Spatial tissue analysis of secondary sarcoma following CAR T cell therapy for B cell lymphoma

CD19-directed chimeric antigen receptor (CAR)-engineered T cells have transformed cellular therapy for hematologic malignancies but have also raised concerns about secondary malignancies. A spatial profiling method was used to analyze the tumor microenvironment and define native and CAR T cell association with a pleomorphic sarcoma arising 12 months post-CAR T therapy for B cell lymphoma. Although CAR T sequences were absent in the secondary tumor, our approach enabled profiling of the stroma, tumor, and infiltrating T cells. Spatial analysis incorporated proteomics via serial antibody staining and transcriptomics using RNA hybridization on an automated MACSima imaging cyclic staining (MICS) system, which allows for in situ detection of CAR T cells. We report here the prevalence of CAR-positive T cells in patient-derived tissue sections, observed metabolic and proliferative shifts in the tumor and its microenvironment, and immune checkpoint analysis. These findings provide insights into post-CAR T secondary cancers and highlight tools that may guide future targeted therapies.