Innate Immune Landscape in Early Lung Adenocarcinoma by Paired Single-Cell Analyses. Homo sapiens

We perform massively parallel single cell RNA-seq (MARS-Seq) on non-lymphocytic immune cells sorted from a human stage IA lung adenocarcinoma lesion and from the adjacent non-involved lung. With an unbiased single cell transcriptomic analysis of non-lymphocyte cells accumulating in these tissues, we sought to capture the heterogeneity of the tumor-infiltrating myeloid (TIM) compartment. Using a previously described unbiased expectation-maximization algorith (Paul et al., 2015), we identified clusters that were then named according to literature-reported marker profiles. This revealed a CD141+ DC subets, a CD1c+ DC subset, and a macrophage subset that clustered separately and was found to be enriched in the lesion as compared to other macrophage subsets. Overall design: Using singlet, CD45+ DAPI- CD3- CD19- gating, over 1100 cells from a human stage IA lung adenocarcinoma lesion and over 700 cells from the non-involved lung were sorted into individual wells of a 384-well plate, then processed by MARS-Seq.

我们对从人类IA期肺腺癌病灶及邻近未受累肺组织中分选得到的非淋巴细胞免疫细胞，开展大规模并行单细胞RNA测序（MARS-Seq）。通过对这两类组织中积聚的非淋巴细胞开展无偏单细胞转录组分析，我们旨在解析肿瘤浸润髓系区室（tumor-infiltrating myeloid, TIM）的异质性。我们采用此前报道的无偏期望最大化算法（Paul等，2015）对细胞簇进行鉴定，随后依据文献报道的标志物特征对各细胞簇予以命名。分析结果显示存在CD141阳性树突状细胞（Dendritic Cell, DC）亚群、CD1c阳性树突状细胞亚群，以及一个单独聚类的巨噬细胞亚群；与其他巨噬细胞亚群相比，该亚群在病灶中呈现富集状态。
总体实验设计：通过采用单峰细胞、CD45阳性、DAPI阴性、CD3阴性、CD19阴性的设门策略，我们从人类IA期肺腺癌病灶中分选得到超过1100个细胞，从邻近未受累肺组织中分选得到超过700个细胞，将这些细胞接种至384孔板的单个孔中，随后通过MARS-Seq完成实验处理。