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MicroRNA-155 coordinates the immunological landscape within murine melanoma and correlates with immunity in human cancers
H. Atakan Ekiz, Thomas B. Huffaker, Allie H. Grossmann, W. Zac Stephens, Matthew A. Williams, June L. Round, Ryan M. O’Connell
H. Atakan Ekiz, Thomas B. Huffaker, Allie H. Grossmann, W. Zac Stephens, Matthew A. Williams, June L. Round, Ryan M. O’Connell
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Research Article Immunology Oncology

MicroRNA-155 coordinates the immunological landscape within murine melanoma and correlates with immunity in human cancers

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Abstract

miR-155 has recently emerged as an important promoter of antitumor immunity through its functions in T lymphocytes. However, the impact of T cell–expressed miR-155 on immune cell dynamics in solid tumors remains unclear. In the present study, we used single-cell RNA sequencing to define the CD45+ immune cell populations at different time points within B16F10 murine melanoma tumors growing in either wild-type or miR-155 T cell conditional knockout (TCKO) mice. miR-155 was required for optimal T cell activation and reinforced the T cell response at the expense of infiltrating myeloid cells. Further, myeloid cells from tumors growing in TCKO mice were defined by an increase in wound healing genes and a decreased IFN-γ–response gene signature. Finally, we found that miR-155 expression predicted a favorable outcome in human melanoma patients and was associated with a strong immune signature. Moreover, gene expression analysis of The Cancer Genome Atlas (TCGA) data revealed that miR-155 expression also correlates with an immune-enriched subtype in 29 other human solid tumors. Together, our study provides an unprecedented analysis of the cell types and gene expression signatures of immune cells within experimental melanoma tumors and elucidates the role of miR-155 in coordinating antitumor immune responses in mammalian tumors.

Authors

H. Atakan Ekiz, Thomas B. Huffaker, Allie H. Grossmann, W. Zac Stephens, Matthew A. Williams, June L. Round, Ryan M. O’Connell

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Figure 4

miR-155 expression defines an immune-enriched phenotype in human cutaneous melanoma.

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miR-155 expression defines an immune-enriched phenotype in human cutaneo...
(A) Kaplan-Meier survival curves showing an improved clinical outcome in miR-155–high subpopulation of skin cutaneous melanoma (SKCM) patients (red line). For this analysis, miRseq data from The Cancer Genome Atlas (TCGA) was categorized at the top and bottom thirds, resulting in 148 patients per group. P value of the log-rank test is shown in the graph. (B) Volcano plots showing differentially expressed genes in miR-155–high SKCM subpopulation. This plot was generated by analyzing RNAseq data from the same patients categorized in panel A. T cell–associated genes are indicated, showing a significant upregulation in the miR-155–high cohort. A linear fit model was used and the P values were corrected using the Benjamini-Hochberg method. (C) Comparison of the T cell–associated gene expression between miR-155–high and miR-155–low SKCM subpopulations. (D) Heatmap showing the correlation between miR-155 expression and SKCM clinical subtype and lymphocyte infiltration scores. Lymphocyte score and tumor subtype for SKCM were defined in a study from TCGA consortium (29). Several immune-related genes showed higher levels of expression in the miR-155–high SKCM subset. Hierarchical clustering was performed by using Euclidean distances and the ward.D2 algorithm. (E) Scatter plots showing the positive correlation between miR-155 host gene (MIR155HG) and immune-associated gene expression in TCGA-SKCM. Color gradient indicates the lymphocyte infiltration score of tumors, and the symbol shape indicates the molecular subtype of tumors (▲ immune, ■ keratin, + MITF-low, ● uncategorized). Student’s t test was used for the statistical analysis of the slope of regression line.

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