Single cell-derived clonal analysis of human glioblastoma links functional and genomic heterogeneity

Abstract

Glioblastoma (GBM) is a cancer comprised of morphologically, genetically, and phenotypically diverse cells. However, an understanding of the functional significance of intratumoral heterogeneity is lacking. We devised a method to isolate and functionally profile tumorigenic clones from patient glioblastoma samples. Individual clones demonstrated unique proliferation and differentiation abilities. Importantly, naïve patient tumors included clones that were temozolomide resistant, indicating that resistance to conventional GBM therapy can preexist in untreated tumors at a clonal level. Further, candidate therapies for resistant clones were detected with clone-specific drug screening. Genomic analyses revealed genes and pathways that associate with specific functional behavior of single clones. Our results suggest that functional clonal profiling used to identify tumorigenic and drug-resistant tumor clones will lead to the discovery of new GBM clone-specific treatment strategies.cancer | glioblastoma | clonal heterogeneity | genomic analysis | functional analysis

Prognostic Relevance of Tumor Purity and Interaction with MGMT Methylation in Glioblastoma

“…Heterogeneity of MGMT methylation within the tumor cell population has been reported as another source of variability of MGMT promoter methylation. One study observed the presence of both methylated and unmethylated clones in gliomaspheres derived from single cells of the same parental tumor by analyzing both protein expression and promoter methylation (34). Notably, neither MGMT methylation nor protein expression correlated with temozolomide resistance in this study.…”

Cancer stem cells in glioblastoma

“…Furthermore, these investigators described an inverse correlation between stem signature and cell cycle gene expression, suggesting that the cells that form neurospheres in culture cycle more slowly compared with differentiated and differentiating tumor cells. A parallel, single-cell functional analysis of GBMs confirmed a strong variation of genomics and response to therapy (Meyer et al 2015). Additional detailed analysis of heterogeneity of this type will greatly expand our understanding of the differences between tumor cells both within and among GBM patients and improve the characterization of glioma CSCs.…”

Overcoming therapeutic resistance in glioblastoma: the way forward

“…Molecular heterogeneity exists even at the cellular level between cells that carry similar genetic alterations (50,51). Recently, single-cell transcriptional profiling of 430 cells from five different primary GBM tumors uncovered intratumoral heterogeneity at the cellular level.…”

“…Recurrence shows a high degree of variability tures for genes that regulate cell cycle, hypoxia, immune response, and stemness (50). Expanding single cells into clonal populations further demonstrated unique functionality including proliferation, differentiation abilities, and different sensitivities to temozolomide (51). The complexity of intercellular heterogeneity also relates to variations in epigenetic or transcriptional programs, which define a hierarchy of cells showing variable degrees of differentiation and stemness.…”

“…This subpopulation had low expression of cell cycle genes, suggesting slower growth than the remainder of tumor cells. There is emerging evidence that GSCs vary in different GBM subtypes (66)(67)(68), between treatment-naive and recurrent GBM (51,55,63,69), and even within alternate niches in the same tumor (i.e., perivascular and hypoxic) (54,66,70). Which subpopulations of GSCs can initiate tumor recurrence needs further clarification.…”