The Aging vs Disease Trajectory Trees of CNS Cell Types Based on Simultaneous Single Nuclear Global Genomic Analyses

摘要 在这里，我们提出了一个补充的研究提出的父母补助金的组合监管的 增强子在衰老中的编码，以执行我们最初关于细胞的特定目标的逻辑扩展。 衰老/衰老，以实现对这些事件和不同病理学之间的区别的初步见解 每种CNS细胞类型中的因果特征，可能代表散发性 阿尔茨海默病（AD）。初始赠款的具体目标采用和开发生物统计工具 与细胞衰老和复制性衰老有关，包括对潜在的表观基因组 改变和增强激活码最终导致细胞衰老的方法，并提出了 应用单细胞方法。应用这些具体目标/方法特别适合于 提高我们对临床散发性AD中最终发生的潜在初始因果事件的理解， 相关疾病影响男性，并在更大程度上影响女性。与最初的目标一致， 了解增强子介导的细胞衰老和衰老程序的分子基础， 补充，我们建议扩展我们原来的具体目标，以揭示增强程序的基础， 在每种CNS细胞类型中的衰老事件，以允许检查改变的增强子是否 在每种细胞类型中，AD的转录组变化代表了与正常衰老相关的 这些细胞类型的变化。我们假设，虽然每种细胞类型当然都会表现出特定的特征， 衰老甚至细胞衰老的增强子激活特征，正如我们在亲本中发现的那样， 格兰特，AD代表了这些细胞类型的独特轨迹。本补充材料由我们的能力许可， 开发同时定量单核（sn）RNA-seq和 snATAC-seq使用存储在Shiley-Marcos阿尔茨海默病脑库中的档案样本 研究中心（ADRC）在UCSD。我们已经仔细地试验了这种方法，以确保我们在技术上 能够获得高质量的数据，所有拟议的信息管道和我们成功地 如此庞大的数据集已经完全建立起来。补充协议将授权我们扩大 分析，以获得能够产生统计学显著结果的数据集，因此， 结论，这最终可以进一步验证插补从现有的数据库和使用 hiPSC以产生用于验证转录分析的特定细胞类型。我们在这方面的首要目标 补充是将所描述的技术和新的信息方法应用于足够数量的 存档的标本，以允许制定实际的转录因子和途径，区分启动 在特定的中枢神经系统细胞类型中的AD过程。

ABSTRACT Here we propose a Supplement to the research proposed in the parent grant Combinatorial regulation of the enhancer codes in senescence to perform a logical extension of our initial Specific Aims regarding cellular aging/senescence to achieve initial insights into the distinction between these events and distinct pathological causal features in each CNS cell type that may represent the underlying mechanisms underlying sporadic Alzheimer’s Disease (AD). The Specific Aims of the initial grant employed and developed biostatistical tools relevant to cellular aging and replicative senescence, including an examination of underlying epigenomic alterations and enhancer activation codes ultimately leading to cellular senescence approaches and proposed application of single cells approaches. Appling these specific aims/approaches is particularly suitable for enhancing our understanding of the potential initial causal events that eventuate in clinical sporadic AD, an aging- associated disease affecting both men and, to a greater extent, women. In concert with the original Aim of understanding the molecular basis for enhancer-mediated programs of cellular aging and senescence, in this Supplement, we propose to extend our original Specific Aims to uncover the enhancer program underlying the aging events in each CNS cell type, to permit examination of the central question whether the altered enhancer and transcriptome changes in AD in each cell type represent a trajectory distinct from the normal aging-related alterations in these cell types. We hypothesize that, while each cell type will, of course, exhibit specific features of enhancer activation characteristic of aging and even cellular senescence, as we have uncovered in the parent grant, AD represents a distinct trajectory for these cell types. This Supplement is licensed by our ability by our development of the technology to perform simultaneous quantitation of single nucleus (sn) RNA-seq and snATAC-seq using archival samples stored at the brain bank of the Shiley-Marcos Alzheimer's Disease Research Center (ADRC) at UCSD. We have carefully piloted this approach to ensure that we are technically able to obtain high quality data and that all of the proposed informatic pipelines and our ability to successfully aggregate such massive data sets is fully established. The Supplement would license our ability to scale the analysis to obtain data sets capable of generating statistically significant results and, therefore, informative conclusions, which can be ultimately be further validated by imputation from available data bases and using hiPSCs to generate specific cell types for validating transcriptional analyses. Our overarching goal in this Supplement is to apply the described technologies and new informatic approaches to a sufficient number of archived specimens to permit formulating the actual transcription factors and pathways that distinguish initiation of the AD process in specific CNS cell types.