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We have described the process for multiplex cyclic fluorescence immunohistochemistry staining. The primary antibody selection is a crucial aspect of the fluorescence immunohistochemistry assay, and monoclonal antibodies are recommended for better specificity and repeatability. To optimize the working concentration of the primary antibody, a series of dilutions have been tested through immunohistochemistry experiments. Both positive controls (to assess target antigen expression) and negative controls (no primary antibody incubation) are essential and should be set up.
In this protocol, the primary antibodies are diluted and prepared for a mixture from different species. The fluorescence-labeled secondary antibodies are also pooled and incubated in the same way, derived from different species. So, the critical step is choosing the species for different primary antibodies based on the antigens, and the monoclonal antibody is preferred compared with polyclonal antibody. These can ensure that the combination between primary antibody and secondary antibody is specific. The mixed liquid should achieve the working concentration for both primary antibodies and cross-reactivity should not exist between the two antibodies simultaneously. If the primary antibodies are of the same species, one secondary antibody is incubated first, then the second one. When determining the sequence of primary antibody incubation in a panel, priority should be given to antibodies that are sensitive to the antigen-antibody reaction, for the low expression antigens, the intensity would strengthen during second epitope retrieval. Before the second round of antibody incubation, repeating antigen retrieval takes less time (1 min) compared to the first operation (2 min). The fluorescence intensity from previous cyclic staining will not decrease even though the sections undergo heat-induced retrieval twice. For avoiding non-specific immunoreactivity, the incubation conditions need to be optimized including antibody working concentration, incubation time, and environmental temperature.
Various methods of epitope retrieval have been developed in recent decades, primarily divided into heat-induced epitope retrieval (HIER) and protease-induced epitope retrieval (PIER). Heating is an efficient antigen retrieval method that exposes antigen epitopes, making them more effectively detected by antibodies13. The two main options for antigen retrieval are based on citrate buffer and high pH EDTA buffer14. The optimized retrieval condition is identified according to the target antigen.
Autofluorescence can interfere with fluorescent imaging on sections caused by endogenous fluorophores and reagents used in tissue processing15. The use of an associated reagent is required for elution. Fluorophores are selected with emission peaks avoiding autofluorescence peaks (around 490 nm)16,17. Sudan Black B and NaBH4 have been reported for quenching tissue autofluorescence18,19. The combination of Sudan Black B and NaBH4 reduced fluorescence background in targeted renal formalin-fixed paraffin-embedded tissue20. In this protocol, the tissue treatment of KMnO4 in a concentration of 0.15 M/L is time saving for 1 min. KMnO4 covers a layer on the tissue for shielding spontaneous fluorescence and reduces background fluorescence, the specific staining of detected protein is more visualized.
The whole slides are scanned in four different filters channels, image alignment analysis is necessary, it is a great challenge to align the localization of single-cell and subcellular structures. For multispectral images from this technique, professional light imaging equipment and quantitative analysis software are needed for avoiding spectral crosstalk. The expensive cost of the instrument limits its application. Co-incubation of two antibodies saves time, especially when dealing with a 6-marker panel, which requires 3 cycles of incubation. This technique is used to visualize more detailed characterization of immune cells in tumor immune microenvironments. In future, the method will be applied for quantitative analysis of tumor-associated tertiary lymphoid structures.
In summary, multiplex cyclic fluorescence immunohistochemistry enables multiple targets to be stained by individually labeled fluorophores on a single slide. This assay provides an improved understanding of the spatial distribution of cells in the tumor immune microenvironment, and the spatial proximity of tumor-immune cells contributes to screening patients who will benefit from immunotherapy.