Development of m6A-related prognostic models for survival in lung squamous cell carcinoma with different PD-L1 expression levels

Background: Programmed death-ligand 1 (PD-L1) is widely used in the clinical context of immune checkpoint inhibitor therapy, but its relationship with N6-methyladenosine (m6A) RNA methylation in lung squamous cell carcinoma (LUSC) has not been well defined. This study aimed to investigate the association between PD-L1 mRNA expression and m6A regulator expression patterns and to develop exploratory m6A-based prognostic models in LUSC.

Methods: Transcriptome data from 502 patients with LUSC were obtained from The Cancer Genome Atlas (TCGA). Patients were divided into PD-L1 high-expression (PHE) and PD-L1 low-expression (PLE) groups according to the median PD-L1 messenger RNA (mRNA) level. Differential expression and correlation analyses were performed for 30 m6A regulators. Transcriptome sequencing data from surgical specimens from 28 Asian patients with LUSC were used for expression-pattern comparison. Principal component analysis (PCA), univariate Cox regression, and least absolute shrinkage and selection operator (LASSO)-Cox regression were used to construct prognostic models in the TCGA cohort.

Results: In the TCGA cohort, the main differentially expressed m6A regulators between the two PD-L1 groups were YTHDF2 (p < 0.001), IGF2BP3 (p < 0.001), and YTHDC2 (p < 0.001). In the Asian cohort, ALKBH5 (p = 0.008) and ZC3H13 (p = 0.035) showed significant differences. LASSO-Cox models were constructed for the overall LUSC cohort and for the PHE and PLE subgroups. The overall model included METTL3, HNRNPC, and CBLL1, with a 5-year time-dependent area under the receiver operating characteristic curve (AUC) of 0.579. The 5-year AUCs were 0.742 in the PHE subgroup and 0.652 in the PLE subgroup. The risk score remained independently associated with prognosis in multivariate Cox analysis.

Conclusions: In LUSC, PD-L1 mRNA status was associated with distinct m6A regulator expression profiles. In the TCGA cohort, the PHE subgroup showed higher expression of CBLL1, G3BP1, IGF2BP3, FMR1, and YTHDC2, but lower expression of VIRMA, YTHDF2, and PRRC2A compared with the PLE subgroup. In the CICAMS cohort, ALKBH5 and ZC3H13 were more highly expressed in the PHE subgroup. Moreover, m6A-based risk models were associated with survival outcomes, with significant prognostic separation in the overall TCGA cohort and the PHE subgroup, whereas the PLE subgroup showed a weaker survival separation.