Curtis Sarah W, Cook Laura E, Paraiso Kitt, Visel Axel, Cotney Justin L, Murray Jeffrey C, Beaty Terri H, Marazita Mary L, Carlson Jenna C, Leslie-Clarkson Elizabeth J
Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, USA.
Environmental Genomics and Systems Biology Division, National Laboratsory, Berkeley, California, USA.
Birth Defects Res. 2025 Jul;117(7):e2499. doi: 10.1002/bdr2.2499.
Orofacial clefts (OFCs) are the most common craniofacial birth defects, affecting 1 in 700 births, and have a strong genetic basis with a high recurrence risk within families.
While many of the previous studies have associated common, noncoding genetic loci with OFCs, previous studies on de novo variants (DNVs) in OFC cases have focused on coding variants that could have a functional impact on protein structure, and the contribution of noncoding DNVs to the formation of OFCs has largely been ignored and is not well understood.
We reanalyzed an existing dataset of DNVs from 1409 trios with OFCs that had undergone targeted sequencing of known OFC-associated loci. We then annotated these DNVs with information from datasets of predicted epigenetic function during human craniofacial development.
Of the 66 DNVs called in the targeted regions in this study, 17 (25.7%) were within a predicted enhancer or promoter region. Two DNVs fell within the same enhancer region (hs1617), which is more than expected by chance (p = 0.0017). The sequence changes caused by these hs1617 DNVs are predicted to create binding sites not seen in the reference sequence for transcription factors PAX6 and ZBTB7A and to disrupt binding sites for STAT1 and STAT3.
The hs1617 enhancer region is within the same topologically associated domain as HHAT, SERTAD4, and IRF6, all of which are involved in craniofacial development. All three genes are highly expressed in human neural crest cells. Knockout mice for Hhat and Irf6 have abnormal embryonic development including a cleft palate, and variants in and around IRF6 are associated with nonsyndromic and syndromic forms of OFCs in humans.
Taken together, this suggests that noncoding DNVs contribute to the genetic architecture of OFCs, with an excess of DNVs in OFC trios in enhancer regions near known OFC-associated genes. Overall, this adds to our understanding of the genetic mechanisms that underlie OFC formation.
口面部裂隙（OFCs）是最常见的颅面先天性缺陷，每700例出生中就有1例受影响，并且具有很强的遗传基础，在家族内复发风险很高。
虽然之前的许多研究已将常见的非编码基因座与OFCs相关联，但之前关于OFC病例中新生变异（DNVs）的研究主要集中在可能对蛋白质结构产生功能影响的编码变异上，非编码DNVs对OFCs形成的贡献在很大程度上被忽视且未得到充分理解。
我们重新分析了一个现有的来自1409个患有OFCs的三联体的DNV数据集，这些三联体已对已知的OFC相关基因座进行了靶向测序。然后，我们利用人类颅面发育过程中预测的表观遗传功能数据集的信息对这些DNV进行注释。
在本研究的靶向区域中检测到的66个DNV中，17个（25.7%）位于预测的增强子或启动子区域内。两个DNV位于同一增强子区域（hs1617），这一情况比随机预期的更为常见（p = 0.0017）。预计这些hs1617 DNV引起的序列变化会产生参考序列中未出现的转录因子PAX6和ZBTB7A的结合位点，并破坏STAT1和STAT3的结合位点。
hs1617增强子区域与HHAT、SERTAD4和IRF6处于相同的拓扑相关结构域内，所有这些基因都参与颅面发育。这三个基因在人类神经嵴细胞中均高度表达。Hhat和Irf6基因敲除小鼠具有异常的胚胎发育，包括腭裂，并且IRF6及其周围的变异与人类非综合征性和综合征性OFCs相关。
综上所述，这表明非编码DNVs对OFCs的遗传结构有贡献，在已知OFC相关基因附近的增强子区域中，OFC三联体中的DNV数量过多。总体而言，这增加了我们对OFC形成潜在遗传机制的理解。
