A multi-component view of the glioma transcriptome identifies unique immune infiltration patterns in primary glioblastomas and patients with inferior prognosis.
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE111260 | GEO | 2018/03/01
REPOSITORIES: GEO
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Project description:A multi-component view of the glioma transcriptome identifies unique immune infiltration patterns in primary glioblastomas and patients with inferior prognosis.
| PRJNA436366 | ENA
Project description:Comparison of polysomal profiles of murine adult olig2 cortical progenitors, murine tumor olig2 cells derived from hPDGF-B-driven glioblastomas, and murine olig2 proliferative recruited glioma cells contributing to the tumor mass but not derived from the cell of origin An unbiased way to define a cell population lies in identification of its gene expression signature and subsequent comparison to gene expression signatures of known normal or cancer cells to define its position on the axis of tumorigenesis. To quantify similarities and differences in the expression profiles of recruited cells and tumor cells using microarray analysis, we used the bacTRAP technology that allows immunoprecipitation of polysomes from specific cell types in vivo (Heiman et al 2008, Doyle et al 2008). We compared polysomal expression profiles of hPDGFb-driven Ntv-a Ink4a/Arf+/- olig2 mouse glioma cells representing a histologically defined glioma population, recruited olig2 cells derived from Ink4a/Arf+/- olig2 RP-eGFP mice transplanted with non-fluorescent glioma cells, and normal adult cortical olig2 mouse progenitors, using Affymetrix 430 mouse 2.0 chips and Genespring GX10 software (Doyle et al 2008, Heiman et al 2008). Translational profiles of recruited olig2 cells and glioma olig2 cells were similar to each other and clearly distinct from the normal olig2 progenitors, majority of the differences accounted for by the “statistically significantly changed” set of mRNAs (ANOVA, p<0.05), and sample clustering reduced upon removal of the ANOVA-tested mRNA set. Unsupervised hierarchical mRNA clustering likewise indicated that recruited olig2 cells clustered more closely to glioma olig2 cells. The caveat is that olig2 expression in the adult normal brain of bacTRAP olig2 RP-eGFP mice labels both progenitors and mature oligodendrocytes, while recruited and tumor olig2 cells are almost entirely progenitors; therefore, some of the differences seen in the comparative analysis of normal, tumor and recruited olig2 cells may in part result from the shift in relative abundance of different progenitor and mature olig2 cell populations. Normal olig2 progenitors were collected from three replicates of pooled cortices of three olig2 RP-eGFP bacTRAP reporter mice. Mouse gliomas induced by injection of a non-fluorescent RCAS-hPDGFb (Shih et al 2004) or by transplantation of muring glioma cells derived from Ntv-a gliomas induced by the non-fluorescent RCAS-hPDGFb were collected from Ntv-a olig2 RP-eGFP bacTRAP reporter mice and immunoprecipitated; each tumor was processed as a separate sample. Briefly, mouse tissues were collected into ice-cold cyclohexamide-containing buffer, homogenized, cells were lysed in NP-40 and DHPC-containing buffer, centrifuged at 20,000g for 15 min, supernatant incubated with anti-eGFP-conjugated protein G beads 30 min at 4C, washed and RNA collected using Trizol reagent as per manufacturer’s instructions (Doyle et al., 2008; Heiman et al., 2008). RNA was purified, concentrated using Qiagen RNeasy kit, its quality confirmed by Agilent Bioanalyzer, 15ng per sample amplified using Affymetrix Two-Cycle Amplification kit and hybridized to Affymetrix 430 mouse 2.0 chips as described in Doyle et al., 2008; Heiman et al., 2008. Data was analyzed using Genespring GX10 software, as described in the text and in Doyle et al., 2008; Heiman et al., 2008. Briefly, samples were normalized using GCRMA, filtered to remove probe sets with low intensity, and analyzed using ANOVA (p<0.05) with SNK post-hoc and Benjamini and Hochberg FDR multiple testing correction. Probe quality, Pearson’s correlation, hierarchical clustering, heatmaps, gene profile plots were generated using Genespring GX10 software. Pathway analysis was performed using Ingenuity as per manufacturer’s instructions. Gliomas are thought to form by clonal expansion from a single cell-of-origin, and progression-associated mutations to occur in its progeny cells. Glioma progression is associated with elevated growth factor signaling and loss of function of tumor suppressors Ink4a, Arf and Pten. Yet, gliomas are cellularly heterogeneous; they recruit and trap normal cells during infiltration. We performed lineage tracing in a retrovirally mediated, molecularly and histologically accurate mouse model of hPDGFb-driven gliomagenesis. We were able to distinguish cells in the tumor that were derived from the cell-of-origin from those that were not. Phenotypic, tumorogenic and expression analyses were performed on both populations of these cells. Here we show that during progression of hPDGFb-induced murine gliomas, tumor suppressor loss can expand the recruited cell population not derived from the cell-of-origin within glioma microenvironment to dominate regions of the tumor, with essentially no contribution from the progeny of glioma cell-of-origin. Moreover, the recruited cells can give rise to gliomas upon transplantation and passaging, acquire polysomal expression profiles and genetic aberrations typically present in glioma cells rather than normal progenitors, aid progeny cells in glioma initiation upon transplantation, and become independent of PDGFR signaling. These results indicate that non-cell-of-origin derived cells within glioma environment in the mouse can be corrupted to become bona fide tumor, and deviate from the generally established view of gliomagenesis.
2011-06-17 | E-GEOD-30016 | biostudies-arrayexpress
Project description:Gene expression profiling in 50 glial brain tumors and 4 normal brains using 42,000-feature cDNA microarrays (from total RNA). Tumors: 50 fresh-frozen glioma specimens subjected to standard WHO classification. Specimens included astrocytic [2 juvenile pilocytic astrocytomas, 1 low-grade astrocytic glioma, 1 anaplastic astrocytomas, 31 glioblastomas (of these 2 secondary glioblastomas and 2 gliosarcomas)], oligodendroglial [5 oligodendrogliomas, 3 anaplastic oligodendrogliomas], and 6 anaplastic oligoastrocytomas tumors. One tumor had been classified as glioneuronal neoplasm. Normal brain was purchased from Stratagene. Stratagene Universal Common Reference was used as reference RNA. The results provide insights into molecular mechanisms and pathways associated with gliomagenesis.
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