Correlation of tumor-infiltrating immune cells of melanoma with overall survival by immunogenomic analysis

Abstract

Aims: Different types of tumor-infiltrating immune cells not only augment but also dampen antitumor immunity in the microenvironment of melanoma. Therefore, it is critical to provide an overview of tumor-infiltrating immune cells in melanoma and explore a novel strategy for immunotherapies.

Methods: We analyzed the immune states of different stages in melanoma patients by the immune, stromal, and estimation of stromal and immune cells in malignant tumor tissues using expression data (ESTIMATE) scores. Immune cell types were identified by the estimating relative subsets of RNA transcripts (CIBERSORTx) algorithm in 471 melanoma and 324 healthy tissues. Moreover, we performed a gene set variation analysis (GSVA) to determine the differentially regulated pathways in the tumor microenvironment.

Results: In melanoma cohorts, we found that ESTIMATE and immune scores were involved in survival or tumor clinical stage. Among the 22 immune cells, CD8⁺ T cells, M2 macrophages, and regulatory T cells (Tregs) showed significant differences using the CIBERSORTx algorithm. Furthermore, GSVA identified the immune cell-related pathways; the primary immunodeficiency pathway, intestinal immune network for IgA, and TGF-β pathways were identified as participants of the crosstalk in CD8⁺ T cells, Tregs, and M2 macrophages in the melanoma microenvironment.

Conclusion: These results reveal the cellular and molecular characteristics of immune cells in melanoma, providing a method for selecting targets of immunotherapies and promoting the efficacy of therapies for the treatment of melanoma.

Keywords: CD8+ T cells; M2 macrophage; melanoma; tumor-infiltrating immune cells.

Figure 1

ESTIMATE, stroma, and immune scores in TCGA‐SKCM of melanoma patients by ESTIMATE algorithm analysis. (A–D): ESTIMATE, stroma, and immune scores and tumor purity, respectively, at different stages. The lowest ESTIMATE, stroma, and immune scores were in stage II. (E–H): Association between survival curves and different ESTIMATE, stroma, and immune scores and tumor purity, respectively, in melanoma patients in TCGA‐SKCM. (n = 471, * P < .05, *** P < .001, and **** P < .0001)

Figure 2

Analyses of immune cells between melanoma and healthy tissues using the CIBERSORTx algorithm. (A) Heatmap of normalized absolute abundance of immune cell types in an individual sample. (B) Boxplots of different immune cells between melanoma and healthy control samples. The blue boxplot (NC) represents healthy control; the red boxplot (T) represents tumors. (* P < .05    and *** P < .001)

Figure 3

Association between survival curves and the different fractions of immune cells, including CD8⁺ T cells (A), M2 macrophages (B), M0 macrophages (C), and Tregs (D) in melanoma patients in TCGA‐SKCM. Survival curves of resting mast cells (E), resting dendritic cells (F), M1 macrophages (G), and activated memory CD4⁺ T cells (H) in melanoma patients in TCGA‐SKCM. The number of tumor patients and healthy control participants was 471 and 324, respectively.‐

Figure 4

Assessment of immune cells in melanoma. Immunofluorescence analysis of CD8, CD206, CD68, and Foxp3 expression in melanoma and normal skin tissue samples. Representative images from three patients displayed positive staining in the stromal regions. CD8 (A), CD206 (B), CD68 (C), and Foxp3 (D) staining. × 20X magnification

Figure 5

Co‐expression of immune cells in melanoma tissues. (A) Correlation heatmaps of immune cells and altered pathways in melanoma tissues. Relationship between CD8⁺ T cells and M2 macrophages (B), CD8⁺ T cells and Treg (C), and M2 macrophages with Treg (D) in melanoma tissues after analysis. (E) Circos plot of the relationship between altered immune cells CD8⁺ T cells, M2 macrophages, Tregs, and the intestinal immune network for IgA, primary immunodeficiency, and TGF‐β signaling pathway

Figure 6

Correlation between immune cells and pathways in melanoma. CD8⁺ T cells (A–C) and Tregs (G–I) showed a positive correlation with the intestinal immune network for IgA, primary immunodeficiency pathways, and a negative correlation with the TGF‐β signaling pathway. M2 macrophages (D–F) showed a negative correlation with CD8⁺ T cells and Tregs