A novel SMARCC1 -mutant BAFopathy implicates epigenetic dysregulation of neural progenitors in hydrocephalus.
A novel SMARCC1 -mutant BAFopathy implicates epigenetic dysregulation of neural progenitors in hydrocephalus.
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一种新的 SMARCC1 突变 BAF 病涉及脑积水神经祖细胞的表观遗传失调。
DOI：
10.1101/2023.03.19.23287455
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发表时间：
2023
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作者：
Singh,AmritaK;Viviano,Stephen;Allington,Garrett;McGee,Stephen;Kiziltug,Emre;Mekbib,KedousY;Shohfi,JohnP;Duy,PhanQ;DeSpenza,Tyrone;Furey,CharutaG;Reeves,BenjaminC;Smith,Hannah;Ma,Shaojie;Sousa,AndréMM;Cherskov,Adriana;
重要性脑积水，以脑室扩大为特征，是最常见的需要脑部手术的疾病。先天性脑积水（CH）的一些家族形式已被确定，但大多数散发病例的CH的原因仍然难以捉摸。最近的研究表明，SMARCC 1是B RG 1-相关因子（BAF）染色质重塑复合物的一个组成部分，是CH基因的候选基因。然而，SMARCC 1变异体尚未在大型患者队列中进行系统性检查，也未与人类综合征最终相关。此外，CH相关SMARCC 1变体尚未在体内进行功能验证或机制研究。本研究的目的是（i）评估SMARCC 1中罕见的、破坏性的新生突变（DNM）与脑室扩大相关的程度;（ii）描述SMARCC 1突变患者的临床和放射学表型;（iii）评估CH相关SMARCC 1突变的体内致病性和机制。设计、设置和参与者使用全外显子组测序进行了一项遗传关联研究，该研究来自一个由2，697名脑室扩大三人组组成的队列，包括接受神经外科治疗的CH患者，共收集了5年（2016-2021）的8，091个外显子组。2023年数据分析。比较对照队列由来自自闭症谱系障碍患者的未受影响的兄弟姐妹及其未受影响的父母的1，798个外显子组组成，这些外显子组来自Simons simplex财团。主要成果和措施使用严格、经过验证的标准识别和过滤基因变体。富集试验评估基因水平变异负荷。计算机生物物理建模估计了变体对蛋白质结构影响的可能性和程度。通过分析RNA测序数据评估CH相关SMARCC 1突变对人胎脑转录组的影响。Smarcc 1敲除和患者特异性Smarcc 1变体在非洲爪蟾中进行了测试，并使用光学相干断层扫描成像，原位杂交和免疫荧光显微镜进行了研究。结果SMARCC 1在DNM富集试验中超过全基因组显著性阈值。在无关患者中检测到6种罕见的蛋白质改变DNM，包括4种功能丧失突变和1种复发性典型剪接位点突变（c.1571+1G>A）。DNM定位于SMARCC 1的高度保守的DNA相互作用的SWE 3、Myb-DNA结合、富含Glu和染色体结构域。患者表现出发育迟缓（DD）、导水管狭窄和其他结构性脑和心脏缺陷。G 0和G1 Smarcc 1爪蟾突变体表现出导水管狭窄和心脏缺陷，并被人类野生型SMARCC 1拯救，但不是患者特异性SMARCC 1突变体。脑积水SMARCC 1突变的人胎脑和Smarcc 1突变的爪蟾脑表现出类似的改变表达的关键基因与妊娠中期神经发生，包括转录因子NEUROD 2和MAB 21 L2。结论SMARCC 1是一个真正的CH危险基因。SMARCC 1中的DNM引起一种新的人类BAF病，我们称之为“SMARCC 1-相关发育不全综合征（SaDDS）"，其特征在于脑室扩大、导水管狭窄、DD和各种结构性脑或心脏缺陷。这些数据强调了SMARCC 1和BAF染色质重塑复合物对人脑形态发生的重要性，并为人类CH发病机制的“神经干细胞”范例提供了证据。这些结果突出了基于三重的WES用于识别风险的实用性。
Importance Hydrocephalus, characterized by cerebral ventriculomegaly, is the most common disorder requiring brain surgery. A few familial forms of congenital hydrocephalus (CH) have been identified, but the cause of most sporadic cases of CH remains elusive. Recent studies have implicated SMARCC1 , a component of the B RG1- a ssociated factor (BAF) chromatin remodeling complex, as a candidate CH gene. However, SMARCC1 variants have not been systematically examined in a large patient cohort or conclusively linked with a human syndrome. Moreover, CH-associated SMARCC1 variants have not been functionally validated or mechanistically studied in vivo . Objectives The aims of this study are to (i) assess the extent to which rare, damaging de novo mutations (DNMs) in SMARCC1 are associated with cerebral ventriculomegaly; (ii) describe the clinical and radiographic phenotypes of SMARCC1 -mutated patients; and (iii) assess the pathogenicity and mechanisms of CH-associated SMARCC1 mutations in vivo . Design, setting, and participants A genetic association study was conducted using whole-exome sequencing from a cohort consisting of 2,697 ventriculomegalic trios, including patients with neurosurgically-treated CH, totaling 8,091 exomes collected over 5 years (2016-2021). Data were analyzed in 2023. A comparison control cohort consisted of 1,798 exomes from unaffected siblings of patients with autism spectrum disorder and their unaffected parents sourced from the Simons simplex consortium. Main outcomes and measures Gene variants were identified and filtered using stringent, validated criteria. Enrichment tests assessed gene-level variant burden. In silico biophysical modeling estimated the likelihood and extent of the variant impact on protein structure. The effect of a CH-associated SMARCC1 mutation on the human fetal brain transcriptome was assessed by analyzing RNA-sequencing data. Smarcc1 knockdowns and a patient-specific Smarcc1 variant were tested in Xenopus and studied using optical coherence tomography imaging, in situ hybridization, and immunofluorescence microscopy. Results SMARCC1 surpassed genome-wide significance thresholds in DNM enrichment tests. Six rare protein-altering DNMs, including four loss-of-function mutations and one recurrent canonical splice site mutation (c.1571+1G>A) were detected in unrelated patients. DNMs localized to the highly conserved DNA-interacting SWIRM, Myb-DNA binding, Glu-rich, and Chromo domains of SMARCC1 . Patients exhibited developmental delay (DD), aqueductal stenosis, and other structural brain and heart defects. G0 and G1 Smarcc1 Xenopus mutants exhibited aqueductal stenosis and cardiac defects and were rescued by human wild-type SMARCC1 but not a patient-specific SMARCC1 mutant. Hydrocephalic SMARCC1 -mutant human fetal brain and Smarcc1 -mutant Xenopus brain exhibited a similarly altered expression of key genes linked to midgestational neurogenesis, including the transcription factors NEUROD2 and MAB21L2 . Conclusions SMARCC1 is a bona fide CH risk gene. DNMs in SMARCC1 cause a novel human BAFopathy we term “ S MARCC1- a ssociated D evelopmental D ysgenesis S yndrome (SaDDS)”, characterized by cerebral ventriculomegaly, aqueductal stenosis, DD, and a variety of structural brain or cardiac defects. These data underscore the importance of SMARCC1 and the BAF chromatin remodeling complex for human brain morphogenesis and provide evidence for a “neural stem cell” paradigm of human CH pathogenesis. These results highlight the utility of trio-based WES for identifying risk …