SLC5A12 defines an invasive epithelial state associated with immune remodeling and therapeutic vulnerability in HNSCC

Abstract

Head and neck squamous cell carcinoma (HNSCC) is characterized by marked epithelial and immune heterogeneity. The malignant epithelial states associated with tumor progression, immune remodeling, and potential therapeutic vulnerability remain incompletely defined. Single-cell RNA-sequencing datasets from three HNSCC cohorts were integrated with TCGA-HNSC and five GEO cohorts. Epithelial-state heterogeneity, inferred trajectories, regulons, cell-cell communication, prognostic features, spatial localization, and ferroptosis-associated transcriptional programs were analyzed. SLC5A12 was prioritized through convergent computational analyses and was subsequently tested by loss-of-function assays and xenograft experiments. CellOracle perturbation, ferroptosis-related drug-sensitivity analyses, and molecular docking were treated as computational predictions. Five epithelial states were identified, among which the Invasive population increased with disease progression and exhibited the highest inferred CNV burden. Invasive cells showed enrichment of malignant and extracellular-matrix programs and prominent predicted MIF-CD74/CXCR4 communication with regulatory T cells. Machine-learning, WGCNA, single-cell, and spatial analyses converged on SLC5A12 as an Invasive-state-associated prognostic feature. Computational analyses further indicated a ferroptosis-associated vulnerability profile in the Invasive state and predicted attenuation of invasive and immunoregulatory programs after virtual SLC5A12 loss. Experimentally, SLC5A12 knockdown reduced proliferation, clonogenicity, migration, invasion, and xenograft growth while increasing apoptosis. Structure-based virtual screening nominated ledipasvir (ZINC000150338819) and elbasvir (ZINC000150588351) as top-ranked candidate SLC5A12-binding compounds. SLC5A12 is a molecular feature of an Invasive epithelial state associated with HNSCC progression, adverse outcome, and predicted immune-remodeling and therapeutic-vulnerability programs. Experimental loss-of-function data support a tumor-promoting role for SLC5A12, whereas the MIF-Treg communication, ferroptosis vulnerability, CellOracle perturbation, and molecular-docking findings remain computational hypotheses requiring direct validation.