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

摘要 在这里，我们建议对父母拨款中提出的研究提出补充意见 增强子在衰老过程中编码，以执行我们最初关于细胞的特定目标的逻辑扩展 衰老/衰老以获得对这些事件之间的区别的初步见解和明显的病理 每种中枢神经系统细胞类型中可能代表散发性潜在机制的因果特征 阿尔茨海默病(AD)。最初赠款的具体目标是采用和开发生物统计工具 与细胞衰老和复制衰老有关，包括对潜在的表观基因组的检查 改变和增强子激活密码最终导致细胞衰老的途径，并提出 单细胞方法的应用。应用这些具体的目标/方法特别适合于 加强我们对临床散发性AD的潜在初始原因事件的理解，这是一种衰老- 影响男性和在更大程度上影响女性的相关疾病。与……的初衷一致 了解增强子介导的细胞衰老和衰老程序的分子基础 作为补充，我们建议扩展我们最初的特定目标，以揭示支持 每种中枢神经系统细胞类型中的老化事件，以允许检查中心问题是否改变的增强子 在每种细胞类型中，AD的转录组变化代表了不同于正常衰老相关的轨迹 这些细胞类型的改变。我们假设，虽然每种细胞类型都会表现出特定的特征 就像我们在亲代中发现的那样，衰老甚至细胞衰老的增强子激活特征 格兰特，AD代表了这些细胞类型的不同轨迹。本副刊是根据我们的能力由我们的 单核(SN)RNA-SEQ和DNA同时定量技术的发展 使用Shiley-Marcos阿尔茨海默病脑库存储的档案样本进行SnATAC-SEQ 加州大学洛杉矶分校研究中心(ADRC)。我们已经仔细地试行了这种方法，以确保我们在技术上 能够获得高质量的数据，所有拟议的信息化管道和我们成功的能力 汇总如此海量的数据集是完全确定的。《副刊》将授权我们扩大 分析以获得能够产生统计上有意义的结果的数据集，从而提供信息 结论，这些结论最终可以通过从现有数据库中推算和使用 HiPSCs产生特定的细胞类型，用于验证转录分析。我们在这方面的首要目标是 补充是将所描述的技术和新的信息学方法应用于足够数量的 存档的样本，以允许制定区分启动的实际转录因子和途径 在特定的中枢神经系统细胞类型中AD过程的研究。

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.