Epithelial-mesenchymal transition (EMT) signature is inversely associated with T-cell infiltration in non-small cell lung cancer (NSCLC)

Abstract

Epithelial-mesenchymal transition (EMT) is able to drive metastasis during progression of multiple cancer types, including non-small cell lung cancer (NSCLC). As resistance to immunotherapy has been associated with EMT and immune exclusion in melanoma, it is important to understand alterations to T-cell infiltration and the tumor microenvironment during EMT in lung adenocarcinoma and squamous cell carcinoma. We conducted an integrated analysis of the immune landscape in NSCLCs through EMT scores derived from a previously established 16 gene signature of canonical EMT markers. EMT was associated with exclusion of immune cells critical in the immune response to cancer, with significantly lower infiltration of CD4 T-cells in lung adenocarcinoma and CD4/CD8 T-cells in squamous cell carcinoma. EMT was also associated with increased expression of multiple immunosuppressive cytokines, including IL-10 and TGF-β. Furthermore, overexpression of targetable immune checkpoints, such as CTLA-4 and TIM-3 were associated with EMT in both NSCLCs. An association may exist between immune exclusion and EMT in NSCLC. Further investigation is merited as its mechanism is not completely understood and a better understanding of this association could lead to the development of biomarkers that could accurately predict response to immunotherapy.

Figure 1

16 canonical gene markers of EMT. The 16 canonical genes consist of 3 ‘epithelial’ and 13 ‘mesenchymal’ genes.

Figure 2

Immune cell infiltration landscape by EMT score status. (A) Immune infiltration of ‘mesenchymal’ lung ADC compared to ‘epithelial’ lung ADC. (B) Fold change of infiltration of immune cells compared between ‘epithelial’ and ‘mesenchymal’ lung ADC. (C) Immune infiltration of ‘mesenchymal’ lung SqCC compared to ‘epithelial’ lung SqCC. (D) Fold change of infiltration of immune cells compared between ‘epithelial’ and ‘mesenchymal’ lung SqCC. *p < 0.05, **p < 0.01, ***p < 0.001.

Figure 3

Box plot of RNA-seq z-scores of 16 cytokine genes for ‘mesenchymal’ and ‘epithelial’ groups. (A) Distribution of RNA-seq z-scores of ‘mesenchymal’ lung ADC compared to ‘epithelial’ lung ADC (B) Distribution of RNA-seq z-scores of ‘mesenchymal’ lung SqCC compared to ‘epithelial’ lung SqCC *p < 0.05, **p < 0.01, ***p < 0.001.

Figure 4

Box plot of RNA-seq z-scores of 6 immune checkpoint genes and FASLG for ‘mesenchymal’ and ‘epithelial’ groups. (A) Distribution of RNA-seq z-scores of ‘mesenchymal’ lung ADC compared to ‘epithelial’ lung ADC (B) Distribution of RNA-seq z-scores of ‘mesenchymal’ lung SqCC compared to ‘epithelial’ lung SqCC *p < 0.05, **p < 0.01, ***p < 0.001.