Chromatin dynamics reveal circadian control of human in vitro islet maturation [ATAC-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.

干细胞衍生组织有望彻底变革疾病研究与治疗格局，但当前多数技术手段所生成的产物功能尚未成熟。本研究通过全景分析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，系统性探究人类干细胞体外定向分化为胰岛（pancreatic islets）的分子机制。研究发现，细胞谱系定型（lineage commitment）过程中，增强子潜能（enhancer potential）会发生重编程；同时本研究揭示了广泛存在的表观遗传预启动（epigenetic priming）如何调控内分泌细胞命运（endocrine cell fates）。通过构建胰岛分化与成熟的调控回路（regulatory circuits）模型，本研究鉴定出内分泌细胞生成所必需的关键基因，并明确昼夜节律调控（circadian control）是限制体外胰岛功能的核心瓶颈。将干细胞衍生胰岛同步化至昼夜节律性进食/禁食周期后，可通过诱导能量代谢与胰岛素分泌效应因子的周期性合成——包括反相的胰岛素与胰高血糖素脉冲（antiphasic insulin and glucagon pulses）——触发胰岛的代谢成熟（metabolic maturation）过程。经上述同步化处理后，干细胞衍生胰岛可获得稳定的染色质改变，并产生具有升高葡萄糖阈值（glucose threshold）的节律性胰岛素应答反应——这正是功能成熟的标志性特征——且在移植（transplantation）后数日内即可发挥生理功能。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与提升。