Single‐cell RNA‐seq reveals the invasive trajectory and molecular cascades underlying glioblastoma progression

Abstract

Glioblastoma (GBM) is the most common and aggressive primary brain tumor, in which GBM stem cells (GSCs) were identified to contribute to aggressive phenotypes and poor prognosis. Yet, how GSCs progress to invasive cells remains largely unexplored. Here, we revealed the cell subpopulations with distinct functional status and the existence of cells with high invasive potential within heterogeneous primary GBM tumors. We reconstructed a branched trajectory by pseudotemporal ordering of single tumor cells, in which the root showed GSC‐like phenotype while the end displayed high invasive activity. Thus, we further determined a path along which GSCs gradually transformed to invasive cells, called the ‘stem‐to‐invasion path’. Along this path, cells showed incremental expression of GBM invasion‐associated signatures and diminishing expression of GBM stem cell markers. These findings were validated in an independent single‐cell data set of GBM. Through analyzing the molecular cascades underlying the path, we identify crucial factors controlling the attainment of invasive potential of tumor cells, including transcription factors and long noncoding RNAs. Our work provides novel insights into GBM progression, especially the attainment of invasive potential in primary tumor cells, and supports the cancer stem cell model, with valuable implications for GBM therapy.

Dissecting the Invasion-Associated Long Non-coding RNAs Using Single-Cell RNA-Seq Data of Glioblastoma

“…For negatively correlated lncRNAs, ENSG00000254528 ( RP11-728F11.4 ) and ENSG00000267062 ( CTD-2659N19.10 ) ranked among the top four and ten, both of which showed significantly higher expression levels in GBM cells and nearly no expression in normal cells. Notably, VIM-AS1 and WWTR1-AS1 were the top two lncRNAs with the highest correlations between their expression levels and pseudotime along the “stem-to-invasion path” in our previous work ( Pang et al, 2019 ). These findings promoted us to explore the dynamic changes of GBM invasion-associated lncRNAs along the “stem-to-invasion path.” We found that the expression levels of many lncRNAs such as ENSG00000258232 ( RP11-161H23.5 ), ENSG00000267607 ( CTD-2369P2.8 ), and ENSG00000238258 ( RP11-342D11.2 ), gradually increased as cells transferred from cancer stem cell-like state to invasive state ( Figure 4A ).…”

“…To validate the above observations, we combined the results from our previous work ( Pang et al, 2019 ), in which we identified 12 cell clusters using the same data set. And cluster 3, 4, 7, and 9 showed relatively higher expression of EMT-associated genes.…”

“…Notably, many DEGs in M1 have been reported to be associated with migration and invasion. For example, EPAS1 was an important transcription factor (TF) that was validated to promote the invasive potential of GBM cells by our previous work ( Pang et al, 2019 ). Many studies revealed that ANX family proteins (ANXA1 and ANXA2), especially ANXA2, could promote cancer progression including proliferation, invasion and metastasis ( Chen C.Y.…”

A Single Cell but Many Different Transcripts: A Journey into the World of Long Non-Coding RNAs

“…They used scRNA-seq based on SMART-seq to analyze a novel parameter they describe as "pseudotime", which refers to transcriptional changes in cells during GBM progression. They were able to describe the path along which GBM stem cells (GSCs) gradually transform into invasive cells, called the "stem-to-invasion path" [172]. The path contains transcription factors and lncRNAs supporting one more time their importance in cancer development.…”

A Complex Systems Analysis of Cancer Networks

“…It is paving the future of precision oncology. [150]). A droplet-based scRNA-Seq of patient-derived GBM cells, generated two or three distinct clusters by t-SNE and the Louvain community structure detection algorithm.…”