Mutant TP53 Physically Sequesters FOXP3 to Abrogate PD-L1 Transcriptional Regulation and Drive Immune Evasion in Lung Adenocarcinoma: A Multi-Scale Computational Proof

Background Immune checkpoint therapy (ICT) targeting PD-1/PD-L1 fails in nearly half of lung adenocarcinoma (LUAD) patients. FOXP3, confirmed to be expressed tumor-cell-intrinsically in LUAD epithelium, directly regulates CD274 (PD-L1) transcription. I hypothesized that gain-of-function (GOF) mutant p53 (mutp53) physically sequesters FOXP3, preventing occupancy of its cognate CD274 promoter binding sites and enabling unchecked PD-L1 expression and immune evasion in a lineage-specific manner. Methods Six-layer multi-scale computational analysis: (1) clinical survival meta-analysis across three independent LUAD cohorts (TCGA PanCancer Atlas n = 510, OncoSG n = 181, CPTAC n = 110; N = 670); (2) FIMO in silico transcription factor occupancy analysis (JASPAR 2024 MA0850.1) on the CD274 promoter; (3) ATAC-seq chromatin accessibility profiling across LUAD/HNSC lineages; (4) AlphaFold 3 mutp53-FOXP3 complex prediction with PAE analysis; (5) AMBER ff19SB/TIP3P molecular dynamics (2 ns NPT production trajectory, 310K, 0.15M NaCl, A100 GPU; Making-it-Rain pipeline); (6) foundational pan-cancer transcriptomic analysis (8 TCGA cohorts, N = 4,205; DESeq2/Spearman coupling) from preprint [36]. Results Clinical meta-analysis: disrupted FOXP3-PD-L1 axis significantly predicted inferior OS (log-rank p = 6×10⁻⁴, N = 670). FIMO identified 8 high-confidence FOXP3 consensus binding sites (GTAAACA; p = 7.93×10⁻⁵) on the CD274 promoter. ATAC-seq revealed lineage-specific chromatin remodelling. AlphaFold 3 predicted a stable mutp53-FOXP3 heterodimer (pLDDT > 70 at interface). AMBER MD simulation (2 ns NPT, 310K) demonstrated progressive complex compaction (radius of gyration: 46.7→43.9 Å), significant inter-chain correlated motion confirming mutp53-FOXP3 physical coupling, rigid interface geometry at the mutp53 DNA-binding domain (RMSF 1–2 Å, residues 150–300), and estimated interaction energy of − 55.33 kcal/mol (MM energy decomposition). From preprint [36]: mutp53 upregulates CD274 (log₂FC = 0.53, padj < 0.0001) without altering FOXP3 (log₂FC = 0.014, padj = 0.889) in 517 TCGA-LUAD samples; 67% adenocarcinoma vs 0% non-adenocarcinoma FOXP3-checkpoint uncoupling across N = 4,205 tumors. Conclusions First multi-scale computational proof that GOF mutp53 sequesters FOXP3, blocking 8 confirmed CD274 promoter sites, driving PD-L1 overexpression and significantly inferior survival across 670 LUAD patients. This lineage-specific mechanism defines the mutp53-FOXP3 interface as a novel therapeutic target for ICT sensitization.