Abstract 2704: Deciphering the tumor microenvironment with spatially-resolved protein and comprehensive gene expression profiling using the Visium spatial platform

Abstract

Spatially-resolved measurements of gene and protein expression are crucial for understanding tissue and cell organization and function. High resolution analyses of gene expression within a spatial context can be particularly informative in heterogeneous tumor types, where a deeper understanding of the underlying biology can improve treatment efficacy and patient outcomes. Here, using the 10x Genomics Visium Spatial Gene Expression Solution we demonstrate the use of curated gene expression panels with simultaneous immunofluorescence protein detection for a comprehensive view of the tumor microenvironment in a human ovarian endometrial adenocarcinoma. This approach enabled unbiased assessment of proteins of interest simultaneously with gene expression at high resolution in tissue sections without pre-selecting specific regions. We used three separate curated gene expression panels, each containing more than 1,000 genes: the Human Pan-Cancer panel; the Human Immunology Panel; and the Human Gene Signature Panel. For all three panels, high concordance of panel gene expression between targeted and untargeted (whole transcriptome) Visium Gene Expression libraries was observed. Immunofluorescence staining enabled us to discern the tumor and stromal compartments, and when combined with cellular gene expression, allowed identification of adaptive and innate immune cell subpopulations localization within the tissue. We examined the distribution of tumor-infiltrating lymphocytes and found that CD4 and CD8 T cells were dispersed throughout the tumor, whereas CD79A and CD79B B cells clustered in specific areas of the stromal compartment. The localized presence of plasma B cells (JCHAIN+, MZB1, IGHA1+, IGHG1+, IGKC+) suggests that a tumor-specific B cell response may have been mounted. We also identified the presence of classical (CD14+ CD16-) and non-classical (CD14- CD16+) monocytes in the tumor compartment, and NK (NKG7+) cells dispersed across the entire tissue section. The characterization and spatial localization of these cell types within the tumor is key to understanding the tumor biology and can impact prognoses and treatments. Detailed spatially-resolved multi-analyte views of the tumor microenvironment provide essential insights into the underlying biology for development of new therapeutic targets. Here, we have applied this technology to study ovarian cancer, however, we envision its broad application to characterize the complex tumor microenvironment of many different cancers. A greater understanding of region-specific cellular behavior in and around tumors will drive development of targeted therapies, improve treatment strategies, and may ultimately lead to better relapse control and improve survival. Citation Format: Valeria Giangarra, Jennifer Chew, Cedric Uytingco, Sarah E. Taylor, Michael J. Stubbington, Stephen R. Williams, Zachary Bent, Yifeng Yin. Deciphering the tumor microenvironment with spatially-resolved protein and comprehensive gene expression profiling using the Visium spatial platform [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2704.