Diverse reprogramming codes for neuronal identity

The transcriptional programs that establish neuronal identity evolved to produce a rich diversity of neuronal cell types that arise sequentially during development. Remarkably, transient expression of certain transcription factors (TFs) can also endow non-neural cells with neuronal properties. To decipher the relationship between reprogramming factors and transcriptional networks that produce neuronal identity and diversity, we screened ~600 TF pairs and identified 76 that produce induced neurons (iNs) from fibroblasts. By intersecting the transcriptomes of iNs with those of endogenous neurons, we define a “core” cell-autonomous neuronal signature. The iNs also exhibit diversity; each TF pair produces iNs with unique transcriptional patterns that can predict their pharmacological responses. By linking distinct TF input “codes” to defined transcriptional outputs, this study uncovers cell autonomous features of neuronal identity and expands the reprogramming toolbox to enable more facile engineering of induced neurons with desired patterns of gene expression and related functional properties. RNA-Seq profiles for 35 TauEGFP-positive induced neuron populations, 1 embryonic fibroblast population, and 7 endogenous neural populations in biological duplicates. 2 endogenous neural populations were sequenced in biological triplicates. Single-cell RNA-Seq profiles for 4 TauEGFP-positive induced neuron populations and 1 Tau-EGFP-negative/positive mixed population.

调控神经元身份确立的转录程序经演化产生了丰富多样的神经元细胞类型，且此类细胞在发育进程中依次生成。值得注意的是，部分转录因子（Transcription Factors, TFs）的瞬时表达同样可赋予非神经细胞神经元特性。为解析重编程因子与调控神经元身份及多样性的转录网络之间的关联，本研究筛选了约600对转录因子，最终鉴定出76对可将成纤维细胞诱导为诱导神经元（induced neurons, iNs）的因子组合。通过将诱导神经元的转录组与内源性神经元的转录组进行交集分析，本研究定义了一套“核心”细胞自主性神经元特征谱。诱导神经元同样展现出多样性：每一对转录因子组合所诱导产生的神经元均具备独特的转录模式，且该模式可预测其药物反应特征。本研究通过将不同的转录因子输入“编码”与明确的转录输出结果建立关联，揭示了神经元身份的细胞自主性特征，并拓展了重编程工具库，从而能够更便捷地工程化构建具备目标基因表达模式与相关功能特性的诱导神经元。本研究的测序数据集包含：35个Tau增强绿色荧光蛋白（Tau enhanced green fluorescent protein, TauEGFP）阳性诱导神经元群体、1个胚胎成纤维细胞群体以及7个内源性神经细胞群体的RNA测序（RNA-Sequencing, RNA-Seq）图谱，所有样本均设置生物学重复；另有2个内源性神经细胞群体完成了生物学三次重复测序。此外还包含4个TauEGFP阳性诱导神经元群体以及1个Tau-EGFP阴性/阳性混合群体的单细胞RNA测序（single-cell RNA-Sequencing, scRNA-Seq）图谱。