101
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Zhao X, Ruan Y, Wei CL. Tackling the epigenome in the pluripotent stem cells. J Genet Genomics 2009; 35:403-12. [PMID: 18640620 DOI: 10.1016/s1673-8527(08)60058-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2008] [Revised: 05/23/2008] [Accepted: 05/24/2008] [Indexed: 11/26/2022]
Abstract
Embryonic stem cells are unique in their abilities of self-renewal and to differentiate into many, if not all, cellular lineages. Transcriptional regulation, epigenetic modifications and chromatin structures are the key modulators in controlling such pluripotency nature of embryonic stem cell genomes, particularly in the developmental decisions and the maintenance of cell fates. Among them, epigenetic regulation of gene expression is mediated partly by covalent modifications of core histone proteins including methylation, phosphorylation and acetylation. Moreover, the chromatins in stem cell genome appear as a highly organized structure containing distinct functional domains. Recent rapid progress of new technologies enables us to take a global, unbiased and comprehensive view of the epigenetic modifications and chromatin structures that contribute to gene expression regulation and cell identity during diverse developmental stages. Here, we summarized the latest advances made by high throughput approaches in profiling epigenetic modifications and chromatin conformations, with an emphasis on genome-wide analysis of histone modifications and their implications in pluripotency nature of embryonic stem cells.
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Affiliation(s)
- Xiaodong Zhao
- Genome Technology and Biology Group, Genome Institute of Singapore, 138672, Singapore
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102
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Sepulveda DE, Andrews BA, Asenjo JA, Papoutsakis ET. Comparative transcriptional analysis of embryoid body versus two-dimensional differentiation of murine embryonic stem cells. Tissue Eng Part A 2009; 14:1603-14. [PMID: 18433312 DOI: 10.1089/ten.tea.2007.0331] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Understanding the process of ex vivo embryonic stem (ES) cell differentiation is important for generating higher yields of desirable cell types or lineages and for understanding fundamental aspects of ES differentiation. We used DNA microarray analysis to investigate the differentiation of mouse ES cells cultured under three differentiation conditions. Embryoid body (EB) formation was compared to differentiation on surfaces coated with either gelatin (GEL) or matrigel (MAT). Based on the transcriptional patterns of a list of literature-based "stemness" genes, ES cell differentiation on the two coated surfaces appeared similar but not identical to EB differentiation. A notable difference was the GEL and MAT upregulation but EB downregulation of nine such stemness genes, which are related to cell adhesion and epithelial differentiation. Further, GEL and MAT differentiation showed higher expression of bone formation-related genes (Spp1, Csf1, Gsn, Bmp8b, Crlf1). Gene ontology analysis shows an increase in the expression of genes related to migration and cell structure in all three conditions. Overall, GEL and MAT conditions resulted in a more similar to each other transcriptional profile than to the EB condition, and such differences are apparently related to higher nutrient and metabolite gradients and limitations in the EB versus the GEL or MAT cultures.
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Affiliation(s)
- Dario E Sepulveda
- Department of Chemical Engineering and Biotechnology, Centre for Biochemical Engineering and Biotechnology, Institute for Cell Dynamics and Biotechnology (ICDB), University of Chile, Santiago, Chile
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103
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Mansergh FC, Daly CS, Hurley AL, Wride MA, Hunter SM, Evans MJ. Gene expression profiles during early differentiation of mouse embryonic stem cells. BMC DEVELOPMENTAL BIOLOGY 2009; 9:5. [PMID: 19134196 PMCID: PMC2656490 DOI: 10.1186/1471-213x-9-5] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2008] [Accepted: 01/09/2009] [Indexed: 11/18/2022]
Abstract
Background Understanding the mechanisms controlling stem cell differentiation is the key to future advances in tissue and organ regeneration. Embryonic stem (ES) cell differentiation can be triggered by embryoid body (EB) formation, which involves ES cell aggregation in suspension. EB growth in the absence of leukaemia inhibitory factor (LIF) leads EBs to mimic early embryonic development, giving rise to markers representative of endoderm, mesoderm and ectoderm. Here, we have used microarrays to investigate differences in gene expression between 3 undifferentiated ES cell lines, and also between undifferentiated ES cells and Day 1–4 EBs Results An initial array study identified 4 gene expression changes between 3 undifferentiated ES cell lines. Tissue culture conditions for ES differentiation were then optimized to give the maximum range of gene expression and growth. -Undifferentiated ES cells and EBs cultured with and without LIF at each day for 4 days were subjected to microarray analysis. -Differential expression of 23 genes was identified. 13 of these were also differentially regulated in a separate array comparison between undifferentiated ES cells and compartments of very early embryos. A high degree of inter-replicate variability was noted when confirming array results. Using a panel of marker genes, RNA amplification and RT-PCR, we examined expression pattern variation between individual -D4-Lif EBs. We found that individual EBs selected from the same dish were highly variable in gene expression profile. Conclusion ES cell lines derived from different mouse strains and carrying different genetic modifications are almost invariant in gene expression profile under conditions used to maintain pluripotency. Tissue culture conditions that give the widest range of gene expression and maximise EB growth involve the use of 20% serum and starting cell numbers of 1000 per EB. 23 genes of importance to early development have been identified; more than half of these are also identified using similar studies, thus validating our results. EBs cultured in the same dish vary widely in terms of their gene expression (and hence, undoubtedly, in their future differentiation potential). This may explain some of the inherent variability in differentiation protocols that use EBs.
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104
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Oback B. Cloning from stem cells: different lineages, different species, same story. Reprod Fertil Dev 2009; 21:83-94. [DOI: 10.1071/rd08212] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Following nuclear transfer (NT), the most stringent measure of extensive donor cell reprogramming is development into viable offspring. This is referred to as cloning efficiency and quantified as the proportion of cloned embryos transferred into surrogate mothers that survive into adulthood. Cloning efficiency depends on the ability of the enucleated recipient cell to carry out the reprogramming reactions (‘reprogramming ability’) and the ability of the nuclear donor cell to be reprogrammed (‘reprogrammability’). It has been postulated that reprogrammability of the somatic donor cell epigenome is inversely proportional to its differentiation status. In order to test this hypothesis, reprogrammability was compared between undifferentiated stem cells and their differentiated isogenic progeny. In the mouse, cells of divergent differentiation status from the neuronal, haematopoietic and skin epithelial lineage were tested. In cattle and deer, skeletal muscle and antler cells, respectively, were used as donors. No conclusive correlation between differentiation status and cloning efficiency was found, indicating that somatic donor cell type may not be the limiting factor for cloning success. This may reflect technical limitations of the NT-induced reprogramming assay. Alternatively, differentiation status and reprogrammability may be unrelated, making all cells equally difficult to reprogramme once they have left the ground state of pluripotency.
