Abstract
ABSTRACT
Mitochondrial apoptosis is a key regulator of tumor progression, therapeutic resistance, and immune evasion in non‐small cell lung cancer (NSCLC), yet promising candidate biomarkers remain inadequately defined. Using an integrative multi‐omics systems biology framework, we identified 16 mitochondrial apoptosis‐associated genes and uncovered a highly interconnected apoptotic network centered on MCL1, BCL2L1, BAX, CASP8, and CASP9. Comprehensive transcriptomic, genomic, and epigenetic analyses revealed recurrent genomic alterations, subtype‐specific dysregulation, copy number variation‐driven transcriptional changes, differential DNA methylation, and significant survival associations, highlighting their clinical relevance. Independent validation across external transcriptomic cohorts confirmed robust differential expression of the prioritized biomarkers, while physiological transcriptomic and protein atlas analyses demonstrated conserved transcript architecture, widespread tissue expression, and mitochondrial localization of MCL1. Importantly, spatial transcriptomic profiling in a mouse NSCLC model experimentally provided complementary evidence consistent with the computational findings by demonstrating markedly increased and spatially heterogeneous expression of MCL1, BCL2L1, and CASP9 within tumor tissues and their enrichment in distinct cellular populations, supporting their role in tumor heterogeneity and mitochondrial apoptosis regulation. Integrative analysis consistently prioritized MCL1 as the dominant mitochondrial apoptosis biomarker, with BCL2L1 and CASP9 emerging as additional high‐confidence candidates and CASP8 and BAX serving as complementary prognostic biomarkers. These findings establish MCL1 as a promising candidate biomarker and promising precision therapeutic target, while demonstrating that the integration of multi‐omics discovery with spatial transcriptomic validation provides a comprehensive molecular framework for apoptosis‐driven precision oncology in NSCLC.