Human islet open chromatin profiling reveals epigenomic changes elicited by genetic and environmental factors

Type 2 Diabetes (T2D) is a complex disorder with both genetic and environmental risk factors. The epigenome integrates these factors to control transcriptional regulatory programs under steady state, stimulatory, and pathogenic conditions. However, knowledge of how genetic and environmental factors alter the islet chromatin/regulatory landscape is limited. To fill this knowledge gap and to assess the genome-wide effects of SNVs and the diabetic state on islet chromatin accessibility and regulatory element (RE) use, we measured and compared islet chromatin accessibility patterns from 19 genotyped individuals (14 non-diabetic [ND] and 5 T2D) using ATAC-seq. Chromatin accessibility quantitative trait locus (caQTL) analyses identified 3001 SNVs that alter putative RE use/activity. Islet caQTL were significantly and specifically enriched in islet stretch enhancers and islet transcription factor binding motifs, such as FOXA2, NKX6.1, RFX5, and PDX1. Moreover, islet caQTLs were enriched in T2D and fasting glucose-related GWAS loci, including SNVs associated with altered islet expression of ADCY5, MTNR1B, and ZMIZ1. For X/Y sequences tested, the allelic effect on chromatin accessibility matched enhancer activity in luciferase reporter assays. As anticipated, T2D islets did not exhibit concerted, dramatic shifts in chromatin accessibility compared to ND islets. Motif analysis of the 1882 sites exhibiting modest but significant chromatin accessibility changes revealed suggesting that which were roles in responding to oxidative stress, such as BACH1, BACH2 and NRF2. Together, these results provide new insights into the relative impact of genetic and environmental perturbation on the islet epigenome and chromatin-based evidence that a subset of T2D-associated functional variant(s) and their direction-of-effect underlying genetic association with T2D and islet dysfunction. the genetic and environmental Our study uncovers chromatin accessibility signatures of T2D, highlighting the central role of oxidative stress in the etiology of T2D, and provides insights into how T2D associated SNPs modulate the activity of REs in human islets.

2型糖尿病（Type 2 Diabetes, T2D）是一种兼具遗传与环境风险因素的复杂代谢紊乱疾病。表观基因组（epigenome）可整合上述两类风险因素，在稳态、刺激及致病条件下调控转录调控程序。然而，目前对于遗传与环境因素如何改变胰岛染色质与调控景观的认知仍十分有限。为填补这一认知空白，并评估单核苷酸变异（Single Nucleotide Variants, SNVs）与糖尿病状态对胰岛染色质开放性及调控元件（regulatory element, RE）使用情况的全基因组效应，我们利用转座酶可及性测序（Assay for Transposase-Accessible Chromatin using sequencing, ATAC-seq）对19名基因分型个体（14名非糖尿病个体[non-diabetic, ND]与5名2型糖尿病患者）的胰岛染色质开放性模式进行了检测与比较。

染色质开放性数量性状位点（chromatin accessibility quantitative trait locus, caQTL）分析共鉴定出3001个可改变推定调控元件使用与活性的单核苷酸变异。胰岛caQTL显著且特异性地富集于胰岛伸展增强子（stretch enhancers）及胰岛转录因子结合基序（transcription factor binding motifs），例如FOXA2、NKX6.1、RFX5与PDX1。此外，胰岛caQTL在2型糖尿病及空腹血糖相关的全基因组关联分析（Genome-Wide Association Study, GWAS）位点中存在富集，包括与ADCY5、MTNR1B及ZMIZ1的胰岛表达改变相关的单核苷酸变异。针对检测到的X/Y序列，等位基因对染色质开放性的影响与荧光素酶报告基因实验（luciferase reporter assays）中观察到的增强子活性相符。

如预期一致，与非糖尿病个体的胰岛相比，2型糖尿病患者的胰岛并未出现协同性的显著染色质开放性改变。对1882个呈现轻度但显著染色质开放性改变的位点进行基序分析后发现，这些位点涉及氧化应激（oxidative stress）应答相关的功能，例如BACH1、BACH2与NRF2。综上，本研究为遗传与环境扰动对胰岛表观基因组的相对影响提供了新的认知，并为部分与2型糖尿病相关的功能变异及其介导2型糖尿病与胰岛功能异常的遗传关联的效应方向提供了基于染色质的证据。本研究揭示了2型糖尿病的胰岛染色质开放性特征，强调了氧化应激在2型糖尿病发病机制中的核心作用，并阐明了2型糖尿病相关单核苷酸多态性（Single Nucleotide Polymorphisms, SNPs）如何调控人胰岛内调控元件的活性。