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105
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Chambery A, Colucci-D’Amato L, Vissers JPC, Scarpella S, Langridge JI, Parente A. Proteomic Profiling of Proliferating and Differentiated Neural mes-c-myc A1 Cell Line from Mouse Embryonic Mesencephalon by LC−MS. J Proteome Res 2008; 8:227-38. [DOI: 10.1021/pr800454n] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Angela Chambery
- Dipartimento di Scienze della Vita, Seconda Università di Napoli, I-81100 Caserta, Italy, Istituto di Genetica e Biofisica “A. Buzzati-Traverso”, Consiglio Nazionale delle Ricerche, 80131-Napoli, Italy, and Waters Corporation, MS Technologies Center, M22 5PP Manchester, United Kingdom
| | - Luca Colucci-D’Amato
- Dipartimento di Scienze della Vita, Seconda Università di Napoli, I-81100 Caserta, Italy, Istituto di Genetica e Biofisica “A. Buzzati-Traverso”, Consiglio Nazionale delle Ricerche, 80131-Napoli, Italy, and Waters Corporation, MS Technologies Center, M22 5PP Manchester, United Kingdom
| | - Johannes P. C. Vissers
- Dipartimento di Scienze della Vita, Seconda Università di Napoli, I-81100 Caserta, Italy, Istituto di Genetica e Biofisica “A. Buzzati-Traverso”, Consiglio Nazionale delle Ricerche, 80131-Napoli, Italy, and Waters Corporation, MS Technologies Center, M22 5PP Manchester, United Kingdom
| | - Simona Scarpella
- Dipartimento di Scienze della Vita, Seconda Università di Napoli, I-81100 Caserta, Italy, Istituto di Genetica e Biofisica “A. Buzzati-Traverso”, Consiglio Nazionale delle Ricerche, 80131-Napoli, Italy, and Waters Corporation, MS Technologies Center, M22 5PP Manchester, United Kingdom
| | - James I. Langridge
- Dipartimento di Scienze della Vita, Seconda Università di Napoli, I-81100 Caserta, Italy, Istituto di Genetica e Biofisica “A. Buzzati-Traverso”, Consiglio Nazionale delle Ricerche, 80131-Napoli, Italy, and Waters Corporation, MS Technologies Center, M22 5PP Manchester, United Kingdom
| | - Augusto Parente
- Dipartimento di Scienze della Vita, Seconda Università di Napoli, I-81100 Caserta, Italy, Istituto di Genetica e Biofisica “A. Buzzati-Traverso”, Consiglio Nazionale delle Ricerche, 80131-Napoli, Italy, and Waters Corporation, MS Technologies Center, M22 5PP Manchester, United Kingdom
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106
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Tzelepi V, Grivas P, Kefalopoulou Z, Kalofonos H, Varakis JN, Sotiropoulou-Bonikou G. Expression of estrogen receptor co-regulators NCoR and PELP1 in epithelial cells and myofibroblasts of colorectal carcinomas: cytoplasmic translocation of NCoR in epithelial cells correlates with worse prognosis. Virchows Arch 2008; 454:41-53. [DOI: 10.1007/s00428-008-0708-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2008] [Revised: 11/16/2008] [Accepted: 11/18/2008] [Indexed: 02/03/2023]
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107
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Distaso A, Abatangelo L, Maglietta R, Creanza TM, Piepoli A, Carella M, D'Addabbo A, Ancona N. Biological and functional analysis of statistically significant pathways deregulated in colon cancer by using gene expression profiles. Int J Biol Sci 2008; 4:368-78. [PMID: 18953405 PMCID: PMC2567814 DOI: 10.7150/ijbs.4.368] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2008] [Accepted: 10/07/2008] [Indexed: 01/07/2023] Open
Abstract
Gene expression profiling offers a great opportunity for studying multi-factor diseases and for understanding the key role of genes in mechanisms which drive a normal cell to a cancer state. Single gene analysis is insufficient to describe the complex perturbations responsible for cancer onset, progression and invasion. A deeper understanding of the mechanisms of tumorigenesis can be reached focusing on deregulation of gene sets or pathways rather than on individual genes. We apply two known and statistically well founded methods for finding pathways and biological processes deregulated in pathological conditions by analyzing gene expression profiles. In particular, we measure the amount of deregulation and assess the statistical significance of predefined pathways belonging to a curated collection (Molecular Signature Database) in a colon cancer data set. We find that pathways strongly involved in different tumors are strictly connected with colon cancer. Moreover, our experimental results show that the study of complex diseases through pathway analysis is able to highlight genes weakly connected to the phenotype which may be difficult to detect by using classical univariate statistics. Our study shows the importance of using gene sets rather than single genes for understanding the main biological processes and pathways involved in colorectal cancer. Our analysis evidences that many of the genes involved in these pathways are strongly associated to colorectal tumorigenesis. In this new perspective, the focus shifts from finding differentially expressed genes to identifying biological processes, cellular functions and pathways perturbed in the phenotypic conditions by analyzing genes co-expressed in a given pathway as a whole, taking into account the possible interactions among them and, more importantly, the correlation of their expression with the phenotypical conditions.
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Affiliation(s)
- Angela Distaso
- Istituto di Studi sui Sistemi Intelligenti per l'Automazione, CNR, Via Amendola 122/D-I, 70126 Bari, Italy
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108
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Lim CY, Tam WL, Zhang J, Ang HS, Jia H, Lipovich L, Ng HH, Wei CL, Sung WK, Robson P, Yang H, Lim B. Sall4 regulates distinct transcription circuitries in different blastocyst-derived stem cell lineages. Cell Stem Cell 2008; 3:543-54. [PMID: 18804426 DOI: 10.1016/j.stem.2008.08.004] [Citation(s) in RCA: 178] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2008] [Revised: 07/13/2008] [Accepted: 08/15/2008] [Indexed: 12/21/2022]
Abstract
Stem cells self-renew or differentiate under the governance of a stem-cell-specific transcriptional program, with each transcription factor orchestrating the activities of a particular set of genes. Here we demonstrate that a single transcription factor is able to regulate distinct core circuitries in two different blastocyst-derived stem cell lines, embryonic stem cells (ESCs) and extraembryonic endoderm (XEN) cells. The transcription factor Sall4 is required for early embryonic development and for ESC pluripotency. Sall4 is also expressed in XEN cells, and depletion of Sall4 disrupts self-renewal and induces differentiation. Genome-wide analysis reveals that Sall4 is regulating different gene sets in ESCs and XEN cells, and depletion of Sall4 targets in the respective cell types induces differentiation. With Oct4, Sox2, and Nanog, Sall4 forms a crucial interconnected autoregulatory network in ESCs. In XEN cells, Sall4 regulates the key XEN lineage-associated genes Gata4, Gata6, Sox7, and Sox17. Our findings demonstrate how Sall4 functions as an essential stemness factor for two different stem cell lines.
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Affiliation(s)
- Chin Yan Lim
- Stem Cell and Developmental Biology, Genome Institute of Singapore, 138672 Singapore
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109
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Shen Q, Wang Y, Kokovay E, Lin G, Chuang SM, Goderie SK, Roysam B, Temple S. Adult SVZ stem cells lie in a vascular niche: a quantitative analysis of niche cell-cell interactions. Cell Stem Cell 2008; 3:289-300. [PMID: 18786416 PMCID: PMC2747473 DOI: 10.1016/j.stem.2008.07.026] [Citation(s) in RCA: 798] [Impact Index Per Article: 46.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2007] [Revised: 05/02/2008] [Accepted: 07/29/2008] [Indexed: 11/26/2022]
Abstract
There is an emerging understanding of the importance of the vascular system within stem cell niches. Here, we examine whether neural stem cells (NSCs) in the adult subventricular zone (SVZ) lie close to blood vessels, using three-dimensional whole mounts, confocal microscopy, and automated computer-based image quantification. We found that the SVZ contains a rich plexus of blood vessels that snake along and within neuroblast chains. Cells expressing stem cell markers, including GFAP, and proliferation markers are closely apposed to the laminin-containing extracellular matrix (ECM) surrounding vascular endothelial cells. Apical GFAP+ cells are admixed within the ependymal layer and some span between the ventricle and blood vessels, occupying a specialized microenvironment. Adult SVZ progenitor cells express the laminin receptor alpha6beta1 integrin, and blocking this inhibits their adhesion to endothelial cells, altering their position and proliferation in vivo, indicating that it plays a functional role in binding SVZ stem cells within the vascular niche.
