Abstract A074: Spatially resolved deep antigen profiling of single cells in FFPE tissue samples through CODEXTM
Authors: Gallina Maria Elena , Choksi Atri , Nikulina Nadya , Singh Jaskirat , Dakshinamoorthy Gajalakshmi , Kim Joseph , Mistry Sejal , Kennedy-Darling Julia 
Published: February 2019

Abstract
Spatially resolved, deep antigen profiling of tissue specimens is crucial for investigating the architecture and cell diversity in complex matrices, such as the tumor microenvironment (TME). The correlation of these two parameters with the progression of a variety of pathologies, ranging from cancer to autoimmune diseases, is still vastly unknown due to the lack of technologies that enable the detection of both high content and spatial resolution. Formalin-fixed, paraffin-embedded (FFPE) tissues constitute the ideal sample for these investigations as they retain tissue morphology at room temperature for long periods of time, which is convenient and cost-effective, and are available in vast specimen archives. Akoya Biosciences, Inc., is commercializing CODEXTM (CO-Detection by indEXing), a multiparameteric imaging platform that performs the concurrent detection and quantification of dozens of antigens with single cell resolution within a tissue specimen. The CODEX platform uses a DNA-based barcode library to label antibodies and iterative cycles of adding and removing cognate dye-labeled oligonucleotides to reveal the staining pattern for a subset of the target markers per cycle. The entire data acquisition process is fully automated using the CODEX instrument, which integrates with existing microscopes. To support high-multiplexing capabilities, more than 45 different antibody clones have been screened and validated for the detection of target epitopes in human FFPE secondary lymphoid tissues for both healthy and cancerous specimens using the CODEX platform. Proof-of-concept data have also been obtained for different cancer types, including melanoma and head and neck cancer in both normal and TMA formats. Analysis software has been developed to extract meaning from CODEX datasets and is included as part of the CODEX platform. The analysis pipeline includes image drift compensation, deconvolution and segmentation to measure integrated fluorescence intensity for each cell across tens of parameters. In this manner, infiltrating lymphocytes and other immune cells have been identified within the TME. With the high multiplexing capabilities, a variety of T-cells can be identified to detect the ratios of both immunosuppressive and immune-activating subtypes. Analysis of FFPE tissues using the CODEX platform demonstrates the unparalleled opportunities for simultaneously detecting tens of antigens with single-cell resolution within a tissue specimen.
Citation Format: Maria Elena Gallina, Atri Choksi, Nadya Nikulina, Jaskirat Singh, Gajalakshmi Dakshinamoorthy, Joseph Kim, Sejal Mistry, Julia Kennedy-Darling. Spatially resolved deep antigen profiling of single cells in FFPE tissue samples through CODEXTM [abstract]. In: Proceedings of the Fourth CRI-CIMT-EATI-AACR International Cancer Immunotherapy Conference: Translating Science into Survival; Sept 30-Oct 3, 2018; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2019;7(2 Suppl):Abstract nr A074.