Supplementary Materials1: Supplemental Shape 1. *p 0.05, **p 0.01 and ***p 0.001 by paired t-test). (F) Relationship of tumor CX3CL1 focus (pg/ml) and rate of recurrence of mononuclear phagocyte (MP) infiltrate in the Brequinar tyrosianse inhibitor tumor (Spearmans rank-based relationship). (G) Pub plots displaying the rate of recurrence of two B cell metaclusters across cells (remaining), as demonstrated by heatmap indicating normal relative manifestation of indicated markers across individuals (ideal; Brequinar tyrosianse inhibitor n=18), determined by Phenograph evaluation on Compact disc3- cells using CyTOF Panel 1 (strategies). (H) Pub plots stratifying the main immune system lineages by TLS enrichment (*p 0.05, **p 0.01 and ***p 0.001 by unpaired t-test). (I) MICSSS for Compact disc3, Compact disc68, and Compact disc20 for tumor and nLung lesions, showing consultant TLS enriched (TLS+) and non-enriched (TLS-) tumors. Pub plots display mean SEM. NIHMS873618-health supplement-1.pdf (11M) Mmp8 GUID:?53C4FE86-D1B6-47F4-8A58-2A9DB1E809D5 2: Supplemental Figure 2. Tregs upregulate immunosuppressive substances in the tumor site, Linked to Shape 2 (A) viSNE plots of Compact disc3+ solitary cells across cells showing normalized manifestation of 30 indicated markers of the representative individual.(B) Pub plots teaching frequencies across cells for leftover metaclusters from Shape 2B (n=18). (C) Percentage of Compact disc8+ GranzymeB+ T cells to Tregs metacluster frequencies across cells (n=18). (D) Normalized manifestation of ICOS, 41BB, and Compact disc38 on tumor Compact disc3+ cells demonstrated on viSNE plots to get a representative individual (left) and bar pots showing normalized expression across patients for indicated metaclusters in tumor (n=18) (right). (E) Heatmap of CD8- T cell bulk sequencing normalized UMI counts grouped by tissues across 6 patients (left). Scatter plot showing relative expression level of genes differentially expressed between nLung and tumor, with genes significantly different between tissue colored red (p 0.01, log2|FC| 1). (F) Heat map illustrating single cell marker expression on Brequinar tyrosianse inhibitor Tregs from mass Brequinar tyrosianse inhibitor cytometry in a representative patient. Each row represents a single Treg cell and are grouped by tissue (left). Bar plots stratifying the normalized expression of indicated proteins in Tregs across tissue (right; n=18). (G) Bar plots show the normalized expression of Granzyme B (top) and IFN (bottom) on indicated T cell metaclusters for 9 patient stratified by tissue type upon stimulation. (H) Bar plots showing normalized expression of PD-1 found on CD4+ and CD8+ T cells in 10 lung adenocarcinoma patients. (I) MICSSS for CD8 and CD20 showing a TLS in tumor of a representative patient. (J) Frequency of CD8+ PD-1+ T cells in nLung to overall TCR repertoire clonality correlation plot (Spearmans rank-based correlation). Bar plots show mean SEM; *p 0.05, **p 0.01 and ***p 0.001 by paired t-test NIHMS873618-supplement-2.pdf (12M) GUID:?8DFB1F89-BE5E-47C3-83B4-FFD22F3531B5 3: Supplemental Figure 3. NK Cells correlate with CD16+ monocytes and tumor MHC I expression, Related to Figure 3 (A) Bar plots of frequency of CD16+ and CD16- NK cell metaclusters stratified by tissue for 10 additional lung adenocarcinoma patients (*p 0.05, **p 0.01 and ***p 0.001 by paired t-test).(B) Correlation plot showing the relationship of CD16+ monocyte frequency with CD16+ NK cell frequency (Spearmans rank-based correlation). (C) Bar plots of the normalized expression of granzyme B by CD16+ NK cells across nLung and tumor, upon stimulation (n=9; *p 0.05, **p 0.01 and ***p 0.001 by paired t-test). (D) Correlation plot illustrating an indirect relationship of HLA-ABC expression on CD45- Compact disc326+ cells and Compact disc16+ NK cell rate of recurrence (n=10; Spearmans rank-based relationship). Pub plots display mean SEM. NIHMS873618-health supplement-3.pdf (183K) GUID:?E6FB6078-ECA1-46DB-9BD7-11154915E533 4: Supplemental Figure 4. Differential proteins and transcript marker manifestation of tumor myeloid populations by single-cell RNA sequencing and mass cytometry, Related to Shape 4 (A) Manifestation degrees of indicated transcripts by MARS-seq, normalized across mononuclear phagocyte clusters from Shape 3A.(B) viSNE of Compact disc3- immune system cells generated across cells of a consultant individual colored by normalized expression of 28 indicated markers. (C) Pub plots displaying frequencies across cells for staying metaclusters from Shape 4C (n=18). (D) Pub plots of Compact disc16+ and Compact disc14+ monocyte metacluster frequencies stratified by cells for 10 extra lung adenocarcinoma individuals. (E) Normalized manifestation of IL-6, IL-8, TNF and IL-1 across myeloid metaclusters in tumor for 10 adenocarcinoma individuals. (F) Normalized IL-1 manifestation across MARS-seq clusters (remaining) and of normalized proteins manifestation from go for Phenograph metaclusters in the tumor (correct) with related viSNE plots. (G) Bar plots of normalized IL-1 expression by CD14+ monocytes across tissues (n=10) Bar plots show mean SEM; *p 0.05, **p 0.01 and ***p 0.001 by.