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Affiliation(s)
- Qin Shen
- New York Neural Stem Cell Institute, Rensselaer, NY 12144, USA
- Center for Neuropharmacology and Neuroscience, Albany Medical College, Albany, NY 12208, USA
| | - Yue Wang
- New York Neural Stem Cell Institute, Rensselaer, NY 12144, USA
| | - Erzsebet Kokovay
- New York Neural Stem Cell Institute, Rensselaer, NY 12144, USA
- Center for Neuropharmacology and Neuroscience, Albany Medical College, Albany, NY 12208, USA
| | - Gang Lin
- Rensselaer Polytechnic Institute, Rensselaer, NY 12180, USA
| | - Shu-Mien Chuang
- Graduate Institute of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | | | | | - Sally Temple
- New York Neural Stem Cell Institute, Rensselaer, NY 12144, USA
- Center for Neuropharmacology and Neuroscience, Albany Medical College, Albany, NY 12208, USA
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110
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Halley JD, Winkler DA, Burden FR. Toward a Rosetta stone for the stem cell genome: Stochastic gene expression, network architecture, and external influences. Stem Cell Res 2008; 1:157-68. [DOI: 10.1016/j.scr.2008.03.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/16/2008] [Revised: 03/17/2008] [Accepted: 03/21/2008] [Indexed: 02/05/2023] Open
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111
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Sohal D, Yeatts A, Ye K, Pellagatti A, Zhou L, Pahanish P, Mo Y, Bhagat T, Mariadason J, Boultwood J, Melnick A, Greally J, Verma A. Meta-analysis of microarray studies reveals a novel hematopoietic progenitor cell signature and demonstrates feasibility of inter-platform data integration. PLoS One 2008; 3:e2965. [PMID: 18698424 PMCID: PMC2495035 DOI: 10.1371/journal.pone.0002965] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2007] [Accepted: 07/18/2008] [Indexed: 01/27/2023] Open
Abstract
Microarray-based studies of global gene expression (GE) have resulted in a large amount of data that can be mined for further insights into disease and physiology. Meta-analysis of these data is hampered by technical limitations due to many different platforms, gene annotations and probes used in different studies. We tested the feasibility of conducting a meta-analysis of GE studies to determine a transcriptional signature of hematopoietic progenitor and stem cells. Data from studies that used normal bone marrow-derived hematopoietic progenitors was integrated using both RefSeq and UniGene identifiers. We observed that in spite of variability introduced by experimental conditions and different microarray platforms, our meta-analytical approach can distinguish biologically distinct normal tissues by clustering them based on their cell of origin. When studied in terms of disease states, GE studies of leukemias and myelodysplasia progenitors tend to cluster with normal progenitors and remain distinct from other normal tissues, further validating the discriminatory power of this meta-analysis. Furthermore, analysis of 57 normal hematopoietic stem and progenitor cell GE samples was used to determine a gene expression signature characteristic of these cells. Genes that were most uniformly expressed in progenitors and at the same time differentially expressed when compared to other normal tissues were found to be involved in important biological processes such as cell cycle regulation and hematopoiesis. Validation studies using a different microarray platform demonstrated the enrichment of several genes such as SMARCE, Septin 6 and others not previously implicated in hematopoiesis. Most interestingly, alpha-integrin, the only common stemness gene discovered in a recent comparative murine analysis (Science 302(5644):393) was also enriched in our dataset, demonstrating the usefulness of this analytical approach.
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Affiliation(s)
- Davendra Sohal
- Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Andrew Yeatts
- Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Kenny Ye
- Albert Einstein College of Medicine, Bronx, New York, United States of America
| | | | - Li Zhou
- Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Perry Pahanish
- Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Yongkai Mo
- Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Tushar Bhagat
- Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - John Mariadason
- Albert Einstein College of Medicine, Bronx, New York, United States of America
| | | | - Ari Melnick
- Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - John Greally
- Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Amit Verma
- Albert Einstein College of Medicine, Bronx, New York, United States of America
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112
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Shi L, Jones WD, Jensen RV, Harris SC, Perkins RG, Goodsaid FM, Guo L, Croner LJ, Boysen C, Fang H, Qian F, Amur S, Bao W, Barbacioru CC, Bertholet V, Cao XM, Chu TM, Collins PJ, Fan XH, Frueh FW, Fuscoe JC, Guo X, Han J, Herman D, Hong H, Kawasaki ES, Li QZ, Luo Y, Ma Y, Mei N, Peterson RL, Puri RK, Shippy R, Su Z, Sun YA, Sun H, Thorn B, Turpaz Y, Wang C, Wang SJ, Warrington JA, Willey JC, Wu J, Xie Q, Zhang L, Zhang L, Zhong S, Wolfinger RD, Tong W. The balance of reproducibility, sensitivity, and specificity of lists of differentially expressed genes in microarray studies. BMC Bioinformatics 2008; 9 Suppl 9:S10. [PMID: 18793455 PMCID: PMC2537561 DOI: 10.1186/1471-2105-9-s9-s10] [Citation(s) in RCA: 185] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Reproducibility is a fundamental requirement in scientific experiments. Some recent publications have claimed that microarrays are unreliable because lists of differentially expressed genes (DEGs) are not reproducible in similar experiments. Meanwhile, new statistical methods for identifying DEGs continue to appear in the scientific literature. The resultant variety of existing and emerging methods exacerbates confusion and continuing debate in the microarray community on the appropriate choice of methods for identifying reliable DEG lists. RESULTS Using the data sets generated by the MicroArray Quality Control (MAQC) project, we investigated the impact on the reproducibility of DEG lists of a few widely used gene selection procedures. We present comprehensive results from inter-site comparisons using the same microarray platform, cross-platform comparisons using multiple microarray platforms, and comparisons between microarray results and those from TaqMan - the widely regarded "standard" gene expression platform. Our results demonstrate that (1) previously reported discordance between DEG lists could simply result from ranking and selecting DEGs solely by statistical significance (P) derived from widely used simple t-tests; (2) when fold change (FC) is used as the ranking criterion with a non-stringent P-value cutoff filtering, the DEG lists become much more reproducible, especially when fewer genes are selected as differentially expressed, as is the case in most microarray studies; and (3) the instability of short DEG lists solely based on P-value ranking is an expected mathematical consequence of the high variability of the t-values; the more stringent the P-value threshold, the less reproducible the DEG list is. These observations are also consistent with results from extensive simulation calculations. CONCLUSION We recommend the use of FC-ranking plus a non-stringent P cutoff as a straightforward and baseline practice in order to generate more reproducible DEG lists. Specifically, the P-value cutoff should not be stringent (too small) and FC should be as large as possible. Our results provide practical guidance to choose the appropriate FC and P-value cutoffs when selecting a given number of DEGs. The FC criterion enhances reproducibility, whereas the P criterion balances sensitivity and specificity.
