Classification of cancer cell lines using a promoter-targeted liquid hybridization capture-based bisulfite sequencing approach

DNA methylation plays a significant role in assuring cell identity, thus potentiating its application in molecular classification of cancers in respect of tissue origins or clinically and aetiologically distinct subtypes. In this study, we adapted our liquid hybridization capture-based bisulfite sequencing approach on the targeted sequencing of promoter methylomes. We detected ten cell lines originated from different tissue origins and demonstrated a similar potentiality of promoter methylomes as classifiers for cancer cell lines from different tissue origins in comparison with gene expression profiles. Furthermore, promoter methylome can sensitively differentiate two different cell lines from the same tissue origin in respect of the CpG island methylator phenotype (CIMP), as in the case of AGS and BGC-823 gastric cancer cell lines. These results potentiate the targeted sequencing of promoter methylomes as a means for comprehensive screening and classifying cancer cells with respect to tissue-origins and CIMP subtypes in the future studies. Overall design: We proved the potentiality of promoter-targeted LHC-BS that requires reduced experimental cost and less amount of initial DNA samples in comparison with a previous design [23] using YH cell line. In addition, we generated single-base promoter methylomes for ten cell lines, including eight cancer cell lines generated from four types of tissues and one pair of model cell lines for ovarian cancer (T29 and T29H). We proved the potentiality of promoter-targeted LHC-BS that requires reduced experimental cost and less amount of initial DNA samples in comparison with a previous design using YH cell line. In addition, we generated single-base promoter methylomes for ten cell lines, including eight cancer cell lines generated from four types of tissues and one pair of model cell lines for ovarian cancer (T29 and T29H).

DNA甲基化（DNA methylation）在维持细胞身份稳态中发挥关键作用，使其在基于组织来源或临床与病因学差异亚型的癌症分子分类领域具备重要应用潜力。
本研究针对启动子甲基化组的靶向测序，优化了基于液相杂交捕获的亚硫酸氢盐测序（bisulfite sequencing）方法。我们完成了10株不同组织来源细胞系的测序检测，结果证实启动子甲基化组与基因表达谱类似，均可作为区分不同组织来源癌细胞系的分类标志物。此外，启动子甲基化组还可依据CpG岛甲基化表型（CpG island methylator phenotype，CIMP）敏感区分同一组织来源的不同细胞系，例如AGS与BGC-823胃癌细胞系。本研究结果表明，未来可通过启动子甲基化组靶向测序实现癌症细胞的组织来源与CIMP亚型的全面筛查与分型。

整体实验设计：我们以YH细胞系为验证材料，证实相较于既往研究设计[23]，靶向启动子的液相杂交捕获亚硫酸氢盐测序可降低实验成本并减少初始DNA样本投入量。此外，我们完成了10株细胞系的单碱基分辨率启动子甲基化组测序，其中包括源自4类组织的8株癌细胞系，以及1对卵巢癌模型细胞系（T29与T29H）。我们以YH细胞系为验证材料，证实相较于既往研究设计[23]，靶向启动子的液相杂交捕获亚硫酸氢盐测序可降低实验成本并减少初始DNA样本投入量。此外，我们完成了10株细胞系的单碱基分辨率启动子甲基化组测序，其中包括源自4类组织的8株癌细胞系，以及1对卵巢癌模型细胞系（T29与T29H）。