Prognostic biomarkers and immune cell infiltration characteristics in small cell lung cancer

Background

Small cell lung cancer (SCLC) is a highly malignant and aggressive neuroendocrine tumor. With the rise of immunotherapy, it has provided a new direction for SCLC. However, due to the lack of prognostic biomarkers, the median overall survival of SCLC is still to be improved. This study aimed to explore novel biomarkers and tumor-infiltrating immune cell characteristics that may serve as potential diagnostic and prognostic markers in SCLC.

Methods

Gene expression profiles from patients with SCLC were downloaded from the Gene Expression Omnibus (GEO) database, and tumor microenvironment (TME) infiltration profile data were obtained using CIBERSORT. The robust rank aggregation (RRA) method was utilized to integrate three SCLC microarray datasets downloaded from the GEO database and identify robust differentially expressed genes (DEGs) between normal and tumor tissue samples. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed to explore the functions of the robust DEGs. Subsequently, protein–protein interaction networks and key modules were constructed by Cytoscape, and hub genes were selected from the whole network using the plugin cytoHubba. Survival analysis of hub genes was performed by Kaplan–Meier plotter in 18 patients with extensive-stage SCLC.

Results

A total of 312 robust DEGs, including 55 upregulated and 257 downregulated genes, were screened from 129 SCLC tissue samples and 44 normal tissue samples. GO and KEGG enrichment analyses revealed that the robust DEGs were predominantly involved in human T-cell leukemia virus 1 infection, focal adhesion, complement and coagulation cascades, tumor necrosis factor (TNF) signaling pathway, and ECM-receptor interaction, which are closely associated with the development and progression of SCLC. Subsequently, three DEGs modules and six hub genes (ITGA10, DUSP12, PTGS2, FOS, TGFBR2, and ICAM1) were identified through screening with the Cytoscape plugins MCODE and cytoHubba, respectively. Immune cell infiltration analysis by the CIBERSORT algorithm revealed that resting memory CD4⁺ T cells were the predominant infiltrating immune cells in SCLC. In addition, Kaplan–Meier plotter revealed that the gene prostaglandin-endoperoxide synthase 2 (PTGS2) was a potential prognostic biomarker of SCLC.

Conclusions

Hub genes and tumor-infiltrating immune cells may be the molecular mechanisms underlying the development of SCLC, and this finding could contribute to the formulation of individualized immunotherapy strategies for SCLC.