During human organogenesis, lung development is a timely and tightly regulated developmental process under the control of a large number of signaling molecules. Understanding how genetic variants can disturb normal lung development causing different lung malformations is a major goal for dissecting molecular mechanisms during embryogenesis. Here, through exome sequencing (ES), array CGH, genome sequencing (GS) and Hi-C, we aimed at elucidating the molecular basis of bilateral isolated lung agenesis in three fetuses born to a non-consanguineous family. We detected a complex genomic rearrangement containing duplicated, triplicated and deleted fragments involving the SHH locus in fetuses presenting complete agenesis of both lungs and near-complete agenesis of the trachea, diagnosed by ultrasound screening and confirmed at autopsy following termination. The rearrangement did not include SHH itself, but several regulatory elements for lung development, such as MACS1, a major SHH lung enhancer, and the neighboring genes MNX1 and NOM1. The rearrangement incorporated parts of two topologically associating domains (TADs) including their boundaries. Hi-C of cells from one of the affected fetuses showed the formation of two novel TADs each containing SHH enhancers and the MNX1 and NOM1 genes. Hi-C together with GS indicate that the new 3D conformation is likely causative for this condition by an inappropriate activation of MNX1 included in the neo-TADs by MACS1 enhancer, further highlighting the importance of the 3D chromatin conformation in human disease.

在人体器官发生过程中，肺发育是在大量信号分子控制下的及时且严格调控的发育过程。了解遗传变异如何干扰正常的肺发育导致不同的肺畸形是剖析胚胎发生过程中分子机制的主要目标。在这里，我们通过外显子组测序 (ES)、阵列 CGH、基因组测序 (GS) 和 Hi-C，旨在阐明非近亲家庭所生三个胎儿双侧孤立肺发育不全的分子基础。我们检测到一个复杂的基因组重排，其中包含重复、三次重复和缺失的片段，这些片段涉及胎儿的 SHH 基因座，表现为双肺完全发育不全和气管几乎完全发育不全，通过超声筛查诊断并在终止后的尸检中确认。重排不包括SHH本身，但是肺发育的几个调节元件，例如 MACS1，一种主要的SHH肺增强剂，以及邻近的基因MNX1和NOM1。重排合并了两个拓扑关联域 (TAD) 的部分，包括它们的边界。来自其中一个受影响胎儿的细胞的 Hi-C 显示形成了两个新的 TAD，每个 TAD 都含有SHH增强子和MNX1和NOM1基因。Hi-C 与 GS 一起表明，新的 3D 构象可能是由MNX1的不适当激活引起的MACS1 增强子包含在 neo-TAD 中，进一步强调了 3D 染色质构象在人类疾病中的重要性。