单细胞转录组探究胃癌转移过程中MHC-Ⅱ类分子的演进缺失

Single-cell transcriptome analysis revealed the evolutionary deletion of MHC-Ⅱ expression in gastric cancer metastasis

目的:使用单细胞转录组数据绘制胃癌免疫微环境组成图谱,探究胃癌转移过程中MHC-Ⅱ类分子演进缺失的免疫机制。方法:在GEO数据库中获取胃癌原发癌和转移癌单细胞数据集,基于R(4.1.2)、Python(3.7),对该数据集进行分群、拷贝数变异(CNV)、拟时序、基因集变异(GSVA)分析、转录因子分析、非负矩阵分解、免疫细胞细分亚群和基因集富集分析,并结合来自TCGA等数据库的多个公共转录组数据集,验证所得出的结论。结果:拟时序分析反映MHC-Ⅱ类分子在癌症转移过程中演进缺失,转录因子分析观察到IRF1、STAT1等转录因子在原发癌中的高表达,非负矩阵分解探查到原发癌中独有的干扰素(IFN)γ表达模块,但原发癌展现了较冷的免疫微环境。免疫细胞的亚群分类展示了树突状细胞、巨噬细胞、T细胞等在微环境中的分布。细胞通讯分析显示MDSC样和SPP1+肿瘤相关巨噬细胞(TAM)抑制了转移癌中IFNγ的分泌并表现了促血管生成活性。基于这两种TAM的生物标志构建的评分在胃癌中具有预后意义(Log-Rank P<0.05)。scPAGE在较大规模的bulk转录组层面对单细胞分析获得的结果进行了验证。结论:TAM介导IFNγ分泌抑制,其在转移癌较原发癌中分泌相对较少,是MHC-Ⅱ在两者间表达出现差异的原因之一。针对MDSC样TAM和SPP1+TAM的研究可能是肿瘤免疫治疗的另一突破点。

Objective:To depict the immune microenvironment atlas of gastric cancer and to explore the immune mechanism under the evolutionary deletion of MHC-Ⅱ expression in gastric cancer metastasis with single-cell transcriptome data. Methods:A single-cell data set of primary and metastatic gastric cancer was obtained from the Gene Expression Omnibus(GEO)database,combined with multiple datasets like TCGA. With R(4.1.2)and Python(3.7),clustering,copy number variation(CNV)analysis,pseudotime analysis,gene set variation analysis(GSVA),transcription factor analysis,consensus non-negative matrix factorization analysis,immune cell subpopulation analysis and gene set enrichment analysis were conducted. Combined with multiple public transcriptome data sets from TCGA and other databases,the conclusions were verified. Results:The depleted expression of MHC-Ⅱ in metastatic cancer was observed by pseudotime analysis,while a high expression of IRF1 and STAT1 in primary carcinoma was observed by transcription factor analysis. Consensus Non-negative Matrix Factorization obtained a unique IFNγ expression module from the primary tumor,but a colder immune microenvironment was observed in primary tumor. Immune cell subpopulation analysis reveals the distribution of dendritic cells,macrophages and T cells in the tumor microenvironment. Cell chat analysis shows that MDSC-like and SPP1+Tumor-associated Macrophages(TAM) were found to play a crucial part in angiogenesis. The score constructed on the basis of TAMs′ biomarkers shows prognostic significance in gastric cancer(Log-Rank P<0.05). ScPAGE verified the results of single cell analysis at the bulk transcriptome level. Conclusion:The inhibition of IFNγ emission mediated by TAM in metastatic tumor may contribute to the difference of MHC-Ⅱexpression between the primary and metastatic sites. Research on MDSC-like and SPP1+TAM may become another breakthrough point of tumor immunotherapy.