Spatially resolved proteomics provides insights into the normal-dysplasia-tumor continuum in oral squamous cell carcinoma.

Background

Oral epithelial dysplasia is a recognized precursor lesion for oral squamous cell carcinoma (OSCC), yet the proteomic changes underlying the progression from normal epithelium to dysplasia and ultimately to OSCC remain incompletely characterized. This gap is partially due to the high interpatient heterogeneity of OSCC, the frequent reliance on cross-patient comparisons, and the omission of dysplasia as a critical intermediate stage.

Methods

A histology-guided, spatially resolved proteomics workflow was applied to formalin-fixed paraffin-embedded tissue blocks from six patients with primary OSCC. For each case, spatially contiguous normal (N), dysplasia (D), and tumor (T) regions from the same lesion-bearing block, yielding 18 regional proteomes. Proteins were profiled using data-independent acquisition liquid chromatography-tandem mass spectrometry. Downstream analyses included differential expression analysis, Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment, soft-clustering trajectory analysis, protein-protein interaction analysis, exploratory clinicopathological stratification, and immunohistochemistry validation.

Results

The spatially matched N-D-T dataset identified 1,683 proteins in N, 2,100 in D, and 1,966 in T. Under the predefined differential-expression threshold, the N vs. D comparison yielded more differentially expressed proteins than the D vs. T comparison, suggesting that threshold-detectable proteomic alterations may already be present at dysplasia. Functionally, the N-to-D transition was associated with cell-cycle activation, proliferative signaling, hypoxia-associated responses, and metabolic alterations, whereas the D-to-T transition was more closely related to cytoskeletal organization, motor activity, and structural remodeling. Across the overall N-to-T contrast, glycolysis, pyruvate metabolism, and broader metabolic reprogramming predominated. Trajectory analysis resolved Early Warning, Progression, and dysplasia-restricted transient modules, suggesting a non-linear architecture of proteomic evolution during OSCC progression. MYO1B showed progression-associated spatial increase from N to D and T regions, whereas HSP90AB1 was prioritized as a candidate invasion-associated hub supported by proteomic, protein-protein interaction network, and external transcriptomic analyses.

Conclusions

Spatially resolved proteomics of archived formalin-fixed paraffin-embedded tissues provides a morphology-anchored proteomic continuum of oral malignant transformation in a small spatially matched cohort. The data suggest that OSCC progression involves early-shift, progressive, and transient dysplasia-specific programs. These findings offer candidate proteins and biological hypotheses for further validation in larger oral cancer cohorts.