An End-to-End Workflow for Interrogating Tumor-Infiltrating Myeloid Cells Using Mass Cytometry.

Myeloid cells are a highly heterogeneous group of innate immune cells which include a diverse collection of cell types and cell states. Distinct subsets can impact tumor progression differently, with conventional type 1 DCs important in protective anti-tumor immune responses, while immunosuppressive tumor-associated macrophages and myeloid-derived suppressive cells (MDSCs) play tumor-promoting roles. Deep phenotyping of myeloid cells using single-cell technologies such as mass cytometry provides the unprecedented opportunity to comprehensively characterize the underlying heterogeneity of myeloid cells. Here we provide a detailed end-to-end workflow including both experimental and computational protocols enabling deep phenotyping of tumor-infiltrating myeloid cells using mass cytometry. A protocol that facilitates interrogation of phosphoproteins in circulating and tumor-infiltrating myeloid cells has been provided together with detailed scripts for Phenograph analysis of tumor-infiltrating myeloid cells.