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pmid:33787354
Identification of an Immune Gene Signature Based on Tumor Microenvironment Characteristics in Colon Adenocarcinoma.
Ying Chen · Jia Zhao
Cell transplantation · 2021 doi:10.1177/09636897211001314
Paper
complete
Experiment
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Data
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Analysis
partial
Execution
absent
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Complete file
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Based on The Cancer Genome Atlas (TCGA) and GSE39582 cohorts, the scores of 22 tumor infiltrating lymphocytes (TILs) were calculated using CIBERSORT. ConsensusClusterPlus was used for unsupervised clustering. Three TME subtypes (TMEC1, TMEC2, and TME3) were identified based on TIL scores. TMEC2 was associated with the worst prognosis. Random forest, k-means clustering, and principal component analysis were used to construct the TME score risk signature. The median TME score was used to divide the samples into high- and low-risk groups. The prognoses of the patients with high TME scores were worse than those of the patients with low TME scores. A high TME score was an independent prognostic risk factor for patients with colon cancer. The Gene Set Enrichment Analysis (GSEA) results showed that those with high TME scores were enriched in FOCAL_ADHESION, ECM_RECEPTOR_INTERACTION, and PATHWAYS_IN_CANCER. 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