Mapping open chromatin in iPSCs derived from beta-cells

Current in-vitro islet differentiation protocols suffer from heterogeneity and low efficiency. Induced-pluripotent stem cells (iPSCs) derived from pancreatic beta-cells (BiPSCs) preferentially differentiate towards endocrine pancreas-like cells versus those from fibroblasts (FiPSCs). We interrogated genome-wide open chromatin in BiPSCs and FiPSCs via ATAC-seq, and identified ~8.3k significant, differential open chromatin sites (DOCS) between the two iPSC subtypes (FDR<0.05). DOCS where chromatin was more accessible in BiPSCs (Bi-DOCS) were significantly enriched for known regulators of endodermal development, including bivalent and weak enhancers, and FOXA2 binding sites (FDR<0.05). Bi-DOCS were associated with genes related to pancreas development and beta-cell function, including transcription factors mutated in monogenic diabetes (PDX1, NKX2-2, HNF1A; FDR<0.05). Moreover, Bi-DOCS correlated with enhanced gene expression in BiPSC-derived definitive endoderm and pancreatic progenitor cells. Bi-DOCS therefore highlight both known and novel genes and pathways governing islet-lineage commitment, which can be exploited for differentiation protocol optimisation, diabetes disease modelling, and therapeutic purposes.

当前体外胰岛分化方案存在异质性高、效率低下的缺陷。相较于成纤维细胞来源的诱导多能干细胞（FiPSCs），胰腺β细胞来源的诱导多能干细胞（BiPSCs）更倾向于分化为内分泌胰腺样细胞。本研究通过转座酶可及性测序（ATAC-seq）分析了BiPSCs与FiPSCs的全基因组开放染色质状态，鉴定得到两类诱导多能干细胞亚型间约8300个具有统计学意义的差异开放染色质位点（DOCS，错误发现率FDR<0.05）。在BiPSCs中染色质开放性更高的DOCS（即Bi-DOCS）显著富集于已知的内胚层发育调控因子，涵盖二价调控元件与弱增强子，以及FOXA2结合位点（FDR<0.05）。Bi-DOCS所关联的基因涉及胰腺发育与β细胞功能相关通路，包括单基因糖尿病中发生突变的转录因子（如PDX1、NKX2-2、HNF1A，FDR<0.05）。此外，Bi-DOCS的染色质开放状态与BiPSC来源的定型内胚层及胰腺祖细胞中的基因表达上调显著相关。因此，Bi-DOCS揭示了调控胰岛谱系定向的已知与全新基因及通路，可用于优化体外胰岛分化方案、构建糖尿病疾病模型，并应用于治疗领域。