Transcriptomic profiling of BrO, DMGO and GD2 CAR T cells: Processed datasets

Diffuse midline glioma (DMG) is a rare yet highly aggressive paediatric cancer primarily arising in the pontine region of the brainstem, necessitating the development of patient-representative models for treatment advance. Here, we developed an FGF4-driven human brainstem organoid model. By genetically engineering de novo H3.3K27M-altered DMG, we demonstrate that brainstem-pontine glial specification is critical for DMG tumorigenesis, yielding infiltrative tumors that recapitulate patient-specific molecular heterogeneity. Prolonged GD2 CAR T cell treatment mirrors clinical outcome variability, reveals extensive transcriptional heterogeneity, and enables identification of both potent effector and dysfunctional populations. Furthermore, incorporation of brain-resident myeloid cells generated DMG-specific microglia that reduced GD2 CAR T cell efficacy and revealed the functional states most vulnerable to microglia-mediated immune suppression. Thus, we present a novel human DMG model offering a months-long experimental window in vitro, which we leverage to delineate CAR T cell functionality and microglial impact, aiding therapy development for this devastating disease.