Clinical and Translational Research Center, Canon Stroke and Vascular Research Center, 875 Ellicott Street, 14203, Buffalo, NY, USA.
Department of Biomedical Engineering, University at Buffalo, Buffalo, NY, USA.
BMC Med Genomics. 2019 Oct 30;12(1):149. doi: 10.1186/s12920-019-0591-7.
Genetics play an important role in intracranial aneurysm (IA) pathophysiology. Genome-wide association studies have identified several single nucleotide polymorphisms (SNPs) that are linked to IA but how they affect disease pathobiology remains poorly understood. We used Encyclopedia of DNA Elements (ENCODE) data to investigate the epigenetic landscapes surrounding genetic risk loci to determine if IA-associated SNPs affect functional elements that regulate gene expression and if those SNPs are most likely to impact a specific type of cells.
We mapped 16 highly significant IA-associated SNPs to linkage disequilibrium (LD) blocks within the human genome. Within these regions, we examined the presence of H3K4me1 and H3K27ac histone marks and CCCTC-binding factor (CTCF) and transcription-factor binding sites using chromatin immunoprecipitation-sequencing (ChIP-Seq) data. This analysis was conducted in several cell types relevant to endothelial (human umbilical vein endothelial cells [HUVECs]) and inflammatory (monocytes, neutrophils, and peripheral blood mononuclear cells [PBMCs]) biology. Gene ontology analysis was performed on genes within extended IA-risk regions to understand which biological processes could be affected by IA-risk SNPs. We also evaluated recently published data that showed differential methylation and differential ribonucleic acid (RNA) expression in IA to investigate the correlation between differentially regulated elements and the IA-risk LD blocks.
The IA-associated LD blocks were statistically significantly enriched for H3K4me1 and/or H3K27ac marks (markers of enhancer function) in endothelial cells but not in immune cells. The IA-associated LD blocks also contained more binding sites for CTCF in endothelial cells than monocytes, although not statistically significant. Differentially methylated regions of DNA identified in IA tissue were also present in several IA-risk LD blocks, suggesting SNPs could affect this epigenetic machinery. Gene ontology analysis supports that genes affected by IA-risk SNPs are associated with extracellular matrix reorganization and endopeptidase activity.
These findings suggest that known genetic alterations linked to IA risk act on endothelial cell function. These alterations do not correlate with IA-associated gene expression signatures of circulating blood cells, which suggests that such signatures are a secondary response reflecting the presence of IA rather than indicating risk for IA.
遗传学在颅内动脉瘤（IA）发病机制中起着重要作用。全基因组关联研究已经确定了几个与 IA 相关的单核苷酸多态性（SNP），但它们如何影响疾病的病理生物学仍知之甚少。我们使用 DNA 元件百科全书（ENCODE）数据来研究遗传风险位点周围的表观遗传景观，以确定与 IA 相关的 SNP 是否影响调节基因表达的功能元件，以及这些 SNP 是否最有可能影响特定类型的细胞。
我们将 16 个与 IA 高度相关的 SNP 映射到人类基因组中的连锁不平衡（LD）块内。在这些区域内，我们使用染色质免疫沉淀测序（ChIP-Seq）数据检查 H3K4me1 和 H3K27ac 组蛋白标记以及 CCCTC 结合因子（CTCF）和转录因子结合位点的存在。这项分析是在与血管内皮（人脐静脉内皮细胞[HUVEC]）和炎症（单核细胞、中性粒细胞和外周血单核细胞[PBMC]）生物学相关的几种细胞类型中进行的。对扩展的 IA 风险区域内的基因进行基因本体论分析，以了解哪些生物学过程可能受到 IA 风险 SNP 的影响。我们还评估了最近发表的数据，该数据显示 IA 中存在差异甲基化和差异核糖核酸（RNA）表达，以研究差异调节元件与 IA 风险 LD 块之间的相关性。
IA 相关的 LD 块在血管内皮细胞中统计学上显著富集 H3K4me1 和/或 H3K27ac 标记（增强子功能的标记），但在免疫细胞中则不然。IA 相关的 LD 块在血管内皮细胞中也包含更多的 CTCF 结合位点，尽管没有统计学意义。IA 组织中鉴定的差异甲基化 DNA 区域也存在于几个 IA 风险 LD 块中，这表明 SNP 可能会影响这种表观遗传机制。基因本体论分析支持受 IA 风险 SNP 影响的基因与细胞外基质重组和内肽酶活性有关。
这些发现表明，与 IA 风险相关的已知遗传改变作用于血管内皮细胞功能。这些改变与循环血液细胞中与 IA 相关的基因表达特征不相关，这表明这些特征是 IA 的继发反应，而不是表明 IA 的风险。
