Human breast epithelial stem cells and their regulation

Gene expression of Epithelial Membrane Protein 2 gene and β1-Integrin gene in patients with breast cancer

Background

Breast cancer is the most common invasive cancer and the leading cause of cancer death in women. The function of over a thousand genes is reported as affected by genetic modifications in breast cancer.

Objectives

To study the gene expression of Epithelial Membrane 2 (EMP2) and β1-Integrin genes in patients with breast cancer.

Subjects and methods

This study was carried out by cooperation between the Biochemistry Division Department of Chemistry, Faculty of Science and Medical Biochemistry and Molecular Biology Department, Faculty of Medicine, Menoufia University. This study included 120 subjects divided into 2 groups Group I: Included 60 women with breast cancer undergoing modified radical mastectomy. Tissue specimens were taken from the cancerous breast tissue and from the marginal healthy breast tissues. Group II: Included 60 age and sex-matched apparently healthy women served as a control group. All patients participants were subjected to full history taking, general clinical examination, abdominal ultrasound, CT-scan for abdomen, mammography, fine needle biopsy, histopathological examination, immunostaining of tissues, metastatic work up (chest x-ray and bone scan) and laboratory investigations including: Complete blood count (patients and controls), serum carbohydrate antigen 15–3 (patients and controls), detection of EMP2 and β1-Integrin genes expression in the tissue samples by formation of cDNA by reverse transcription PCR after RNA extraction and real-time PCR using SYBR Green technique.

Results

Compared to healthy tissues, the breast cancer tissues had significant higher EMP2 and β1-Integringene expression levels. Also, there was a significant increase in CA15-3 in patients group as compared with the control group. It was found that EMP2 and β1-Integrin expression in malignant tissue samples correlates with advanced and metastatic disease.

Conclusion

The gene expression of EMP2 and β1-Integrin are important markers for the severity of breast cancer and they are good indicators of its prognosis.

The Role of Intra-Tumoral Heterogeneity and Its Clinical Relevance in Epithelial Ovarian Cancer Recurrence and Metastasis

Epithelial ovarian cancer is the deadliest gynecologic cancer, due in large part to recurrent tumors. Recurrences tend to have metastasized, mainly in the peritoneal cavity and developed resistance to the first line chemotherapy. Key to the progression and ultimate lethality of ovarian cancer is the existence of extensive intra-tumoral heterogeneity (ITH). In this review, we describe the genetic and epigenetic changes that have been reported to give rise to different cell populations in ovarian cancer. We also describe at length the contributions made to heterogeneity by both linear and parallel models of clonal evolution and the existence of cancer stem cells. We dissect the key biological signals from the tumor microenvironment, both directly from other cell types in the vicinity and soluble or circulating factors. Finally, we discuss the impact of tumor heterogeneity on the choice of therapeutic approaches in the clinic. Variability in ovarian tumors remains a major barrier to effective therapy, but by leveraging future research into tumor heterogeneity, we may be able to overcome this barrier and provide more effective, personalized therapy to patients.

Isolation and characterization of adult mammary stem cells from breast cancer-adjacent tissues

Normal adult mammary stem cells (AMSCs) are promising sources for breast reconstruction, particularly following the resection of breast tumors. However, carcinogenic events can potentially convert normal AMSCs to cancer stem cells, posing a safety concern for the use of AMSCs for clinical tissue regeneration. In the present study, AMSCs and autologous primary breast cancer cells were isolated and compared for their ability to differentiate, their gene expression profile, and their potential to form tumors in vivo. AMSCs were isolated from normal tissue surrounding primary breast tumors by immunomagnetic sorting. The pluripotency of these cells was investigated by differentiation analysis, and gene expression profiles were compared with microarrays. Differentially expressed candidate genes were confirmed by reverse transcription-polymerase chain reaction and western blot analyses. The in vivo tumorigenicity of these cells, compared with low-malignancy MCF-7 cells, was also investigated by xenograft tumor formation analysis. The results revealed that AMSCs isolated from normal tissues surrounding primary breast tumors were positive for the stem cell markers epithelial-specific antigen and keratin-19. When stimulated with basic fibroblast growth factor, a differentiation agent, these AMSCs formed lobuloalveolar structures with myoepithelia that were positive for common acute lymphoblastic leukemia antigen. The gene expression profiles revealed that, compared with cancer cells, AMSCs expressed low levels of oncogenes, including MYC, RAS and ErbB receptor tyrosine kinase 2, and high levels of tumor suppressor genes, including RB transcriptional corepressor 1, phosphatase and tensin homolog, and cyclin-dependent kinase inhibitor 2A. When injected into nude non-obese diabetic/severe combined immunodeficiency-type mice, the AMSCs did not form tumors, and regular mammary ductal structures were generated. The AMSCs isolated from normal tissue adjacent to primary breast tumors had the normal phenotype of mammary stem cells, and therefore may be promising candidates for mammary reconstruction subsequent to breast tumor resection.

