Uncovering new mechanisms of craniosynostosis associated with structural and copy number variation, using mouse modelling and human neural crest cells

使用小鼠模型和人类神经嵴细胞揭示与结构和拷贝数变异相关的颅缝早闭的新机制

• 批准号: MR/T031670/1
• 负责人: Andrew O M Wilkie
• 金额: $ 100.54万
• 依托单位: University of Oxford
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2020
• 资助国家: 英国
• 起止时间: 2020 至 无数据
• 项目状态: 未结题
• 来源: https://gtr.ukri.org/projects?ref=MR%2FT031670%2F1
• 关键词: Uncovering; new; mechanisms; craniosynostosis; associated

Growth of the skull to make space for the growing brain is possible because new bone is added to narrow gaps between the skull bones, termed cranial sutures, as the head grows. When one of these gaps fuses, this prevents further growth at the fused suture, a disorder termed craniosynostosis (CRS). This serious condition affects about 350 babies annually in the UK.CRS has many causes, but we know that in about 25% it occurs because of an altered genetic instruction regulating the complex signalling processes in the cranial sutures. Finding a genetic cause is important for many reasons. For parents, it ends the diagnostic odyssey; for clinical geneticists, it enables correct risks to be given and tests to be recommended; for the medical team, there may be specific complications to screen for. In biochemical disorders, the information can be critical for correct treatment. We can also learn more about how cranial sutures normally function.Despite this progress, there are many children with CRS in whom a genetic cause is suspected, but cannot be identified. For example in the 100,000 Genomes whole genome sequencing (WGS) Project (100kGP), 119 carefully selected patients/families with CRS have been analysed, but a diagnosis has only been achieved in ~18%. How might we be missing some genetic causes?Although DNA sequencing technology has achieved remarkable advances, there is still "dark matter" in the genome that is poorly characterised. For example 70% of our genome is made up of repetitive DNA that is hard to sequence and often gets scrambled when it is being copied. Consequently sections of DNA may be present in too many or too few copies (copy number variants - CNVs), or pieces may be altered in their position or orientation (structural variants - SVs). These CNVs and SVs can cause changes to the way nearby genes are expressed (RNA is made); as a result, a protein might be made in a tissue where the gene should normally be silent.In this project we want to look in more detail for these SVs and CNVs in children with complex CRS who remain without a diagnosis, as we suspect these could cause misexpression in cranial sutures leading to CRS. The 100kGP resource is ideal to study, because it represents the largest resource of WGS of these children in the world.Our proposed work comprises four broad elements: First, we want to take another look at the WGS data, using combinations of computational methods to find SV or CNV that might be causative. We will also use two relatively new technologies, nanopore sequencing and optical mapping, which look at genomes in different ways to the previous WGS; we expect these will reveal previously unknown SV and CNV. Second, for carefully chosen SV or CNV that we suspect may cause CRS, we will make the equivalent rearrangement in mice by genome engineering. If the mice show abnormal skull growth, this provides strong support that the rearrangement is causative of the human condition too. We plan to construct 4 different mouse mutants during the project.Third, we will test how well a different technology, that avoids the use of mice, might work. This involves inducing human cells to change into a type of cell termed neural crest, starting from a patient blood sample. This cell type is one of the major constituents of cranial sutures. We plan to construct 6 different neural crest lines during the project.Fourth, we will perform detailed tests comparing mouse tissues and neural crest cells, to see if cell function is disturbed. We will measure expression of the genes around the SV/CNV; assess how the DNA is folded inside the cell; and analyse the chemical modifications of proteins wrapping around the DNA.Our overall goals will be to extend understanding of the ways by which SV/CNV cause CRS and other diseases; obtain specific comparative data on methods of genome mapping and functional assessment to improve future analyses; and find new diagnoses for patients and families.

