Abstract 5089: Cross-platform comparison of snRNAseq, Visium, and Xenium on lung and breast cancer samples

Abstract Background: Spatial transcriptomics is revolutionizing biology and pathology of cancer by enabling the spatial analysis of RNA profiles in formalin-fixed tissues. However, the comparative performance of different platforms and their potential complementarity remain unclear. Methods: We conducted a comprehensive analysis of single-nuclei RNA sequencing (snRNAseq, n=15), full-transcriptome Visium v2 (n=10), and Xenium (n=40) on lung and breast cancer samples. This allowed a direct comparison between Visium and Xenium and an assessment of how snRNAseq can complement these spatial platforms. Results: Our findings highlight that Xenium provides high-resolution spatial data with single-cell accuracy and robust performance on FFPE tissues. We demonstrate that snRNAseq enhances Xenium analysis by facilitating automated cell annotation, quality control, and imputing missing gene expression profiles. Although Visium’s full transcriptome capabilities offer broader coverage, its resolution is limited and remains a challenge for interpretation, even when refined with super-resolution modeling (e.g., BayesSpace). Conclusion: Xenium excels in resolution and single-cell spatial mapping, seamlessly integrating with snRNAseq without requiring additional normalization. While Visium offers full transcriptome data, its resolution restricts biological interpretation. Together, Xenium and snRNAseq provide a powerful framework for spatial transcriptomics, advancing insights into tissue biology and pathology. Citation Format: Mariia Bilous, Daria Buszta, Jonathan Bac, Yixing Dong, Sylvie André, Marina Alexandre-Gaveta, Senbai Kang, Krisztian Homicsko, Raphael Gottardo. Cross-platform comparison of snRNAseq, Visium, and Xenium on lung and breast cancer samples [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 5089.