CDKN3, PKP2, ADM, MS4A1, FAM83A, and DKK1 Define a Posttranslational Modification (PTM)-Associated Prognostic Model...

Posttranslational modification (PTM) plays an important role in protein regulation and may influence tumor initiation and progression. However, the role of PTM-related programs in lung adenocarcinoma (LUAD) remains incompletely understood.

Single-cell RNA sequencing (scRNA-seq) data were analyzed to quantify the activity of PTM-related gene set using the AUCell algorithm and to characterize intercellular communication using CellChat. Molecular subtypes and differentially expressed genes (DEGs) were identified using ConsensusClusterPlus and limma packages, respectively, followed by functional enrichment analysis. Univariate Cox regression, LASSO regression with 10-fold cross-validation, and stepwise multivariable Cox regression based on the Akaike information criterion (AIC) were used to construct a prognostic model. Immune infiltration was evaluated using ESTIMATE, CIBERSORT, MCP-counter, and TIMER algorithms, and drug sensitivity was predicted using oncoPredict package. The IMvigor210 cohort was used for exploratory assessment of immunotherapy response. Quantitative real-time reverse transcription PCR (qRT-PCR) was used to measure the expressions of the model genes. CCK-8, wound-healing, and Transwell assays were performed to evaluate the effects of CDKN3 knockdown on LUAD cells.

Comparison between two PTM groups revealed that receptor ligands such as MIF-(CD74+CXCR4) and MIF-(CD74+CD44) had higher communication probabilities in the high-PTM-score group. Two molecular subtypes were identified, and a six-gene risk model for LUAD was established based on CDKN3, PKP2, ADM, MS4A1, FAM83A, and DKK1. The high-risk group showed a lower immune score, and drugs such as Docetaxel_1007 may have therapeutic potential for LUAD. Immunotherapy response prediction further demonstrated that the low-risk group may be more likely to benefit from immunotherapy. In vitro experiments demonstrated that CDKN3, PKP2, ADM, FAM83A, and DKK1 were upregulated, whereas MS4A1 was downregulated in A549 cells compared with BEAS-2B cells. Additionally, knockdown of CDKN3 significantly suppressed the viability, migration, and invasion of LUAD cells.

The PTM-related six-gene model showed potential for prognostic stratification and characterization of immune-related features in LUAD. However, further prospective and experimental validation is required before direct clinical application.