Precision Omic Portrait Spots 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 metastasis, whether lymphatic or systemic. Cellular identity plasticity endows carcinoma cells with the capacity to reshape their phenotype, thereby promoting enhanced metastatic potential.Following validation of protein homology and molecular biology assays, we employed Cleavage Under Targets and Tagmentation (CUT&Tag) sequencing to profile the epigenetic reprogramming of histone marks H3K4me3 and H4K16ac in three patient-derived HNSCC organoid lines with WDR54 knockdown or overexpression and their matched controls. Briefly, raw data generated from CUT&Tag sequencing are publicly accessible via the SRA Run Selector. Organoids were cultured for seven days and processed using the Hyperactive Universal CUT&Tag Assay Kit (Vazyme, TD903-01, China), with each epigenetic mark assayed in six biological replicates. After the CUT&Tag reaction, DNA purification, pre-amplification, library construction, and quality control (including assessments of tagmentation efficiency, DNA integrity, and library concentration) were performed. Sequencing was carried out on a DNBSEQ-T7 instrument (BGI, China) in PE150 mode, achieving approximately 6 Gb per sample. Subsequent analysis included quality control and annotation of sequencing reads, peak calling and annotation, motif discovery, and differential functional analysis of genes. In summary, our study establishes WDR54 as an epigenetic regulator that establishes cellular identity in HNSCC and drives metastatic progression.