Development and Clinical Validation of a Novel 4-Gene Prognostic Signature Predicting Survival in Colorectal Cancer

Frontiers in Oncology
Yihang YuanLeilei Liang

Abstract

In this study, we collected genes related to energy metabolism, used gene expression data from public databases to classify molecular subtypes of colon cancer (COAD) based on the genes related to energy metabolism, and further evaluated the relationships between the molecular subtypes and prognosis and clinical characteristics. Differential expression analysis of the molecular subtypes yielded 1948 differentially expressed genes (DEGs), whose functions were closely related to the occurrence and development of cancer. Based on the DEGs, we constructed a 4-gene prognostic risk model and identified the high expression of FOXD4, ENPEP, HOXC6, and ALOX15B as a risk factor associated with a high risk of developing COAD. The 4-gene signature has strong robustness and a stable predictive performance in datasets from different platforms not only in patients with early COAD but also in all patients with colon cancer. The enriched pathways of the 4-gene signature in the high- and low-risk groups obtained by GSEA were significantly related to the occurrence and development of colon cancer. Moreover, the results of qPCR, immunohistochemistry staining and Western blot assay revealed that FOXD4, ENPEP, HOXC6, and ALOX15B are over expressed in...Continue Reading

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Datasets Mentioned

BETA
GSE39582

Methods Mentioned

BETA
RNA-Seq
chip
PCR
Assay
xenograft

Software Mentioned

randomForestSRC
DESeq2
randomForestSRC R
R package “ NMF ”
TCGA GDC API
R package clusterProfiler
R
R timeROC
Bioconductor
Tumor Immune Estimation Resource ( TIMER )

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