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Development of 42 marker panel for in-depth study of cancer associated fibroblast niches in breast cancer using imaging mass cytometry
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Description: Imaging Mass Cytometry (IMC) is a novel, and formidable high multiplexing imaging method emerging as a promising tool for in-depth studying of tissue architecture and intercellular communications. Several studies have reported various IMC antibody panels mainly focused on studying the immunological landscape of the tumor microenvironment (TME). With this paper, we wanted to address cancer associated fibroblasts (CAFs), an unfairly neglected component of the TME in present IMC studies. Therefore, we focused on the development of a comprehensive IMC panel that can be used for a thorough description of the CAF composition of breast cancer TME and for an in-depth study of different CAF niches in relation to both immune and breast cancer cell communication. We established and validated a 42 marker panel using a variety of control tissues and rigorous quantification methods. The final panel contained 6 CAF-specific markers (aSMA, FAP, PDGFRa, PDGFRb, YAP1, pSMAD2). Breast cancer tissues (4 cases of luminal, 5 cases of triple negative breast cancer) and a modified CELESTA pipeline were used to demonstrate the usefulness of our IMC panel for detailed profiling of different CAF, cancer cell and immune cell phenotypes. Using our modified cell classification approach, and together with the implementation of our panel for staining the breast cancer tissue, we were able to identify different CAF and immune cell phenotypes in a very high resolution, not described before using this type of data. Keywords: Imaging mass cytometry, tumor microenvironment, cancer associated fibroblasts, microniches, breast cancer
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