Convergent chromatin remodeling enables pan-aerodigestive detection of advanced malignancies in plasma cfDNA

Background: Liquid biopsy approaches for cancer detection often rely on tissue-specific methylation or fragmentation features to infer tumor origin. However, a pan-aerodigestive cancer detection strategy is clinically valuable given shared risk exposures, field cancerization, and frequent diagnostic ambiguity among lung, esophageal, and head & neck cancers. We hypothesized that advanced-stage disease exhibits convergent chromatin remodeling, producing a dominant malignancy-associated fragmentomic signal that supersedes subtler tissue-of-origin patterns. Methods: Whole-genome EM-seq (~15×) was performed on plasma cfDNA from 120 patients with stage III/IV aerodigestive cancers (lung, esophageal, head & neck; squamous and adenocarcinoma) and 60 age-matched controls. Four fragmentomic modalities were assessed: (1) genome-wide fragmentation in 5-Mb bins (DELFI-like), (2) NMF spectral components, (3) 4-mer end motifs, and (4) promoter-centric nucleosome scores (Griffin). All preprocessing occurred strictly within each training fold of a repeated stratified 10-fold CV (100 repeats) to prevent data leakage. No test-sample information was used in training. Hyperparameters were tuned only within training partitions. Random Forest classifiers were trained under this fully nested scheme. Results: The multimodal classifier robustly detected advanced aerodigestive malignancies with a mean AUROC 0.86 and AUPRC 0.94. However, modality dissection revealed a clear performance hierarchy: nucleosome positioning (Griffin) alone achieved AUROC 0.85 and AUPRC 0.93, nearly matching the full integrated model, whereas end motifs performed poorly (AUROC 0.61). Biological interpretation demonstrated prominent nucleosome depletion centered at promoters of proliferation-associated genes, indicating a convergent epigenetic state of promoter opening across late-stage aerodigestive malignancies. Conclusions: Advanced aerodigestive cancers exhibit a dominant, convergent chromatin remodeling signature detectable in plasma cfDNA, driven primarily by altered nucleosome positioning. In late-stage disease, this shared malignancy-associated fragmentomic signal outweighs tissue-of-origin-dependent patterns. These findings highlight the utility of nucleosome-based fragmentomics not merely for detection, but for resolving diagnostic ambiguity in patients with indeterminate masses and for monitoring total tumor burden in high-risk aerodigestive malignancies.