Experimental Cardiology, Department of Cardiology, Thoraxcenter Erasmus University Medical Center, Rotterdam, The Netherlands; and.
Department of Pediatrics, Wilhelmina Children's Hospital.
J Am Soc Nephrol. 2018 Feb;29(2):462-476. doi: 10.1681/ASN.2016080875. Epub 2017 Nov 1.
Genome-wide association studies (GWASs) have identified many genetic risk factors for CKD. However, linking common variants to genes that are causal for CKD etiology remains challenging. By adapting self-transcribing active regulatory region sequencing, we evaluated the effect of genetic variation on DNA regulatory elements (DREs). Variants in linkage with the CKD-associated single-nucleotide polymorphism rs11959928 were shown to affect DRE function, illustrating that genes regulated by DREs colocalizing with CKD-associated variation can be dysregulated and therefore, considered as CKD candidate genes. To identify target genes of these DREs, we used circular chromosome conformation capture (4C) sequencing on glomerular endothelial cells and renal tubular epithelial cells. Our 4C analyses revealed interactions of CKD-associated susceptibility regions with the transcriptional start sites of 304 target genes. Overlap with multiple databases confirmed that many of these target genes are involved in kidney homeostasis. Expression quantitative trait loci analysis revealed that mRNA levels of many target genes are genotype dependent. Pathway analyses showed that target genes were enriched in processes crucial for renal function, identifying dysregulated geranylgeranyl diphosphate biosynthesis as a potential disease mechanism. Overall, our data annotated multiple genes to previously reported CKD-associated single-nucleotide polymorphisms and provided evidence for interaction between these loci and target genes. This pipeline provides a novel technique for hypothesis generation and complements classic GWAS interpretation. Future studies are required to specify the implications of our dataset and further reveal the complex roles that common variants have in complex diseases, such as CKD.
全基因组关联研究（GWAS）已经确定了许多与 CKD 相关的遗传风险因素。然而，将常见变体与导致 CKD 病因的基因联系起来仍然具有挑战性。通过适应自转录活性调控区测序，我们评估了遗传变异对 DNA 调控元件（DREs）的影响。与 CKD 相关的单核苷酸多态性 rs11959928 连锁的变体被证明会影响 DRE 功能，这表明受 DRE 调控的基因与 CKD 相关变异所在的区域发生失调，因此可以被视为 CKD 的候选基因。为了确定这些 DRE 的靶基因，我们在肾小球内皮细胞和肾小管上皮细胞上使用了圆形染色体构象捕获（4C）测序。我们的 4C 分析揭示了与 CKD 相关的易感性区域与 304 个靶基因的转录起始位点之间的相互作用。与多个数据库的重叠证实，这些靶基因中的许多都参与了肾脏的稳态。表达数量性状基因座分析显示，许多靶基因的 mRNA 水平与基因型有关。通路分析表明，靶基因在对肾功能至关重要的过程中富集，确定了调节性香叶基香叶基二磷酸生物合成作为一种潜在的疾病机制。总的来说，我们的数据将多个基因注释到先前报道的与 CKD 相关的单核苷酸多态性上，并提供了这些基因座与靶基因之间相互作用的证据。该研究为假设的产生提供了一种新的技术，并补充了经典的 GWAS 解释。需要进一步的研究来明确我们数据集的意义，并进一步揭示常见变异在复杂疾病（如 CKD）中的复杂作用。
