Identifying M1-like macrophage related genes for prognosis prediction in lung adenocarcinoma based on a gene co-expression network

Zhiyuan Wang; Shan Yan; Ying Yang; Xuan Luo; Xiaofang Wang; Kun Tang; Juan Zhao; Yongwen He; Li Bian

doi:10.1016/j.heliyon.2023.e12798

Identifying M1-like macrophage related genes for prognosis prediction in lung adenocarcinoma based on a gene co-expression network

Heliyon. 2023 Jan 4;9(1):e12798. doi: 10.1016/j.heliyon.2023.e12798. eCollection 2023 Jan.

Authors

Zhiyuan Wang^{1

2}, Shan Yan³, Ying Yang², Xuan Luo¹, Xiaofang Wang⁴, Kun Tang⁵, Juan Zhao¹, Yongwen He^{6

7}, Li Bian²

Affiliations

¹ School of Basic Medicine, Kunming Medical University, Kunming, 650500, China.
² Department of Pathology, The First Affiliated Hospital of Kunming Medical University, Kunming, 650031, China.
³ Institute of Biomedical Engineering, Kunming Medical University, Kunming, 650031, China.
⁴ Department of Pathology, The Second Affiliated Hospital of Kunming Medical University, Kunming, 650031, China.
⁵ Intensive Care Unit, The First Affiliated Hospital of Kunming Medical University, Kunming, 650031, China.
⁶ School of Stomatology, Kunming Medical University, Kunming, 650021, China.
⁷ Qujing Medical College, Qujing, 655099, China.

Abstract

Macrophages are one of the most important players in the tumor microenvironment. But the contribution of macrophages to lung adenocarcinoma (LUAD) is still controversial. The current study aimed to display an immune landscape to clarify the function of macrophages and detect prognostic hub genes in LUAD. The transcriptome data were adopted to screen differently expressed genes (DEGs) in The Cancer Genome Atlas database (TCGA). The cell type identification by estimating relative subsets of RNA transcripts (CIBERSORT) algorithm was used to reveal the immune landscape. Weighted gene co-expression network analysis (WGCNA) analysis was performed to identify the hub module associated with macrophages. Function Enrichment analysis was conducted on hub module genes. Moreover, univariate and multivariate Cox regression analyses were performed to identify prognostic hub genes. Kaplan-Meier (KM) and Time-dependent receiver operating characteristic (ROC) curves were plotted to assess the prognostic capacity of the four prognostic hub genes. The GES1196959 dataset from the Gene Expression Omnibus (GEO) database was downloaded to verify the differential expression of the 4 prognostic hub genes.

Keywords: Immune landscape; Lung adenocarcinoma; Macrophages; Prognostic hub genes; WGCNA.