HPV-negative tongue squamous cell carcinoma (TSCC) is an aggressive subtype of oral squamous cell carcinoma (OSCC) with limited targeted therapies and poor prognosis, particularly in advanced stages. TSCC is frequently diagnosed at a late stage, when lymph node metastasis and local invasion are already present, contributing to poor clinical outcomes and limited therapeutic options. Despite advances in treatment, the 5-year survival rate for advanced TSCC remains around 40%, with minimal improvement over recent decades. To address the urgent need for more effective, biologically informed interventions, this thesis investigates the epigenomic and transcriptomic landscape of TSCC using both patient tissues and patient-derived xenograft (PDX) models. We generated the first enhancer and super-enhancer (ESE) data in primary TSCC by performing H3K27ac ChIP-seq and RNA-seq on matched tumor and adjacent normal tissues from 15 HPV-negative patients. This matched design enabled sensitive detection of tumor-specific regulatory alterations, identifying over 159,000 ESEs, including 6,473 disease-specific regions. Integration with transcriptomic data revealed that tumor-specific ESEs drive oncogene upregulation (e.g., KIF17, MET, PLEK2, SH2D5), while normal-specific ESEs are linked to downregulated tumor suppressors (e.g., SMIM5, SOSTDC1). To evaluate the fidelity of PDX models in recapitulating TSCC biology, we conducted a pilot study integrating spatial ATAC-seq and bulk RNA-seq across two matched tumor–PDX pairs. Twelve distinct clusters were identified, revealing differential expression of epithelial, mesenchymal, and partial epithelial-to-mesenchymal transition (pEMT) markers. Tumor samples exhibited elevated mesenchymal and pEMT signatures, one at invasive fronts, while PDXs retained higher epithelial marker expression. Cell type deconvolution uncovered diverse populations—including malignant cells, CAFs, TAMs, T cells, B cells, and endothelial cells—with spatial co-localization in perivascular niches suggesting functional crosstalk in immune infiltration and tumor expansion. Comparison to a larger TSCC cohort confirmed transcriptional similarity between tumors and PDXs, with regulatory RNA profiles showing stronger conservation across matched pairs. Together, these findings provide a spatially resolved, epigenetically informed framework for understanding TSCC heterogeneity and progression. They underscore the role of enhancer reprogramming, pEMT, and mesenchymal-like stromal cells in shaping tumor behavior and therapeutic resistance, and highlight the utility of PDX models and regulatory RNAs in guiding precision oncology for HPV-negative tongue cancer.