Molecular mechanisms of asymmetric divisions in mammary stem cells

Stem cells have the remarkable ability to undergo proliferative symmetric divisions and self-renewing asymmetric divisions. Balancing of the two modes of division sustains tissue morphogenesis and homeostasis. Asymmetric divisions of Drosophila neuroblasts (NBs) and sensory organ precursor (SOP) cells served as prototypes to learn what we consider now principles of asymmetric mitoses. They also provide initial evidence supporting the notion that aberrant symmetric divisions of stem cells could correlate with malignancy. However, transferring the molecular knowledge of circuits underlying asymmetry from flies to mammals has proven more challenging than expected. Several experimental approaches have been used to define asymmetry in mammalian systems, based on daughter cell fate, unequal partitioning of determinants and niche contacts, or proliferative potential. In this review, we aim to provide a critical evaluation of the assays used to establish the stem cell mode of division, with a particular focus on the mammary gland system. In this context, we will discuss the genetic alterations that impinge on the modality of stem cell division and their role in breast cancer development.

Targeting metabolism to induce cell death in cancer cells and cancer stem cells

Abnormal metabolism and the evasion of apoptosis are considered hallmarks of cancers. Accumulating evidence shows that cancer stem cells are key drivers of tumor formation, progression, and recurrence. A successful therapy must therefore eliminate these cells known to be highly resistant to apoptosis. In this paper, we describe the metabolic changes as well as the mechanisms of resistance to apoptosis occurring in cancer cells and cancer stem cells, underlying the connection between these two processes.

The Hedgehog signaling pathway in ovarian teratoma is stimulated by Sonic Hedgehog which induces internalization of Patched

The Hedgehog-Gli (Hh-Gli) signaling pathway was examined in ovarian dermoids, which show characteristics of both tumors and developmental malformations. Dermoids are classified as mature teratomas that present differentiation into various tissues, mostly epidermal elements such as glands, multilayered epithelium, hair follicles and occasionally bone and cartilage. Their development is attributed to aberrant meiosis of germinal cells within the ovary. We showed activation of the Hh-Gli signaling in ovarian dermoid primary cultures. Cyclopamine treatment slows down cell proliferation, while the Sonic Hedgehog (Shh) protein stimulates cell proliferation and induces internalization of the Patched (Ptch) protein, which accumulates in the form of granules in the cytoplasm, colocalized with the Shh protein. Cyclopamine treatment decreases Gli1 localization in the nucleus compared to non-treated cells. Based on our observations, the mechanism of Hedgehog activation in the ovarian dermoids could be the ligand-dependent autocrine pathway, which can also be stimulated by paracrine signals.

Why does oestrogen-only hormone therapy have such a small impact on breast cancer risk? A hypothesis

There seems to be irrefutable evidence that oestrogen is involved in the pathogenesis of breast cancer. The disease mostly affects women and the epidemiology of breast cancer relates to reproductive markers such as pregnancy, age at menarche and age of menopause. Most breast cancers elaborate oestrogen receptors (ER) and in such cases endocrine therapies such as tamoxifen and aromatase-inhibitors (AIs) are effective adjuvant treatments. However, high-quality randomised controlled trials (RCTs) (such as the WHI study) have shown that oestrogen-only hormone therapy (ET) does not increase breast cancer risk at all. This would seem to be a remarkable paradox. There appears to be at least two reasons for this apparent contradiction. First, it has been known for two decades that the breast itself produces oestrogens locally and the microenvironment around a breast cancer is more important that the impact of systemic-oestrogens. Second, breast cancer stem cells (breast CSC) have been identified and it seems likely that these long-lived, multipotential cells are responsible for the genesis of many breast cancers, as well as their malignant behaviour. Breast CSC usually do not contain sex-hormone receptors, but their offspring often elaborate ER and progesterone receptor (PR). Thus, it appears unlikely that oestrogen per se initiates breast cancer, but rather might stimulate an existing tumour.

