Deep profiling of mouse splenic architecture with CODEX multiplexed imaging.

A highly multiplexed cytometric imaging approach, called CO-Detection by indEXing (CODEX), is used here to create multidimensional imaging datasets of normal mouse and lupus (MRL/lpr) spleens. In this procedure, antibody binding events are rendered iteratively using DNA barcodes, fluorescent dNTP analogs, and an in-situ polymerization-based indexing procedure. An algorithmic pipeline enabling single cell antigen quantification in tightly packed tissues was developed and used to overlay well known morphological features with de novo characterization of lymphoid tissue architecture at a single cell and cellular neighboorhood levels. We observed an unexpected, profound impact of the cellular neighborhood on the expression of protein receptors on immune cells. By comparing normal murine spleen to spleens from animals with systemic autoimmune disease (MRL/lpr), extensive and previously uncharacterized splenic cell interaction dynamics in the healthy versus diseased state was observed. The fidelity of multiplexed imaging data analysis demonstrated here will allow deep proteomic analysis and systematic characterization of complex tissue architecture in normal and clinically aberrant samples. CODEX_MRLdataset_expression.csv table contains cell types annotation, expression profiles and coordinates of all segmented objected identified in spleen sections analyzed in this study. CODEX_MRLdataset_neighborhood_graph.csv contains annotation and coordinates of all pairwise cell to cell contacts (interactions) mapped across samples imaged in the study.