Subtype-specific expression and prognostic significance of creatine kinase family genes in non-small cell lung cancer: a TCGA-based integrated analysis
Abstract
Abstract Background Non-small cell lung cancer (NSCLC), primarily comprising lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC), remains a leading cause of cancer-related mortality worldwide. While creatine kinase (CK) enzymes are central to cellular energy homeostasis, their subtype-specific transcriptional dysregulation and prognostic relevance in NSCLC remain poorly characterized. Methods RNA-seq STAR counts and clinical metadata for TCGA-LUAD and TCGA-LUSC were retrieved using TCGAbiolinks. Matched tumor (TP) and normal tissue (NT) samples were analyzed for paired differential expression analysis (DEA). Data processing included edgeR filtering, TMM normalization, and limma-voom modeling for LUAD, LUSC and pooled cohorts. The analysis focused on five CK family genes: CKM , CKB , CKMT1A , CKMT1B , and CKMT2 . Clinical characteristics and ESTIMATE-based tumor purity were incorporated into univariate and multivariate Cox regression models. Kaplan-Meier survival analysis was performed to evaluate the prognostic impact of key CK members. Results The paired cohort consisted of 109 patients (58 LUAD and 51 LUSC). DEA and volcano plots revealed distinct subtype-dependent expression patterns: While CKMT1A and CKMT1B were consistently upregulated across all cohorts, their fold-change was markedly higher in LUSC than in LUAD. Conversely, subtype-specific dysregulation was observed for other members: CKM was significantly upregulated specifically in LUAD, whereas…
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Evidence Hub reads this as a cohort study, done in people. Its evidence level is 3 of 5 (Moderate · trial / cohort / secondary analysis). Trials without a large randomized design, cohorts and secondary analyses give moderate evidence. Reported size: 109 participants or records.
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