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. 2024 Feb 9;27(3):109179. doi: 10.1016/j.isci.2024.109179

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© 2024 The Authors

This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).

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Immunofluorescence and immunohistochemistry workflow and immune cell characterization

(A) Workflow of the mIF and IHC methods. Multiple visits from the same patients are marked with different letters, and numbers following letters mark samples collected from the same clinical visit. Sections stained with different mIF panels or antibodies are shown in the order it was applied. Examples of analyzed regions of interest (ROIs) are shown.

(B) From top bar to bottom bar: percentage of immune cells in ROIs. Immune cell proportions in regions where all stainings were available. Heatmap indicating the levels of immune cells and markers in different ROIs/patients. Bottom annotation includes sample information with patient of origin, sample types, and ROIs as well as clinical information with prior BCG treatment, post-BCG outcome (CR: complete response at 6 months. Failure: any persistent high-grade cancer), and progression status (T-stage progression).

(C) Comparisons of the levels of immune cell types and markers in different ROIs. All stromal areas have been combined to one ROI. Adjusted p values are indicated when below-significance level of 0.05 (Wilcoxon rank-sum test).