Background Highly multiplexed cyclic immunofluorescence (MxIF) platforms, such as the PhenoCycler system (formerly CODEX) by Akoya Biosciences allow users to stain and visualize up to 100 markers on a single formalin-fixed paraffin-embedded (FFPE) tissue section. The Phenocycler accomplishes this feat by staining the tissue with antibodies that have been conjugated to a unique single-stranded oligonucleotide barcode (BX). Reporters (RX), containing the complimentary sequence and tagged with one of 3 spectrally-resolved fluorophores, are subsequently added, imaged and then gently removed via isothermal reaction.1 With the advent of this type of technology, comes the opportunity to apply it to the study of diverse tissues and biological conditions. However, in this pursuit, investigators are often faced with the challenge of developing custom reagents for the platform. Factors such as tissue auto-fluorescence, antigen density, cell density, fluorophore signal sensitivity, and conjugation efficiency need to be considered to optimize panel development.
Methods To increase probability of success, expedite panel development, and optimize reagent utilization, we have developed the ‘Joker’ panel development kit. The ‘Joker’ kit consists of (1) BX007, (2) three versions of RX007, each conjugated to one of the 3 antibody-reading channels (AlexaFluor®750, Atto550, and AlexaFluor®647), and (3) a tissue microarray (TMA) containing 16 unique human tissues. As proof of concept, we conjugated a previously validated CD45 monoclonal antibody to our ‘Joker’ BX007.
Results Conjugation of CD45 to BX007 was verified via flow cytometry and by tissue using the ‘Joker’ TMA (figure 1A,B). Cycles in which no markers were revealed provided information on backgrounds present in different tissue types (figure 2A). A representative immune cell for each tissue was identified and pixel intensity was calculated for CD45-BX007 with respect to background (table 1). We demonstrated that this kit could be used to quickly screen custom markers across tissue types in a single run. We show that CD45-BX007 is compatible with all channels over multiple tissues (figure 2A,B).
Conclusions Utilizing the ‘Joker’ kit we can expedite determination of the best channel-tissue combination for any given custom-developed antibody under the biological conditions we seek to study. This is critical for MxIF panel development and especially important for low expression markers that may give out false positive results if acquired on channels with high background. Alternatively, false negative results may occur if the antibody is visualized on a low sensitivity channel. The ‘Joker’ kit can greatly facilitate the panel development effort of researchers using the PhenoCycler MxIF system.
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