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Affiliation(s)
- Leming Shi
- National Center for Toxicological Research, US Food and Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, USA
| | - Wendell D Jones
- Expression Analysis Inc., 2605 Meridian Parkway, Durham, NC 27713, USA
| | - Roderick V Jensen
- University of Massachusetts Boston, Department of Physics, 100 Morrissey Boulevard, Boston, MA 02125, USA
| | - Stephen C Harris
- National Center for Toxicological Research, US Food and Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, USA
| | - Roger G Perkins
- Z-Tech Corporation, an ICF International Company at NCTR/FDA, 3900 NCTR Road, Jefferson, AR 72079, USA
| | - Federico M Goodsaid
- Center for Drug Evaluation and Research, US Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20993, USA
| | - Lei Guo
- National Center for Toxicological Research, US Food and Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, USA
| | - Lisa J Croner
- Biogen Idec Inc., 5200 Research Place, San Diego, CA 92122, USA
| | - Cecilie Boysen
- ViaLogy Inc., 2400 Lincoln Avenue, Altadena, CA 91001, USA
| | - Hong Fang
- Z-Tech Corporation, an ICF International Company at NCTR/FDA, 3900 NCTR Road, Jefferson, AR 72079, USA
| | - Feng Qian
- Z-Tech Corporation, an ICF International Company at NCTR/FDA, 3900 NCTR Road, Jefferson, AR 72079, USA
| | - Shashi Amur
- Center for Drug Evaluation and Research, US Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20993, USA
| | - Wenjun Bao
- SAS Institute Inc., SAS Campus Drive, Cary, NC 27513, USA
| | | | - Vincent Bertholet
- Eppendorf Array Technologies, rue du Séminaire 20a, 5000 Namur, Belgium
| | - Xiaoxi Megan Cao
- Z-Tech Corporation, an ICF International Company at NCTR/FDA, 3900 NCTR Road, Jefferson, AR 72079, USA
| | - Tzu-Ming Chu
- SAS Institute Inc., SAS Campus Drive, Cary, NC 27513, USA
| | - Patrick J Collins
- Agilent Technologies Inc., 5301 Stevens Creek Boulevard, Santa Clara, CA 95051, USA
| | - Xiao-hui Fan
- National Center for Toxicological Research, US Food and Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, USA
- Pharmaceutical Informatics Institute, Zhejiang University, Hangzhou 310027, China
| | - Felix W Frueh
- Center for Drug Evaluation and Research, US Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20993, USA
| | - James C Fuscoe
- National Center for Toxicological Research, US Food and Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, USA
| | - Xu Guo
- Affymetrix Inc., 3420 Central Expressway, Santa Clara, CA 95051, USA
| | - Jing Han
- Center for Biologics Evaluation and Research, US Food and Drug Administration, 8800 Rockville Pike, Bethesda, MD 20892, USA
| | - Damir Herman
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Huixiao Hong
- Z-Tech Corporation, an ICF International Company at NCTR/FDA, 3900 NCTR Road, Jefferson, AR 72079, USA
| | - Ernest S Kawasaki
- National Cancer Institute Advanced Technology Center, 8717 Grovemont Circle, Gaithersburg, MD 20877, USA
| | - Quan-Zhen Li
- University of Texas Southwestern Medical Center, 6000 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Yuling Luo
- Panomics Inc., 6519 Dumbarton Circle, Fremont, CA 94555, USA
| | - Yunqing Ma
- Panomics Inc., 6519 Dumbarton Circle, Fremont, CA 94555, USA
| | - Nan Mei
- National Center for Toxicological Research, US Food and Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, USA
| | - Ron L Peterson
- Novartis Institutes for Biomedical Research, 250 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Raj K Puri
- Center for Biologics Evaluation and Research, US Food and Drug Administration, 8800 Rockville Pike, Bethesda, MD 20892, USA
| | - Richard Shippy
- GE Healthcare, 7700 S River Parkway, Tempe, AZ 85284, USA
| | - Zhenqiang Su
- National Center for Toxicological Research, US Food and Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, USA
| | | | - Hongmei Sun
- Z-Tech Corporation, an ICF International Company at NCTR/FDA, 3900 NCTR Road, Jefferson, AR 72079, USA
| | - Brett Thorn
- Z-Tech Corporation, an ICF International Company at NCTR/FDA, 3900 NCTR Road, Jefferson, AR 72079, USA
| | - Yaron Turpaz
- Pharmaceutical Informatics Institute, Zhejiang University, Hangzhou 310027, China
| | - Charles Wang
- UCLA David Geffen School of Medicine, Transcriptional Genomics Core, Cedars-Sinai Medical Center, 8700 Beverly Boulevard, Los Angeles, CA 90048, USA
| | - Sue Jane Wang
- Center for Drug Evaluation and Research, US Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20993, USA
| | | | - James C Willey
- Ohio Medical University, 3000 Arlington Avenue, Toledo, OH 43614, USA
| | - Jie Wu
- Z-Tech Corporation, an ICF International Company at NCTR/FDA, 3900 NCTR Road, Jefferson, AR 72079, USA
| | - Qian Xie
- Z-Tech Corporation, an ICF International Company at NCTR/FDA, 3900 NCTR Road, Jefferson, AR 72079, USA
| | - Liang Zhang
- CapitalBio Corporation, 18 Life Science Parkway, Changping District, Beijing 102206, China
| | - Lu Zhang
- Solexa Inc., 25861 Industrial Boulevard, Hayward, CA 94545, USA
| | - Sheng Zhong
- University of Illinois at Urbana-Champaign, Department of Bioengineering, 1304 W. Springfield Avenue, Urbana, IL 61801, USA
| | | | - Weida Tong
- National Center for Toxicological Research, US Food and Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, USA
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113
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Abstract
Embryonic stem (ES) cells are pluripotent and capable of self-renewal, thus holding promise for regenerative medicine. Recent studies have begun to provide insights into the molecular mechanisms underlying pluripotency and self-renewal. In this article, we discuss the roles of transcriptional regulation, epigenetic regulation and miRNAs in the maintenance of pluripotency and the differentiation of ES cells.
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Affiliation(s)
- Lingyi Chen
- Division of Pediatric Hematology/Oncology, Children's Hospital Boston, Dana Farber Cancer Institute, Boston, MA 02115, USA
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114
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Abstract
Androgen refractory prostate cancer metastasis is a major clinical challenge. Mechanism-based approaches to treating prostate cancer metastasis require an understanding of the developmental origin of the metastasis-initiating cell. Properties of prostate cancer metastases such as plasticity with respect to differentiated phenotype and androgen independence are consistent with the transformation of a prostate epithelial progenitor or stem cell leading to metastasis. This review focuses upon current evidence and concepts addressing the identification and properties of normal prostate stem or progenitor cells and their transformed counterparts.
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115
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Doherty JM, Geske MJ, Stappenbeck TS, Mills JC. Diverse adult stem cells share specific higher-order patterns of gene expression. Stem Cells 2008; 26:2124-30. [PMID: 18511597 PMCID: PMC2610416 DOI: 10.1634/stemcells.2008-0380] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Adult tissue stem cells (SCs) share functional properties regardless of their tissue of residence. It had been thought that SCs might also share expression of certain "stemness" genes, although early investigations for such genes were unsuccessful. Here, we show that SCs from diverse tissues do preferentially express certain types of genes and that SCs resemble other SCs in terms of global gene expression more than they resemble the differentiated cells (DCs) of the tissues that they supply. Genes associated with nuclear function and RNA binding were over-represented in SCs. In contrast, DCs from diverse tissues shared enrichment in genes associated with extracellular space, signal transduction, and the plasma membrane. Further analysis showed that transit-amplifying cells could be distinguished from both SCs and DCs by heightened expression of cell division and DNA repair genes and decreased expression of apoptosis-related genes. This transit-amplifying cell-specific signature was confirmed by de novo generation of a global expression profile of a cell population highly enriched for transit-amplifying cells: colonic crypt-base columnar cells responding to mucosal injury. Thus, progenitor cells preferentially express intracellular or biosynthetic genes, and differentiation correlates with increased expression of genes for interacting with other cells or the microenvironment. The higher-order, Gene Ontology term-based analysis we use to distinguish SC- and DC-associated gene expression patterns can also be used to identify intermediate differentiation states (e.g., that of transit-amplifying cells) and, potentially, any biological state that is reflected in changes in global gene expression patterns. Disclosure of potential conflicts of interest is found at the end of this article.
