New Down syndrome brain organization revealed by single-cell genomics

项目概要/摘要 近100%的唐氏综合症（DS;人类21号染色体三体）患者活到了50岁 显示阿尔茨海默病（AD）样痴呆和神经病理学（DS-AD），代表了一种 突出的DS合并症，最近被报道为DS成人死亡的主要原因。超出 21号染色体三体，包括关键的AD基因，淀粉样前体蛋白（APP），分子 DS-AD的潜在机制一直难以确定。没有疾病修饰疗法（DMT） 预防或治疗DS-AD，从而改善DS生活质量和寿命。 这个INCLUDE提案将通过揭示转录组学（RNA）和 基因组（DNA）单细胞景观的老化DS个人，特别是DS-AD大脑，通过集中 一种新的人类大脑分子机制，可能是DS-AD的基础：体细胞基因重组（SGR） 以及由此产生的基因组和转录组异质性。SGR有可能改变人类的DNA蓝图， DS脑细胞导致脑细胞的功能后果，可以解释DS-AD的发作以及 其他DS脑合并症，如自闭症和癫痫。SGR尚未在DS大脑中进行检查，如果 操作，将提供一个从根本上新的观点如何基因和基因剂量的行动，以促进DS-AD 随着时间已知SGR作用于正常和散发性AD神经元中的APP，导致数千个新的APP 人类大脑中的变异，并已在科学文献中得到独立证实。的 已证实的DS脑基因表达增加，结合已鉴定的基因表达与SGR的联系， 提示通过21三体在转录上增加的基因是DS-AD中SGR的新靶点。APP很可能是 神经元和非神经元细胞中受DS影响的基因的“冰山一角”，这对DS和 以及正常和患病人脑的其他状态。三个独立的，但紧密相连的， 研究要素（RE）将由一个经过验证的分子生物学家协作团队完成， 神经科学家，神经学家，生物工程师和生物信息学家来检验SGR有助于 通过改变单细胞中已知和未知的疾病基因， 在DS脑内的转录组和基因组水平。RE 1和RE 2将使用尖端测序技术 用于询问DS和DS-AD单核的转录组和基因组异质性的技术 与对照组相比，并将信息整合转录组表达，染色质可及性， 跨细胞类型的单细胞内的新同种型检测和基因组嵌合形式，包括基因组DNA 随着年龄的增长RE 3将探索SGR在原代神经元和诱导多能神经元中的功能后果。 干细胞（iPSC）模型，以了解疾病增强SGR的功能意义， SGR揭示的治疗机会。

PROJECT SUMMARY/ABSTRACT Nearly 100% of Down syndrome (DS; trisomy of human chromosome 21) individuals that live into their 5th decade of life and beyond, show Alzheimer’s disease (AD)-like dementia and neuropathology (DS-AD), representing a prominent DS comorbidity that has recently been reported as the leading cause of death for DS adults. Beyond trisomy of chromosome 21, which includes the key AD gene, amyloid precursor protein (APP), the molecular mechanisms underlying DS-AD have resisted identification. There are no disease-modifying therapies (DMTs) to prevent or treat DS-AD, which could improve DS quality of life and lifespan. This INCLUDE proposal will transform our understanding of DS by revealing the transcriptomic (RNA) and genomic (DNA) single-cell landscape of the aging DS individual, and especially the DS-AD brain, by centering upon a novel human brain molecular mechanism that might underlie DS-AD: somatic gene recombination (SGR) and resultant genomic and transcriptomic heterogeneity. SGR has the potential to change the DNA blueprint of DS brain cells resulting in functional consequences for brain cells that could explain DS-AD onset as well as other DS brain comorbidities such as autism and epilepsy. SGR has not been examined in DS brains, which if operational, would provide a fundamentally new view on how genes and gene dosage act to promote DS-AD over time. SGR is known to act on APP in normal and sporadic AD neurons, resulting in thousands of new APP variants within individual human brains and has been independently confirmed in the scientific literature. The proven increases in DS brain gene expression, combined with the identified linkage of gene expression to SGR, implicates genes transcriptionally increased by trisomy 21 as new targets for SGR in DS-AD. APP is likely the “tip of the iceberg” for DS-affected genes in neurons and non-neuronal cells, with implications for both DS as well as other states of the normal and diseased human brain. Three independent, but deeply-connected, Research Elements (REs) will be completed by a proven, collaborative team of molecular biologists, neuroscientists, neurologists, bioengineers, and bioinformaticians to test the hypothesis that SGR contributes to DS brain deficits and DS-AD by altering known and unknown disease genes at the single-cell transcriptomic and genomic level within the DS brain. RE1 and RE2 will use cutting-edge sequencing technologies to interrogate the transcriptomic and genomic heterogeneity of single nuclei from DS and DS-AD brains compared to controls, and will informatically integrate transcriptomic expression, chromatin accessibility, novel isoform detection and genomic mosaicism forms, including gencDNAs, within single cells across cell types and with age. RE3 will explore the functional consequences SGR in primary neuronal and induced pluripotent stem cell (iPSC) models towards understanding the functional implications of disease enhanced SGR, and the therapeutic opportunities that SGR unveils.