Abstract A073: CODEXTM: A novel platform for spatially resolved deep antigen profiling of single cells in tissue samples
Authors: Gallina Maria Elena , Choksi Atri , Nikulina Nadya , Singh Jaskirat , Dakshinamoorthy Gajalakshmi , Kim Joseph , Mistry Sejal , Kennedy-Darling Julia 
Published: February 2019

Abstract
The tumor microenvironment (TME) comprises a multitude of cell types that collectively create an immunosuppressive environment, enabling tumor growth. Understanding the spatial organization of these tissues requires a technology that can identify the presence of multiple markers and correlate it to their specific spatial location within the same tissue. Characteristics of the TME including infiltrating immune cells, angiogenesis and the presence of other nonmalignant cells influence important phenomena like drug delivery, treatment effectiveness and, ultimately, clinical outcomes. Current methodologies for analyzing the spatial dimension of tissues, e.g., traditional immunofluorescence (IF) and immunohistochemistry (IHC), are limited to measuring a few parameters simultaneously, thereby restricting the number of phenotypes that can be identified. Conversely, single-cell technologies like mass cytometry and next-generation sequencing-based tools provide multiplexing capabilities, but at the expense of the associated spatial information. Akoya Biosciences, Inc., is commercializing CODEXTM (CO-Detection by indEXing), a multiparameteric imaging platform that allows the simultaneous detection and quantification of dozens of target epitopes in single cells within a single tissue section. This innovative platform is an end-to-end solution that comprises three components: 1) the CODEX fluidics instrument, 2) a suite of specialized CODEX reagents, and 3) an analysis pipeline. The CODEX workflow involves a barcoding system such that each antibody moiety is conjugated to a proprietary tag. Panels of CODEX antibodies are used to stain tissue specimens en masse in a single step. Staining data for sets of antibodies are revealed across iterative cycles using corresponding dye-labeled barcodes. The CODEX fluidics instrument integrates with existing microscope units for a fully automated data collection process. CODEX data are processed to achieve noise reduction and analyzed at the single-cell level through a segmentation algorithm based on nuclear staining.More than 80 antibodies have been validated on the CODEX platform for analysis of human and mouse fresh-frozen and FFPE tissues. Preliminary studies on fresh-frozen tissues with developed antibodies demonstrate an unprecedented capability for revealing the spatial correlation between a variety of target epitopes. These results demonstrate the enormous potential of the CODEX technology to identify spatial correlations in the TME through highly multiplexed detection with single-cell resolution.
Citation Format: Maria Elena Gallina, Atri Choksi, Nadya Nikulina, Jaskirat Singh, Gajalakshmi Dakshinamoorthy, Joseph Kim, Sejal Mistry, Julia Kennedy-Darling. CODEXTM: A novel platform for spatially resolved deep antigen profiling of single cells in tissue samples [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 A073.