Breast cancer, stem cells and sex hormones: part 1. The impact of fetal life and infancy

Like other organs, the breast contains rare somatic stem cells (SCs) that are long-lived and slowly dividing. In the adult breast, they are closely regulated in areas located along the breast ducts called SC niches. Breast SCs can produce offspring that become ductal, alveoli or myoepithelial cells. In fetal life, SCs form the primitive breast ducts and up to 30 weeks of gestational age, this process appears to be largely independent of estrogen. Early life risk factors for breast cancer include birth weight, rapid growth during infancy and diet. The impact of these risk factors may be mediated through SC number. These somatic breast SCs persist into adult life and so they are exposed to oncogenic influences for much longer than the short-lived differentiated breast ductal and alveolar cells. As such, it is likely that the breast SC is a prominent target for carcinogenesis and so SC number may be an important determinant of breast cancer risk later in life.

Malignant precursor cells pre-exist in human breast DCIS and require autophagy for survival

Background

While it is accepted that a majority of invasive breast cancer progresses from a ductal carcinoma in situ (DCIS) precursor stage, very little is known about the factors that promote survival of DCIS neoplastic cells within the hypoxic, nutrient deprived intraductal microenvironment.

Methodology and Principal Findings

We examined the hypothesis that fresh human DCIS lesions contain pre-existing carcinoma precursor cells. We characterized these cells by full genome molecular cytogenetics (Illumina HumanCytoSNP profile), and signal pathway profiling (Reverse Phase Protein Microarray, 59 endpoints), and demonstrated that autophagy is required for survival and anchorage independent growth of the cytogenetically abnormal tumorigenic DCIS cells. Ex vivo organoid culture of fresh human DCIS lesions, without enzymatic treatment or sorting, induced the emergence of neoplastic epithelial cells exhibiting the following characteristics: a) spontaneous generation of hundreds of spheroids and duct-like 3-D structures in culture within 2–4 weeks; b) tumorigenicity in NOD/SCID mice; c) cytogenetically abnormal (copy number loss or gain in chromosomes including 1, 5, 6, 8, 13, 17) compared to the normal karyotype of the non-neoplastic cells in the source patient's breast tissue; d) in vitro migration and invasion of autologous breast stroma; and e) up-regulation of signal pathways linked to, and components of, cellular autophagy. Multiple autophagy markers were present in the patient's original DCIS lesion and the mouse xenograft. We tested whether autophagy was necessary for survival of cytogenetically abnormal DCIS cells. The lysosomotropic inhibitor (chloroquine phosphate) of autophagy completely suppressed the generation of DCIS spheroids/3-D structures, suppressed ex vivo invasion of autologous stroma, induced apoptosis, suppressed autophagy associated proteins including Atg5, AKT/PI3 Kinase and mTOR, eliminated cytogenetically abnormal spheroid forming cells from the organ culture, and abrogated xenograft tumor formation.

Conclusions

Cytogenetically abnormal spheroid forming, tumorigenic, and invasive neoplastic epithelial cells pre-exist in human DCIS and require cellular autophagy for survival.

Stem cells in normal mammary gland and breast cancer

The mammary gland is a structurally dynamic organ that undergoes dramatic alterations with age, menstrual cycle, and reproductive status. Mammary gland stem cells, the minor cell population within the mature organ, are thought to have multiple functions in regulating mammary gland development, tissue maintenance, major growth, and structural remodeling. In addition, accumulative evidence suggests that breast cancers are initiated and maintained by a subpopulation of tumor cells with stem cell features (called cancer stem cells). A variety of methods have been developed to identify and characterize mammary stem cells, and several signal transduction pathways have been identified to be essential for the self-renewal and differentiation of mammary gland stem cells. Understanding the origin of breast cancer stem cells, their relationship to breast cancer development, and the differences between normal and cancer stem cells may lead to novel approaches to breast cancer diagnosis, prevention, and treatment.

