Spatial transcriptomics of glioblastoma second surgery samples to compare progression and pseudoprogression

We performed spatial transcriptomics on a case series of different clinical subtypes of glioblastoma second surgery samples due to novel enhancement following chemoradiation that were confirmed based on clinico-pathologic outcome as disease progression (PD) or pseudoprogression (psPD). All samples showed mixed histologic presentation (Control, Inflammatory, or Hypercellular) which complicated disease interpretation by pathology. Our goals were to (1) determine if spatial transcriptomics could better distinguish between PD and psPD than bulk RNA approaches in mixed samples, (2) determine which differentially expressed genes (DEGs) and estimated immune cell populations distinguish PD and psPD in similar histologic sites, and (3) identify varying molcular processes through gene ontology that separate PD and psPD in similar presenting areas. Overall design: NanoString Digital Spatial Profiling (DSP) with human Whole Transcriptome Atlas (WTA) was performed on glioblastoma samples with 4 showing progression (PD) and 4 showing pseudoprogression (psPD) taken from brain resection at second surgery.