使用CSI-微生物从多个单细胞RNA-seq平台中识别细胞内细菌
Welles Robinson1,2,3,4,5, Joshua K Stone6, Fiorella Schischlik1
1Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA.
Science advances
|July 3, 2024
概括
这项研究引入了CSI-Microbes,用于使用单细胞RNA测序 (scRNA-seq) 分析瘤微生物组. 它揭示了包围细菌的髓状细胞可能驱动炎症并影响免疫疗法反应.
科学领域:
- 在瘤学瘤学.
- 微生物学 微生物学
- 生物信息学是一种生物信息学.
背景情况:
- 瘤微生物组对于癌症的进展和治疗反应至关重要.
- 了解瘤细胞内的微生物存在是必不可少的.
研究的目的:
- 开发和验证一个计算管道 (CSI-Microbes) 用于单细胞RNA测序 (scRNA-seq) 数据中的微生物分析.
- 系统地评估用于微生物恢复的scRNA-seq技术.
- 为了研究微生物的同时发生和宿主细胞相互作用在癌症.
主要方法:
- 开发CSI-微生物计算管道的开发.
- 系统评估多种scRNA-seq技术用于微生物独特分子标识符的恢复.
- 对患者食道和结直肠癌样本的分析.
主要成果:
- 10倍的基因组学化学 (3'v3和5') 显示出优异的微生物恢复.
- 不同的微生物属在宿主细胞内共同存在,这表明细胞内相互作用.
- 微生物RNA在表达益炎性细胞因子 (例如IL1Β,CXCL8) 的髓状细胞中得到丰富.
- 瘤细胞在感染时对抗原处理和呈现途径进行上调.
结论:
- 含有吞细菌的骨髓状细胞是瘤微环境 (TME) 中细菌RNA的重要来源.
- 这些髓状细胞可能会促进TME炎症并影响免疫治疗结果.
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