Figure 4. Unbiased characterization of the mononuclear phagocyte compartment.

(A) MARS-seq of 1473 cells pooled from tumor and nLung of a Stage IA adenocarcinoma patient. Cells were gated in silico and clustering on 770 mononuclear phagocytes is shown (see STAR methods). Columns represent single cells, with most variable genes from low (white) to high (purple). Normalized frequency of each cluster in tumor or nLung (top). Macrophages (MΦ), monocytes (Mono).

(B) viSNE analysis of CD3- immune cells colored and labeled by Phenograph metaclusters (left) and tissue (right), for a representative patient.

(C) Heatmap of Phenograph clusters of CD3- cells; rows represent clusters of single cells within individual patients grouped by metacluster across multiple patients.

(D) Bar plots of metacluster frequencies from 18 lung adenocarcinoma patients across tissue (*p<0.05, **p<0.01 and ***p<0.001 by paired t-test).

(E, F) Expression of corresponding transcript and protein by MARS-seq and CyTOF, respectively. Normalized transcript expression of MARS-seq clusters (left) and normalized protein expression of select Phenograph metaclusters in the tumor (right) for phenotypic markers (E; n=18), and cytokines (F; n=10) with corresponding viSNE plots.

(G) Bar plot of normalized IL-8 expression by CD14+ monocytes across tissue (n=10; *p<0.05, **p<0.01 and ***p<0.001 by paired t-test).

Bar plots show mean ± SEM.

See also Figure S4