Epigenetic activation of SLC7A11 defines a ferroptosis—immune axis and enables robust DNA methylation-based diagnosis of lung squamous cell carcinoma

TL;DR

This study identifies SLC7A11 as a key epigenetically activated gene in lung squamous cell carcinoma, enabling a highly accurate DNA methylation-based diagnostic model and linking it to immune evasion and treatment resistance.

Contribution

The study introduces a novel DNA methylation-based diagnostic model for LUSC using SLC7A11 and reveals its role in ferroptosis resistance and immune suppression.

Findings

SLC7A11 is epigenetically activated in LUSC with promoter hypomethylation and increased expression.

A four-probe methylation model achieved high diagnostic accuracy (AUC = 0.985 and 1.000 in TCGA and GSE121849 datasets).

High SLC7A11 levels correlate with immune evasion and resistance to certain therapies but sensitivity to rTRAIL and 17-allylamino-17-demethoxygeldanamycin.

Abstract

Lung squamous cell carcinoma (LUSC) currently lacks reliable biomarkers for early diagnosis and precision therapy. While Solute Carrier Family 7 Member 11 (SLC7A11) plays key roles in ferroptosis resistance, redox homeostasis and tumor progression, its epigenetic regulation, diagnostic potential, and immunological functions in LUSC remain poorly understood.

Multi-omics data from The Cancer Genome Atlas (TCGA), Clinical Proteomic Tumor Analysis Consortium (CPTAC), Gene Expression Omnibus (GEO) and an in-house cohorts of 173 LUSC patients were integrated to characterize SLC7A11 DNA methylation, mRNA, and protein levels. Four methylation probes were utilized to construct diagnostic models, including Generalized Linear Model (GLM), Least Absolute Shrinkage and Selection Operator (LASSO), Random Forest (RF), and Extreme Gradient Boosting (XGB). These models were validated internally (via 10-fold cross-validation and bootsrtapping) and externally using the GSE121849 dataset. Model interpretability was examined through SHapley Additive exPlanations (SHAP). Additionally, immune infiltration, pathway enrichment and drug sensitivity analyses were performed to explore ferroptosis-associated and immunity-related mechanisms.

SLC7A11 exhibited LUSC-specific epigenetic activation, characterized by promoter hypomethylation, mRNA upregulation, and protein overexpression across cohorts. The four-probe GLM diagnostic model achieved superior performance (AUC = 0.985 in TCGA; AUC = 1.000 in GSE121849), with SHAP identifying cg02102889 (TSS1500) as the most influential probe. While SLC7A11 expression and methylation were not significantly associated with survival in the overall cohort, high SLC7A11 predicted poorer outcomes in female patients and those with pathologic T3 & T4 stage disease. Mechanistically, SLC7A11-high tumors displayed ferroptosis-resistant and immunosuppressive phenotypes, including increased Programmed Death-Ligand 1 (PD-L1) expression and enrichment of regulatory T cells and M2 macrophages. Drug sensitivity profiling suggested resistance to Reactive Oxygen Species (ROS) inducers and Histone Deacetylase (HDAC) inhibitors, but enhanced sensitivity to recombinant tumor necrosis factor-related apoptosis-inducing ligand (rTRAIL) and 17-Allylamino-17-demethoxygeldanamycin.

SLC7A11 undergoes epigenetic activation in LUSC and enables a robust four-probe, methylation-based diagnostic model. Its expression is linked to ferroptosis resistance, immune evasion, and therapeutic response, supporting SLC7A11 as a promising biomarker for early diagnosis and personalized treatment in LUSC.

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