Background Cell-free DNA (cfDNA) analysis offers an attractive noninvasive means of detecting and monitoring diseases. cfDNA cleavage patterns within a short range (e.g., 11 nucleotides) have been reported to correlate with cytosine-phosphate-guanine (CpG) methylation, allowing fragmentomics-based methylation analysis (FRAGMA). Here, we adopted FRAGMA to the extended region harboring multiple nucleosomes, termed FRAGMAXR. Methods We profiled cfDNA nucleosomal patterns over the genomic regions from −800 to 800 bp surrounding differentially methylated CpG sites, harboring approximately 8 nucleosomes, referred to as CpG-associated cfDNA nucleosomal patterns. Such nucleosomal patterns were analyzed by FRAGMAXR in cancer patients and pregnant women. Results We identified distinct cfDNA nucleosomal patterns around differentially methylated CpG sites. Compared with subjects without cancer, patients with hepatocellular carcinoma (HCC) showed reduced amplitude of nucleosomal patterns, with a gradual decrease over tumor stages. Nucleosomal patterns associated with differentially methylated CpG sites could be used to train a machine learning model, resulting in the detection of HCC patients with an area under the receiver operating characteristic curve of 0.93. We further demonstrated the feasibility of multicancer detection using a dataset comprising lung, breast, and ovarian cancers. The tissue-of-origin analysis of plasma cfDNA from pregnant women and cancer patients revealed that the placental DNA and tumoral DNA contributions deduced by FRAGMAXR correlated well with values measured using genetic variants (Pearson r: 0.85 and 0.94, respectively). Conclusions CpG-associated cfDNA nucleosomal patterns of cfDNA molecules are influenced by DNA methylation and might be useful for biomarker developments for cancer liquid biopsy and noninvasive prenatal testing.

中文翻译：

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癌症患者和孕妇游离 DNA 的甲基化相关核小体模式


背景 游离 DNA （cfDNA） 分析提供了一种有吸引力的无创检测和监测疾病的方法。据报道，短范围内的 cfDNA 切割模式（例如 11 个核苷酸）与胞嘧啶-磷酸-鸟嘌呤 （CpG） 甲基化相关，因此可以进行基于片段组学的甲基化分析 （FRAGMA）。在这里，我们将 FRAGMA 采用到含有多个核小体的扩展区域，称为 FRAGMAXR。方法 我们分析了差异甲基化 CpG 位点周围 -800 至 800 bp 基因组区域的 cfDNA 核小体模式，其中包含大约 8 个核小体，称为 CpG 相关 cfDNA 核小体模式。通过 FRAGMAXR 分析癌症患者和孕妇的这种核小体模式。结果我们在差异甲基化 CpG 位点周围鉴定了不同的 cfDNA 核小体模式。与无癌症的受试者相比，肝细胞癌 （HCC） 患者表现出核小体模式的振幅降低，并在肿瘤分期逐渐减少。与差异甲基化 CpG 位点相关的核小体模式可用于训练机器学习模型，从而检测到受试者工作特征曲线下面积为 0.93 的 HCC 患者。我们使用包含肺癌、乳腺癌和卵巢癌的数据集进一步证明了多癌检测的可行性。孕妇和癌症患者血浆 cfDNA 的组织来源分析显示，FRAGMAXR 推断的胎盘 DNA 和肿瘤 DNA 贡献与使用遗传变异测量的值（Pearson r：分别为 0.85 和 0.94）密切相关。 结论 cfDNA 分子的 CpG 相关 cfDNA 核小体模式受 DNA 甲基化的影响，可能有助于癌症液体活检和无创产前检测的生物标志物开发。