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Affiliation(s)
- Jason M. Doherty
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110
| | - Michael J. Geske
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110
| | - Thaddeus S. Stappenbeck
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110
| | - Jason C. Mills
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110
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116
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Trajkovski I, Lavrač N, Tolar J. SEGS: Search for enriched gene sets in microarray data. J Biomed Inform 2008; 41:588-601. [DOI: 10.1016/j.jbi.2007.12.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2007] [Revised: 10/08/2007] [Accepted: 12/04/2007] [Indexed: 01/21/2023]
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117
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Rielland M, Hue I, Renard JP, Alice J. Trophoblast stem cell derivation, cross-species comparison and use of nuclear transfer: new tools to study trophoblast growth and differentiation. Dev Biol 2008; 322:1-10. [PMID: 18680738 DOI: 10.1016/j.ydbio.2008.07.017] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2008] [Revised: 07/04/2008] [Accepted: 07/09/2008] [Indexed: 12/25/2022]
Abstract
The trophoblast is a supportive tissue in mammals that plays key roles in embryonic patterning, foetal growth and nutrition. It shows an extensive growth up to the formation of the placenta. This growth is believed to be fed by trophoblast stem cells able to self-renew and to give rise to the differentiated derivatives present in the placenta. In this review, we summarize recent data on the molecular regulation of the trophoblast in vivo and in vitro. Most data have been obtained in the mouse, however, whenever relevant, we compare this model to other mammals. In ungulates, the growth of the trophoblast displays some striking features that make these species interesting alternative models for the study of trophoblast development. After the transfer of somatic nuclei into oocytes, studies in the mouse and the cow have both underlined that the trophoblast may be a direct target of reprogramming defects and that its growth seems specifically affected. We propose that the study of TS cells derived from nuclear transfer embryos may help to unravel some of the epigenetic abnormalities which occur therein.
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Affiliation(s)
- Maite Rielland
- INRA, UMR 1198 Biologie du Developpement et Reproduction, F-78350 Jouy en Josas, France
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118
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Edwards YJK, Bryson K, Jones DT. A meta-analysis of microarray gene expression in mouse stem cells: redefining stemness. PLoS One 2008; 3:e2712. [PMID: 18628962 PMCID: PMC2444034 DOI: 10.1371/journal.pone.0002712] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2008] [Accepted: 05/27/2008] [Indexed: 11/21/2022] Open
Abstract
Background While much progress has been made in understanding stem cell (SC) function, a complete description of the molecular mechanisms regulating SCs is not yet established. This lack of knowledge is a major barrier holding back the discovery of therapeutic uses of SCs. We investigated the value of a novel meta-analysis of microarray gene expression in mouse SCs to aid the elucidation of regulatory mechanisms common to SCs and particular SC types. Methodology/Principal Findings We added value to previously published microarray gene expression data by characterizing the promoter type likely to regulate transcription. Promoters of up-regulated genes in SCs were characterized in terms of alternative promoter (AP) usage and CpG-richness, with the aim of correlating features known to affect transcriptional control with SC function. We found that SCs have a higher proportion of up-regulated genes using CpG-rich promoters compared with the negative controls. Comparing subsets of SC type with the controls a slightly different story unfolds. The differences between the proliferating adult SCs and the embryonic SCs versus the negative controls are statistically significant. Whilst the difference between the quiescent adult SCs compared with the negative controls is not. On examination of AP usage, no difference was observed between SCs and the controls. However, comparing the subsets of SC type with the controls, the quiescent adult SCs are found to up-regulate a larger proportion of genes that have APs compared to the controls and the converse is true for the proliferating adult SCs and the embryonic SCs. Conclusions/Significance These findings suggest that looking at features associated with control of transcription is a promising future approach for characterizing “stemness” and that further investigations of stemness could benefit from separate considerations of different SC states. For example, “proliferating-stemness” is shown here, in terms of promoter usage, to be distinct from “quiescent-stemness”.
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Affiliation(s)
- Yvonne J. K. Edwards
- Bioinformatics Group, Department of Computer Science, University College London, London, United Kingdom
| | - Kevin Bryson
- Bioinformatics Group, Department of Computer Science, University College London, London, United Kingdom
| | - David T. Jones
- Bioinformatics Group, Department of Computer Science, University College London, London, United Kingdom
- * E-mail:
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119
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Gerrits A, Dykstra B, Otten M, Bystrykh L, de Haan G. Combining transcriptional profiling and genetic linkage analysis to uncover gene networks operating in hematopoietic stem cells and their progeny. Immunogenetics 2008; 60:411-22. [PMID: 18560825 PMCID: PMC2493868 DOI: 10.1007/s00251-008-0305-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2008] [Accepted: 05/15/2008] [Indexed: 11/28/2022]
Abstract
Stem cells are unique in that they possess both the capacity to self-renew and thereby maintain their original pool as well as the capacity to differentiate into mature cells. In the past number of years, transcriptional profiling of enriched stem cell populations has been extensively performed in an attempt to identify a universal stem cell gene expression signature. While stem-cell-specific transcripts were identified in each case, this approach has thus far been insufficient to identify a universal group of core “stemness” genes ultimately responsible for self-renewal and multipotency. Similarly, in the hematopoietic system, comparisons of transcriptional profiles between different hematopoietic cell stages have had limited success in revealing core genes ultimately responsible for the initiation of differentiation and lineage specification. Here, we propose that the combined use of transcriptional profiling and genetic linkage analysis, an approach called “genetical genomics”, can be a valuable tool to assist in the identification of genes and gene networks that specify “stemness” and cell fate decisions. We review past studies of hematopoietic cells that utilized transcriptional profiling and/or genetic linkage analysis, and discuss several potential future applications of genetical genomics.
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Affiliation(s)
- Alice Gerrits
- Department of Cell Biology, Section Stem Cell Biology, University Medical Center Groningen, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
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120
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Affiliation(s)
- Ying Liang
- Department of Internal Medicine, Markey Cancer Center, Division of Hematology/Oncology, University of Kentucky, Lexington, Kentucky, United States
- Department of Physiology, College of Medicine, University of Kentucky, Lexington, Kentucky, United States
| | - Gary Van Zant
- Department of Internal Medicine, Markey Cancer Center, Division of Hematology/Oncology, University of Kentucky, Lexington, Kentucky, United States
- Department of Physiology, College of Medicine, University of Kentucky, Lexington, Kentucky, United States
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121
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Zhao X, Heng JIT, Guardavaccaro D, Jiang R, Pagano M, Guillemot F, Iavarone A, Lasorella A. The HECT-domain ubiquitin ligase Huwe1 controls neural differentiation and proliferation by destabilizing the N-Myc oncoprotein. Nat Cell Biol 2008; 10:643-53. [PMID: 18488021 PMCID: PMC2680438 DOI: 10.1038/ncb1727] [Citation(s) in RCA: 217] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2008] [Accepted: 03/25/2008] [Indexed: 02/06/2023]
Abstract
Development of the nervous system requires that timely withdrawal from the cell cycle be coupled with initiation of differentiation. Ubiquitin-mediated degradation of the N-Myc oncoprotein in neural stem/progenitor cells is thought to trigger the arrest of proliferation and begin differentiation. Here we report that the HECT-domain ubiquitin ligase Huwe1 ubiquitinates the N-Myc oncoprotein through Lys 48-mediated linkages and targets it for destruction by the proteasome. This process is physiologically implemented by embryonic stem (ES) cells differentiating along the neuronal lineage and in the mouse brain during development. Genetic and RNA interference-mediated inactivation of the Huwe1 gene impedes N-Myc degradation, prevents exit from the cell cycle by opposing the expression of Cdk inhibitors and blocks differentiation through persistent inhibition of early and late markers of neuronal differentiation. Silencing of N-myc in cells lacking Huwe1 restores neural differentiation of ES cells and rescues cell-cycle exit and differentiation of the mouse cortex, demonstrating that Huwe1 restrains proliferation and enables neuronal differentiation by mediating the degradation of N-Myc. These findings indicate that Huwe1 links destruction of N-Myc to the quiescent state that complements differentiation in the neural tissue.
