Comprehensive Network Analysis of Lung Cancer Biomarkers Identifying Key Genes Through RNA-Seq Data and PPI Networks

Abstract

This study addresses the pressing need for improved lung cancer diagnosis and treatment by leveraging computational methods and omics data analysis. Lung cancer remains a leading cause of cancer-related deaths globally, highlighting the urgency for more effective diagnostic and therapeutic approaches. Current diagnostic methods, such as imaging and biopsies, suffer from limitations in sensitivity, specificity, and accessibility, often due to factors such as poor data quality, small sample sizes, and variability in data sources. These limitations highlight the necessity for the development of advanced noninvasive techniques. Computational methods utilizing omics data have shown promise in overcoming these challenges by comprehensively understanding the molecular pathways involved in lung cancer. We propose a novel approach that utilizes RNA-Seq data and employs LASSO regression with attention mechanisms to identify lung cancer biomarkers. Our results demonstrate the effectiveness of this approach in identifying potential biomarkers for lung cancer, including well-known genes such as TP53, EGFR, KRAS, ALK, and PIK3CA, validating the model’s ability to uncover key genes associated with lung cancer development and progression. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses revealed significant associations of the identified genes with critical biological processes and pathways, including protein synthesis, folding, cell adhesion, gene regulation, and immune responses. The PPI network analysis, constructed using the STRING database and Cytoscape application, highlighted a highly interconnected interaction landscape, with central hub genes playing pivotal roles in lung cancer progression. RPSA emerged as a crucial hub gene, consistently identified across different centrality measures. This study sheds light on the potential of computational methods and omics data analysis in improving lung cancer diagnosis and treatment, offering new insights for future research directions and personalized medicine strategies.