Single-Cell Study Links Invasive Stem Cells to Poor Glioblastoma Outcomes
Summary
The quantification of chromatin accessibility serves as a means of differentiating stem cells from mature cell populations, thereby enabling the identification of primitive stem-like cells within primary tumors, such as glioblastoma (GBM). The self-renewing cells that drive cancer progression and recurrence within primary GBMs are of paramount importance for therapeutic intervention, and therefore, must be the focus of intensive study. Through the utilization of single-cell chromatin accessibility analysis, they demonstrate that primary human GBMs harbor a heterogeneous population of self-renewing cells, which is captured in patient-derived glioblastoma stem cells (GSCs). their in-depth characterization of chromatin accessibility within GSCs reveals the existence of three distinct GSC states: Reactive, Constructive, and Invasive, each governed by a unique set of essential transcription factors, and present within GBMs in varying proportions. The results of the orthotopic xenograft studies reveal that GSC states have a direct correlation with patient survival, and the identification of an invasive GSC signature that is predictive of low patient survival is in line with the greater invasive properties of Invasive state GSCs compared to Reactive and Constructive GSCs, as demonstrated through both in vitro and in vivo assays. In conclusion, their chromatin-driven characterization of GSC states not only improves the precision of prognostication, but also identifies therapeutic dependencies that may be targeted through combination therapies.
Research Criteria
Consequently, it is established that primary Glioblastoma Multiforme (GBM) encompasses distinct states, within which stem-like cells are believed to be situated. Yet, the question of whether these stem-like cells found across the GBM states correspond to functionally diverse populations of Glioblastoma Stem Cells (GSCs) with tumor-initiating potential and exclusive dependencies remains unanswered, a crucial issue that must be addressed to foster therapeutic advancements. In order to resolve this conundrum, they have implemented a synergistic combination of single-cell technologies and functional assays to precisely define the composition of GSCs within primary GBM and to expose the distinctive dependencies across these cells, reflecting the reactive, constructive, and invasive states that have implications for patient outcome.
Sample Type
Nuclei isolated from human glioblastoma tissues.
Result—The Diverse GBM Cancer Stem Cell Pool
Cells were classified into one of four cellular states using single-cell RNA sequencing (scRNA-seq) based on the chromatin accessibility enrichment fraction of the promoter region of the signature gene specific to each state. The percentage of cells that were highly enriched for signature genes in at least one state ranged from 35% to 55.2% in the four cancers examined. In each malignancy, the cell state known as the MES state (identified by scRNA-seq) was found to be the predominant identity among two or more modules identified by chromatin accessibility. On the other hand, NPC and OPC states are mixed together in a chromatin accessibility-based module and are usually preferred over other states in at least two modules. Based on chromatin accessibility, cells assigned to the AC state did not show a preference for aggregation within a single module. When considered as a whole, our results show that chromatin accessibility identifies heterogeneity within AC states, identifies commonality between OPC and NPC states, and gives a more precise stratification of MES states.
Fig.1 In four primary glioblastoma tumors, the UMAP representation of chromatin accessibility shows the grouping of UMAP modules by dominant cellular state, with tumor cells assigned to these states. (Guilhamon, 2021)
In order to determine the existence of potential cancer stem cells inside each initial glioblastoma tumor, a complete investigation of the chromatin accessibility levels at the promoters of 19 transcription factors known to be involved in self-renewal and tumor propagation was performed. Individual cells deemed to be cancer stem cells are not restricted to a single module characterized by chromatin accessibility, but are instead spread throughout a variety of modules, indicating the heterogeneity of cancer stem cells in primary glioblastoma. These findings are consistent with prior research that employed single-cell labeling to evaluate the diverse nature of self-renewing, tumor-initiating cells inside glioblastoma. Their scATAC-seq analysis of putative cancer stem cells within primary glioblastoma revealed that they were present in all four cellular states defined by gene expression, with the majority found in modules designated as NPC and OPC, and a smaller proportion (10%) in MES-specific modules across all four tumors. This shows that the core transcriptional unit of cancer stem cells in primary glioblastoma is not constrained to a specific population characterized by its transcriptional profile or chromatin accessibility profile, given the limits of single-cell technologies.
Fig.2 Cancer stem cells, identified by the enrichment of specific transcription factor promoters, are distributed across gene expression-dominated cellular states in UMAP representations. (Guilhamon, 2021)
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Creative Biolabs provides a comprehensive range of customized, high-quality services in single cell ATAC profiling to support various scientific research worldwide. Examining gene regulation at the single cell level through the analysis of chromatin accessibility can provide insights into the underlying mechanisms at play.
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Reference
- Guilhamon, P.; et al. Single-cell chromatin accessibility profiling of glioblastoma identifies an invasive cancer stem cell population associated with lower survival. Elife. 2021, 10: e64090.
