Abstract 2066: Magnifying glass on sinonasal NUT carcinoma heterogeneity using spatial transcriptomics

Abstract Introduction: Nuclear protein in testis (NUT) carcinomas (NCs) are clinically aggressive, with signature translocation NUTM1::BRD4 genes (70%), BRD3::NUTM1 (15%), NSD3::NUTM1 (6%). Histologically, NCs depict undifferentiated basaloid cells with squamous differentiation; broad lineage immunomarkers lack in NCs. Demonstration of translocation is imperative for NC diagnosis; NUT immunostaining is a surrogate. NC treatment faces obstacles (drug resistance, metastasis). Spatial transcriptomics (ST) technology emerged as ideal approach to elucidate cancer cell heterogeneity and spatial distributions within tissues. Methods: 3 cases of sinonasal NC carcinoma with FFPE formed the study material. Next generation sequencing confirmed NC diagnosis: BRD3::NUTM1 in NC #1, BRD4::NUTM1 in NC # 2, NC # 3. A representative region of each of NCs was subjected to 10X Genomics Visium Spatial Gene Expression analysis. Ingenuity Pathway Analysis (IPA) employed for pathways and network analyses. Resulting data were visualized/ analyzed in 10X Genomics Loupe Browser. Results: All cases demonstrated statistically distinct (graph-neural network based) transcriptomic clusters. These clusters were correlated with histologic characteristics by parsing all spots by region types based on tissue distribution including tumor, limited stroma and normal epithelium. Cluster constitution and transcriptomic pattern were consistent with the morphologic features of each tissue region. NC #3 had relatively low number of tumor clusters in comparison to NC #1, NC#2. Table 1 Table 1 Summary of results Case NC #1 NC #2 NC #3 Age (yo) 63 53 28 Sex F M M Outcome NED AWD DOD Fusion type BRD3::NUTM1 BRD4::NUTM1 BRD4::NUTM1 #Tumor Cell Clusters 5 3 1 Shared within top 100 of all 3 cases Rank NTS 28 30 9 HOXB3 41 21 10 HOXB6 59 62 21 PRSS21 55 39 38 NUTM1 48 33 49 KRT14 40 41 99 Top 10 Genes LOR, SPRR2A, DLK1, IV/involucrin, SPINK5, SPRR1B, SPINK6, SPINK7, SPRR2F, HMGCS2 SPINK6, SPINK5, CA9, CA2, EPHA7, TRPC6, GPR174, HDAC9, PIK3C2G, PTPRD OPN5, NRN1, NTS, DSG1, DSC1, NKX2-8, HOXB3, MMP12, AFP, ALB . Conclusions: Spatial transcriptomic profiling corresponds to histopathologic features in NC and yet highlights cell type diversity across tumors and in the case of NC#2, within a given tumor. Behavior correlates are speculative, but NC#3 for which the patient had a rapidly lethal outcome showed a preponderance of neural gene expression which may be of interest in tumor cell progression/ evolution. Citation Format: Diana Bell, Garret Choby, Michelle Afkhami, Ellie Maghami, Ehab Hanna, Raja Seethala. Magnifying glass on sinonasal NUT carcinoma heterogeneity using spatial transcriptomics [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 2066.