Epigenetic destabilization of chromatin compartments defines chromosomal weak links enriched for driver mutations in head and neck squamous cell carcinoma

Head and neck squamous cell carcinoma (HNSCC) is marked by extensive epigenetic remodeling and recurrent mutations in a limited set of cancer driver genes. Although large-scale chromatin compartments are known to influence mutation rates, whether cancer-associated epigenetic erosion destabilizes higher-order genome architecture in primary tumors-and thereby shapes mutational vulnerability-remains unresolved. Here, we identify chromosomal “weak links” as regions of compromised A/B compartment integrity that recurrently harbor driver mutations in HNSCC. We analyzed genome-wide DNA methylation profiles from multiple independent HNSCC cohorts, including TCGA and institutional datasets spanning oral tongue, floor of mouth, and laryngeal tumors, together with matched normal epithelium. A/B chromatin compartments were inferred directly from long-range DNA methylation correlation structure, enabling analysis of higher-order genome organization in primary tumors at population scale. Beyond compartment switching, we quantified compartment strength, eigenvector magnitude, and fragmentation to capture architectural destabilization. Across cohorts and anatomical subsites, HNSCC tumors exhibited pervasive but non-random weakening of A/B compartment organization relative to normal tissues. These chromosomal weak links were characterized by reduced long-range methylation correlation, intermediate methylation variability, and low compartment eigenvector magnitude, consistent with erosion of higher-order chromatin architecture. Strikingly, weak-link regions were significantly enriched for recurrently mutated HNSCC driver gene including TP53, FAT1, NOTCH1, CDKN2A, KMT2D, SMARCA4, and PIK3CA. These loci were preferentially localized to compartment boundaries or intrinsically low-stability regions that showed reproducible weakening across datasets. Together, our findings reveal that global epigenetic erosion in HNSCC destabilizes chromatin compartment architecture, generating conserved chromosomal weak links that repeatedly concentrate driver mutations. This work uncovers a previously unrecognized mechanistic coupling between global DNA methylation erosion and large-scale chromatin compartment destabilization that defines chromosomal weak links selectively vulnerable to oncogenic mutation in HNSCC. This layer of genome vulnerability establishes epigenetically inferred compartment destabilization as a scalable framework for mapping structural fragility in cancer genomes.