Development of necroptosis-related gene signature to predict the prognosis of colon adenocarcinoma

Abstract

Colon adenocarcinoma (COAD) is a common malignancy and has a high mortality rate. However, the current tumor node metastasis (TNM) staging system is inadequate for prognostic assessment of COAD patients. Therefore, there is an urgent need to identify reliable biomarkers for the prognosis COAD patients. The aberrant expression of necroptosis-related genes (NRGs) is reported to be associated with tumorigenesis and metastasis. In the present work, we compared the expression profiles of NRGs between COAD patients and normal individuals. Based on seven differentially expressed NRGs, a risk score was defined to predict the prognosis of COAD patients. The validation results from both training and independent external cohorts demonstrated that the risk score is able to distinguish the high and low risk COAD patients with higher accuracies, and is independent of the other clinical factors. To facilitate its clinical use, by integrating the proposed risk score, a nomogram was built to predict the risk of individual COAD patients. The C-index of the nomogram is 0.75, indicating the reliability of the nomogram in predicting survival rates. Furthermore, two candidate drugs, namely dapsone and xanthohumol, were screed out and validated by molecular docking, which hold the potential for the treatment of COAD. These results will provide novel clues for the diagnosis and treatment of COAD.

Keywords: colon adenocarcinoma; gene signature; molecular docking; necroptosis; nomogram; survival analysis.

FIGURE 1

The flow chart of this study.

FIGURE 2

The differentially expressed NRGs. (A) Heatmap for the 105 differentially expressed NRGs. Red is tumor tissue samples, and blue is normal samples (*p < 0.05; **p < 0.01; ***p < 0.001). (B) A volcano plot of NRGs. Up-regulated and down-regulated genes are indicated by red and blue, respectively.

FIGURE 3

Validation of the prognostic NRGs signature in COAD patients (A–B) The TCGA-COAD samples were divided into high and low risk groups according to the median risk score. The larger the risk score, the more the samples of deaths. (C) Differentially expression of prognostic genes in high and low risk groups are depicted in a boxplot. Red is the high risk group and green is the low risk group (***p < 0.001). (D) Kaplan-Meier curve for predicting OS in the TCGA cohort. Red is the high risk group and blue is the low risk group. (E) ROC curve in the TCGA cohort. (F) Kaplan–Meier curve for predicting OS in the GEO cohort. (G) ROC curve in the GEO cohort.

FIGURE 4

Independent prognostic analysis. (A) Univariate independent prognostic analysis in the TCGA cohort. (B) Multivariate independent prognostic analysis in the TCGA cohort. (C–F) NRGs signature based outcome stratification of different clinicopathological features (Status, Stage, N, M).

FIGURE 5

Functional gene set enrichment analysis. (A–C) The pathways enriched in high risk group; (D–F) The pathways enriched in low risk group.

FIGURE 6

Construction and evaluation of the prognostic nomogram. (A) The nomogram predicts the probability of the 1-, 3-, and 5-year OS. (B) The calibration plot of the nomogram for predicting the probability of the 1-, 3-, and 5-year OS. (C) AUC smooth curve for evaluating the accuracy of nomogram predictions.

FIGURE 7

Candidate drugs screening for high risk patients and target identification. (A–C) The identified targets (confidence score>0.8) from STRING for dapsone, xanthohumol and flucytosine, respectively. (D) Eight of the 17 targets were significantly differentially expressed, of which five were significantly under-expressed in the high risk group and three were significantly over-expressed (**p < 0.01; ***p < 0.001). (E,F) Patients with a high NAT2 expression and patients with a low LCAT expression had a higher survival rate.

FIGURE 8

The result of molecular docking between candidate drugs and targets. (A) The molecular docking results between dapsone and its target NAT2. (B) The molecular docking results between xanthohumol and its target LCAT.