Comprehensive pan-cancer analysis reveals ENC1 as a promising prognostic biomarker for tumor microenvironment and therapeutic responses

Abstract

Accumulating research showed that ENC1 plays a critical role in maintaining the physiological functions. However, little is known about its role in predicting prognosis and immunotherapy response across cancers. In our results, compared to normal tissues, most cancer tissues exhibit increased ENC1 expression. We found that the most common type of genetic variation was gene mutation. In addition, a positive correlation was found between CNV and ENC1 expression. Moreover, the overexpression of ENC1 was positively correlated with poor clinical outcomes. The GSEA results showed that ENC1 is closely correlated with tumor-promoting biological functions in most cancers. ENC1 is also closely negatively associated with the infiltration levels of T cells, activated NK cells, and B cells. Most immunomodulators are positively associated with ENC1. Further, we verified that inhibition of ENC1 expression suppressed the proliferation and migration of breast cancer, pancreatic cancer and glioma cells. In conclusion, our study demonstrated that ENC1 plays a protumorigenic role in most cancers. Additionally, ENC1 is closely correlated with tumor microenvironment features and immune checkpoint inhibitors expression. Overall, ENC1 could serve as a promising potential prognostic biomarker in various tumors.

Keywords: ENC1; Immunomodulators; Immunotherapy; Pan-cancer; Prognostic biomarker; Tumor immune infiltration.

Fig. 1

The expression of ENC1 in normal tissues and cancer tissues. (A) ENC1 expression across cancers based on the TCGA and GTEx databases. (B) The expression of ENC1 in paired samples from the TCGA datasets. (C) The correlation between ENC1 expression and pathological stages in ACC, BLCA, SKCM, LIHC, KICH, and PAAD. *p < 0.05; ** p < 0.01; ***p < 0.001.

Fig. 2

Genetic alteration analysis of ENC1. (A) The alteration frequency of ENC1. (B) The correlation of CNV with ENC1 expression in 33 types of cancer. (C) The methylation difference in a subset of cancers (left). The correlation of methylation with ENC1 expression in 33 types of cancer.

Fig. 3

The prognostic value of ENC1 across cancers. (A–C) Forest plot of the correlation of ENC1 expression with OS, DSS, and PFI in 33 types of cancer. OS (overall survival), DSS (disease-specific survival), PFI (progression-free interval).

Fig. 4

Kaplan‒Meier analysis of the correlation between ENC1 expression and OS. (A–P) Survival and prognosis analysis of ENC1 in different cancers.

Fig. 5

The expression of ENC1 correlated with biological functional status across cancers. (A) The association of ENC1 expression with 14 functional states in 25 types of cancer in CancerSEA. (B) Correlation analysis between the 50 hallmark pathways and ENC1 expression across TCGA cancers.

Fig. 6

Correlation of ENC1 with tumor immune infiltration across cancers. Immune cell infiltration analyzed by CIBERSORT (A) and xCell (B).

Fig. 7

Relationship between the expression of ENC1 and immune response across cancers. (A) Correlation between ENC1 expression and the expression of immune-related genes (chemokine genes, receptor genes, and MHC genes). (B) Correlation between ENC1 expression and the expression of immunoinhibitors and immunostimulators. Bar chart of the relationship between ENC1 expression and TMB (C) and MSI (D). TMB (tumor mutational burden), MSI (microsatellite instability).

Fig. 8

Value of ENC1 in predicting the immunotherapy response across cancers. Value of ENC1 in predicting the immunotherapy response in murine tumor model immunotherapy cohorts based on in vivo studies (A) and in cell line cytokine treatment cohorts based on in vitro studies (B). Correlation analysis between ENC1 expression and drug sensitivity based on the GDSC (C) and CTRP (D) datasets.

Fig. 9

The effect of ENC1 on proliferation and migration. (A-C) The knockdown efficiency of ENC1 mRNA and protein level in BT-549, LN229 and PANC-1 cell line verified by qRT-PCR and WB respectively. Quantitative comparisons for WB between samples was derived from the same experiment and that blots were processed in parallel. (D-F) The cell proliferation of BT-549, LN229 and PANC-1 about the ENC1-siRNA group compared to the control group though CCK-8 assay. (G-H) The cell proliferation was analyzed by EdU assay. (I-J) Transwell assays was performed to analysis the migration of BT-549, LN229 and PANC-1 cell transferred by si-RNA comparing the control group. *p < 0.05, **p < 0.01, and ***p < 0.001.