Spatially resolved transcriptomic profiles reveal unique defining molecular features of infiltrative 5ALA-metabolizing cells associated with glioblastoma recurrence

• Published in: Genome medicine 2023-07, Vol.15 (1), p.48-34, Article 48
• Main Authors: Andrieux, Geoffroy, Das, Tonmoy, Griffin, Michaela, Straehle, Jakob, Paine, Simon M L, Beck, Jürgen, Boerries, Melanie, Heiland, Dieter H, Smith, Stuart J, Rahman, Ruman, Chakraborty, Sajib
• Format: Article
• Language: English
• Subjects: 5ALA; Algorithms; Aminolevulinic acid; Brain cancer; Chemotherapy; Diseases; Flow cytometry; Fluorescence; Gene Expression Profiling; Genetic transcription; Glioblastoma; Glioblastoma - genetics; Glioblastoma multiforme; Glycolysis; Humans; Isocitrate dehydrogenase; Localization; Magnetic resonance imaging; Mesenchymal subtype; Metabolism; Metabolites; Microscopy; Myeloid; Myeloid cells; Neoplasm Recurrence, Local - genetics; Neurosurgery; Patients; Physiological aspects; Radiation therapy; Relapse; Spatial transcriptomics; Stem cells; Surgery; Transcriptome; Transcriptomics; Tumor cells; Tumors; Wound response
• ISSN: 1756-994X; 1756-994X
• DOI: 10.1186/s13073-023-01207-1

Spatiotemporal heterogeneity originating from genomic and transcriptional variation was found to contribute to subtype switching in isocitrate dehydrogenase-1 wild-type glioblastoma (GBM) prior to and upon recurrence. Fluorescence-guided neurosurgical resection utilizing 5-aminolevulinic acid (5ALA) enables intraoperative visualization of infiltrative tumors outside the magnetic resonance imaging contrast-enhanced regions. The cell population and functional status of tumor responsible for enhancing 5ALA-metabolism to fluorescence-active PpIX remain elusive. The close spatial proximity of 5ALA-metabolizing (5ALA +) cells to residual disease remaining post-surgery renders 5ALA + biology an early a priori proxy of GBM recurrence, which is poorly understood. We performed spatially resolved bulk RNA profiling (SPRP) analysis of unsorted Core, Rim, Invasive margin tissue, and FACS-isolated 5ALA + /5ALA - cells from the invasive margin across IDH-wt GBM patients (N = 10) coupled with histological, radiographic, and two-photon excitation fluorescence microscopic analyses. Deconvolution of SPRP followed by functional analyses was performed using CIBEROSRTx and UCell enrichment algorithms, respectively. We further investigated the spatial architecture of 5ALA + enriched regions by analyzing spatial transcriptomics from an independent IDH-wt GBM cohort (N = 16). Lastly, we performed survival analysis using Cox Proportinal-Hazards model on large GBM cohorts. SPRP analysis integrated with single-cell and spatial transcriptomics uncovered that the GBM molecular subtype heterogeneity is likely to manifest regionally in a cell-type-specific manner. Infiltrative 5ALA + cell population(s) harboring transcriptionally concordant GBM and myeloid cells with mesenchymal subtype, -active wound response, and glycolytic metabolic signature, was shown to reside within the invasive margin spatially distinct from the tumor core. The spatial co-localization of the infiltrating MES GBM and myeloid cells within the 5ALA + region indicates PpIX fluorescence can effectively be utilized to resect the immune reactive zone beyond the tumor core. Finally, 5ALA + gene signatures were associated with poor survival and recurrence in GBM, signifying that the transition from primary to recurrent GBM is not discrete but rather a continuum whereby primary infiltrative 5ALA + remnant tumor cells more closely resemble the eventual recurrent GBM. Elucidating the unique molecular and cellular features of