A CD133-related gene expression signature identifies an aggressive glioblastoma subtype with excessive mutations

Abstract

Cancer cells are heterogeneous and, it has been proposed, fall into at least two classes: the tumor-initiating cancer stem cells (CSC) and the more differentiated tumor cells. The transmembrane protein CD133 has been widely used to isolate putative CSC populations in several cancer types, but its validity as a CSC marker and hence its clinical ramifications remain controversial. Here, we conducted transcriptomic profiling of sorted CD133 + and CD133 − cells from human glioblastoma multiforme (GBM) and, by subtractive analysis, established a CD133 gene expression signature composed of 214 differentially expressed genes. Extensive computational comparisons with a compendium of published gene expression profiles reveal that the CD133 gene signature transcriptionally resembles human ES cells and in vitro cultured GBM stem cells, and this signature successfully distinguishes GBM from lower-grade gliomas. More importantly, the CD133 gene signature identifies an aggressive subtype of GBM seen in younger patients with shorter survival who bear excessive genomic mutations as surveyed through the Cancer Genome Atlas Network GBM mutation spectrum. Furthermore, the CD133 gene signature distinguishes higher-grade breast and bladder cancers from their lower-grade counterparts. Our systematic analysis provides molecular and genetic support for the stem cell-like nature of CD133 + cells and an objective means for evaluating cancer aggressiveness. molecular profiling | systems biology T he identification of tumor-initiating cancer stem cell (CSC) subpopulations in leukemia (1) and subsequently in breast cancer (2) has led to the hypothesis that tumor proliferation arises largely from these stem/progenitor-like cells and raises the possibility that a similar hypothesis can be applied to a number of solid tumor types (3) including glioblastoma multiforme (GBM) (4), the most deadly form of brain cancer with a diverse cellular phenotype and genetic heterogeneity (5-7). A CD133 + cell population has been isolated from brain as well as other cancers and has been shown to possess stem-cell properties (4, 8), to be more tumorigenic than the CD133 − cells in xenografted animal models (4,8,9), and to confer radiation resistance (10). Gene-expression signatures derived from both tumorigenic and normal stem cells have been correlated to expression profiles of patient samples in an attempt to stratify these patients according to their disease aggressiveness (presumably more CSCs indicate greater aggressiveness). For instance, an invasiveness gene signature derived from tumorigenic breast CSCs has been related to poor survival in breast cancer patients, suggesting that CSCs may contribute to tumor invasion and metastasis (11). A recent computational analysis linking an ES cell-like gene expression signature to the poorly differentiated states of aggressive human tumors, including breast cancer and GBM, further strengthens the putative stem-cell origins of cancer cell proliferation (12). However, this ES cell signature was unable to stratify t...

Stem cell characteristics in glioblastoma are maintained by the ecto-nucleotidase E-NPP1

“…To examine this in greater detail, gene expression microarray-based transcriptome analysis was conducted on NCH421k cells transduced with shNT and ENPP1-shRNA1 4 days post-transduction and significance analysis of microarray (SAM) revealed 2104 differentially regulated genes (FDRo0.05). Using gene set enrichment analysis (GSEA), we tested an enrichment of the CD133-up signature 24 and the consensus stemness ranking-up (CSR-up) signature 25 with their autologous CD133 À counterparts, whereas the CSR-up signature contains genes (n ¼ 70) upregulated in a broader array of stem cell populations reflecting a common stem cell signature. GSEA demonstrates a significant enrichment of both stem cell-associated gene sets in the most downregulated genes upon knockdown (FDR q-valueo0.001; 57 genes out of 76 CD133-up associated genes; 56 genes out of 70 CSR-up signature genes; Figure 3f; Supplementary Table S1).…”

“…Even though there is evidence for the existence of a tumourigenic CD133-negative GSC population, the stem cell-related marker CD133 has proven to be useful to isolate and further characterise tumourigenic GSCs. 4,10,14,24 Analysis of the extracellular CD133 epitope AC133 led to the identification of 12 phosphatases (B7% hit rate) that significantly decreased CD133 level upon knockdown, and hence genes potentially required for the GSC phenotype. Among the candidate genes PPEF1, PTPN7, PPP4C and PPP2R5E were previously shown to be important regulators of CD133 level emphasising the validity of our screen.…”

“…E-NPP1-deficient GSCs are characterised by downregulation of known stem cell markers, such as CD133, LHX2, MSI1, LGR5 and CD15, 4,8,9,34,35 as well as an overall downregulation of stem cell-associated genes as seen by comparison with published stem cell gene signatures. 24,25 Moreover, GFAP and S100 beta, differentiation marker delineating the astrocytic cell lineage, are upregulated upon knockdown of ENPP1 in cultured GSCs. Hence, the change in expression of the studied markers upon ENPP1 knockdown suggests a switch towards a differentiated phenotype.…”

“…GSEA utilising the pre-ranked tool was performed at http://www.broadinstitute.org/gsea/ 57 using default settings. Significant differentially expressed genes between shNT and ENPP1-shRNA1 transduced samples were pre-ranked based on mean fold change and analysed for the enrichment of the following gene sets: CD133-up signature, 24 CSR-up signature, 25 direct E2F1 targets (MetaCore database, https://portal.genego.com/) and KEGG pathways (gene set c2.cp.kegg, version v3.1) as compiled in the Molecular Signatures Database. 57 The gene symbols of the signature genes were updated and annotated for HUGO symbols; duplicates were removed.…”

Colorectal micropapillary carcinomas are associated with poor prognosis and enriched in markers of stem cells

“…In fact, the expression of stem cell markers and their prognostic significance have been reported in several solid tumors, including colorectal cancer. 16,[18][19][20][21][22][23] Several cell surface markers, including CD44, CD133, and CD166, have been used for identification of colorectal cancer stem cells. [24][25][26] Activity of aldehyde dehydrogenase 1 (ALDH1), a detoxifying enzyme that oxidizes intracellular aldehydes, has also been used as a colorectal cancer stem cell marker.…”