Chakraborty Maynak, Jandhyam Harithalakshmi, Basak Samar Kumar, Das Sujata, Alone Debasmita Pankaj
School of Biological Sciences, National Institute of Science Education and Research (NISER) Bhubaneswar, P.O. Bhimpur-Padanpur, Jatni, Khurda, Odisha, 752050, India; Homi Bhabha National Institute (HBNI), Training School Complex, Anushaktinagar, Mumbai, 400094, India.
Disha Eye Hospitals, Barrackpore, Kolkata, 700120, India.
Exp Eye Res. 2023 Mar;228:109403. doi: 10.1016/j.exer.2023.109403. Epub 2023 Feb 1.
Fuchs endothelial corneal dystrophy (FECD) is an age-related, bilateral corneal condition, characterized by apoptosis of the terminally differentiated endothelial cells. A genome-wide association study (GWAS) conducted in the European population in 2017, identified a new single nucleotide polymorphism (SNP), rs1200114 in the intergenic region between long intergenic non-protein coding RNA 970 (LINC00970) and ATPase Na/K transporting subunit beta 1 (ATP1B1). The major focus of the current study is to understand the genetic association of this intergenic variant, rs1200114 with FECD in the Indian population. Sanger sequencing followed by statistical analysis indicated a significant difference in the allelic frequency between controls and cases (P = 0.01) with the minor allele 'G' of rs1200114 imparting a 1.64 fold increased risk for the disease. Luciferase reporter assay revealed no significant difference in the luciferase activity between allele 'A' and 'G' of rs1200114. However, quantitative RT-PCR assay revealed lower expression of ATP1B1 in FECD subjects compared with controls (P = 0.007). Therefore, to find whether another nearby SNP imparts regulatory effect, tag SNP association analysis was carried out; which revealed a significant association of another SNP, rs1200108, present in the intergenic region between LINC00970 and ATP1B1 with FECD (P = 0.009). The protective allele 'A' of rs1200108 displayed reduced reporter activity as opposed to the risk allele 'G' (P = 0.014). Furthermore, haplotype 'A-A' of rs1200108 - rs1200114 was present at a higher frequency in control subjects, suggesting it as a protective haplotype. Altogether, this study inferred the genetic association of rs1200114 and rs1200108 along with the decreased expression of ATP1B1 related to FECD pathogenesis in the Indian population.
富克斯内皮性角膜营养不良（FECD）是一种与年龄相关的双侧角膜疾病，其特征是终末分化的内皮细胞发生凋亡。2017年在欧洲人群中进行的一项全基因组关联研究（GWAS），在长链基因间非编码RNA 970（LINC00970）和ATP酶钠/钾转运亚基β1（ATP1B1）之间的基因间区域发现了一个新的单核苷酸多态性（SNP），rs1200114。本研究的主要重点是了解该基因间变异rs1200114与印度人群中FECD的遗传关联。桑格测序及后续统计分析表明，对照组和病例组之间的等位基因频率存在显著差异（P = 0.01），rs1200114的次要等位基因“G”使疾病风险增加1.64倍。荧光素酶报告基因检测显示，rs1200114的等位基因“A”和“G”之间的荧光素酶活性无显著差异。然而，定量逆转录-聚合酶链反应检测显示，与对照组相比，FECD患者中ATP1B1的表达较低（P = 0.007）。因此，为了确定另一个附近的SNP是否具有调节作用，进行了标签SNP关联分析；结果显示，LINC00970和ATP1B1之间基因间区域存在的另一个SNP rs1200108与FECD存在显著关联（P = 0.009）。与风险等位基因“G”相反，rs1200108的保护性等位基因“A”显示出较低的报告基因活性（P = 0.014）。此外，rs1200108 - rs1200114的单倍型“A - A”在对照组中的出现频率较高，表明它是一种保护性单倍型。总之，本研究推断了rs1200114和rs1200108的遗传关联，以及与印度人群中FECD发病机制相关的ATP1B1表达降低。
