Del Rocío Pérez Baca María, Jacobs Eva Z, Vantomme Lies, Leblanc Pontus, Bogaert Elke, Dheedene Annelies, De Cock Laurenz, Haghshenas Sadegheh, Foroutan Aidin, Levy Michael A, Kerkhof Jennifer, McConkey Haley, Chen Chun-An, Batzir Nurit Assia, Wang Xia, Palomares Maria, Carels Marieke, Demaut Bart, Sadikovic Bekim, Menten Björn, Yuan Bo, Vergult Sarah, Callewaert Bert
medRxiv. 2023 May 24:2023.05.22.23289895. doi: 10.1101/2023.05.22.23289895.
Neurodevelopmental disorders (NDDs) result from impaired development and functioning of the brain. Here, we identify loss-of-function variation in as a novel cause for syndromic intellectual disability (ID). ZFHX3, previously known as ATBF1, is a zinc-finger homeodomain transcription factor involved in multiple biological processes including cell differentiation and tumorigenesis. Through international collaboration, we collected clinical and morphometric data (Face2Gene) of 41 individuals with protein truncating variants (PTVs) or (partial) deletions of . We used data mining, RNA and protein analysis to identify the subcellular localization and spatiotemporal expression of ZFHX3 in multiple models. We identified the DNA targets of ZFHX3 using ChIP seq. Immunoprecipitation followed by mass spectrometry indicated potential binding partners of endogenous ZFHX3 in neural stem cells that were subsequently confirmed by reversed co-immunoprecipitation and western blot. We evaluated a DNA methylation profile associated with haploinsufficiency using DNA methylation analysis on whole blood extracted DNA of six individuals with PTVs and four with a (partial) deletion of . A reversed genetic approach characterized the orthologue in . Loss-of-function variation of consistently associates with (mild) ID and/or behavioural problems, postnatal growth retardation, feeding difficulties, and recognizable facial characteristics, including the rare occurrence of cleft palate. Nuclear abundance of ZFHX3 increases during human brain development and neuronal differentiation in neural stem cells and SH-SY5Y cells, ZFHX3 interacts with the chromatin remodelling BRG1/Brm-associated factor complex and the cleavage and polyadenylation complex. In line with a role for chromatin remodelling, haploinsufficiency associates with a specific DNA methylation profile in leukocyte-derived DNA. The target genes of ZFHX3 are implicated in neuron and axon development. In , z considered to be the orthologue, is expressed in the third instar larval brain. Ubiquitous and neuron-specific knockdown of zfh2 results in adult lethality underscoring a key role for zfh2 in development and neurodevelopment. Interestingly, ectopic expression of zfh2 as well as ZFHX3 in the developing wing disc results in a thoracic cleft phenotype. Collectively, our data shows that loss-of-function variants in are a cause of syndromic ID, that associates with a specific DNA methylation profile. Furthermore, we show that ZFHX3 participates in chromatin remodelling and mRNA processing.
神经发育障碍（NDDs）是由大脑发育和功能受损引起的。在此，我们鉴定出[基因名称]功能丧失性变异是综合征性智力残疾（ID）的一个新病因。ZFHX3，以前称为ATBF1，是一种锌指同源域转录因子，参与包括细胞分化和肿瘤发生在内的多个生物学过程。通过国际合作，我们收集了41名携带蛋白质截短变异（PTV）或[基因名称]（部分）缺失个体的临床和形态学数据（Face2Gene）。我们使用数据挖掘、RNA和蛋白质分析来确定ZFHX3在多个[模型名称]模型中的亚细胞定位和时空表达。我们使用ChIP seq鉴定ZFHX3的DNA靶点。免疫沉淀后进行质谱分析表明神经干细胞中内源性ZFHX3的潜在结合伙伴，随后通过反向共免疫沉淀和蛋白质印迹法得到证实。我们使用对6名携带[基因名称]PTV和4名携带[基因名称]（部分）缺失个体的全血提取DNA进行DNA甲基化分析，评估与[基因名称]单倍剂量不足相关的DNA甲基化谱。一种反向遗传学方法对[物种名称]中的[基因名称]直系同源物进行了表征。[基因名称]功能丧失性变异始终与（轻度）ID和/或行为问题、出生后生长发育迟缓、喂养困难以及可识别的面部特征相关，包括腭裂的罕见发生。在人类大脑发育以及神经干细胞和SH - SY5Y细胞的神经元分化过程中，ZFHX3的核丰度增加，ZFHX3与染色质重塑BRG1/Brm相关因子复合物以及切割和聚腺苷酸化复合物相互作用。与染色质重塑的作用一致，[基因名称]单倍剂量不足与白细胞衍生DNA中的特定DNA甲基化谱相关。ZFHX3的靶基因与神经元和轴突发育有关。在[物种名称]中，z[基因名称]被认为是[基因名称]的直系同源物，在三龄幼虫大脑中表达。zfh2在全身和神经元特异性敲低会导致成虫死亡，突出了zfh2在发育和神经发育中的关键作用。有趣的是，在发育中的翅芽盘中异位表达zfh2以及ZFHX3会导致胸裂表型。总体而言，我们的数据表明[基因名称]功能丧失性变异是综合征性ID的一个病因，与特定的DNA甲基化谱相关。此外，我们表明ZFHX3参与染色质重塑和mRNA加工。
