Core C: CODEX Core

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ABSTRACT (Core C) A central focus of our program is understanding the roles of specific cell types, including immune cell populations, throughout the initiation, development and spread of PDAC in mouse models and in humans. A key aspect of this effort is to define the frequency, spatial relationships and activation states of cell types within tumors, and to learn how these parameters change over time and in response to therapy. Additionally, while each project focuses on a different aspect of PDAC, a comprehensive understanding of the role of the epithelial compartment and the immune system in PDAC will require simultaneous analysis of each of these cell types in multiple tissues. To achieve these goals, we will use CO-Detection by indEXing (CODEX), a new method generated by Dr. Nolan’s group at Stanford. CODEX will allow cytometric imaging of tissue sections with dozens of antibodies. CODEX data from this Core can then be linked to complementary data from CyTOF and scRNASeq used in individual projects. The Specific Aims of Core C for human and mouse pancreas studies are: 1. Provide CODEX processing to investigators, including staining, imaging and quality control 2. Provide CODEX analysis, including antigen clustering, cell type annotation and neighborhood mapping 3. Develop new antibodies and reagents for CODEX in consultation with P01 investigators 4. Develop standard workflows for tissue procurement, processing, storage and retrieval in partnership with the human pancreas tissue core (Core B). Projects 1, 2 and 3 will specifically use the CODEX core platform for studies of both mouse and human tissues. Core C will work closely with the Human Tissue Core B to ensure appropriate human tissue preparation to support CODEX analysis. Thus, Core C will provide services technically difficult and not available in most laboratories, materials not available commercially or impossible to obtain elsewhere, and services more reliably and cost-effectively performed than if performed in an individual investigator’s laboratory. This CODEX Core would be new, and unique at Stanford.