Spatial transcriptomics reveals molecular differences associated with malignant transformation in oral epithelial dysplasia

Abstract

Background Oral epithelial dysplasia (OED) is a precancerous oral lesion with variable risk of progression to oral squamous cell carcinoma (OSCC). The molecular basis underlying this progression remains incompletely understood. To address this gap, this study applied spatial transcriptomics to characterize benign, OED and OSCC biopsies with a focus on the comparison between transforming and non-transforming OED. Methods Spatial transcriptomic profiling was performed on 13 benign, 15 OED (8 transforming, 7 non-transforming), and 14 OSCC biopsies using the NanoString GeoMx Digital Spatial Profiler. Regions of interest were segmented into epithelial and immune-enriched compartments with morphological markers. Gene expression was measured using the GeoMx Cancer Transcriptome Atlas (~1, 800 genes) and differentially expressed genes (DEGs) were identified using linear mixed-effects modeling. Exploratory bioinformatic analyses were performed to provide biological context. Results Comparison of OED with and without transformation identified a limited set of 11 epithelial DEGs, including genes associated with antigen presentation and interferon signaling (e.g., B2M, STAT1, and CD74), while no significant DEGs were detected in immune-enriched regions. Pathway analyses indicated enrichment of immune- and interferon-related processes. Given the modest sample size and targeted gene panel, these findings should be considered exploratory in nature. Conclusions This study provides spatially resolved, exploratory insights into molecular differences between OED lesions with distinct clinical outcomes. The results suggest altered epithelial-immune interactions in transforming lesions, though these findings require validation. Spatial transcriptomics may offer a useful framework for investigating early molecular changes in oral carcinogenesis.