Single cell chromatin accessibility identifies pancreatic islet cell type- and state-specific regulatory programs of diabetes risk [Hi-C]

Single-nucleus assay for transposase-accessible chromatin using sequencing (snATAC-seq) creates new opportunities to dissect cell type-specific mechanisms of complex diseases. Since pancreatic islets are central to type 2 diabetes (T2D), we profiled 15,298 islet cells by using combinatorial barcoding snATAC-seq and identified 12 clusters, including multiple alpha, beta and delta cell states. We cataloged 228,873 accessible chromatin sites and identified transcription factors underlying lineage- and state-specific regulation. We observed state-specific enrichment of fasting glucose and T2D genome-wide association studies for beta cells and enrichment for other endocrine cell types. At T2D signals localized to islet-accessible chromatin, we prioritized variants with predicted regulatory function and co-accessibility with target genes. A causal T2D variant rs231361 at the KCNQ1 locus had predicted effects on a beta cell enhancer co-accessible with INS and genome editing in embryonic stem cell-derived beta cells affected INS levels. Together our findings demonstrate the power of single-cell epigenomics for interpreting complex disease genetics. Overall design: Hi-C of ES-derived beta cells

基于测序的单细胞核转座酶可及性测定（single-nucleus assay for transposase-accessible chromatin using sequencing，snATAC-seq）为解析复杂疾病的细胞类型特异性致病机制提供了全新契机。鉴于胰岛在2型糖尿病（type 2 diabetes，T2D）中的核心作用，我们采用组合条码标记的snATAC-seq技术对15298个胰岛细胞开展了染色质开放谱分析，并鉴定得到12个细胞簇，涵盖多种α细胞、β细胞和δ细胞的细胞状态。我们共编录了228873个染色质可及位点，并鉴定出介导谱系及细胞状态特异性调控的转录因子。我们观察到，β细胞的空腹血糖相关及T2D全基因组关联研究信号呈现细胞状态特异性富集，其他内分泌细胞类型也存在此类富集现象。针对定位于胰岛染色质可及区域的T2D关联信号，我们优先筛选出具备预测调控功能且与靶基因存在共可及性的遗传变异位点。位于KCNQ1基因座的T2D致病遗传变异rs231361，被预测可调控与胰岛素基因（INS）存在共可及性的β细胞增强子；在胚胎干细胞（embryonic stem，ES）分化得到的β细胞中进行基因组编辑后，INS基因的表达水平发生了显著改变。综上，本研究结果证实了单细胞表观基因组学在解析复杂疾病遗传学机制中的重要应用价值。实验整体设计：胚胎干细胞（ES）分化β细胞的Hi-C测序。