Research Projects

Rationale: Intra-tumoral heterogeneity (ITH) is a hallmark of glioblastoma (GBM) that challenges its treatment efficacy. Vascular aberrancy is a major extrinsic factor shaping ITH by influencing microenvironmental cues with varying oxygen, nutrients, and acidity, compartmentalizing the tumor into perivascular and hypoxic niches. Dysregulated angiogenic secretions by tumor endothelial cells actively shape cancer cell plasticity. This complex interaction ecosystem allows GBM to switch tumor states and remodel its immunosuppressive environment, promoting tumor progression. Hypothesis: A thorough spatial understanding of how tumor, immune, and other tumor microenvironmental (TME) cells interact on different proximity scales over the continuum of perfusion gradient in GBM is needed to understand aggressive and therapy-resistant mechanisms. Besides, controlled experimentation in physiologically relevant, patient-derived ex vivo model is essential to validate these spatial transcriptional interactions. This project aims to refine this understanding via the implementation of cutting edge techniques and model systems. Scientific Objectives and Main Experiments: This project aims to: 1) Unveil the spatially distinct transcriptional landscape of GBM cells and TME components across varying vascular perfusion gradients using NanoString GeoMx DSP spatial platform to understand immune suppression in GBM. 2) Validation of spatial signatures using immune-organoid cocultures from GBM patient samples under different perfusion insults. For spatial analysis, region of interests (ROIs) from GBM patient tissue sections will be chosen to represent hypoxic and perivascular niches based on staining for hypoxia (GLUT1) and endothelial marker (CD31). We will leverage this spatial data to understand and characterize immune suppression in GBM. We will determine infiltrating scores of immune cells in each ROI and perform pairwise cell-type correlation analysis to assess co-occurrence of cell types over different proximity scales. Subsequent validation of the observations will be done by immunohistochemistry. We will also unravel direct ligand-receptor communication between tumor and endothelial cells and correlate these with GBM subtype and immune cellular pool. Enrichment analysis of gene sets from databases of hallmark gene sets and canonical pathways will be performed to investigate the biological processes. Finally, we will establish and validate the patient-derived GBM organoid model and utilize gene knockdown approach to evaluate the effect of candidate prognostic genes on invasion ability of organoids. Significance: This project aims to identify vasculature-influenced spatial GBM signatures driving its immunosuppressive nature to nominate biomarkers for GBM progression and design potential combinatorial treatment strategies or repurposed drugs. We aim to better understand how ITH can potentially inform and improve immunotherapeutic strategies.