Tedja Milly S, Swierkowska-Janc Joanna, Enthoven Clair A, Meester-Smoor Magda A, Hysi Pirro G, Felix Janine F, Cowan Cameron S, Cherry Timothy J, van der Spek Peter J, Ghanbari Mohsen, Erkeland Stefan J, Barakat Tahsin Stefan, Klaver Caroline C W, Verhoeven Virginie J M
Department of Ophthalmology, Erasmus University Medical Center, Rotterdam, The Netherlands.
Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands.
Hum Genet. 2025 Jan;144(1):67-91. doi: 10.1007/s00439-024-02721-x. Epub 2025 Jan 8.
Refractive error (RE) and myopia are complex polygenic conditions with the majority of genome-wide associated genetic variants in non-exonic regions. Given this, and the onset during childhood, gene-regulation is expected to play an important role in its pathogenesis. This prompted us to explore beyond traditional gene finding approaches. We performed a genetic association study between variants in non-coding RNAs and enhancers, and RE and myopia. We obtained single-nucleotide polymorphisms (SNPs) in microRNA (miRNA) genes, miRNA-binding sites, long non-coding RNAs genes (lncRNAs) and enhancers from publicly available databases: miRNASNPv2, PolymiRTS, VISTA Enhancer Browser, FANTOM5 and lncRNASNP2. We investigated whether SNPs overlapping these elements were associated with RE and myopia leveraged from a large GWAS meta-analysis (N = 160,420). With genetic risk scores (GRSs) per element, we investigated the joint effect of associated variants on RE, axial length (AL)/corneal radius (CR), and AL progression in an independent child cohort, the Generation R Study (N = 3638 children). We constructed a score for biological plausibility per SNP in highly confident miRNA-binding sites and enhancers in chromatin accessible regions. We found that SNPs in two miRNA genes, 14 enhancers and 81 lncRNA genes in chromatin accessible regions and 54 highly confident miRNA-binding sites, were in RE and myopia-associated loci. GRSs from SNPs in enhancers were significantly associated with RE, AL/CR and AL progression. GRSs from lncRNAs were significantly associated with all AL/CR and AL progression. GRSs from miRNAs were not associated with any ocular biometric measurement. GRSs from miRNA-binding sites showed suggestive but inconsistent significance. We prioritized candidate miRNA binding sites and candidate enhancers for future functional validation. Pathways of target and host genes of highly ranked variants included eye development (BMP4, MPPED2), neurogenesis (DDIT4, NTM), extracellular matrix (ANTXR2, BMP3), photoreceptor metabolism (DNAJB12), photoreceptor morphogenesis (CHDR1), neural signaling (VIPR2) and TGF-beta signaling (ANAPC16). This is the first large-scale study of non-coding RNAs and enhancers for RE and myopia. Enhancers and lncRNAs could be of large importance as they are associated with childhood myopia. We provide a confident blueprint for future functional validation by prioritizing candidate miRNA binding sites and candidate enhancers.
屈光不正（RE）和近视是复杂的多基因疾病，大多数全基因组关联的遗传变异位于非外显子区域。鉴于此，以及其在儿童期发病，基因调控预计在其发病机制中起重要作用。这促使我们超越传统的基因发现方法进行探索。我们开展了一项非编码RNA和增强子中的变异与RE和近视之间的遗传关联研究。我们从公开可用的数据库：miRNASNPv2、PolymiRTS、VISTA增强子浏览器、FANTOM5和lncRNASNP2中获取了微小RNA（miRNA）基因、miRNA结合位点、长链非编码RNA基因（lncRNA）和增强子中的单核苷酸多态性（SNP）。我们利用一项大型全基因组关联研究荟萃分析（N = 160,420），调查了与这些元件重叠的SNP是否与RE和近视相关。通过每个元件的遗传风险评分（GRS），我们在一个独立的儿童队列即Generation R研究（N = 3638名儿童）中，研究了相关变异对RE、眼轴长度（AL）/角膜半径（CR）以及AL进展的联合效应。我们为染色质可及区域中高度可信的miRNA结合位点和增强子中的每个SNP构建了一个生物学合理性评分。我们发现，两个miRNA基因、14个增强子、染色质可及区域中的81个lncRNA基因以及54个高度可信的miRNA结合位点中的SNP，位于与RE和近视相关的基因座中。增强子中SNP的GRS与RE、AL/CR和AL进展显著相关。lncRNA的GRS与所有AL/CR和AL进展显著相关。miRNA的GRS与任何眼部生物测量指标均无关联。miRNA结合位点的GRS显示出提示性但不一致的显著性。我们对候选miRNA结合位点和候选增强子进行了优先排序，以便未来进行功能验证。排名靠前的变异的靶基因和宿主基因的通路包括眼睛发育（BMP4、MPPED2）、神经发生（DDIT4、NTM）、细胞外基质（ANTXR2、BMP3）、光感受器代谢（DNAJB12）、光感受器形态发生（CHDR1）、神经信号传导（VIPR2）和TGF-β信号传导（ANAPC16）。这是第一项针对RE和近视的非编码RNA和增强子的大规模研究。增强子和lncRNA可能非常重要，因为它们与儿童近视相关。我们通过对候选miRNA结合位点和候选增强子进行优先排序，为未来的功能验证提供了一个可靠的蓝图。
