Abstract 3649: A novel spatial multi-omic approach for biological discoveries in colonic diseased tissues using a comprehensive Immuno-Oncology Proteome Atlas and Whole Transcriptome Atlas
Authors: Alyssa Rosenbloom, Shilah Bonnett, Mark Conner, Christine Kang, Erin Piazza, Brian Filanoski, Rhonda Meredith, Hye Son Yi, Lori Hamanishi, Eduardo Ignacio, Nadine Nelson, Michael Prater, Vik Devgan, Rudy Van Eijsden, Melanie Moon, Lesley Isgur, Terence Theisen, Margaret Hoang, Gary Geiss, Joseph M. Beechem
Journal: Cancer Research (2024)

Abstract The advancement of spatially resolved, multiplex proteomic and transcriptomic technologies has revolutionized and redefined the approaches to complex biological questions pertaining to tissue heterogeneity, tumor microenvironments, cellular interactions, cellular diversity, and therapeutic response. While spatial transcriptomics has traditionally led the way in plex, multiple studies have demonstrated a poor correlation between RNA expression and protein abundance, owing to transcriptional and translational regulation, target turnover, and most critically, post-translational protein modifications. Therefore, a more holistic, ultra-high-plex, and high-throughput proteomic atlas approach becomes critical for the next phase of discovery biology. Here, we present a barrier-breaking, spatial proteomics panel that was designed to accelerate scientific discoveries. A Digital Spatial Profiler platform is uniquely suited to support high-plex proteomics, allowing for the simultaneous analyses of proteins from discrete regions of interest (ROIs) in FFPE tissue sections while preserving spatial context. The assay relies upon abcam antibodies coupled to photocleavable DNA barcodes readout with NGS sequencing, allowing for theoretically unlimited plex. Here we introduce the Human Immuno-Oncology Proteome Atlas (IPA), a 570+ antibody-based proteomic discovery panel, compatible with immunohistochemistry on FFPE tissues with NGS readout. IPA is the highest-plex, most comprehensive, antibody-based multi-omic panel to date focusing on key areas of immuno-oncology, oncology, immunology, epigenetics, metabolism, cell death, and signaling pathway regulation. Here we demonstrate the performance of IPA on various cell lines and tissue. Additionally, we show the power of IPA, using the spatial multi-omic assay along with the GeoMx® Whole Transcriptome Atlas (&amp;gt; 18,000 transcripts), a 40-plex custom antibody panel and microbiome-curated RNA custom spike-in (~220 transcripts) to evaluate 70 different colon disease samples across 5 pathologies including adenocarcinoma, hyperplasia, and chronic inflammation. This is the highest-plex multi-omic (~610-plex proteins and &amp;gt;18,220 genes) study ever implemented for spatial biology. When we compared the diseased tissue to normal tissue, we observed an upregulation of specific pathways associated with tumorigenesis and inflammation. Furthermore, we observed distinct differences in proteomic and transcriptomic landscape between pathologies. The cutting-edge, data-driven, expert-curated IPA panel is at the forefront of spatial proteomics, empowering the researcher for the acceleration of biological discoveries. FOR RESEARCH USE ONLY. Not for use in diagnostic procedures. Citation Format: Alyssa Rosenbloom, Shilah Bonnett, Mark Conner, Christine Kang, Erin Piazza, Brian Filanoski, Rhonda Meredith, Hye Son Yi, Lori Hamanishi, Eduardo Ignacio, Nadine Nelson, Michael Prater, Vik Devgan, Rudy Van Eijsden, Melanie Moon, Lesley Isgur, Terence Theisen, Margaret Hoang, Gary Geiss, Joseph M. Beechem. A novel spatial multi-omic approach for biological discoveries in colonic diseased tissues using a comprehensive Immuno-Oncology Proteome Atlas and Whole Transcriptome Atlas [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3649.