Spatial assessment of stromal B cell aggregates predicts response to checkpoint inhibitors in unresectable melanoma

Quantitative assessment of multiplex immunofluorescence (mIF) data represents a powerful tool for immunotherapy biomarker discovery in melanoma and other solid tumors. In addition to providing detailed phenotypic information of immune cells of the tumor microenvironment, these datasets contain spatial information that can reveal biologically relevant interactions among cell types. To assess quantitative mIF analysis as a platform for biomarker discovery, we used a 12-plex mIF panel to characterize tumor samples collected from 50 patients with melanoma prior to treatment with immune checkpoint inhibitors (ICI). Consistent with prior studies, we identified a strong association between stromal B cell percentage and response to ICI therapy. We then compared pathologist assessment of lymphoid aggregates with a density based clustering algorithm, DBSCAN, to both automatically detect B cell aggregates and quantify their size, morphology, and distance to tumor. Spatial neighborhood analysis identified TCF1+ and LAG3-T cell subpopulations enriched near stromal B cells. These analyses provide a roadmap for the further development and validation of spatial immunotherapy biomarkers in melanoma and other diseases.