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Affiliation(s)
- Xudong Zhao
- Institute for Cancer Genetics, Columbia University Medical Center, New York, New York 10032, USA
- Shanghai Research Center for Model Organisms, Shanghai 201203, China
| | - Julian Ik-Tsen Heng
- Division of Molecular Neurobiology, National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK
| | - Daniele Guardavaccaro
- Department of Pathology, NYU Cancer Institute, New York University School of Medicine, 550 First Avenue MSB 599, New York, New York 10016, USA
| | - Richeng Jiang
- Institute for Cancer Genetics, Columbia University Medical Center, New York, New York 10032, USA
| | - Michele Pagano
- Department of Pathology, NYU Cancer Institute, New York University School of Medicine, 550 First Avenue MSB 599, New York, New York 10016, USA
| | - Francois Guillemot
- Division of Molecular Neurobiology, National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK
| | - Antonio Iavarone
- Institute for Cancer Genetics, Columbia University Medical Center, New York, New York 10032, USA
- Department of Pathology, Columbia University Medical Center, New York, New York 10032, USA
- Department of Neurology, Columbia University Medical Center, New York, New York 10032, USA
| | - Anna Lasorella
- Institute for Cancer Genetics, Columbia University Medical Center, New York, New York 10032, USA
- Department of Pathology, Columbia University Medical Center, New York, New York 10032, USA
- Department of Pediatrics, Columbia University Medical Center, New York, New York 10032, USA
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122
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Izadpanah R, Kaushal D, Kriedt C, Tsien F, Patel B, Dufour J, Bunnell BA. Long-term in vitro expansion alters the biology of adult mesenchymal stem cells. Cancer Res 2008; 68:4229-38. [PMID: 18519682 PMCID: PMC2713721 DOI: 10.1158/0008-5472.can-07-5272] [Citation(s) in RCA: 261] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Mesenchymal stem cells (MSC) derived from bone marrow stem cells (BMSC) and adipose tissue stem cells (ASC) of humans and rhesus macaques were evaluated for their cell cycle properties during protracted culture in vitro. Human ASCs (hASC) and rhesus BMSCs (rBMSC) underwent significantly more total population doublings than human BMSCs (hBMSC) and rhesus ASCs (rASC). The cell cycle profile of all MSCs was altered as cultures aged. hMSCs underwent an increase in the frequency of cells in the S phase at P20 and P30. However, rhesus MSCs from both sources developed a distinct polyploid population of cells at P20, which progressed to aneuploidy by P30. Karyotype analysis of MSCs revealed the development of tetraploid or aneuploid karyotypes in the rhesus cells at P20 or P30. Analysis of the transcriptome of the MSCs from early and late passages revealed significant alterations in the patterns of gene expression (8.8% of the genes were differentially expressed in hBMSCs versus hASCs, and 5.5% in rBMSCs versus rASCs). Gene expression changes were much less evident within the same cell type as aging occurred (0.7% in hMSCs and 0.9% in rMSC). Gene ontology analysis showed that functions involved in protein catabolism and regulation of pol II transcription were overrepresented in rASCs, whereas the regulation of I kappa B/nuclear factor-kappaB cascade were overrepresented in hBMSCs. Functional analysis of genes that were differentially expressed in rASCs and hBMSCs revealed that pathways involved in cell cycle, cell cycle checkpoints, protein-ubiquitination, and apoptosis were altered.
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Affiliation(s)
- Reza Izadpanah
- Division of Gene Therapy, Tulane National Primate Research Center, Tulane University Health Sciences Center, Covington, Louisiana
| | - Deepak Kaushal
- Division of Bacteriology and Parasitology, Tulane National Primate Research Center, Tulane University Health Sciences Center, Covington, Louisiana
| | - Christopher Kriedt
- Division of Gene Therapy, Tulane National Primate Research Center, Tulane University Health Sciences Center, Covington, Louisiana
| | - Fern Tsien
- Department of Human Genetics, Louisiana State University Health Sciences Center, New Orleans, Louisiana
| | - Bindiya Patel
- Department of Pharmacology, Tulane University, New Orleans, Louisiana
| | - Jason Dufour
- Division of Veterinary Medicine, Tulane National Primate Research Center, Tulane University Health Sciences Center, Covington, Louisiana
| | - Bruce A. Bunnell
- Division of Gene Therapy, Tulane National Primate Research Center, Tulane University Health Sciences Center, Covington, Louisiana
- Department of Pharmacology, Tulane University, New Orleans, Louisiana
- Center for Gene Therapy, School of Medicine, Tulane University, New Orleans, Louisiana
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123
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Colucci-D'Amato L, di Porzio U. Neurogenesis in adult CNS: from denial to opportunities and challenges for therapy. Bioessays 2008; 30:135-45. [PMID: 18200551 DOI: 10.1002/bies.20703] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The discovery of neurogenesis and neural stem cells (NSC) in the adult CNS has overturned a long-standing and deep-routed "dogma" in neuroscience, established at the beginning of the 20(th) century. This dogma lasted for almost 90 years and died hard when NSC were finally isolated from the adult mouse brain. The scepticism in accepting adult neurogenesis has now turned into a rush to find applications to alleviate or cure the devastating diseases that affect the CNS. Here we highlight a number of methodological, technical and conceptual drawbacks responsible for the historical denial of adult neurogenesis. Furthermore, we discuss old and new issues that need to be faced before NSC or endogenous neurogenesis can safely enter into the doctor's bag for therapies.
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Affiliation(s)
- Luca Colucci-D'Amato
- Dipartimento di Scienze della Vita, Seconda Università di Napoli, Caserta, Italy.
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124
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Collas P, Noer A, Sørensen AL. Epigenetic Basis for the Differentiation Potential of Mesenchymal and Embryonic Stem Cells. ACTA ACUST UNITED AC 2008; 35:205-215. [PMID: 21547118 DOI: 10.1159/000127449] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2007] [Accepted: 02/06/2008] [Indexed: 12/13/2022]
Abstract
SUMMARY: Stem cells have the ability to self-renew, and give rise to one or more differentiated cell types. Embryonic stem cells can differentiate into all cell types of the body and have unlimited self-renewal capacity. Somatic stem cells are found in many adult tissues. They have an extensive but finite lifespan and can differentiate into a more restricted range of cell types. Increasing evidence indicates that the multilineage differentiation ability of stem cells is defined by the potential for expression of developmentally regulated transcription factors and of lineage specification genes. Gene expression, or as emphasized here, the potential for gene expression, is largely controlled by epigenetic modifications of DNA (DNA methylation) and chromatin (such as post-translational histone modifications) in the regulatory regions of specific genes. Epigenetic modifications can also influence the timing of DNA replication. We highlight here how mechanisms by which genes are poised for transcription in undifferentiated stem cells are being uncovered through the mapping of DNA methylation profiles on differentiation-regulated promoters and at the genome-wide level, histone modifications, and transcription factor binding. Epigenetic marks on developmentally regulated and lineage specification genes in stem cells seem to define a state of pluripotency.