颅骨的生长为大脑的生长腾出空间是可能的，因为随着头部的生长，新骨被添加到颅骨之间的狭窄间隙中，称为颅缝。当其中一个间隙融合时，这会阻止融合缝的进一步生长，这种疾病称为颅缝早闭（CRS）。这种严重的疾病每年影响英国约350名婴儿。CRS有许多原因，但我们知道，大约25%的婴儿是因为改变了调节颅缝中复杂信号过程的遗传指令而发生的。找到一个遗传原因是很重要的，原因有很多。对父母来说，它结束了诊断的艰难历程;对临床遗传学家来说，它使正确的风险得到了给予，并推荐了测试;对医疗团队来说，可能有特定的并发症需要筛查。在生化疾病中，这些信息对于正确的治疗至关重要。我们还可以了解更多关于颅缝正常功能的信息。尽管取得了这些进展，但仍有许多儿童患有CRS，其遗传原因被怀疑，但无法确定。例如，在100，000个基因组全基因组测序（WGS）项目（100 kGP）中，已经分析了119名精心挑选的CRS患者/家庭，但仅在~ 18%中实现了诊断。我们怎么可能遗漏一些遗传原因呢？虽然DNA测序技术已经取得了显着的进步，但基因组中仍然存在“暗物质”，其特征很差。例如，我们基因组的70%是由重复的DNA组成的，这些DNA很难测序，而且在复制时经常会被打乱。因此，DNA片段可能存在太多或太少的拷贝（拷贝数变异-CNV），或者片段的位置或方向可能发生改变（结构变异-SV）。这些CNVs和SV可以引起附近基因表达方式的改变（产生RNA）;因此，一种蛋白质可能会在一个基因通常应该沉默的组织中产生。在这个项目中，我们想更详细地研究这些SV和CNVs在患有复杂CRS但没有得到诊断的儿童中的作用，因为我们怀疑这些SV和CNVs可能会导致颅缝中的错误表达，从而导致CRS。100 kGP资源是理想的研究，因为它代表了世界上最大的WGS资源，我们的工作包括四个主要内容：首先，我们想再看看WGS数据，使用计算方法的组合来找到可能是病因的SV或CNV。我们还将使用两种相对较新的技术，纳米孔测序和光学作图，它们以与以前的WGS不同的方式观察基因组;我们预计这些技术将揭示以前未知的SV和CNV。其次，对于我们怀疑可能导致CRS的SV或CNV，我们将通过基因组工程在小鼠中进行等效重排。如果小鼠显示出异常的头骨生长，这就有力地支持了这种重排也是人类疾病的原因。我们计划在项目期间构建4种不同的小鼠突变体。第三，我们将测试一种避免使用小鼠的不同技术的效果。这涉及从患者血液样本开始诱导人类细胞转变为一种称为神经嵴的细胞。这种细胞类型是颅缝的主要成分之一。我们计划在项目中构建6种不同的神经嵴线。第四，我们将进行详细的测试，比较小鼠组织和神经嵴细胞，看看细胞功能是否受到干扰。我们将测量SV/CNV周围基因的表达，评估DNA在细胞内是如何折叠的，并分析包裹在DNA周围的蛋白质的化学修饰。我们的总体目标是扩大对SV/CNV引起CRS和其他疾病的方式的理解;获得基因组定位和功能评估方法的具体比较数据，以改善未来的分析;为病人和家属找到新的诊断方法。

项目成果

Characterising clinically relevant complex structural variants in craniosynostosis using long-range technologies

使用远程技术表征颅缝早闭的临床相关复杂结构变异

• 发表时间: 2024
• 期刊: EUROPEAN JOURNAL OF HUMAN GENETICS
• 影响因子: 5.2
• 作者: Pei Yang

Pathogenic variants in the paired-related homeobox 1 gene (PRRX1) cause craniosynostosis with incomplete penetrance.

配对相关同源框 1 基因 (PRRX1) 的致病性变异会导致外显率不完全的颅缝早闭。

• DOI: 10.1016/j.gim.2023.100883
• 发表时间: 2023
• 期刊: official journal of the American College of Medical Genetics
• 作者: Tooze RS

Craniosynostosis, inner ear, and renal anomalies in a child with complete loss of SPRY1 (sprouty homolog 1) function.

• DOI: 10.1136/jmg-2022-108946
• 发表时间: 2023-07
• 期刊: Journal of medical genetics
• 影响因子: 4

Evaluating the performance of a clinical genome sequencing program for diagnosis of rare genetic disease, seen through the lens of craniosynostosis.

• DOI: 10.1038/s41436-021-01297-5
• 发表时间: 2021-12
• 期刊: Genetics in medicine : official journal of the American College of Medical Genetics
• 作者: Hyder Z;Calpena E;Pei Y;Tooze RS;Brittain H;Twigg SRF;Cilliers D;Morton JEV;McCann E;Weber A;Wilson LC;Douglas AGL;McGowan R;Need A;Bond A;Tavares ALT;Thomas ERA;Genomics England Research Consortium;Hill SL;Deans ZC;Boardman-Pretty F;Caulfield M;Scott RH;Wilkie AOM
• 通讯作者: Wilkie AOM