Abstract 3646: A spatially resolved single cell proteomic atlas of small bowel adenocarcinoma

Abstract

Abstract Small bowel adenocarcinoma (SBA) is a rare malignancy associated with poor prognosis. The cellular and proteomic heterogeneity within the tumor immune microenvironment (TIME) of SBA is a likely driver of prognosis, disease progression and response to therapy. There is, however, a major gap in our knowledge of tumor and immune interactions in SBA. Cyclic Immunofluorescence (CycIF), an antibody-based, highly multiplexed imaging technology for spatially resolved single cell level proteomic profiling, is well suited to map the proteomic heterogeneity and organization of TIME in SBA. Here, using CycIF, we have generated a spatially resolved single-cell proteomic atlas of TIME for 136 tumor and normal samples from clinically and genomically annotated SBA patients (N=37). The SBA TIME Atlas covers information on expression levels, spatial position, and cell morphology for > 40 proteomic markers of tumor-intrinsic processes and states, diverse immune cell types, immune checkpoints, and tumor vascularization. In total, we collected proteomics data from > 600,000 cells. Using a hierarchical decision tree of cell type markers, we have generated the cell identity annotations for > 350,000 cells, with positional information. A comprehensive computational analysis of the SBA atlas revealed various spatial and heterogeneity features that may impact the TIME organization in fine detail. Using those features, we have compared the proteomic heterogeneity in tumor vs. normal cell populations, identifying spatial and single-cell correlates of key clinical variables (e.g., patient survival, age, sex, disease stage, metastatic status). We have also performed differential analyses of spatial features involving protein markers and cell types with respect to genomic alteration states and have mapped the spatial enrichment of likely actionable immune check proteins to immune and tumor cells. Such mapping may guide future therapeutic decisions. Overall, we expect that the SBA TIME Atlas will provide a useful resource and inform future translational studies, as well as basic research for better mechanistic understanding and treatment of this disease. Citation Format: Zeynep Dereli, Behnaz Bozorgui, Huamin Wang, John Weinstein, Michael Overman, Anil Korkut. A spatially resolved single cell proteomic atlas of small bowel adenocarcinoma [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 3646.