Fig. 2: Association of neoantigen load score (NLS) with immune infiltration and construction of CD8-Tex model.
From: A novel integrated approach to predicting cancer immunotherapy efficacy
A Heatmap depicting the correlations of mRNA expression levels of T cell receptor-related gene signatures with NLS of three types in TCGA-LUNG. Significant regression coefficient is indicated by *P < 0.05; **P < 0.01; ***P < 0.001. B Heatmap of GSEA normalized enrichment scores (NESs) for immune cell marker genes. Specifically, for each of three classes of NLS (fusion, SNV and indel), GSEA was performed on genes ranked by the t value from each linear regression model. Gene signatures with q-value <0.3 are retained and color-scaled. C The correlations of SNV-, indel- and fusion-derived NLS with CIBERSORTx-inferred exhausted CD8+ T cells in TCGA-LUNG samples. D The overview of multivariate linear regression approach modeling both tumor features and CD8+ T-cell exhaustion. The NLS of three types was denoted as x1, x2 and x3, respectively. The integrated neoantigen model (CD8-Tex) was fit to estimate the overall immunogenicity of predicted neoantigens and represent the degree of neoantigen-based CD8+ T-cell exhaustion in TME.
