Department of Endocrinology and Metabolism, the First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China.
Department of Endocrinology, Affiliated Hospital 2 of Nantong University, Nantong First People's Hospital, Nantong, 226000, China.
BMC Med. 2024 Sep 4;22(1):357. doi: 10.1186/s12916-024-03583-w.
Our previous genome‑wide association studies (GWAS) have suggested rs912304 in 14q12 as a suggestive risk variant for type 1 diabetes (T1D). However, the association between this risk region and T1D subgroups and related clinical risk features, the underlying causal functional variant(s), putative candidate gene(s), and related mechanisms are yet to be elucidated.
We assessed the association between variant rs912304 and T1D, as well as islet autoimmunity and islet function, stratified by the diagnosed age of 12. We used epigenome bioinformatics analyses, dual luciferase reporter assays, and expression quantitative trait loci (eQTL) analyses to prioritize the most likely functional variant and potential causal gene. We also performed functional experiments to evaluate the role of the causal gene on islet function and its related mechanisms.
We identified rs912304 as a risk variant for T1D subgroups with diagnosed age ≥ 12 but not < 12. This variant is associated with residual islet function but not islet-specific autoantibody positivity in T1D individuals. Bioinformatics analysis indicated that rs912304 is a functional variant exhibiting spatial overlaps with enhancer active histone marks (H3K27ac and H3K4me1) and open chromatin status (ATAC-seq) in the human pancreas and islet tissues. Luciferase reporter gene assays and eQTL analyses demonstrated that the biallelic sites of rs912304 had differential allele-specific enhancer activity in beta cell lines and regulated STXBP6 expression, which was defined as the most putative causal gene based on Open Targets Genetics, GTEx v8 and Tiger database. Moreover, Stxbp6 was upregulated by T1D-related proinflammatory cytokines but not high glucose/fat. Notably, Stxbp6 over-expressed INS-1E cells exhibited decreasing insulin secretion and increasing cell apoptosis through Glut1 and Gadd45β, respectively.
This study expanded the genomic landscape regarding late-onset T1D risk and supported islet function mechanistically connected to T1D pathogenesis.
我们之前的全基因组关联研究（GWAS）表明，14q12 上的 rs912304 是 1 型糖尿病（T1D）的一个提示性风险变异。然而，该风险区域与 T1D 亚组及相关临床风险特征、潜在的因果功能变异、候选基因及相关机制之间的关联尚未阐明。
我们评估了 rs912304 与 T1D、胰岛自身免疫和胰岛功能之间的关联，按 12 岁时确诊的年龄进行分层。我们使用表观基因组生物信息学分析、双荧光素酶报告基因检测和表达数量性状基因座（eQTL）分析来确定最可能的功能变异和潜在的因果基因。我们还进行了功能实验，以评估因果基因对胰岛功能及其相关机制的作用。
我们发现 rs912304 是诊断年龄≥12 岁而非<12 岁的 T1D 亚组的风险变异。该变异与 T1D 个体的胰岛功能残留但与胰岛特异性自身抗体阳性无关。生物信息学分析表明，rs912304 是一个功能变异，在人胰腺和胰岛组织中与增强子活性组蛋白标记（H3K27ac 和 H3K4me1）和开放染色质状态（ATAC-seq）具有空间重叠。荧光素酶报告基因检测和 eQTL 分析表明，rs912304 的双等位基因位点在β细胞系中具有不同的等位基因特异性增强子活性，并调节 STXBP6 的表达，根据 Open Targets Genetics、GTEx v8 和 Tiger 数据库，STXBP6 被定义为最可能的候选基因。此外，T1D 相关促炎细胞因子而非高葡萄糖/脂肪可上调 Stxbp6。值得注意的是，过度表达 Stxbp6 的 INS-1E 细胞通过 Glut1 和 Gadd45β 分别表现出胰岛素分泌减少和细胞凋亡增加。
本研究扩展了关于迟发性 T1D 风险的基因组图谱，并支持与 T1D 发病机制有机制联系的胰岛功能。
