ABSTRACT

Saliva and buccal samples are popular for epigenome wide association studies (EWAS) due to their ease of collection compared and their ability to sample a different cell lineage compared to blood. As these samples contain a mix of white blood cells and buccal epithelial cells that can vary within a population, this cellular heterogeneity may confound EWAS. This has been addressed by including cellular heterogeneity obtained through cytology at the time of collection or by using cellular deconvolution algorithms built on epigenetic data from specific cell types. However, to our knowledge, the two methods have not yet been compared. Here we show that the two methods are highly correlated in saliva and buccal samples (R = 0.84, P < 0.0001) by comparing data generated from cytological staining and Infinium MethylationEPIC arrays and the EpiDISH deconvolution algorithm from buccal and saliva samples collected from twenty adults. In addition, by using an expanded dataset from both sample types, we confirmed our previous finding that age has strong, non-linear negative correlation with epithelial cell proportion in both sample types. However, children and adults showed a large within-population variation in cellular heterogeneity. Our results validate the use of the EpiDISH algorithm in estimating the effect of cellular heterogeneity in EWAS and showed DNA methylation generally underestimates the epithelial cell content obtained from cytology.

摘要

唾液和口腔样本在表观基因组广泛关联研究 (EWAS) 中很受欢迎，因为它们比较容易收集，并且与血液相比，它们能够对不同的细胞谱系进行采样。由于这些样本包含可能在人群中变化的白细胞和颊上皮细胞的混合物，因此这种细胞异质性可能会混淆 EWAS。这已通过包括在收集时通过细胞学获得的细胞异质性或通过使用基于特定细胞类型的表观遗传数据的细胞去卷积算法来解决。但是，据我们所知，这两种方法尚未进行比较。在这里，我们表明这两种方法在唾液和口腔样本中高度相关（R = 0.84，P < 0. 0001）通过比较细胞学染色和 Infinium MethylationEPIC 阵列产生的数据以及从 20 名成年人收集的口腔和唾液样本中的 EpiDISH 反卷积算法。此外，通过使用来自两种样本类型的扩展数据集，我们证实了我们之前的发现，即年龄与两种样本类型中的上皮细胞比例具有很强的非线性负相关性。然而，儿童和成人在细胞异质性方面表现出很大的群体内差异。我们的结果验证了 EpiDISH 算法在估计 EWAS 中细胞异质性的影响方面的使用，并显示 DNA 甲基化通常低估了从细胞学获得的上皮细胞含量。通过使用来自两种样本类型的扩展数据集，我们证实了我们之前的发现，即年龄与两种样本类型中的上皮细胞比例具有很强的非线性负相关性。然而，儿童和成人在细胞异质性方面表现出很大的群体内差异。我们的结果验证了 EpiDISH 算法在估计 EWAS 中细胞异质性的影响方面的使用，并显示 DNA 甲基化通常低估了从细胞学获得的上皮细胞含量。通过使用来自两种样本类型的扩展数据集，我们证实了我们之前的发现，即年龄与两种样本类型中的上皮细胞比例具有很强的非线性负相关性。然而，儿童和成人在细胞异质性方面表现出很大的群体内差异。我们的结果验证了 EpiDISH 算法在估计 EWAS 中细胞异质性的影响方面的使用，并显示 DNA 甲基化通常低估了从细胞学获得的上皮细胞含量。