Van Deusen Amy L, Kumar Sushanth, Calhan O Yipkin, Goggin Sarah M, Shi Jiachen, Williams Corey M, Keeler Austin B, Fread Kristen I, Gadani Irene C, Deppmann Christopher D, Zunder Eli R
Department of Biology, College of Arts and Sciences, University of Virginia, Charlottesville, VA, USA.
Neuroscience Graduate Program, School of Medicine, University of Virginia, Charlottesville, VA, USA.
Nat Neurosci. 2025 Jan;28(1):174-188. doi: 10.1038/s41593-024-01786-1. Epub 2024 Dec 18.
Development of the mammalian brain requires precise molecular changes across diverse cell lineages. While single-cell RNA abundances in the developing brain have been characterized by single-cell RNA sequencing (scRNA-seq), single-cell protein abundances have not been characterized. To address this gap, we performed mass cytometry on the whole brain at embryonic day (E)11.5-E12.5 and the telencephalon, the diencephalon, the mesencephalon and the rhombencephalon at E13.5-postnatal day (P)4 from C57/BL6 mice. Using a 40-antibody panel to analyze 24,290,787 cells from two to four biological replicates per sample, we identify 85 molecularly distinct cell clusters from distinct lineages. Our analyses confirm canonical molecular pathways of neurogenesis and gliogenesis, and predict two distinct trajectories for cortical oligodendrogenesis. Differences in protein versus RNA expression from mass cytometry and scRNA-seq, validated by immunohistochemistry and RNAscope in situ hybridization (ISH), demonstrate the value of protein-level measurements for identifying functional cell states. Our findings show the utility of mass cytometry as a scalable platform for single-cell profiling of brain tissues.
哺乳动物大脑的发育需要不同细胞谱系间精确的分子变化。虽然发育中大脑的单细胞RNA丰度已通过单细胞RNA测序（scRNA-seq）进行了表征，但单细胞蛋白质丰度尚未得到表征。为了填补这一空白，我们对C57/BL6小鼠胚胎期第11.5天至12.5天的全脑以及胚胎期第13.5天至出生后第4天（P4）的端脑、间脑、中脑和后脑进行了质谱流式细胞术分析。使用一个包含40种抗体的面板对每个样本两到四个生物学重复中的24,290,787个细胞进行分析，我们从不同谱系中鉴定出85个分子上不同的细胞簇。我们的分析证实了神经发生和胶质发生的经典分子途径，并预测了皮质少突胶质细胞生成的两条不同轨迹。通过免疫组织化学和RNAscope原位杂交（ISH）验证的质谱流式细胞术和scRNA-seq在蛋白质与RNA表达上的差异，证明了蛋白质水平测量在识别功能性细胞状态方面的价值。我们的研究结果表明质谱流式细胞术作为一种可扩展的平台用于脑组织单细胞分析的实用性。
