Precision omic portrait deciphers the epigenetic variable during cellular identity reshaping of metastatic head and neck squamous cell carcinoma

The poor prognosis of head and neck squamous cell carcinoma (HNSCC) is primarily attributed to lymphatic or systemic metastasis. The cellular identity plasticity provides carcinocytes with the motility phenotype fluctuations, which indicates the intensified metastasis. Aiming at elucidating this lineage evolution, this study integrated single-cell RNA sequencing data from 12 primary lesions, 12 lymphatic metastases, and 12 distant metastases to portray the pan-metastatic cellular landscape. With the escalation of metastasis, there was a dramatic increase in the proportion of cancer-associated fibroblasts (CAFs). The spatiotemporal RNA alternative splicing and trajectory tracing methods with/without histopathological constraint observed that the SCGB3A1 + malignant epithelial cells, which becomes conspicuous in metastasis, undergoes partial epithelial-mesenchymal transition (pEMT) to exhibit a CXCL14 + CAF phenotype, and B2M + CAFs serve as a transdifferentiation terminal. Moreover, multimodal genetic detection identified WD repeat domain 54 (WDR54) as a potential initiator of cellular identity reshaping. Functional experiments demonstrated that WDR54-launched dedifferentiation preserves lineage plasticity via epithelial signature erosion, and markedly enhances cellular invasion, migration, and MDSC-mediated immune evasion. Homologous protein structural congruence alignment and CUT&Tag profiling revealed that WDR54 initiates the TGF-β-driven pEMT program by selective H3K4me3 and H4K16ac modifications. Clinically, the practical utility of WDR54 as a diagnostic, prognostic and therapeutic target has received validations from a real-world perspective. In summary, the research establishes WDR54 as an epigenetic regulator that initializes cell identity and triggers metastasis in HNSCC.