Abstract LB331: Integrating multiple spatial transcriptomic and proteomic technologies to generate a cancer atlas to understand the tumor microenvironment
Authors: Price Colles , Nishimura Kazuho , Bandyopadhyay Som , Borger Darrell , Weiner Russell 
Published: April 2024

Abstract
Deep single-cell genomics has provided a monumental leap in our understanding and categorical analysis of cancer cells and their unique molecular properties. With spatial platforms that preserve the tissue architecture, an emerging understanding of complex cell interactions and local environment influences is providing new perspectives for targeted therapies. Here we describe a comprehensive approach at profiling the tumor immune microenvironment across multiple solid malignancies to provide an atlas of tumor biology. To generate this atlas, we created a MERFISH panel of 500 genes representing over 40 cell phenotyping pathways and dozens of signaling pathways including chemokines, cytokines, interferon, and ligand-receptor interactions. This panel was used across 15 patients representing multiple solid malignancies. We also utilized the Immuno-Oncology focused Xenium panel to profile 16 different patients across the same indications. With the Xenium data we simultaneously assessed proteomic expression using a 16 plex panel focused on immuno-oncology targets and subsequently did H&E staining, allowing multiple -omic data collections within a single slide. After initial filtering and quality control this projects produced a total dataset with over 15 million cells and billions of transcripts. The 500 gene MERFISH panel revealed complex relationships between diverse cell types within the tumor microenvironment that was dependent on cellular location and surrounding area. While the presence of major immune cell types was observed in all cancer tissues, the ratio and spatial relationship to cancer cells differed between each tumor. Accordingly, we observed that differences in cellular composition of the microenvironment corresponded with associated changes in cellular signaling. Similarly, with Xenium we identified new spatial relationships between cancer and immune cells with their environment while confirming part of these relationships with subsequent immunofluorescence data. The H&E data provided an opportunity to overlay this data with standard pathological annotation. We further investigated how each cellular microneighborhood varied throughout the tumor and varied from patient. This comprehensive map of the tumor immune microenvironment is a deep cellular dive into cellular architecture. As this Cancer Atlas evolves this will drive the discovery of several new potential biological targets and cell types of interest. This will also be critical for the assessment of current cellular and drug therapies in preclinical and clinical models. This effort will continue with more patient samples across a greater number of disease indications and will include more technologies. We will also expand the development and implementation of analytical tools to maximum the knowledge and insights gained from this Atlas. Together, this will be a critical tool in the continuing fight against cancer.
Citation Format: Colles Price, Kazuho Nishimura, Som Bandyopadhyay, Darrell Borger, Russell Weiner. Integrating multiple spatial transcriptomic and proteomic technologies to generate a cancer atlas to understand the tumor microenvironment [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr LB331.