作者团队

Nelson Johansen, Saroja Somasundaram, ... , Trygve E Bakken, Rebecca D Hodge, Jeremy A Miller

研究方向

人类皮质细胞图谱；snRNA-Seq；WGS

论文题目 

Interindividual variation in human cortical cell type abundance and expression

论文摘要

INTRODUCTION: Interindividual variation is a known feature of the human brain. In neocortical regions, broad classes of neurons and non-neuronal cells vary in abundance and gene expression in healthy adult humans, yet variation remains unexplored within finer divisions of cell types. Characterizing the effects of biological factors such as age, sex, ancestry, disease, or genetic variants on high-resolution cell types requires molecular profiling of single nuclei from large donor cohorts.

RATIONALE: Single-nucleus RNA-sequencing (snRNA-seq) combined with whole-genome sequencing (WGS) applied to a large cohort of donors enable comprehensive assessment of interdonor variation in the neocortex of nonaged adults. Integrated analyses of demographic characteristics, single-nucleotide polymorphisms (SNPs), and gene expression can implicate genes associated with biological factors and gene regulatory regions in specific cell types. Such work can also serve as an important baseline to interpret cellular variation in neurological and psychiatric diseases that affect cortical function, and for understanding changes with age and associated neurodegenerative disorders.

RESULTS: We present comprehensive transcriptomic (snRNA-seq) and genomic (WGS) profiling of cortical tissues from 75 human brain donors comprising nearly 400,000 nuclei covering all major neocortical cell types. We show quantitatively that nearly all cells collected from these adult donors can be confidently assigned to a cell type in a taxonomy defined by using only a few donors. This demonstrates a highly consistent cellular architecture across individuals and confirms the viability of cell type mapping for larger-scale studies. These highly conserved cell types showed substantial variation in gene expression and abundances between individuals driven by multiple biological factors. Underlying medical conditions in our donor cohort affect cellular abundance. For example, PVALB-expressing interneurons show decreased abundance in epilepsy cases, reflecting previously reported cell loss in this disease.

We found differences in gene expression across individuals at the finest cell type resolution. Gene networks in excitatory neurons and glia were particularly variable across donors, irrespective of medical condition or brain region. Deep-layer neuronal types that communicate with distant brain regions showed higher variation than that in superficial types. A substantial proportion of variation in gene expression is explained by donor, including contributions from age, sex, ancestry, and disease state. Furthermore, genomic variation was significantly associated with variable gene expression, with most cell types containing cis-expression quantitative trait loci. Yet much variation remains unexplained by measured factors, paving the way for larger studies of similar design.

CONCLUSION: By profiling the human brain across 75 adult individuals through use of snRNA-seq and WGS, we assessed variation in cortical cellular abundance and gene expression at cell type–level resolution. This study indicates a highly consistent cellular makeup across human individuals but with substantial variation that reflects donor characteristics, disease condition, and genetic regulation that will provide a comprehensive reference for future studies of disease.

    介绍：个体间差异是人类大脑的一个已知特征。在新皮质区域，健康成人中广泛的神经元和非神经元细胞种类在数量和基因表达方面存在差异，但在细胞类型的更精的细胞类型中，差异仍未被探索。为了确定生物学因素（如年龄、性别、血统、疾病或遗传变异）对高分辨率细胞类型的影响，需要分析来自大型队列的单细胞核分子图谱。

    基本原理：单核RNA测序（snRNA-seq）结合全基因组测序（WGS）应用于大量供体队列，可以全面评估非老年成人新皮层供体间的差异。对人口统计学特征、单核苷酸多态性（SNPs）和基因表达的综合分析可以揭示特定细胞类型中与生物因子和基因调控区域相关的基因。这些工作也可以作为重要的基础，用于解释影响皮质功能的神经和精神疾病中的细胞变异，以及理解随年龄变化和相关神经退行性疾病。

    结果：对来自75名人类大脑供体的皮质组织进行了全面的转录组学（snRNA-seq）和基因组学（WGS）分析，其中包括近40万个细胞核，涵盖了所有主要的新皮质细胞类型。定量分析表明，几乎所有从这些成年样本收集的细胞都可以有效地分配到仅使用少数供体定义分类的细胞类型。证明了个体间高度一致的细胞结构，并证实了细胞类型用于更大规模研究的可行性。这些高度保守的细胞类型在受多种生物因素驱动的个体之间显示出显著的基因表达和丰度差异。在这项研究的样本队列中，潜在的健康状况影响细胞丰度。例如，表达pvalb的中间神经元在癫痫病例中显示丰度降低，反映了先前报道的这种疾病的细胞损失。

    研究人员发现在最精细的细胞类型分辨率下，个体间的基因表达存在差异。兴奋性神经元和神经胶质细胞中的基因网络在不同样本中的差异尤其明显，与健康状况或大脑区域无关。与远端脑区交流的深层神经元类型比浅层神经元类型表现出更高的变异。基因表达的很大一部分变异可由样本解释，包括来自年龄、性别、血统和疾病状态的影响。此外，基因组变异与可变基因表达显著相关，大多数细胞类型含有顺式表达的数量性状位点。然而，许多变化仍然无法通过测量因素来解释，这为类似设计的更大规模研究奠定了基础。

    结论：通过使用snRNA-seq和WGS分析75名成年人的大脑，研究人员在细胞类型水平分辨率下评估了皮质细胞丰度和基因表达的变化。本研究表明，人类个体的细胞组成高度一致，但存在反映样本特征、疾病状况和遗传调控的实质性差异，这将为未来的疾病研究提供全面参考。