To characterize benign, oral epithelial dysplasia (OED), and oral squamous cell carcinoma (OSCC) biopsies using spatial transcriptomics, with a focus on comparing transforming and non-transforming OED.
Approach:
Sample Collection: Analyzed 42 archived oral biopsy samples: 13 benign, 15 OED (8 transforming, 7 non-transforming), and 14 OSCC.
Spatial Transcriptomic Profiling: Utilized NanoString GeoMx Digital Spatial Profiler to measure gene expression across ~1,800 genes.
Data Analysis: Identified differentially expressed genes (DEGs) using linear mixed-effects modeling and performed exploratory bioinformatic analyses.
Key Findings:
Identified 11 epithelial DEGs in transforming vs non-transforming OED, including B2M, STAT1, and CD74, which are related to antigen presentation and interferon signaling.
No significant DEGs were found in immune-enriched regions.
Pathway analyses indicated enrichment of immune- and interferon-related processes.
Interpretation:
The study provides exploratory insights into molecular differences between OED lesions with distinct clinical outcomes.
Limitations:
Modest sample size may limit the generalizability of findings, particularly in the context of the identified DEGs.
Targeted gene panel does not capture the full transcriptome.
Conclusion:
Spatial transcriptomics may serve as a framework for investigating early molecular changes in oral carcinogenesis, though findings require validation.
