Spatial and Clonal Dynamics in Glioblastoma: Disentangling Drivers of Migration and Stemness

Glioblastoma (GBM) is an aggressive and incurable brain tumor marked by its high invasiveness, resistance to therapy, and universal recurrence. A key clinical challenge in GBM treatment is the diffuse infiltration of glioblastoma cells (GBCs) into the neighboring brain parenchyma, limiting the efficacy of current treatment plans. GBCs exhibit extensive genetic heterogeneity, with relapse often driven by subclones originally present but genetically distinct from dominant clones during diagnosis. Recent animal models suggest the heterogenous nature of GBCs’s ability to form interconnected networks, with a subset of GBCs becoming unconnected with a heightened invasiveness. Although multi-region whole-genome sequencing of patient samples suggests clonal invasion, technical limitations still obscure whether these migratory and invasive cells are truly (i) clonal in origin and (ii) driven by cell-intrinsic factors such as genetic alterations, or by cell-extrinsic influences from the tumor microenvironment (TME). Understanding how genetics, transcriptional states, and TME drive the evolutionary trajectory of invasive cells is key to disrupting their behavior. This investigation requires addressing two challenges: (1) linking large-scale migratory clones with genomic and transcriptomic data, and (2) uncovering how the tumor microenvironment (TME) influences subclonal evolution and invasive potential. To (1) track and characterize migratory clones, we will utilize the Landau lab’s expertise in joint single- cell whole-genome and transcriptome profiling across spatially distinct tumor regions. By constructing somatic phylogenies using single-nucleotide variants as natural lineage markers, we aim to trace the emergence and spread of invasive clones, providing a "temporal microscope" of tumor evolution. By integrating single-cell multi- region lineage trees with genomics and transcriptomics, we will gain an unprecedented lens of the evolution of invasive clones through time and identify the genetic alterations and molecular drivers of their aggressiveness towards recurrence. To (2) explore how the TME contributes to invasion, we will incorporate Slide-tags— spatially barcoded oligos—to map individual nuclei within their native microenvironment. This integration of high- resolution spatial with transcriptomics and cell lineages will allow us to assess how histological niches such as necrosis impose selective pressures on GBC subclones. Together, with three-dimensional layers of information for each cell, we can gain valuable insights into how the TME shapes the clonal architecture and cellular programming of GBCs to promote invasive phenotypes. This project will be ideal for me as a training scientist, given its use of novel single-cell technologies and my interest in somatic evolution, along with its direct clinical impact. With the mentorship of my sponsor, thesis committee, PhD program, and the support of this fellowship, I am confident I will be well prepared to pursue and achieve my goal of becoming an independent researcher capable of leading my own research group. Project Number: 1F31CA310290-01 | Fiscal Year: 2026 | NIH Institute/Center: National Cancer Institute (NCI) | Principal Investigator: Jake Qiu | Institution: WEILL MEDICAL COLL OF CORNELL UNIV, NEW YORK, NY | Award Amount: $50,114 | Activity Code: F31 | Study Section: Special Emphasis Panel[ZRG1 F09B-W (20)] View on NIH RePORTER: https://reporter.nih.gov/project-details/11315519