Human induced pluripotent stem cells (iPSCs) can be differentiated along various neuronal lineages to generate two-dimensional neuronal cultures as well as three-dimensional brain organoids. Such iPSC-derived cellular models are being utilized to study the basic biology of human neuronal function and to interrogate the molecular underpinnings of disease biology. The different cellular models generated from iPSCs have varying properties in terms of the diversity and organization of the cells as well as the cellular functions that are present. To understand transcriptomic differences in iPSC-derived monolayer neuronal cultures and three-dimensional brain organoids, we differentiated eight human iPSC lines from healthy control subjects to generate cerebral organoids and cortical neuron monolayer cultures from the same set of iPSC lines. We undertook RNA-seq experiments in these model systems and analyzed the gene expression data to identify genes that are differentially expressed in cerebral organoids and two-dimensional cortical neuron cultures. In cerebral organoids, gene ontology analysis showed enrichment of genes involved in tissue development, response to stimuli, and the interferon-γ pathway, while two-dimensional cortical neuron cultures showed enrichment of genes involved in nervous system development and neurogenesis. We also undertook comparative analysis of these gene expression profiles with transcriptomic data from the human fetal prefrontal cortex (PFC). This analysis showed greater overlap of the fetal PFC transcriptome with cerebral organoid gene expression profiles compared to monolayer cortical neuron culture profiles. Our studies delineate the transcriptomic differences between cortical neuron monolayer cultures and three-dimensional cerebral organoids and can help inform the appropriate use of these model systems to address specific scientific questions.

中文翻译：

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来自人类诱导多能干细胞的脑类器官和皮质神经元培养物的比较转录组学分析。

人类诱导多能干细胞 (iPSC) 可以沿着各种神经元谱系分化，以产生二维神经元培养物以及三维脑类器官。此类 iPSC 衍生的细胞模型正被用于研究人类神经元功能的基本生物学和询问疾病生物学的分子基础。从 iPSC 生成的不同细胞模型在细胞的多样性和组织以及存在的细胞功能方面具有不同的特性。为了了解 iPSC 衍生的单层神经元培养物和三维大脑类器官的转录组学差异，我们从健康对照受试者中区分了八种人类 iPSC 系，以从同一组 iPSC 系中生成大脑类器官和皮层神经元单层培养物。我们在这些模型系统中进行了 RNA-seq 实验，并分析了基因表达数据，以确定在大脑类器官和二维皮质神经元培养物中差异表达的基因。在大脑类器官中，基因本体分析显示参与组织发育、对刺激的反应和干扰素-γ途径的基因富集，而二维皮质神经元培养显示参与神经系统发育和神经发生的基因富集。我们还对这些基因表达谱与来自人类胎儿前额叶皮层 (PFC) 的转录组数据进行了比较分析。该分析表明，与单层皮层神经元培养谱相比，胎儿 PFC 转录组与大脑类器官基因表达谱的重叠更大。