Metabolism of oxygen, while central to life, also produces reactive oxygen species (ROS) that have been implicated in processes as diverse as cancer, cardiovascular disease, and aging. It has recently been shown that central nervous system stem cells 1, 2 and hematopoietic stem cells and early progenitors [3][4][5][6] contain lower levels of ROS than their more mature progeny and that these differences appear to be critical for maintaining stem cell function. We hypothesized that epithelial tissue stem cells and their cancer stem cell (CSC) counterparts may also share this property. Here we show that normal mammary epithelial stem cells contain lower concentrations of ROS than their more mature # To whom correspondence should be addressed. mfclarke@stanford.edu. * Contributed equally.Author Contributions M.D. and R.W.C. contributed equally to this work. M.D, R.W.C., N.L., T.K., M.J.D., A.K., D.Q., J.S.L., L.A., and M.W. performed the experiments. B.J., M.J.K, I.W., F.W., G.S., C.G., B.P., J.S., and S.K.L. aided in human tumor tissue acquisition. G.S. designed a pre-operative protocol allowing for tissue acquisition. M.D., R.W.C., and M.F.C. designed the experiments and wrote the manuscript. S.R.Q., J.M.B., and I.L.W. provided intellectual input and aided in experimental design.Author Information Reprints and permissions information is available at npg.nature.com/reprintsandpermissions. Given the conservation of low ROS levels in several types of normal tissue stem cells, we hypothesized that CSCs in some tumors may also contain lower concentrations of ROS than their non-tumorigenic progeny. In order to investigate ROS biology in human CSCs, we began by examining the expression of genes involved in ROS metabolism in primary human breast CSCs and NTCs. Using microarray data from human breast CSC-enriched populations and NTCs 13 and a curated list of genes involved in ROS metabolism 5 (see methods), Gene Set Enrichment Analysis (GSEA) 14 revealed that the expression of ROS genes was highly overrepresented in the CD44 + CD24 -/low Lin -breast CSC-enriched population compared to NTCs (p<0.001; Supplementary Fig. S2). The ROS genes identified as the core enriched genes by GSEA included a number of important antioxidant genes (Supplementary Table 2). Thus, gene expression profiles of human breast CSC-containing populations suggest that they contain higher levels of antioxidant defense systems than NTCs. NIH Public AccessNext, we directly assessed ROS levels in human tumor subpopulations. To do this the CD44 + CD24 -/low Lin -breast CSC-enriched population and the corresponding "Not CD44 + CD24 -/low " Lin -NTC population were purified from surgically resected breast tumors ( Supplementary Fig. S3). DCF-DA staining revealed that the CSC-enriched population in the human breast tumors we examined contained significantly lower levels of prooxidants than the NTC population. In some breast tumors, the vast majority of cells in the CSC-containing fraction displayed a low ROS phenotype compared to NTCs (Fig. 1e) while ...

Summary Human breast tumors contain a breast cancer stem cell (BCSC) population with properties reminiscent of normal stem cells. We found 37 microRNAs that were differentially expressed between human BCSCs and non-tumorigenic cancer cells. Three clusters, miR-200c-141, miR-200b-200a-429 and miR-183-96-182 were down-regulated in human BCSCs, normal human and murine mammary stem/progenitor cells and embryonal carcinoma cells. Expression of BMI1, a known regulator of stem cell self-renewal, was modulated by miR-200c. MiR-200c inhibited the clonogenicity of breast cancer cells and suppressed the growth of embryonal carcinoma cells in vitro. Most importantly, miR-200c strongly suppressed the ability of normal mammary stem cells to form mammary ducts and tumor formation driven by human BCSCs in vivo. The coordinated down-regulation of three microRNA clusters and the similar functional regulation of clonogenicity by miR-200c provide a molecular link that connects breast cancer stem cells with normal stem cells.

The nature and extent of interindividual and temporal variation in gene expression patterns in specific cells and tissues is an important and relatively unexplored issue in human biology. We surveyed variation in gene expression patterns in peripheral blood from 75 healthy volunteers by using cDNA microarrays. Characterization of the variation in gene expression in healthy tissue is an essential foundation for the recognition and interpretation of the changes in these patterns associated with infections and other diseases, and peripheral blood was selected because it is a uniquely accessible tissue in which to examine this variation in patients or healthy volunteers in a clinical setting. Specific features of interindividual variation in gene expression patterns in peripheral blood could be traced to variation in the relative proportions of specific blood cell subsets; other features were correlated with gender, age, and the time of day at which the sample was taken. An analysis of multiple sequential samples from the same individuals allowed us to discern donor-specific patterns of gene expression. These data help to define human individuality and provide a database with which disease-associated gene expression patterns can be compared.

A widespread approach to modern cancer therapy is to identify a single oncogenic driver gene and target its mutant protein product (e.g. EGFR inhibitor treatment in EGFR-mutant lung cancers). However, genetically-driven resistance to targeted therapy limits patient survival. Through genomic analysis of 1122 EGFR-mutant lung cancer cell-free DNA samples and whole exome analysis of seven longitudinally collected tumor samples from an EGFR-mutant lung cancer patient, we identify critical co-occurring oncogenic events present in most advanced-stage EGFR-mutant lung cancers. We define new pathways limiting EGFR inhibitor response, including WNT/β-catenin and cell cycle gene (e.g. CDK4, CDK6) alterations. Tumor genomic complexity increases with EGFR inhibitor treatment and co-occurring alterations in CTNNB1, and PIK3CA exhibit non-redundant functions that cooperatively promote tumor metastasis or limit EGFR inhibitor response. This study challenges the prevailing single-gene driver oncogene view and links clinical outcomes to co-occurring genetic alterations in advanced-stage EGFR-mutant lung cancer patients.