The NRG1 gene is frequently silenced by methylation in breast cancers and is a strong candidate for the 8p tumour suppressor gene

Neuregulin-1 (NRG1) is both a candidate oncogene and candidate tumour suppressor gene. It encodes the heregulins and other mitogenic ligands for the ERBB family, but it also causes apoptosis in NRG1-expressing cells. We found that most breast cancer cell lines had reduced or undetectable expression of NRG1. This included cell lines that had translocation breaks in the gene. Similarly, expression in cancers was generally comparable to or less than various normal breast samples. Many non-expressing cell lines had extensive methylation of the CpG island at the principal transcription start site at exon 2 of NRG1. Expression was reactivated by demethylation. Many tumours also showed methylation, while normal mammary epithelial fragments had none. Lower NRG1 expression correlated with higher methylation. siRNA-mediated depletion of NRG1 increased net proliferation, in a normal breast cell line and a breast cancer cell line that expressed NRG1. The short arm of chromosome 8 is frequently lost in epithelial cancers, and NRG1 is the most centromeric gene that is always affected. NRG1 may therefore be the major tumour suppressor gene postulated to be on 8p: it is in the correct location, is anti-proliferative, and is silenced in many breast cancers.

Cells with characteristics of cancer stem/progenitor cells express the CD133 antigen in human endometrial tumors

PURPOSE

Cancer stem cells represent an attractive therapeutic target for tumor eradication. The present study aimed to determine whether CD133 expression may identify cells with characteristics of cancer stem/progenitor cells in human endometrial tumors.

EXPERIMENTAL DESIGN

We analyzed 113 tumor samples for CD133/1 expression by flow cytometry, immunohistochemistry, and semiquantitative reverse transcription-PCR. CD133(+) cells were isolated and used to assess phenotypic characteristics, self-renewal capacity, ability to maintain CD133 expression and form sphere-like structures in long-term cultures, sensitivity to chemotherapeutic agents, gene expression profile, and ability to initiate tumors in NOD/SCID mice.

RESULTS

Primary tumor samples exhibited a variable degree of immunoreactivity for CD133/1, ranging from 1.3% to 62.6%, but stained negatively for other endothelial and stem cell-associated markers. Isolated CD133(+) cells expanded up to 4.6-fold in serum-replenished cultures and coexpressed the GalNAcalpha1-O-Ser/Thr MUC-1 glycoform, a well-characterized tumor-associated antigen. Dissociated bulk tumors formed sphere-like structures; cells grown as tumor spheres maintained CD133 expression and could be propagated for up to 12 weeks. CD133(+) cells purified from endometrioid adenocarcinomas were resistant to cisplatin-induced and paclitaxel-induced cytotoxicity and expressed a peculiar gene signature consisting of high levels of matrix metalloproteases, interleukin-8, CD44, and CXCR4. When serially transplanted into NOD/SCID mice, CD133(+) cells were capable of initiating tumor formation and recapitulating the phenotype of the original tumor.

CONCLUSIONS

CD133 is expressed by human endometrial cancers and might represent a valuable tool to identify cells with cancer stem cell characteristics.

Phenotypic and functional characterization of human mammary stem/progenitor cells in long term culture

BACKGROUND

Cancer stem cells exhibit close resemblance to normal stem cells in phenotype as well as function. Hence, studying normal stem cell behavior is important in understanding cancer pathogenesis. It has recently been shown that human breast stem cells can be enriched in suspension cultures as mammospheres. However, little is known about the behavior of these cells in long-term cultures. Since extensive self-renewal potential is the hallmark of stem cells, we undertook a detailed phenotypic and functional characterization of human mammospheres over long-term passages.

METHODOLOGY

Single cell suspensions derived from human breast 'organoids' were seeded in ultra low attachment plates in serum free media. Resulting primary mammospheres after a week (termed T1 mammospheres) were subjected to passaging every 7th day leading to the generation of T2, T3, and T4 mammospheres.

PRINCIPAL FINDINGS

We show that primary mammospheres contain a distinct side-population (SP) that displays a CD24(low)/CD44(low) phenotype, but fails to generate mammospheres. Instead, the mammosphere-initiating potential rests within the CD44(high)/CD24(low) cells, in keeping with the phenotype of breast cancer-initiating cells. In serial sphere formation assays we find that even though primary (T1) mammospheres show telomerase activity and fourth passage T4 spheres contain label-retaining cells, they fail to initiate new mammospheres beyond T5. With increasing passages, mammospheres showed an increase in smaller sized spheres, reduction in proliferation potential and sphere forming efficiency, and increased differentiation towards the myoepithelial lineage. Significantly, staining for senescence-associated beta-galactosidase activity revealed a dramatic increase in the number of senescent cells with passage, which might in part explain the inability to continuously generate mammospheres in culture.

