Chromatin dynamics reveal circadian control of human in vitro islet maturation [RNA-seq]

Stem cell-derived tissues could transform disease research and therapy, yet most methods generate functionally immature products. We investigate how human stem cells differentiate into pancreatic islets in vitro by profiling DNA methylation, chromatin accessibility, and histone modification changes. We find that enhancer potential is reset upon lineage commitment, and show how pervasive epigenetic priming steers endocrine cell fates. Modeling islet differentiation and maturation regulatory circuits reveals genes critical for generating endocrine cells and identifies circadian control as limiting for in vitro islet function. Entrainment to circadian feeding/fasting cycles triggers islet metabolic maturation by inducing cyclic synthesis of energy metabolism and insulin secretion effectors, including antiphasic insulin and glucagon pulses. Following entrainment, stem cell-derived islets gain persistent chromatin changes and rhythmic insulin responses with a raised glucose threshold, a hallmark of functional maturity, and function within days of transplantation. Thus, stem cell-derived tissues are amenable to functional improvement by circadian modulation. RNA-seq of purified live cells at defined developmental stages from stem cells to mature pancreatic islet α/β cells. RNA-seq of human islets / islets differentiated from human pluripotent stem cells entrained to circadian metabolic rhythms.

干细胞衍生组织有望革新疾病研究与治疗，但现有多数方法所制备的组织功能成熟度不足。本研究通过分析DNA甲基化（DNA methylation）、染色质可及性（chromatin accessibility）及组蛋白修饰（histone modification）的动态变化，探究人类干细胞体外分化为胰岛的调控机制。研究发现谱系定型过程中增强子潜能（enhancer potential）会发生重置，并揭示了广泛存在的表观遗传预编程（epigenetic priming）如何调控内分泌细胞的命运走向。通过构建胰岛分化与成熟的调控网络模型，本研究筛选出调控内分泌细胞生成的关键基因，并证实昼夜节律调控（circadian control）是体外胰岛功能成熟的限制性因素。通过施加昼夜节律进食-禁食周期（circadian feeding/fasting cycles）的同步化诱导，可通过激活能量代谢与胰岛素分泌效应因子的周期性合成——包括反相（antiphasic）的胰岛素与胰高血糖素脉冲——促进胰岛的代谢成熟（metabolic maturation）。经同步化诱导后，干细胞衍生胰岛会获得稳定的染色质改变，并表现出升高葡萄糖阈值（glucose threshold）的节律性胰岛素应答——这正是功能成熟的标志性特征——且在移植后数天内即可发挥功能。综上，干细胞衍生组织可通过昼夜节律调控实现功能层面的优化。本研究的测序数据集包含两类：其一为从干细胞至成熟胰岛α/β细胞各明确发育阶段的纯化活细胞的RNA测序（RNA-seq）数据；其二为人类原代胰岛，以及经昼夜节律代谢周期同步化诱导的人多能干细胞（human pluripotent stem cells）衍生胰岛的RNA测序数据。