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

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. 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.