DNA methylomes undergo distinct waves of remodeling during thymic T cell development and do not acquire a proliferation-induced imprint.

Dynamic changes of the DNA methylation (DNAmeth) landscape drive differentiation of mature T lymphocytes. However, the role of DNAmeth-mediated regulation in thymocyte development remains unclear. Thus, we generated genome-wide DNAmeth profiles of eight defined human thymocyte subsets, revealing two waves of DNAmeth remodeling: first before TCR rearrangement, then during final maturation. Transcriptomic changes occurred also during phases of DNAmeth stability, indicating decoupled dynamics of epigenetic and transcriptional regulation. In contrast to mature T cells, thymocytes were protected from proliferation-induced changes in the DNA methylome. Finally, the DNAmeth profiles were useful as biomarkers to assess the quality of an in vivo mouse model of human T cell development. This study revealed unexpected dynamics of DNAmeth-mediated control of human thymocyte development and displayed the capacity of DNAmeth profiles to serve as biomarkers for successful T cell generation in model systems and, as a possible future application, during manufacturing of therapeutic cell products. To assess the possible influence of patient's DNA-methylation status on human thymocyte development, we performed comparative analysis of eight thymocyte subsets (n=5). Additionally, DNA methylation profiles were compared to thymocytes from a humanized mouse model (NSGW41hlL7) after umbilical cord blood hematopoietic stem cell graft (n=4).

DNA甲基化（DNA methylation, DNAmeth）组图谱的动态变化驱动成熟T淋巴细胞的分化。然而，DNA甲基化介导的调控在胸腺细胞发育中的作用仍不明确。为此，我们获取了8种已明确界定的人胸腺细胞亚群的全基因组DNA甲基化图谱，揭示出两轮DNA甲基化重塑浪潮：第一轮发生于T细胞受体（TCR）重排之前，第二轮则于最终成熟阶段进行。转录组变化同样发生于DNA甲基化稳定阶段，表明表观遗传调控与转录调控的动态变化存在解偶联现象。与成熟T细胞不同，胸腺细胞可免受增殖诱导的DNA甲基化组变化影响。本研究揭示了DNA甲基化介导的人胸腺细胞发育调控的未预期动态特征，并证实DNA甲基化图谱可作为生物标志物，用于评估人T细胞发育的体内小鼠模型的质量，同时也证明其可作为生物标志物评估模型系统中T细胞的成功生成情况，未来或可应用于治疗性细胞产品的制备过程。为评估患者DNA甲基化状态对人胸腺细胞发育的潜在影响，我们对8组胸腺细胞亚群开展了比较分析（n=5）。此外，我们将脐带血造血干细胞移植后（n=4）的人源化小鼠模型（NSGW41hlL7）来源的胸腺细胞的DNA甲基化图谱与前述亚群进行了比对。