Anderson_LOH_v3

Simultaneous brain cell type and lineage determined by scRNA-seq reveals stereotyped cortical development Mutations are acquired frequently, such that each cell’s genome inscribes its history of cell divisions. Common genomic alterations involve loss of heterozygosity (LOH). LOH accumulates throughout the genome, offering large encoding capacity for inferring cell lineage. Using only single cell RNA sequencing (scRNA-seq) of mouse brain cells, we found that LOH events spanning multiple genes are revealed as tracts of monoallelically expressed, constitutionally heterozygous single nucleotide variants (SNVs). We simultaneously inferred cell lineage, marked developmental time points based on X-chromosome inactivation and the total number of LOH events, while identifying cell types from gene expression patterns. Our results are consistent with progenitor cells giving rise to multiple cortical cell types through stereotyped expansion and distinct waves of neurogenesis. This type of retrospective analysis could be incorporated into scRNA-seq pipelines and, compared to experimental approaches for determining lineage in model organisms, is applicable where genetic engineering is prohibited, such as humans.基于单细胞RNA测序（single cell RNA sequencing, scRNA-seq）同时解析脑细胞类型与细胞谱系，揭示模式化大脑皮层发育进程 体细胞突变的积累频率颇高，每个细胞的基因组均记录了其细胞分裂的完整历程。常见的基因组变异类型包括杂合性缺失（loss of heterozygosity, LOH）。杂合性缺失在全基因组范围内累积，为细胞谱系的推断提供了充足的编码信息容量。仅通过对小鼠脑细胞开展单细胞RNA测序（scRNA-seq），我们发现跨多个基因的杂合性缺失事件，会以单等位基因表达的组成型杂合单核苷酸变异（single nucleotide variants, SNVs）片段的形式被检测到。我们同时开展了细胞谱系推断，基于X染色体失活状态与杂合性缺失事件总数标定发育时间节点，并通过基因表达模式识别细胞类型。我们的研究结果支持下述结论：祖细胞通过模式化的细胞扩增与差异化的神经发生波次，产生多种大脑皮层细胞类型。 这类回顾性分析方法可整合至单细胞RNA测序流程中；相较于模式生物中用于确定细胞谱系的实验手段，该方法适用于禁止基因工程操作的场景，例如人类研究。