groups. On the other hand, global 5-hmC levels of CLL patients were similar to memory B cells and reduced compared to naïve B cells. Interestingly, 5-hmC levels were increased at regulatory regions such as gene-body, CpG island shores and shelves and 5-hmC distribution over the gene-body positively correlated with degree of transcriptional activity. Importantly, CLL samples showed aberrant 5-hmC and 5-mC pattern over gene-body compared to well-defined patterns in normal B-cells. Integrated analysis of 5-hmC and RNA-sequencing from CLL datasets identified three novel oncogenic drivers that could have potential roles in CLL development and progression.
Thus, our study suggests that the global loss of 5-hmC, accompanied by its significant increase at the gene regulatory regions, constitute a novel hallmark of CLL pathogenesis. Our combined analysis of 5-mC and 5-hmC sequencing provided insights into the potential role of 5-hmC in modulating gene expression changes during CLL pathogenesis.
慢性淋巴细胞白血病 (CLL) 一直是一个很好的模型系统，可用于了解 5-甲基胞嘧啶 (5-mC) 在癌症进展中的功能作用。最近，5-mC 的一种氧化形式 5-羟甲基胞嘧啶 (5-hmC) 作为一种具有预后和诊断意义的调节性表观遗传修饰物，引起了广泛关注，它存在于几种癌症中。然而，目前还没有全面的研究探讨 5-羟甲基胞嘧啶 (5-hmC) 水平在 CLL 中的作用。在此，我们使用质谱和 hMeDIP 测序分析了 B 细胞成熟和 CLL 发病机制过程中 5-hmC 的动态变化。
我们发现，与非类别转换和类别转换记忆 B 细胞相比，幼稚 B 细胞的 5-hmC 和 5-mC 水平更高。我们发现，与幼稚 B 细胞和记忆 B 细胞相比，CLL 患者（n=15）的全基因组 5-mC 水平显著降低，而在 CLL 预后组之间未检测到变化。另一方面，CLL 患者的全基因组 5-hmC 水平与记忆 B 细胞相似，且低于幼稚 B 细胞。有趣的是，在调节区域（如基因体、CpG 岛的滨和架），5-hmC 水平增加，并且 5-hmC 在基因体上的分布与转录活性的程度呈正相关。重要的是，与正常 B 细胞中明确的模式相比，CLL 样本的基因体上的 5-hmC 和 5-mC 模式异常。对 CLL 数据集的 5-hmC 和 RNA-seq 的综合分析确定了三个新的致癌驱动子，它们可能在 CLL 的发展和进展中发挥作用。
因此，我们的研究表明，5-hmC 的整体缺失，伴随着其在基因调控区域的显著增加，构成了 CLL 发病机制的一个新标志。我们对 5-mC 和 5-hmC 测序的综合分析为了解 5-hmC 在 CLL 发病机制过程中调节基因表达变化的潜在作用提供了新的见解。
