Abstract 1880: Advancing spatial discovery multiomics: Integration of a novel 1,000+ plex discovery proteome atlas with an 18,000+ plex whole transcriptome atlas for same-slide investigation of multiple cancer pathologies
Authors: Ashley Heck, Hiromi Sato, Christine Kang, Brian Filanoski, Lori Hamanashi, Giang Ong, Terence Theisen, Erin Piazza, Kyla Teplitz, Margaret Hoang, Michael D. Rhodes, Joseph Beechem
Journal: Cancer Research (2025)

Abstract Spatial multiomics at high plex represents a transformative approach to understanding complex biological systems. Whereas high plex spatial transcriptomics have transformed tissue analyses, spatial proteomics have been limited by low plex and lacking coverage of major biological pathways. Proteins, which represent the functional units of cellular response and activity, are essential for studying the heterogeneity of cancer and immune pathology. Furthermore, cellular responses to intrinsic and extrinsic stimuli are often driven by post-translational modifications of proteins. Enabling simultaneous analyses of proteins and RNA in FFPE tissue sections in spatial context with a sequencing readout and theoretically unlimited plex, the GeoMx® Digital Spatial Profiler (DSP) platform is uniquely positioned to support high plex proteomics and multiomics. In prior work, we demonstrated a same slide spatial multiomics workflow using the GeoMx DSP platform with the GeoMx Whole Transcriptome Atlas (18, 000+ genes) and the GeoMx Human Immuno Oncology Proteome Atlas (570+ proteins). In the present study, we expand this platform by adding 500 additional protein targets, increasing the spatial proteomic atlas to over 1, 000 targets. This expanded content allows for the discovery of novel biomarkers and potential therapeutic targets across multiple domains, including immune-oncology, immunology, oncology, neuroscience, signaling pathway regulation, cell death, metabolism, and epigenetics. We introduce the Discovery Proteome Atlas, a 1, 000+ plex antibody-based proteomic assay and validate its performance in terms of specificity, sensitivity and reproducibility of each antibody in multiplex. When applied on the same-slide with the WTA assay to a tumor tissue microarray containing 50+ cases from various organs (e.g., skin, lung, testis, prostate, pancreas), we observe distinct multiomic profiles of cells with specific tumor regions and assess the abundance of multiple phosphorylated targets. Phosphorylation, like other post translational modifications, can only be studied through proteomics. By combining proteomic and transcriptomic atlases with spatial context in the same cell populations, this approach provides comprehensive insights into heterogenous tissues with complex disease mechanisms, offering a discovery portal for novel therapeutic or biomarker identification. -Bruker Confidential- Citation Format: Ashley Heck, Hiromi Sato, Christine Kang, Brian Filanoski, Lori Hamanashi, Giang Ong, Terence Theisen, Erin Piazza, Kyla Teplitz, Margaret Hoang, Michael D. Rhodes, Joseph Beechem. Advancing spatial discovery multiomics: Integration of a novel 1, 000+ plex discovery proteome atlas with an 18, 000+ plex whole transcriptome atlas for same-slide investigation of multiple cancer pathologies [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 1880.