Spatial Transcriptomics Reveals Molecular Differences Associated with Malignant Transformation in Oral Epithelial Dysplasia

Methods

We performed spatial transcriptomics on 13 benign, 15 OED (8 with transformation, 7 without), and 14 OSCC biopsies using the NanoString GeoMx Digital Spatial Profiler. Regions of interest were segmented into epithelial and stromal compartments with morphological markers. Gene expression was profiled using the GeoMx cancer transcriptome atlas assay for ~1,800 tumor related genes.

Differentially expressed genes (DEGs) from next-generation sequencing were subject to bioinformatic analyses. Results Differentially gene expression analysis between OED with and without transformation revealed eight upregulated and three downregulated genes in epithelial cells, with no significant changes in immune cells. Protein-protein interaction network analysis identified B2M, STAT1, and CD74 as central hub genes.

Pathway enrichment analysis suggested interferon and cytokine-mediated immune pathways, along with myeloid and amyloid formation-related pathways, as important contributors to OED transformation. Transcription factor analysis highlighted RELA and RFX as key upstream regulators. Conclusions Malignant transformation of OED appears to be primarily driven by epithelial-intrinsic activation of interferon and inflammatory signaling pathways rather than overt transcriptional reprogramming of immune cells.

These findings suggest that early immune-related alterations in oral carcinogenesis are tumor cell centered and may precede significant changes in immune cell composition.