Laboratory for Genomics, Foundation Jean Dausset-CEPH, 75010, Paris, France.
Laboratory of Excellence GenMed, Paris, France.
Sci Rep. 2022 Mar 18;12(1):4684. doi: 10.1038/s41598-022-08663-6.
Lymphoblastoid cell lines (LCLs) derive from blood infected in vitro by Epstein-Barr virus and were used in several genetic, transcriptomic and epigenomic studies. Although few changes were shown between LCL and blood genotypes (SNPs) validating their use in genetics, more were highlighted for other genomic features and/or in their transcriptome and epigenome. This could render them less appropriate for these studies, notably when blood DNA could still be available. Here we developed a simple, high-throughput and cost-effective real-time PCR approach allowing to distinguish blood from LCL DNA samples based on the presence of EBV relative load and rearranged T-cell receptors γ and β. Our approach was able to achieve 98.5% sensitivity and 100% specificity on DNA of known origin (458 blood and 316 LCL DNA). It was further applied to 1957 DNA samples from the CEPH Aging cohort comprising DNA of uncertain origin, identifying 784 blood and 1016 LCL DNA. A subset of these DNA was further analyzed with an epigenetic clock indicating that DNA extracted from blood should be preferred to LCL for DNA methylation-based age prediction analysis. Our approach could thereby be a powerful tool to ascertain the origin of DNA in old collections prior to (epi)genomic studies.
淋巴母细胞系 (LCL) 源自体外感染 EBV 的血液，已被用于多项遗传、转录组和表观基因组学研究。尽管 LCL 和血液基因型 (SNP) 之间显示出的变化很少，证明了它们在遗传学中的应用价值，但在其他基因组特征和/或转录组和表观基因组中发现的变化更多。这可能使它们不太适合这些研究，尤其是在血液 DNA 仍然可用的情况下。在这里，我们开发了一种简单、高通量且具有成本效益的实时 PCR 方法，该方法能够基于 EBV 相对载量和重排的 T 细胞受体 γ 和 β 的存在，区分血液和 LCL DNA 样本。我们的方法在已知来源的 DNA（458 份血液和 316 份 LCL DNA）上达到了 98.5%的灵敏度和 100%的特异性。进一步将其应用于包含来源不确定的 DNA 的 1957 份 CEPH 衰老队列的 DNA 样本，鉴定出 784 份血液和 1016 份 LCL DNA。这些 DNA 的一部分进一步用表观遗传钟进行了分析，表明基于 DNA 甲基化的年龄预测分析，应优先选择血液提取的 DNA。因此，我们的方法可以在进行 (表观)基因组研究之前，作为一种强有力的工具来确定旧样本库中 DNA 的来源。
