Analyzing the scaffold immune microenvironment using flow cytometry: practices, methods and considerations for immune analysis of biomaterials

The immune system has evolved as a powerful tool for our body to combat infections, and is being engineered for new treatments in cancer and autoimmune disease. More recently, the complex role of the immune system is being recognized in tissue repair, regenerative medicine and biomaterial responses. From these combined interests, the field of immunoengineering is rapidly growing. However, bridging immunology with engineering poses numerous challenges including the biological complexity, language of immunology and accurately leveraging the powerful techniques of immunology to new applications. Elucidating the identity and function of immune cell populations responding to engineering systems will be required for continued advancement. Multi-color flow cytometry is a central technique used by immunologists for this purpose that requires careful control of variables, data acquisition, and interpretation. Here, we present methods for multi-color flow cytometry experimental design and analysis focused on characterizing the scaffold immune microenvironment in regenerative medicine research.