Spatial transcriptomic analysis reveals lack of response to PD-1 blockade in recurrent glioblastoma

Abstract

Immune checkpoint inhibitors have transformed treatment for several cancers, yet clinical trials of programmed cell death protein 1 (PD-1) blockade in glioblastoma (GBM) have consistently failed to show therapeutic benefit. While some studies have reported treatment-related transcriptional changes, particularly in T cells, findings remain limited and inconsistent. The aim of this study was to investigate changes in tumor cells and tumor-associated macrophages (TAMs) after PD-1 blockade in recurrent GBM using spatial transcriptomics. We performed Digital Spatial Profiling (GeoMx, NanoString) on FFPE tumor samples from 26 patients with matched primary and recurrent IDH-wildtype GBM, including 16 patients who received neoadjuvant nivolumab at recurrence. Tumor (SOX2⁺) and TAM (IBA1⁺) segments were selected for targeted spatial analysis. Following quality control and filtering, transcriptomic profiles were compared between nivolumab-treated and untreated recurrent tumors. PD-1 blockade did not induce detectable gene expression changes in either tumor cells or TAMs. There were no significant differences in global expression profiles or in more targeted analyses of malignant cell states, cell cycle activity, interferon signaling, or myeloid transcriptional programs. These results consistently indicate that neoadjuvant PD-1 blockade does not elicit measurable responses at the spatial transcriptomic level in tumor cells or TAMs in recurrent GBM. These findings align with the lack of clinical benefit observed in trials and highlight the need for alternative strategies to improve immunotherapy outcomes in GBM.