近日，美国波士顿儿童医院William T. Pu等研究人员合作完成人类心脏增强子和非编码新生变异在先天性心脏病中的功能剖析。这一研究成果于2024年2月20日在线发表在国际学术期刊《自然—遗传学》上。

研究人员表示，先天性心脏病（CHD）有45%是由罕见的编码突变引起的。扰乱顺式调控元件（CRE）的非编码突变可能是导致其余病例的原因，但它们的鉴定一直是个难题。

研究人员在人类诱导多能干细胞衍生的心肌细胞（iPSC-CM）中使用慢病毒大规模并行报告分析（lentiMPRA），对从750例CHD三倍体全基因组测序中优先排序的6590个非编码新生变异（ncDNV）进行了功能评估。共有403个ncDNV对心脏CRE活性产生了重大影响。大多数基因都增加了增强子的活性，而且往往是在检测不到参考序列活性的区域。通过将十个DNV引入其原生基因组环境进行测试，其中四个DNV改变了邻近基因的表达和iPSC-CM的转录状态。

为了确定未来进行功能测试的DNV的优先顺序，研究人员利用MPRA数据建立了一个回归模型EpiCard。通过EpiCard对独立的CHD队列进行分析，发现了DNV的富集。研究人员共同开发了一个可扩展的系统来测量ncDNV对CRE活性的影响，并将其用于系统评估ncDNV对CHD的贡献。

附：英文原文

Title: Functional dissection of human cardiac enhancers and noncoding de novo variants in congenital heart disease

Author: Xiao, Feng, Zhang, Xiaoran, Morton, Sarah U., Kim, Seong Won, Fan, Youfei, Gorham, Joshua M., Zhang, Huan, Berkson, Paul J., Mazumdar, Neil, Cao, Yangpo, Chen, Jian, Hagen, Jacob, Liu, Xujie, Zhou, Pingzhu, Richter, Felix, Shen, Yufeng, Ward, Tarsha, Gelb, Bruce D., Seidman, Jonathan G., Seidman, Christine E., Pu, William T.

Issue&Volume: 2024-02-20

Abstract: Rare coding mutations cause ～45% of congenital heart disease (CHD). Noncoding mutations that perturb cis-regulatory elements (CREs) likely contribute to the remaining cases, but their identification has been problematic. Using a lentiviral massively parallel reporter assay (lentiMPRA) in human induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs), we functionally evaluated 6,590 noncoding de novo variants (ncDNVs) prioritized from the whole-genome sequencing of 750 CHD trios. A total of 403 ncDNVs substantially affected cardiac CRE activity. A majority increased enhancer activity, often at regions with undetectable reference sequence activity. Of ten DNVs tested by introduction into their native genomic context, four altered the expression of neighboring genes and iPSC-CM transcriptional state. To prioritize future DNVs for functional testing, we used the MPRA data to develop a regression model, EpiCard. Analysis of an independent CHD cohort by EpiCard found enrichment of DNVs. Together, we developed a scalable system to measure the effect of ncDNVs on CRE activity and deployed it to systematically assess the contribution of ncDNVs to CHD.

DOI: 10.1038/s41588-024-01669-y

Source: https://www.nature.com/articles/s41588-024-01669-y