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...