The development of the cerebral cortex involves a series of dynamic events, including cell proliferation and migration, which rely on the motor protein dynein and its regulators NDE1 and NDEL1. While the loss of function in NDE1 leads to microcephaly-related malformations of cortical development (MCDs), NDEL1 variants have not been detected in MCD patients. Here, we identified two patients with pachygyria, with or without subcortical band heterotopia (SBH), carrying the same de novo somatic mosaic NDEL1 variant, p.Arg105Pro (p.R105P). Through single-cell RNA sequencing and spatial transcriptomic analysis, we observed complementary expression of Nde1/NDE1 and Ndel1/NDEL1 in neural progenitors and post-mitotic neurons, respectively. Ndel1 knockdown by in utero electroporation resulted in impaired neuronal migration, a phenotype that could not be rescued by p.R105P. Remarkably, p.R105P expression alone strongly disrupted neuronal migration, increased the length of the leading process, and impaired nucleus–centrosome coupling, suggesting a failure in nucleokinesis. Mechanistically, p.R105P disrupted NDEL1 binding to the dynein regulator LIS1. This study identifies the first lissencephaly-associated NDEL1 variant and sheds light on the distinct roles of NDE1 and NDEL1 in nucleokinesis and MCD pathogenesis.

大脑皮层的发育涉及一系列动态事件，包括细胞增殖和迁移，这些事件依赖于运动蛋白动力蛋白及其调节因子NDE1和NDEL1。虽然 NDE1 功能丧失会导致小头畸形相关的皮质发育畸形 (MCD)，但在 MCD 患者中尚未检测到NDEL1变异。在这里，我们鉴定了两名患有脑回肥大的患者，有或没有皮质下带异位（SBH），携带相同的从头体细胞镶嵌NDEL1变异，p.Arg105Pro（p.R105P）。通过单细胞RNA测序和空间转录组分析，我们分别观察到Nde1 / NDE1和Ndel1 / NDEL1在神经祖细胞和有丝分裂后神经元中的互补表达。通过子宫内电穿孔敲低Ndel1会导致神经元迁移受损，这种表型无法通过 p.R105P 来挽救。值得注意的是，p.R105P 的单独表达会强烈破坏神经元迁移，增加前导过程的长度，并损害核-中心体耦合，表明核运动失败。从机制上讲，p.R105P 破坏了 NDEL1 与动力蛋白调节因子 LIS1 的结合。这项研究鉴定了第一个与无脑畸形相关的NDEL1变异，并揭示了 NDE1 和 NDEL1 在核分裂和 MCD 发病机制中的不同作用。