Integrative analyses of single-cell and bulk RNA sequencing to construct the tumor-associated macrophage-related prognostic signature in lung adenocarcinoma.

BACKGROUND

Tumor-associated macrophages (TAMs) are a type of tumor-infiltrating immune cell that play a crucial role in tumor progression. However, the roles of TAMs and their regulatory mechanisms in lung adenocarcinoma (LUAD) remain poorly understood. Therefore, we aimed to develop a novel TAM-related prognostic signature to predict survival outcomes and constructed a lncRNA-miRNA-mRNA network based on these genes.

METHODS

Transcriptomic data, clinical data, and single-cell RNA-sequencing (scRNA-seq) data were obtained from LUAD patients were obtained from the Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. Differentially expressed-lncRNAs (DE-lncRNAs), miRNAs (DE-miRNAs), and mRNAs (DEGs) were identified in LUAD. Differentially expressed TAM-related genes (DE-TAMGs) were selected and used to construct prognostic signatures. A TAM-related risk score was calculated, and patients were stratified into high- and low-risk groups based on the median risk score. Then, biological functions, immune characteristics, and responses to immunotherapy and chemotherapy were assessed across the risk groups. A TAM-related lncRNA-miRNA-mRNA network was constructed based on DE-lncRNAs, DE-miRNAs, and TAM-related signatures. Quantitative polymerase chain reaction (qPCR) was used to validate the expression of TAM-related genes, and scRNA-seq analysis was used to examine cell-type-specific expression of these genes.

RESULTS

A total of 316 DE-lncRNAs, 162 DE-miRNAs, and 2,601 DEGs were screened in LUAD. Among these, 147 DE-TAMGs were selected. KLF4, GAPDH PDGFB, TIMP1, CD74, and CCL20 were identified as the key prognostic markers in LUAD. Patients were divided into high- and low-risk groups based on the median risk score. Enrichment analysis revealed several cancer-related pathways associated with the high-risk group, and significant differences in terms of immune cell infiltration, HLA-related gene expression, immune checkpoints expression, and therapeutic responses were observed between high- and low-risk groups. We also constructed a lncRNA-miRNA-mRNA network, which included 36 DE-lncRNAs, 23 shared miRNA, and four TAMGs (PDGFB, CD74, KLF4, and CCL20). The qPCR results indicated the increased expression of PDGFB, CD74, and KLF4 but decreased expression of CCL20 in LUAD tumor tissues compared with adjacent normal tissues. scRNA-seq analysis revealed that CD74, KLF4, CCL20, PDGFB were specifically expressed in macrophages.

CONCLUSIONS

In conclusion, we identify the TAM-related prognostic signature that predicts the survival outcome in patients with LUAD. This signature may offer a novel effective therapeutic strategy for LUAD patients.