Noncoding rare variants of TBX6 in congenital anomalies of the kidney and urinary tract

Congenital anomalies of the kidney and urinary tract (CAKUT) are a wide range of congenital structural renal defects. CAKUT is the leading cause of chronic renal failure and end-stage renal disease in children. Studies in humans and animal models have confirmed the large genetic contribution to CAKUT. The previous evidence suggested that human TBX6 coding mutations might cause CAKUT via gene-dosage insufficiency. However, the potential involvement of TBX6 noncoding mutations in CAKUT remains to be elucidated. Here, we described DNA sequencing and copy-number analysis of TBX6 in 269 Chinese subjects with CAKUT. Interestingly, we identified two heterozygous noncoding variants of TBX6 in sporadic subjects with CAKUT: one is c.769-7delT, from a subject with duplex renal and collecting system, and the other is a 3 untranslated region (3-UTR) variant (c.1392C>T) from a subject with unilateral renal hypoplasia. These two TBX6 noncoding variants are novel and extremely rare, respectively, in human populations archived in the ExAC database. The mini-gene splicing assay showed that the TBX6 c.769-7delT variant significantly reduced the splicing efficiency of TBX6 intron 5 when compared to the wild-type control. In this work, we identified a novel splicing variant of TBX6 in human CAKUT. Our experimental observations suggested that the TBX6 noncoding variant can affect gene expression and may potentially be involved in human CAKUT.

先天性肾及尿路畸形（CAKUT）是一系列先天性肾脏结构缺陷。CAKUT是儿童慢性肾衰竭和终末期肾病的主要病因。对人类和动物模型的研究已证实遗传因素对CAKUT有重大影响。先前的证据表明，人类TBX6编码突变可能通过基因剂量不足导致CAKUT。然而，TBX6非编码突变在CAKUT中的潜在作用仍有待阐明。在此，我们描述了对269名中国CAKUT患者进行的TBX6 DNA测序和拷贝数分析。有趣的是，我们在散发的CAKUT患者中鉴定出两种TBX6杂合非编码变异：一种是c.769 - 7delT，来自一名双肾盂及集合系统患者；另一种是3'非翻译区（3 - UTR）变异（c.1392C>T），来自一名单侧肾发育不全患者。这两种TBX6非编码变异在ExAC数据库所收录的人群中分别是新的且极其罕见的。小基因剪接实验表明，与野生型对照相比，TBX6 c.769 - 7delT变异显著降低了TBX6第5内含子的剪接效率。在这项工作中，我们在人类CAKUT中鉴定出一种新的TBX6剪接变异。我们的实验观察结果表明，TBX6非编码变异可影响基因表达，并可能潜在地参与人类CAKUT的发生。