Integrative spatial analysis reveals a multi-layered organization of glioblastoma

Abstract

Glioma contains malignant cells in diverse states. Hypoxic regions are associated with a unique histology of pseudopalisading cells, while other regions appear to have limited histological organization, reflecting the diffuse nature of glioma cells. Here, we combine spatial transcriptomics with spatial proteomics and novel computational approaches to define glioma cellular states at high granularity and uncover their organization. We find three prominent modes of cellular organization. First, cells in any given state tend to be spatially clustered, such that tumors are composed of small local environments that are each typically enriched with one major cellular state. Second, specific pairs of states preferentially reside in proximity across multiple scales. Despite the unique composition of each tumor, this pairing of states remains largely consistent across tumors. Third, the pairwise interactions that we detect collectively define a global architecture composed of five layers. Hypoxia appears to drive this 5-layered organization, as it is both associated with unique states of surrounding cells and with a long-range organization that extends from the hypoxic core to the infiltrative edge of the tumor. Accordingly, tumor regions distant from any hypoxic foci and tumors that lack hypoxia such as IDH-mutant glioma are less organized. In summary, we provide a conceptual framework for the organization of gliomas at the resolution of cellular states and highlight the role of hypoxia as a long-range tissue organizer.

Programs, Origins, and Niches of Immunomodulatory Myeloid Cells in Gliomas

“…A vascular niche straddles the hypoxic niche and the inflammatory niche, indicative of vascular proliferation in response to hypoxia and potentially representing an entry point for immune infiltration. These patterns are generally consistent with recent reports 46 .…”

Glioblastoma is spatially organized by neurodevelopmental programs and a glial-like wound healing response

“…The advent of high-throughput spatial transcriptomics methods has led to some important developments in this regard. Early studies using array-based spatial transcriptomics have revealed a changing spatial organization of tumor and immune cells driven by hypoxia 5,10 , and hybridization-based in situ sequencing (HybISS) has helped characterize intercellular interactions of tumor and stromal cells 11,12 . The recurring patterned co-existence of several transcriptional subtypes suggests that tumor cells form a complex system retaining certain functional and organizational aspects of the healthy brain to survive and evolve together with the tumor microenvironment (TME).…”

2D and 3D multiplexed subcellular profiling of nuclear instability in human cancer

“…Others exhibited gradual accumulation of AC-like markers towards the periphery ( Figure 6F and Figure S4C ). When we analyzed publicly available spatial transcriptomic data from the IVY Glioblastoma Atlas, which was generated from seven spatially distinct regions from 10 adult GBM specimens 48 , we also found that MES markers (NDRG1, CEBPB) were elevated in regions near necrosis, NPC (ELAVL4) and OPC (SOX10) markers were higher toward the infiltrating edge of the tumor, and lamin A/C was lower towards the infiltrating edge ( Figure S4D ).…”