Induced pluripotent stem cells (iPSCs) and their differentiated neurons (iPSC-neurons) are a widely used cellular model in the research of the central nervous system. However, it is unknown how well they capture age-associated processes, particularly given that pluripotent cells are only present during the earliest stages of mammalian development. Epigenetic clocks utilize coordinated age-associated changes in DNA methylation to make predictions that correlate strongly with chronological age. It has been shown that the induction of pluripotency rejuvenates predicted epigenetic age. As existing clocks are not optimized for the study of brain development, we developed the fetal brain clock (FBC), a bespoke epigenetic clock trained in human prenatal brain samples in order to investigate more precisely the epigenetic age of iPSCs and iPSC-neurons. The FBC was tested in two independent validation cohorts across a total of 194 samples, confirming that the FBC outperforms other established epigenetic clocks in fetal brain cohorts. We applied the FBC to DNA methylation data from iPSCs and embryonic stem cells and their derived neuronal precursor cells and neurons, finding that these cell types are epigenetically characterized as having an early fetal age. Furthermore, while differentiation from iPSCs to neurons significantly increases epigenetic age, iPSC-neurons are still predicted as being fetal. Together our findings reiterate the need to better understand the limitations of existing epigenetic clocks for answering biological research questions and highlight a limitation of iPSC-neurons as a cellular model of age-related diseases.

中文翻译：

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胎儿大脑发育的新型表观遗传时钟可预测细胞干细胞模型和衍生神经元的产前年龄


诱导多能干细胞 (iPSC) 及其分化神经元 (iPSC-神经元) 是中枢神经系统研究中广泛使用的细胞模型。然而，尚不清楚它们捕获年龄相关过程的能力如何，特别是考虑到多能细胞仅存在于哺乳动物发育的最早阶段。表观遗传时钟利用 DNA 甲基化中与年龄相关的协调变化来做出与实际年龄密切相关的预测。研究表明，多能性的诱导可以使预测的表观遗传年龄恢复活力。由于现有时钟并未针对大脑发育研究进行优化，我们开发了胎儿脑时钟 (FBC)，这是一种在人类产前大脑样本中进行训练的定制表观遗传时钟，以便更精确地研究 iPSC 和 iPSC 神经元的表观遗传年龄。 FBC 在两个独立的验证队列中对总共 194 个样本进行了测试，证实 FBC 优于胎儿大脑队列中其他已建立的表观遗传时钟。我们将 FBC 应用到 iPSC 和胚胎干细胞及其衍生的神经元前体细胞和神经元的 DNA 甲基化数据中，发现这些细胞类型在表观遗传学上具有早期胎儿年龄的特征。此外，虽然 iPSC 分化为神经元显着增加了表观遗传年龄，但 iPSC 神经元仍被预测为胎儿。我们的研究结果重申，需要更好地了解现有表观遗传时钟在回答生物学研究问题方面的局限性，并强调 iPSC 神经元作为年龄相关疾病的细胞模型的局限性。