Glioblastoma multiforme (GBM) is the most common form of malignant glioma, characterized by genetic instability, intratumoral histopathological variability, and unpredictable clinical behavior. We investigated global gene expression in surgical samples of brain tumors. Gene expression profiling revealed large differences between normal brain samples and tumor tissues and between GBMs and lower-grade oligodendroglial tumors. Extensive differences in gene expression were found among GBMs, particularly in genes involved in angiogenesis, immune cell infiltration, and extracellular matrix remodeling. We found that the gene expression patterns in paired specimens from the same GBM invariably were more closely related to each other than to any other tumor, even when the paired specimens had strikingly divergent histologies. Survival analyses revealed a set of Ϸ70 genes more highly expressed in rapidly progressing tumors that stratified GBMs into two groups that differed by >4-fold in median duration of survival. We further investigated one gene from the group, FABP7, and confirmed its association with survival in two unrelated cohorts totaling 105 patients. Expression of FABP7 enhanced the motility of glioma-derived cells in vitro. Our analyses thus identify and validate a prognostic marker of both biologic and clinical significance and provide a series of putative markers for additional evaluation.brain ͉ glioma ͉ tumor ͉ FABP7 ͉ prognosis

Glioblastoma multiforme (GBM) is the most common and lethal primary brain tumor in adults. We combined neuroimaging and DNA microarray analysis to create a multidimensional map of gene-expression patterns in GBM that provided clinically relevant insights into tumor biology. Tumor contrast enhancement and mass effect predicted activation of specific hypoxia and proliferation gene-expression programs, respectively. Overexpression of EGFR, a receptor tyrosine kinase and potential therapeutic target, was also directly inferred by neuroimaging and was validated in an independent set of tumors by immunohistochemistry. Furthermore, imaging provided insights into the intratumoral distribution of gene-expression patterns within GBM. Most notably, an ''infiltrative'' imaging phenotype was identified that predicted patient outcome. Patients with this imaging phenotype had a greater tendency toward having multiple tumor foci and demonstrated significantly shorter survival than their counterparts. Our findings provide an in vivo portrait of genome-wide gene expression in GBM and offer a potential strategy for noninvasively selecting patients who may be candidates for individualized therapies.cancer ͉ genomics ͉ glioblastoma multiforme ͉ radiogenomics R ecent advances in the molecular analysis of brain tumors have led to an improved understanding of gliablastoma multiforme (GBM) tumor biology and the genomic heterogeneity that typifies the disease (1-7). However, the diagnosis and treatment of GBM is still largely guided by histopathology and immunohistochemistry, approaches that group histologically similar tumors that can often demonstrate markedly distinct clinical behaviors. Overall survival remains poor, with most patients succumbing to their disease within 15 months of diagnosis. Methods that assess molecular differences between GBMs hold promise for improving outcome by potentially allowing for individualized patient management.Magnetic resonance imaging (MRI) is routinely used in the diagnosis, characterization, and clinical management of GBM (8). It is a powerful and noninvasive diagnostic imaging tool that allows global assessment of GBMs and their interaction with their local environment. In its ability to extract structural, compositional, physiological, and functional information, MRI captures multidimensional, in vivo portraits of GBMs. Interestingly, histologically similar tumors often demonstrate highly distinct imaging profiles on MRI (9). Recently, several studies have attempted to correlate imaging findings with molecular markers, but no consistent associations have emerged. and many of the imaging features that characterize tumors currently lack biological or molecular correlates (10-15). Much of the information encoded within neuroimaging studies therefore remains unaccounted for and incompletely characterized at the molecular level. We reasoned that the phenotypic diversity of GBM captured by neuroimaging reflects underlying inter-and intratumoral gene-expression differences and that these relationships ...

Optimal activation of T cells requires effective occupancy of both the antigen-specific T cell receptor and a second coreceptor such as CD28. We used cDNA microarrays to characterize the genomic expression program in human peripheral T cells responding to stimulation of these receptors. We found that CD28 agonists alone elicited few, but reproducible, changes in gene expression, whereas CD3 agonists elicited a multifaceted temporally choreographed gene expression program. The principal effect of simultaneous engagement of CD28 was to increase the amplitude of the CD3 transcriptional response. The induced genes whose expression was most enhanced by costimulation were significantly enriched for known targets of nuclear factor of activated T cells (NFAT) transcription factors. This enhancement was nearly abolished by blocking the nuclear translocation of NFATc by using the calcineurin inhibitor FK506. CD28 signaling promoted phosphorylation, and thus inactivation, of the NFAT nuclear export kinase glycogen synthase kinase-3 (GSK3), coincident with enhanced dephosphorylation of NFATc proteins. These results provide a detailed picture of the transcriptional program of T cell activation and suggest that enhancement of transcriptional activation by NFAT, through inhibition of its nuclear export, plays a key role in mediating the CD28 costimulatory signal

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