CONCLUSIONS

Thus, the self-renewal potential of human breast stem cells is exhausted within five in vitro passages of mammospheres, suggesting the need for further improvisation in culture conditions for their long-term maintenance.

Differential expression of estrogen receptor alpha (ERalpha) protein in MCF-7 breast cancer cells chronically exposed to TCDD

Estrogens play a key role in the development and evolution of breast cancer tumors. Estrogen receptor alpha (ERalpha) mediates many of the biological activities of estrogens, and its expression is associated with low invasiveness and good prognosis. Recent epidemiological reports suggest that long-term exposure to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) is implicated in the increased incidence of breast cancer in exposed women. TCDD interferes with the expression of some ERalpha-dependent genes and inhibits estradiol (E2)- dependent growth of breast cancer cells in vitro. However, E2-dependent xenographs of MCF-7 human breast cancer cells resumed growth after a 2-week exposure to TCDD. The mechanisms involved in the resumption of cell growth are not completely understood. In this study, we show that short term-exposure (16 days) to 1 nM TCDD results in the suppression of ERalpha protein expression, while chronic exposure for more than 1 year (LTDX cells) results in the partial re-expression of the receptor. Immunocytochemistry studies showed that re-expression of ERalpha in LTDX cells occurred in some of the cells. Analysis by Western immunoblots indicated that four out of five LTDX clones expressed ERalpha at levels comparable to those in unexposed MCF-7 cells. Removal of TCDD treatment for 16 days restored the expression of ERalpha in the ERalpha-negative clonal cells. These results suggest that MCF-7 cells chronically exposed to TCDD contain at least two cell subpopulations that may respond differently to the ERalpha-mediated effects of TCDD.

"Stem cell like" breast cancers-a model for the identification of new prognostic/predictive markers in endocrine responsive breast cancer exemplified by Plexin B1

The identification of new biological markers for breast cancer has adopted a new dimension by the use of novel techniques such as global gene expression profiling. While important results have been achieved by these methods not all hopes for a more precise assessment of patients' prognosis have yet been accomplished and validation of prognostic or predictive gene signatures is still often difficult. Several recent approaches suggest that comparisons of differential gene expression could be more instructive if prior classifications of tumors based on molecular or biological characteristics were applied. We previously reported a subtype of breast cancer by using a cluster of coordinately expressed genes many of which has been associated with the mammary epithelial stem cells. While a stringent inverse link of ER status and proliferation of the tumor was observed among those "stem cell like" (SCL) tumors, this link was "uncoupled" in about half of the Non-"stem cell like" (Non-SCL) tumors. This subgroup of SCL tumors can be used as a reference system to analyze changes in the ER pathway by comparing the expression of genes dependent on the ER status. By using this strategy we identified Plexin B1, a cell-surface receptor for the semaphorin Sema4D, whose expression is reduced in the group of "uncoupled" tumors. Loss of Plexin B1 is associated with a poor prognosis in both univariate (all patients: p=0.0062; ER positive: p=0.0107) and multivariate analyses (all patients: p=0.032; ER positive: p=0.022). In conclusion those strategies of gene expression analysis in a context of biological meaningful classifications could be helpful to reveal new prognostic/predictive markers.

Wnt/beta-catenin signaling in murine hepatic transit amplifying progenitor cells

BACKGROUND & AIMS

Oval cells are postnatal hepatic progenitors with high proliferative potential and bipotent differentiation ability to become hepatocytes and cholangiocytes. Because Wnt/beta-catenin signaling is a known regulatory pathway for liver development and regeneration, we studied the role of Wnt signaling in oval cells using a mouse model of chronic liver injury.

METHODS

A 3,5-diethoxycarbonyl-1,4-dihydrocollidine (DDC)-enriched diet was used to stimulate oval cell proliferation. Livers were harvested for histologic analysis and determination of Wnt family gene expression by quantitative reverse transcription-polymerase chain reaction and in situ hybridization. The transgenic beta-catenin reporter mouse (TOPGAL) was use to confirm canonical Wnt/beta-catenin signal transduction in proliferating oval cells within atypical ductal proliferations (ADPs). Confocal fluorescence microscopy and immunohistochemistry was used to confirm colocalization of beta-catenin with the oval cell antigen A-6.

