Tumor type and cell type-specific gene expression alterations in diverse pediatric central nervous system tumors identified using single nuclei RNA-seq. Tumor type and cell type-specific gene expression alterations in diverse pediatric central nervous system tumors identified using single nuclei RNA-seq

Central nervous system (CNS) tumors are the leading cause of pediatric cancer death, and these patients have an increased risk for developing secondary neoplasms. Due to the low prevalence of pediatric CNS tumors, major advances in targeted therapies have been lagging compared to other adult tumors. We collected single nuclei RNA-seq data from 35 pediatric CNS tumors and three non-tumoral pediatric brain tissues (84,700 nuclei) and characterized tumor heterogeneity and transcriptomic alterations. We distinguished cell subpopulations associated with specific tumor types including radial glial cells in ependymomas and oligodendrocyte precursor cells in astrocytomas. In tumors, we observed pathways important in neural stem cell-like populations, a cell type previously associated with therapy resistance. Lastly, we identified transcriptomic alterations among pediatric CNS tumor types compared to non-tumor tissues, while accounting for cell type effects on gene expression. Our results suggest potential tumor type and cell type-specific targets for pediatric CNS tumor treatment. Overall design: Nuclei were isolated from pediatric central nervous system tumors and non-tumor pediatric brain tissue and analyzed using single nuclei RNA-seq (following 10X Genomics 3' VDJ protocol). Majority of the samples were multiplexed into a single 10x run. Please refer to the published paper for the details on the samples that were pooled into the same run.

中枢神经系统（Central nervous system, CNS）肿瘤是儿童癌症死亡的首要诱因，此类患者罹患继发性肿瘤的风险亦显著升高。鉴于儿童中枢神经系统肿瘤患病率较低，其靶向治疗的重大进展相较其他成人肿瘤仍相对滞后。我们收集了35例儿童中枢神经系统肿瘤与3例非肿瘤性儿童脑组织的单细胞核RNA测序（single nuclei RNA-seq）数据，共计84700个细胞核，借此对肿瘤异质性与转录组改变进行了系统表征。我们成功区分出与特定肿瘤类型相关的细胞亚群，包括室管膜瘤中的放射状胶质细胞，以及星形细胞瘤中的少突胶质细胞前体细胞。在肿瘤样本中，我们观测到与神经干细胞样群体密切相关的关键通路——该细胞类型此前已被证实与治疗耐药性存在关联。最后，我们在校正细胞类型对基因表达影响的前提下，鉴定出不同儿童中枢神经系统肿瘤类型相较于非肿瘤组织的转录组差异改变。本研究结果提示了针对儿童中枢神经系统肿瘤的潜在肿瘤类型与细胞类型特异性治疗靶点。
整体实验设计：研究人员从儿童中枢神经系统肿瘤与非肿瘤性儿童脑组织中分离得到细胞核，采用单细胞核RNA测序技术（遵循10X Genomics 3' VDJ实验流程）开展分析。绝大多数样本被混合至单次10X测序流程中。关于混合至同一测序批次的样本详情，请参阅已发表的相关论文。