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RNA-Seq of GPR56+/- populations

ABSTRACT: Insights into the complex clonal architecture of acute myeloid leukemia (AML) unravelled by deep sequencing technologies have challenged the concept of AML as a hierarchically organised disease initiated and driven by rare self-renewing leukemic stem cells (LSCs). The lack of clone-specific surface markers, however, precludes prospective isolation and functional characterisation of distinct clones. Here, we performed RNA-Sequencing and assessed LSC frequencies for 56 primary AML samples in xenograft assays. We found that G-protein coupled receptor 56 (GPR56) identified the engrafting fraction in CD34positive samples and was associated with most high-risk mutations and poor outcome. Furthermore, variant allele frequency analysis revealed different clonal composition of engrafting GPR56+ versus non-engrafting GPR56- fractions identifying GPR56 as a discriminator of leukemic sub-clones with high and low leukemia initiating capacity. Our data suggest that the NSG-model rather than reproducing the full clonal diversity of the human disease selects for leukemic sub-clones based on their distinct functional properties.

ORGANISM(S): Homo sapiens

PROVIDER: GSE68623 | GEO | 2020/05/01

REPOSITORIES: GEO

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Project description:G protein-coupled receptor 56 (GPR56/ADGRG1) is an adhesion GPCR with an essential role in brain development and cancer. Elevated expression of GPR56 was observed in the clinical specimens of Glioblastoma (GBM), a highly invasive primary brain tumor. However, we found the expression to be variable across the specimens, presumably due to the intratumor heterogeneity of GBM. Therefore, we re-examined GPR56 expression in public domain spatial gene expression data and single-cell expression data for GBM, which revealed that GPR56 expression was high in cellular tumors, infiltrating tumor cells, and proliferating cells, low in microvascular proliferation and peri-necrotic areas of the tumor, especially in hypoxic mesenchymal-like cells. To gain a better understanding of the consequences of GPR56 downregulation in tumor cells and other molecular changes associated with it, we generated a sh-RNA-mediated GPR56 knockdown in the GBM cell line U373 and performed transcriptomics, proteomics, and phospho-proteomics analysis. Our analysis revealed enrichment of gene signatures, pathways, and phosphorylation of proteins potentially associated with mesenchymal (MES) transition in the tumor and concurrent increase in cell invasion and migration behavior of the GPR56 knockdown GBM cells. Interestingly, our analysis also showed elevated expression of Transglutaminase 2 (TG2) - a known interactor of GPR56, in the knockdown cells. The inverse expression of GPR56 and TG2 was also observed in intratumoral, spatial gene expression data for GBM and in GBM cell lines cultured in vitro under hypoxic conditions. Integrating all these observations, we infer a functional link between the inverse expression of the two proteins, the hypoxic niche, and the mesenchymal status in the tumor. Hypoxia-induced downregulation of GPR56 and activation of TG2 may result in a network of molecular events that contribute to the mesenchymal transition of GBM cells, and we propose a putative model to explain this functional and regulatory relationship of the two proteins.

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RNA-Seq of GPR56+/- populations

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