RESULTS

Several Wnt ligands were significantly induced in the liver of DDC-fed mice and localized to proliferating cells in and adjacent to the ADPs. Oval cells isolated from DDC-fed mouse livers showed the presence of active beta-catenin in the nucleus along with cell-cycle entry in response to purified Wnt3a in vitro. Moreover, Wnt3a-induced beta-catenin/T-cell factor/lymphoid enhancer factor (TCF/LEF) transcriptional activation was quantified by TCF/LEF luciferase reporter assays.

CONCLUSIONS

From these data, we conclude that oval cells respond to Wnt ligands (Wnt3a) in vitro with an increase in amino-terminus dephosphorylated beta-catenin and cell-cycle entry and that canonical Wnt/beta-catenin/TCF signaling is active in proliferating facultative hepatic progenitor cells in vivo. These findings may lend insight to the consequences of increased canonical Wnt signaling during periods of chronic liver injury.

ERbeta scientific visions translate to clinical uses

Estrogen receptor beta (ERbeta) was discovered in 1995 and reported on in 1996. During the 10 years following this event, our understanding of estrogen signaling has changed remarkably. We now know that estradiol, the major endogenous activator of ER, is non-selective for the two receptors, and that ERalpha and ERbeta are, in many contexts, antagonistic against one another, an example of a yin/yang relationship, perhaps nature's way to accomplish subtle regulatory changes of estrogen signaling as a response to ever-shifting physiological requirements. Needless to say, this knowledge is of paramount significance pharmaceutically, and several ERbeta-selective agonists, intended for use against a multitude of diseases, have already been synthesized and patented by drug companies. Clearly, the next 5-10 years will be extremely exciting in view of results from clinical trials testing the clinical utility of ERbeta targeted drugs.

Origins of breast cancer subtypes and therapeutic implications

This Review summarizes and evaluates the current evidence for the cellular origins of breast cancer subtypes identified by different approaches such as histology, molecular pathology, genetic and gene-expression analysis. Emerging knowledge of the normal breast cell types has led to the hypothesis that the subtypes of breast cancer might arise from mutations or genetic rearrangements occurring in different populations of stem cells and progenitor cells. We describe the common distinguishing features of these breast cancer subtypes and explain how these features relate both to prognosis and to selection of the most appropriate therapy. Recent data indicate that breast tumors may originate from cancer stem cells. Consequently, inhibition of stem-cell self-renewal pathways should be explored because of the likelihood that residual stem cells might be resistant to current therapies.

The hedgehog signaling network, mammary stem cells, and breast cancer: connections and controversies

Several signal transduction networks have been implicated in the regulation of mammary epithelial stem cell self-renewal and maintenance (Kalirai and Clarke 2006; Liu et al. 2005). These signaling networks include those of the Wnt, Notch, TGFO, EGF, FGF, IGF, and most recently, the Hedgehog (Hh) families of secreted ligands. However, we currently know very little about the cellular and molecular mechanisms by which these signaling pathways function to regulate normal epithelial stem/progenitor cells. What is clear is that the regulatory signaling networks thought to control normal stem/progenitor cell self-renewal and maintenance are, with the current sole exception of the hedgehog network, well-documented to have contributory roles in mammary cancer development and disease progression when misregulated. In this review, genetic regulation of mammary gland development by hedgehog network genes is outlined, highlighting a developing controversy as to whether activated hedgehog signaling regulates normal regenerative mammary epithelial stem cells or, indeed, whether activated hedgehog signaling functions at all in ductal development. In addition, the question of whether inappropriate hedgehog network activation influences breast cancer development is addressed, with emphasis on the prospects for using hedgehog signaling antagonists clinically for breast cancer treatment or prevention.

Identification of novel stem cell markers using gap analysis of gene expression data

We describe a method for detecting marker genes in large heterogeneous collections of gene expression data. Markers are identified and characterized by the existence of demarcations in their expression values across the whole dataset, which suggest the presence of groupings of samples. We apply this method to DNA microarray data generated from 83 mouse stem cell related samples and describe 426 selected markers associated with differentiation to establish principles of stem cell evolution.