Spatial organization and stochastic fluctuations of immune cells impact clinical responsiveness to immunotherapy in melanoma patients

High-dimensional, spatial single-cell technologies, such as CyTOF imaging mass cytometry (IMC), provide detailed information regarding locations of a large variety of cancer and immune cells in microscopic scales in tumor microarray slides obtained from patients prior to immune checkpoint inhibitor (ICI) therapy. An important question is how the initial spatial organization of these cells in the tumor microenvironment (TME) changes with time and regulates tumor growth and eventually outcomes as patients undergo ICI therapy. Utilizing IMC data of melanomas of patients who later underwent ICI therapy, we develop a spatially resolved interacting cell system model that is calibrated against patient response data to address the above question. We find that the tumor fate in these patients is determined by the spatial organization of activated CD8⁺ T cells, macrophages, and melanoma cells and the interplay between these cells that regulate exhaustion of CD8⁺ T cells. We find that fencing of tumor cell boundaries by exhausted CD8⁺ T cells is dynamically generated from the initial conditions that can play a protumor role. Furthermore, we find that specific spatial features such as co-clustering of activated CD8⁺ T cells and macrophages in the pretreatment samples determine the fate of the tumor progression, despite stochastic fluctuations and changes over the treatment course. Our framework enables the determination of mechanisms of interplay between a key subset of tumor and immune cells in the TME that regulate clinical response to ICIs.