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Affiliation(s)
- Philippe Collas
- Institute of Basic Medical Sciences, Department of Biochemistry, Faculty of Medicine, University of Oslo, Norway
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125
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Jakt LM, Nishikawa S. DNA chip databases, omics, and gene fishing: commentary. Cancer Sci 2008; 99:829-35. [PMID: 18294276 PMCID: PMC11159018 DOI: 10.1111/j.1349-7006.2008.00767.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2007] [Revised: 12/17/2007] [Accepted: 12/18/2007] [Indexed: 11/30/2022] Open
Abstract
(Cancer Sci 2008; 99: 829–835)
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Affiliation(s)
- Lars Martin Jakt
- Stem Cell Research Group, Center for Developmental Biology, Riken, Minatojima-Minamimachi 2-2-3, Chuoku, Kobe.
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126
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Abstract
Background Significance analysis at single gene level may suffer from the limited number of samples and experimental noise that can severely limit the power of the chosen statistical test. This problem is typically approached by applying post hoc corrections to control the false discovery rate, without taking into account prior biological knowledge. Pathway or gene ontology analysis can provide an alternative way to relax the significance threshold applied to single genes and may lead to a better biological interpretation. Results Here we propose a new analysis method based on the study of networks of pathways. These networks are reconstructed considering both the significance of single pathways (network nodes) and the intersection between them (links). We apply this method for the reconstruction of networks of pathways to two gene expression datasets: the first one obtained from a c-Myc rat fibroblast cell line expressing a conditional Myc-estrogen receptor oncoprotein; the second one obtained from the comparison of Acute Myeloid Leukemia and Acute Lymphoblastic Leukemia derived from bone marrow samples. Conclusion Our method extends statistical models that have been recently adopted for the significance analysis of functional groups of genes to infer links between these groups. We show that groups of genes at the interface between different pathways can be considered as relevant even if the pathways they belong to are not significant by themselves.
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127
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Sepúlveda DE, Andrews BA, Asenjo JA, Papoutsakis ET. Comparative Transcriptional Analysis of Embryoid Body Versus Two-Dimensional Differentiation of Murine Embryonic Stem Cells. Tissue Eng Part A 2008. [DOI: 10.1089/tea.2007.0331] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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128
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Wong DJ, Liu H, Ridky TW, Cassarino D, Segal E, Chang HY. Module map of stem cell genes guides creation of epithelial cancer stem cells. Cell Stem Cell 2008; 2:333-44. [PMID: 18397753 PMCID: PMC2628721 DOI: 10.1016/j.stem.2008.02.009] [Citation(s) in RCA: 573] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2007] [Revised: 01/18/2008] [Accepted: 02/12/2008] [Indexed: 10/22/2022]
Abstract
Self-renewal is a hallmark of stem cells and cancer, but existence of a shared stemness program remains controversial. Here, we construct a gene module map to systematically relate transcriptional programs in embryonic stem cells (ESCs), adult tissue stem cells, and human cancers. This map reveals two predominant gene modules that distinguish ESCs and adult tissue stem cells. The ESC-like transcriptional program is activated in diverse human epithelial cancers and strongly predicts metastasis and death. c-Myc, but not other oncogenes, is sufficient to reactivate the ESC-like program in normal and cancer cells. In primary human keratinocytes transformed by Ras and I kappa B alpha, c-Myc increases the fraction of tumor-initiating cells by 150-fold, enabling tumor formation and serial propagation with as few as 500 cells. c-Myc-enhanced tumor initiation is cell-autonomous and independent of genomic instability. Thus, activation of an ESC-like transcriptional program in differentiated adult cells may induce pathologic self-renewal characteristic of cancer stem cells.
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MESH Headings
- Adult Stem Cells/cytology
- Adult Stem Cells/physiology
- Animals
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Cell Proliferation
- Cell Transformation, Neoplastic
- Cells, Cultured
- Chromatin Immunoprecipitation
- DNA-Binding Proteins/metabolism
- Embryonic Stem Cells/cytology
- Embryonic Stem Cells/physiology
- Epithelium/pathology
- Fibroblasts/cytology
- Fibroblasts/metabolism
- Fluorescent Antibody Technique
- Gene Expression Profiling
- Gene Expression Regulation
- Genes, ras/physiology
- Genomic Instability
- Humans
- Immunoenzyme Techniques
- Keratinocytes/cytology
- Keratinocytes/metabolism
- Mice
- Mice, SCID
- Neoplasms, Experimental/genetics
- Neoplasms, Experimental/metabolism
- Neoplasms, Experimental/pathology
- Neoplastic Stem Cells/pathology
- Oligonucleotide Array Sequence Analysis
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Transcription Factors/metabolism
- Transcription, Genetic
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Affiliation(s)
- David J. Wong
- Program in Epithelial Biology, Stanford University, Stanford CA 94305, USA
| | - Helen Liu
- Program in Epithelial Biology, Stanford University, Stanford CA 94305, USA
| | - Todd W. Ridky
- Program in Epithelial Biology, Stanford University, Stanford CA 94305, USA
| | - David Cassarino
- Department of Pathology, Stanford University, Stanford CA 94305, USA
| | - Eran Segal
- Department of Computer Science and Applied Mathematics, Weizmann Institute, Rehovot, Israel
| | - Howard Y. Chang
- Program in Epithelial Biology, Stanford University, Stanford CA 94305, USA
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129
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Pedotti P, 't Hoen PAC, Vreugdenhil E, Schenk GJ, Vossen RH, Ariyurek Y, de Hollander M, Kuiper R, van Ommen GJB, den Dunnen JT, Boer JM, de Menezes RX. Can subtle changes in gene expression be consistently detected with different microarray platforms? BMC Genomics 2008; 9:124. [PMID: 18331641 PMCID: PMC2335120 DOI: 10.1186/1471-2164-9-124] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2007] [Accepted: 03/10/2008] [Indexed: 11/29/2022] Open
Abstract
Background The comparability of gene expression data generated with different microarray platforms is still a matter of concern. Here we address the performance and the overlap in the detection of differentially expressed genes for five different microarray platforms in a challenging biological context where differences in gene expression are few and subtle. Results Gene expression profiles in the hippocampus of five wild-type and five transgenic δC-doublecortin-like kinase mice were evaluated with five microarray platforms: Applied Biosystems, Affymetrix, Agilent, Illumina, LGTC home-spotted arrays. Using a fixed false discovery rate of 10% we detected surprising differences between the number of differentially expressed genes per platform. Four genes were selected by ABI, 130 by Affymetrix, 3,051 by Agilent, 54 by Illumina, and 13 by LGTC. Two genes were found significantly differentially expressed by all platforms and the four genes identified by the ABI platform were found by at least three other platforms. Quantitative RT-PCR analysis confirmed 20 out of 28 of the genes detected by two or more platforms and 8 out of 15 of the genes detected by Agilent only. We observed improved correlations between platforms when ranking the genes based on the significance level than with a fixed statistical cut-off. We demonstrate significant overlap in the affected gene sets identified by the different platforms, although biological processes were represented by only partially overlapping sets of genes. Aberrances in GABA-ergic signalling in the transgenic mice were consistently found by all platforms. Conclusion The different microarray platforms give partially complementary views on biological processes affected. Our data indicate that when analyzing samples with only subtle differences in gene expression the use of two different platforms might be more attractive than increasing the number of replicates. Commercial two-color platforms seem to have higher power for finding differentially expressed genes between groups with small differences in expression.
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Affiliation(s)
- Paola Pedotti
- Center for Human and Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands.
