DNA methylation patterns in human iPSC-derived sensory neuronal differentiation

Sensory neurons of the peripheral nervous system are critical in health and disease. Sensory neurons derived from induced pluripotent stem (iPS) cells are now being used increasingly for <i>in vitro</i> models of neuropathy, pain, and neurotoxicity. DNA methylation is critical for neurodevelopment and has been implicated in many neuronal diseases, but has not been examined in iPS-derived sensory neurons. In order to better characterize the iPS-derived sensory neuron model, we have undertaken a genome-wide DNA methylation study on the cells from human iPS to iPS-derived sensory neurons during differentiation through reduced representation and bisulfite sequencing. We report decreasing DNA methylation with iPS-derived sensory neuronal differentiation that is reflected in increasing numbers and proportions of hypomethylated individual CpGs and regions, as well as lowered DNMT3b expression. Furthermore, genes with changes in DNA methylation near their TSS suggest key pathways that may be involved in iPS-derived sensory neuronal differentiation. These findings provide insights into sensory neuronal differentiation and can be used for further <i>in vitro</i> modelling of disease states.

外周神经系统的感觉神经元在健康与疾病进程中均发挥关键作用。目前，由诱导多能干细胞（induced pluripotent stem cell，iPS）分化得到的感觉神经元，正日益被应用于周围神经病变、疼痛及神经毒性的体外（in vitro）模型构建。DNA甲基化对神经发育至关重要，且与多种神经元疾病的发生发展密切相关，但目前尚未在iPS来源的感觉神经元中开展系统研究。为更好地表征iPS来源的感觉神经元模型，我们针对人类iPS细胞向iPS来源感觉神经元分化过程中的细胞，采用简化代表性测序与亚硫酸氢盐测序技术，开展了全基因组DNA甲基化研究。本研究发现，随着iPS来源感觉神经元的分化，DNA甲基化水平逐渐降低，具体体现为低甲基化的单个CpG位点及调控区域的数量与占比均持续升高，同时DNA甲基转移酶3b（DNMT3b）的表达水平也随之下调。此外，转录起始位点（transcription start site，TSS）附近DNA甲基化发生改变的基因，提示了一系列可能参与iPS来源感觉神经元分化的关键通路。上述研究结果为感觉神经元分化机制提供了新的理论视角，同时可用于后续疾病状态的体外建模研究。