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Research Article

Specific immune landscapes and immune checkpoint expressions in histotypes and molecular subtypes of sarcoma

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Article: 1792036 | Received 17 Dec 2019, Accepted 01 Jul 2020, Published online: 12 Jul 2020

Figures & data

Table 1. Clinical characteristics of patients among the different cohorts.

Figure 1. Unsupervised clustering analysis of the 93 ICP/MM gene expression signature for all 253 sarcoma samples. Heat map of the full signature for all samples. Sarcoma (in columns) are labeled by their histological subgroup. Genes belonging to the signature (in rows) are labeled by their biological relevance. (TNF: tumor necrosis factor, DR: death receptor, Cytotox: cytotoxic T cell, ICP: immune checkpoint, Mono: monocyte, Macro: macrophage, NK: natural killer and Neutro: neutrophil.).

Figure 1. Unsupervised clustering analysis of the 93 ICP/MM gene expression signature for all 253 sarcoma samples. Heat map of the full signature for all samples. Sarcoma (in columns) are labeled by their histological subgroup. Genes belonging to the signature (in rows) are labeled by their biological relevance. (TNF: tumor necrosis factor, DR: death receptor, Cytotox: cytotoxic T cell, ICP: immune checkpoint, Mono: monocyte, Macro: macrophage, NK: natural killer and Neutro: neutrophil.).

Figure 2. Correlation of ICP/MM genes expression with histological sarcoma subtype with t-SNE. t-SNE analysis processing a non-linear dimension reduction of the signature for all samples. Points are sarcomas highlighted in colors for each histological subtype (Dim: dimension).

Figure 2. Correlation of ICP/MM genes expression with histological sarcoma subtype with t-SNE. t-SNE analysis processing a non-linear dimension reduction of the signature for all samples. Points are sarcomas highlighted in colors for each histological subtype (Dim: dimension).

Figure 3. Expression level of the 93 ICP/MM genes across each sarcoma subtype.

- The gene expression value is displayed by bars representing the 25 and 75 percentile of expression level for each ICP/MM. Each sarcoma subtype is shown (green: GIST; blue: MLPS; red: SCG; orange: SS).- The Z-score is averaged for each gene within each sarcoma subgroup (red corresponding to the highest expression and blue the lowest one; from 2 to −2, respectively).- The significance displays the relationship between expression values across histological subtype given by multiple Bonferroni-adjusted ANOVA, ranked from high significance (top) to non-significant (bottom). Vertical dashed line indicates significance threshold (p = .05), 84 genes out of 93 (90%) are differentially expressed in the different subtypes.- The prognosis represents the impact of an ICP/MM gene expression on MFS. A positive prognostic impact (high expression correlated with longer MFS) and is represented in green. A negative impact (high expression correlated with shorter MFS) and is represented in red.- CT and FDA highlight genes whose protein is targeted in a Clinical Trial or by a Food and Drug Administration approved agent.Citation10
Figure 3. Expression level of the 93 ICP/MM genes across each sarcoma subtype.

Figure 4. Immune population defined by CIBERSORT signature and their relevance across sarcoma subtypes.

- The expression value is displayed by bars representing the 25 and 75 percentile of expression level for each immune cell population. Each sarcoma subtype is shown (green: GIST; blue: MLPS; red: SCG; orange: SS).- The Z-score is averaged for each gene within each sarcoma subgroup (red corresponding to the highest expression and blue the lowest one; from 2 to −2, respectively).- The significance displays the relationship between expression values across histological subtype given by multiple Bonferroni-adjusted ANOVA, ranked from high significance (top) to non-significant (bottom). Vertical dashed line indicates significance threshold (p = .05), 16 immune cell populations out of 22 are differentially expressed in the different subtypes.- The prognosis represents the impact of an immune cell population on MFS. A positive prognostic impact (high expression correlated with longer MFS) and is represented in green. A negative impact (high expression correlated with shorter MFS) and is represented in red.
Figure 4. Immune population defined by CIBERSORT signature and their relevance across sarcoma subtypes.

Figure 5. Kaplan-Meier analysis of metastasis-free survival according to M0-macrophage signature in the group of 137 sarcoma including SCG, MLPS and SS (unadjusted p).

Figure 5. Kaplan-Meier analysis of metastasis-free survival according to M0-macrophage signature in the group of 137 sarcoma including SCG, MLPS and SS (unadjusted p).
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