Single-Cell RNAseq analysis of infiltrating neoplastic cells at the migrating front of human glioblastoma

Abstract

Glioblastoma is the most common primary brain cancer in adults and is notoriously difficult to treat due to its diffuse nature. We performed single-cell RNAseq on 3589 cells in a cohort of four patients. We obtained cells from the tumor core as well as surrounding peripheral tissue. Our analysis revealed cellular variation in the tumor's genome and transcriptome, We were able to identify infiltrating neoplastic cells in regions peripheral to the core lesions. Despite the existence of significant heterogeneity among neoplastic cells, we found that infiltrating GBM cells share a consistent gene signature between patients, suggesting a common mechanism of infiltration. Additionally, in investigating the immunological response to the tumors, we found transcriptionally 2 distinct myeloid cell populations residing in the tumor core and the surrounding peritumoral space. Our data provide a detailed dissection of GBM cell types, revealing an abundance of novel information about tumor formation and migration.

Mesenchymal Transformation: The Rosetta Stone of Glioblastoma Pathogenesis and Therapy Resistance

“…[14,87] Single cell RNAseq revealed that nearly 50% of cells in GBMs TME are infiltrative immune cells, of which 95% are resident microglia/macrophages and the rest are mainly dendritic cells. [88] Similar observation by Wang and colleagues showed enriched infiltrative lymphocytes in the MES subtype. [89] Subtype-specific immune profile also demonstrated that GBM MES phenotype is enriched with pro-inflammatory and immunosuppressive genes (summarized in Figure 3).…”

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

“…The raw data (GSE84465) for validation were downloaded from GEO database, which contains 3589 cells. These data were published by Darmanis et al (2017) and preprocessed with the same steps as the data from Patel et al Finally,882 tumor cells remained for subsequent analysis. We also obtained the oligodendroglioma data (GSE70630) published by Tirosh et al (2016b) and a set of single-cell data of the normal brain (GSE67835) published by Darmanis et al (2015), in which 4044 and 277 cells, respectively, remained after the similar filtration.…”

“…To validate whether the stem-to-invasion path could be recaptured in other GBM data, we obtained another single-cell RNA-seq data set of GBM (published by Darmanis et al (2017) which contains 3589 cells from four patients. Following the same data processing, the final number of tumor cells for validation was 882.…”

A Microglial Subset at the Tumor-Stroma Interface of Glioma

“…In agreement with published results, our analysis identified a discrete cluster of peripheral myeloid cells ( Figure 1B). To further define this population, cells in the myeloid cluster from the 'peripheral' tissue sample were selected for by the expression of previously reported microglia-specific genes 9,25 (TMEM119, P2RY12, GPR34, OLFML3, SLC2A5, SALL1, and ADORA3, Figure 1B). 92.4% of myeloid cells from the peripheral tissue sample were positive for microglia selection criteria.…”

“…We took advantage of this large pool of data to test the robustness of the PGAM signature across healthy and pathological samples. To capture the heterogeneity surrounding HGG, we collected data from primary and recurrent Grade IV GB, Grade III HGG, as well as IDH mutant astrocytoma and oligodenrocytoma 13,22,25,41,42 . It has been proposed that the observed activated GAM-Mg profiles reflect aging-related phenotypes of microglia 23 .…”