Immune gene patterns and characterization of the tumor immune microenvironment associated with cancer immunotherapy efficacy. Issue 3 (March 2023)

• Record Type: Journal Article
• Authors: Lin, Lili; Zhang, Wenda; Chen, Yongjian; Ren, Wei; Zhao, Jianli; Ouyang, Wenhao; He, Zifan; Su, Weifeng; Yao, Herui; Yu, Yunfang
• Is Part Of: Heliyon. Volume 9:Issue 3(2023)
• Publication Date: 2023-03
• Subjects: Cancer -- Immunotherapy -- Tumor immune microenvironment -- Machine learning; AUC Area under the curve -- CIs Confidence intervals -- CTL Cytotoxic T-lymphocyte infiltration -- GEO Gene Expression Omnibus -- GO Gene Ontology -- GSEA Gene set enrichment analysis -- GSVA Gene set variation analysis -- HLAs Human leukocyte antigens -- HRs Hazard ratios -- KEGG Kyoto Encyclopedia of Genes and Genomes -- LASSO Penalized logistic least absolute shrinkage and selector operation -- lncRNA Long non-coding RNA -- NSCLC Non-small cell lung cancer -- OS Overall survival -- PCA Principal componentanalysis -- PD-L1 Programmed death ligand-1 -- PFS Profession-free survival -- RNA-seq Transcriptome RNA sequencing -- ROC receiver operating characteristic curves -- TCGA The Cancer Genome Atlas -- TMB Tumor mutation burden -- TME Tumor immunemicroenvironment -- WGCNA Weighted gene co-expression network analysis; Research -- Periodicals; Medical sciences -- Periodicals; Natural history -- Periodicals; Social sciences -- Periodicals; Earth sciences -- Periodicals; Physical sciences -- Periodicals; 507.2
• DOI: 10.1016/j.heliyon.2023.e14450
• Languages: English
• ISSNs: 2405-8440

Abstract

Abstract: Although immunotherapy has revolutionized cancer management, most patients do not derive benefits from it. Aiming to explore an appropriate strategy for immunotherapy efficacy prediction, we collected 6251 patients' transcriptome data from multicohort population and analyzed the data using a machine learning algorithm. In this study, we found that patients from three immune gene clusters had different overall survival when treated with immunotherapy ( P < 0.001), and that these clusters had differential states of hypoxia scores and metabolism functions. The immune gene score showed good immunotherapy efficacy prediction (AUC was 0.737 at 20 months), which was well validated. The immune gene score, tumor mutation burden, and long non-coding RNA score were further combined to build a tumor immune microenvironment signature, which correlated more strongly with overall survival (AUC, 0.814 at 20 months) than when using a single variable. Thus, we recommend using the characterization of the tumor immune microenvironment associated with immunotherapy efficacy via a multi-omics analysis of cancer.