Exploratory Transcriptomic Profiling of Three RNA-Seq Samples Reveals Heterogeneity in KRAS-Associated Signaling and Epithelial Lineage Programs

KRAS-driven lung adenocarcinoma is molecularly heterogeneous; however, evaluation of mutation-associated programs requires matched mutation and clinical metadata. Here, three GDC STAR-count RNA-sequencing files annotated with GENCODE v۳۶ were analyzed to determine which transcriptomic conclusions could be supported from the available data alone. Protein-coding TPM values were used for library-level quality assessment, transcriptome-wide correlation, principal component analysis, sample-specific expression contrasts, and exploratory scoring of curated KRAS/MAPK, PI۳K–AKT–mTOR, cell-cycle, epithelial-lineage, epithelial–mesenchymal transition, hypoxia, inflammatory, interferon, apoptosis, and NRF۲-related gene sets. The samples contained ۲۴.۳–۴۹.۵ million assigned reads and ۱۲,۸۰۸–۱۴,۵۷۴ protein-coding genes with TPM ≥۱. Pairwise transcriptome correlations ranged from r=۰.۷۴۵ to ۰.۸۲۵. Marked biological heterogeneity was observed. Sample ۱ showed a secretory epithelial profile characterized by PAEP, CEACAM۵, CEACAM۶, BPIFA۱, and EPCAM. Sample ۲ displayed a keratinizing/squamous-like program dominated by KRT۵, KRT۶A, KRT۱۴, KRT۱۷, SPRR family genes, and elevated NRF۲-associated and glycolytic scores. Sample ۳ exhibited a strong alveolar-lineage and immune-associated profile, with high SFTPA۱, SFTPA۲, SFTPB, SFTPC, HLA-DRA, CD۷۴, and inflammatory pathway scores. KRAS expression was detectable in all samples (۱۶.۳۳–۳۰.۰۹ TPM), but RNA expression alone could not establish KRAS mutation status. These findings demonstrate substantial lineage and pathway heterogeneity among the three transcriptomes and provide a hypothesis-generating framework for subsequent mutation-informed analysis. Mutation-stratified differential expression, prognostic modeling, and survival analysis were not performed because mutation and clinical outcome data were unavailable.

کلیدواژه ها:

RNA ، seqKRAS signalingtranscriptomic heterogeneityepithelial lineagelung adenocarcinoma