Abstract 1112: Gene expression characteristics of EBV-positive smooth muscle tumors compared to EBV-positive NPC and LELC
Authors: Harold Yu Chan, Yi Ren, Teo Wei Keat, Joseph W. Foley, Loh Kwok Seng, Raymond KY Tsang, Han Shuting, Jain Amit, Toh Han Chong, Joshua K. Tay, Victor Lee
Journal: Cancer Research (2025)

Abstract Background: EBV SMTs are rare stromal malignancies associated with immunosuppression. Despite diversity in their anatomical location and clinical presentation, EBV SMTs likely share common pathways of EBV-driven tumorigenesis. We aim to evaluate the gene expression characteristics of EBV SMTs and compare them with EBV-negative sarcomas and other EBV-positive tumors such as nasopharyngeal carcinoma (NPC) and lymphoepithelial-like carcinoma (LELC). Methodology: Formalin-fixed paraffin embedded (FFPE) tissue sections were obtained from patients with EBV SMTs, non EBV-SMTs and NPC tumors treated at the National University Hospital, Singapore. FFPE sections for LELC tumors were retrieved from the National Cancer Centre, Singapore. To ensure histological purity, laser-capture microdissection (LCM) was performed for tumor epithelial regions for each tumor specimen. Gene expression libraries were prepared using a specialized mRNA-Seq technique optimized for tiny amounts of FFPE material, followed by next generation sequencing. Differential gene expression analysis and geneset enrichment analysis was performed. Results: Our preliminary cohort comprised 230 gene expression libraries, including 9 EBV SMT, 16 EBV-negative sarcoma, 161 NPC and 44 LELC libraries. Principal component analysis showed distinct clustering of EBV SMTs separate from EBV-negative sarcomas. EBV SMTs also clustered distinctly when compared to NPC and LELC tumors. Compared to EBV-negative sarcomas, EBV SMTs were enriched for immune genes including CD40 (TNF receptor found on antigen presenting cells, p-adj = 1.33e-13) and MHC Class II genes (HLA-DQA1, HLADQA2, p-adj &amp;lt; 0.005 for both). In contrast, pathways involved in epithelial mesenchymal transition (NES = -1.57, p-adj = 0.0429) were enriched in EBV-negative sarcomas. Although EBV SMTs were more inflamed than their EBV-negative counterparts, we observed that NPC and LELC tumors were further enriched for inflammatory processes compared to EBV SMTs. Biological processes that were upregulated in NPC and LELC tumors included neutrophil chemotaxis (NES = 1.46, p-adj = 0.0325 and antimicrobial humoral immune response mediated by antimicrobial peptide (NES = 1.63 , p-adj = 0.0317). Deconvolution of immune cell types with ESTIMATE, showed that NPC and LELC tumors had the highest immune cell score, followed by EBV SMTs and EBV-negative sarcomas (median score = 656, 595 and 329 respectively, p = 0.006). Conclusion: Immune processes, including antigen presentation, are enriched in EBV SMTs compared to EBV-negative sarcomas. However, the extent of inflammation appears limited compared to other EBV-positive cancers. Our current work includes expanding our cohort of EBV SMTs for genomic profiling and identifying potential vulnerabilities for targeted treatment. Citation Format: Harold Yu Chan, Yi Ren, Teo Wei Keat, Joseph W. Foley, Loh Kwok Seng, Raymond KY Tsang, Han Shuting, Jain Amit, Toh Han Chong, Joshua K. Tay, Victor Lee. Gene expression characteristics of EBV-positive smooth muscle tumors compared to EBV-positive NPC and LELC [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 1112.