The chromatin remodeler CHD1L controls human cortical neurogenesis and contributes to distal 1q21.1 deletion/duplication syndrome [CUT&RUN]

Background/objectives: Deletions and duplications of the distal 1q21.1 region are associated with syndromic forms of autism (MIM612474, 612475). Variable phenotypes have been reported, including congenital heart defects, autism, schizophrenia, head circumference and height defects. Methods: To elucidate which gene(s) are responsible for the 1q21.1 duplication/deletion- associated phenotypes, we performed gene manipulation in zebrafish and mice. We deciphered the function of candidate driver(s) by multi-omics approaches on human iPSC- derived neural progenitor cells (NPC) and cerebral organoids (CO). Results: We modeled duplication of the 1q21.1 region by overexpressing the 8 genes in the region in zebrafish. We found that only overexpression of CHD1L led to macrocephaly and increased larval body length. Conversely, deletion of the CHD1L zebrafish ortholog resulted in microcephaly and decreased larval body length. These mirror phenotypes are also observed when Chd1l expression is modulated in a mammalian model, notably with a variation in the number of mature Tbr1-positive neurons in the mouse embryo. NPCs derived from control and CHD1L Knock-out isogenic hiPSCs were subjected to transcriptomic and chromatin accessibility analyses. These approaches revealed that CHD1L regulates the expression levels and accessibility of genes involved in neuronal differentiation and synaptogenesis, including autism susceptibility genes such as UNC5D and DPP6. Strikingly, absence of CHD1L shifts the cellular identity from forebrain to retinal fate in CO. Finally, pathogenic missense and truncating variants of CHD1L were found in individuals with autism and/or height defects. Conclusion: CHD1L is a major contributor of the 1q21.1 duplication/deletion-associated microcephaly and growth defects. CHD1L dosage is required during human brain regionalization. Overall design: Human Neural Progenictor Cells derived from hiPSC were subjected to CUT&RUN analysis targeting the proteins CHD1L and H3K4me2.

研究背景与目的：1q21.1远端区域的缺失与重复与综合征型自闭症（MIM612474、612475）相关。已有研究报道该变异存在多种可变表型，涵盖先天性心脏缺陷、自闭症、精神分裂症、头围异常与身高异常。研究方法：为明确1q21.1重复/缺失相关表型的致病基因，我们分别在斑马鱼与小鼠中开展基因操纵实验，并通过多组学方法对人类诱导多能干细胞（induced pluripotent stem cell, iPSC）分化得到的神经前体细胞（neural progenitor cell, NPC）及脑类器官（cerebral organoid, CO）进行分析，以解析候选致病驱动基因的功能。研究结果：我们通过在斑马鱼中过表达该区域的8个编码基因，构建了1q21.1区域重复的疾病模型。实验发现，仅过表达CHD1L即可导致巨头畸形及仔鱼体长增加。反之，敲除斑马鱼中CHD1L的同源基因则会引发小头畸形与仔鱼体长缩短。这种表型镜像效应在调控哺乳动物模型中Chd1l的表达时同样被观测到，具体体现为小鼠胚胎内成熟Tbr1阳性神经元的数量发生显著变化。我们对来自对照及CHD1L敲除同基因人类诱导多能干细胞（human induced pluripotent stem cell, hiPSC）的神经前体细胞开展了转录组学与染色质开放性分析。上述分析结果显示，CHD1L可调控参与神经元分化与突触发生的基因的表达水平及染色质开放性，其中包括UNC5D、DPP6等自闭症易感基因。值得注意的是，在脑类器官中，CHD1L的缺失会将细胞身份从前脑命运转变为视网膜命运。最终，我们在自闭症患者及/或身高异常患者体内检测到了CHD1L的致病性错义变异与截短变异。研究结论：CHD1L是1q21.1区域重复/缺失相关小头畸形与生长发育缺陷的核心致病因子。在人类大脑区域特化进程中，CHD1L的剂量表达调控不可或缺。整体实验设计：将来自人类诱导多能干细胞的神经前体细胞进行针对CHD1L蛋白与H3K4me2组蛋白修饰的CUT&RUN分析。