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130
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Greene JG, Greenamyre JT, Dingledine R. Sequential and concerted gene expression changes in a chronic in vitro model of parkinsonism. Neuroscience 2008; 152:198-207. [PMID: 18191903 PMCID: PMC2562913 DOI: 10.1016/j.neuroscience.2007.11.029] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2007] [Revised: 10/26/2007] [Accepted: 11/14/2007] [Indexed: 12/21/2022]
Abstract
Many mechanisms of neurodegeneration have been implicated in Parkinson's disease, but which ones are most important and potential interactions among them are unclear. To provide a broader perspective on the parkinsonian neurodegenerative process, we have performed a global analysis of gene expression changes caused by chronic, low-level exposure of neuroblastoma cells to the mitochondrial complex I inhibitor and parkinsonian neurotoxin rotenone. Undifferentiated SK-N-MC human neuroblastoma cells were grown in the presence of rotenone (5 nM), and RNA was extracted at three different time points (baseline, 1 week, and 4 weeks) for labeling and hybridization to Affymetrix Human U133 Plus 2.0 GeneChips. Our results show that rotenone induces concerted alterations in gene expression that change over time. Particularly, alterations in transcripts related to DNA damage, energy metabolism, and protein metabolism are prominent during chronic complex I inhibition. These data suggest that early augmentation of capacity for energy production in response to mitochondrial inhibition might be deleterious to cellular function and survival. These experiments provide the first transcriptional analysis of a rotenone model of Parkinson's disease and insight into which mechanisms of neurodegeneration may be targeted for therapeutic intervention.
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Affiliation(s)
- J G Greene
- Department of Neurology, Emory University School of Medicine, 505 Whitehead Biomedical Research Building, 615 Michael Street, Atlanta, GA 30322, USA.
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131
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Ulloa-Montoya F, Kidder BL, Pauwelyn KA, Chase LG, Luttun A, Crabbe A, Geraerts M, Sharov AA, Piao Y, Ko MSH, Hu WS, Verfaillie CM. Comparative transcriptome analysis of embryonic and adult stem cells with extended and limited differentiation capacity. Genome Biol 2008; 8:R163. [PMID: 17683608 PMCID: PMC2374994 DOI: 10.1186/gb-2007-8-8-r163] [Citation(s) in RCA: 102] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2007] [Revised: 05/04/2007] [Accepted: 08/06/2007] [Indexed: 01/22/2023] Open
Abstract
Comparison of the transcriptomes of pluripotent embryonic stem cells, multipotent adult progenitor cells and lineage restricted mesenchymal stem cells identified a unique gene expression profile of multipotent adult progenitor cells. Background Recently, several populations of postnatal stem cells, such as multipotent adult progenitor cells (MAPCs), have been described that have broader differentiation ability than classical adult stem cells. Here we compare the transcriptome of pluripotent embryonic stem cells (ESCs), MAPCs, and lineage-restricted mesenchymal stem cells (MSCs) to determine their relationship. Results Applying principal component analysis, non-negative matrix factorization and k-means clustering algorithms to the gene-expression data, we identified a unique gene-expression profile for MAPCs. Apart from the ESC-specific transcription factor Oct4 and other ESC transcripts, some of them associated with maintaining ESC pluripotency, MAPCs also express transcripts characteristic of early endoderm and mesoderm. MAPCs do not, however, express Nanog or Sox2, two other key transcription factors involved in maintaining ESC properties. This unique molecular signature was seen irrespective of the microarray platform used and was very similar for both mouse and rat MAPCs. As MSC-like cells isolated under MAPC conditions are virtually identical to MSCs, and MSCs cultured in MAPC conditions do not upregulate MAPC-expressed transcripts, the MAPC signature is cell-type specific and not merely the result of differing culture conditions. Conclusion Multivariate analysis techniques clustered stem cells on the basis of their expressed gene profile, and the genes determining this clustering reflected the stem cells' differentiation potential in vitro. This comparative transcriptome analysis should significantly aid the isolation and culture of MAPCs and MAPC-like cells, and form the basis for studies to gain insights into genes that confer on these cells their greater developmental potency.
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Affiliation(s)
- Fernando Ulloa-Montoya
- Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455, USA
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN 55455, USA
- Stamcel Instituut, Katholieke Universiteit Leuven, Leuven 3000, Belgium
| | - Benjamin L Kidder
- Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455, USA
| | - Karen A Pauwelyn
- Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455, USA
- Stamcel Instituut, Katholieke Universiteit Leuven, Leuven 3000, Belgium
| | - Lucas G Chase
- Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455, USA
| | - Aernout Luttun
- Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455, USA
- Stamcel Instituut, Katholieke Universiteit Leuven, Leuven 3000, Belgium
| | - Annelies Crabbe
- Stamcel Instituut, Katholieke Universiteit Leuven, Leuven 3000, Belgium
| | - Martine Geraerts
- Stamcel Instituut, Katholieke Universiteit Leuven, Leuven 3000, Belgium
| | - Alexei A Sharov
- Developmental Genomics and Aging Section, Laboratory of Genetics, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Yulan Piao
- Developmental Genomics and Aging Section, Laboratory of Genetics, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Minoru SH Ko
- Developmental Genomics and Aging Section, Laboratory of Genetics, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Wei-Shou Hu
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN 55455, USA
| | - Catherine M Verfaillie
- Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455, USA
- Stamcel Instituut, Katholieke Universiteit Leuven, Leuven 3000, Belgium
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132
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Hirst M, Delaney A, Rogers SA, Schnerch A, Persaud DR, O'Connor MD, Zeng T, Moksa M, Fichter K, Mah D, Go A, Morin RD, Baross A, Zhao Y, Khattra J, Prabhu AL, Pandoh P, McDonald H, Asano J, Dhalla N, Ma K, Lee S, Ally A, Chahal N, Menzies S, Siddiqui A, Holt R, Jones S, Gerhard DS, Thomson JA, Eaves CJ, Marra MA. LongSAGE profiling of nine human embryonic stem cell lines. Genome Biol 2008; 8:R113. [PMID: 17570852 PMCID: PMC2394759 DOI: 10.1186/gb-2007-8-6-r113] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2006] [Revised: 04/23/2007] [Accepted: 06/14/2007] [Indexed: 12/20/2022] Open
Abstract
To facilitate discovery of novel human embryonic stem cell (ESC) transcripts, we generated 2.5 million LongSAGE tags from 9 human ESC lines. Analysis of this data revealed that ESCs express proportionately more RNA binding proteins compared with terminally differentiated cells, and identified novel ESC transcripts, at least one of which may represent a marker of the pluripotent state.
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Affiliation(s)
- Martin Hirst
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada, V5Z 1L3
| | - Allen Delaney
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada, V5Z 1L3
| | - Sean A Rogers
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada, V5Z 1L3
| | - Angelique Schnerch
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada, V5Z 1L3
| | - Deryck R Persaud
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada, V5Z 1L3
| | - Michael D O'Connor
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada, V5Z 1L3
| | - Thomas Zeng
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada, V5Z 1L3
| | - Michelle Moksa
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada, V5Z 1L3
| | - Keith Fichter
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada, V5Z 1L3
| | - Diana Mah
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada, V5Z 1L3
| | - Anne Go
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada, V5Z 1L3
| | - Ryan D Morin
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada, V5Z 1L3
| | - Agnes Baross
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada, V5Z 1L3
| | - Yongjun Zhao
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada, V5Z 1L3
| | - Jaswinder Khattra
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada, V5Z 1L3
| | - Anna-Liisa Prabhu
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada, V5Z 1L3
| | - Pawan Pandoh
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada, V5Z 1L3
| | - Helen McDonald
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada, V5Z 1L3
| | - Jennifer Asano
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada, V5Z 1L3
| | - Noreen Dhalla
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada, V5Z 1L3
| | - Kevin Ma
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada, V5Z 1L3
| | - Stephanie Lee
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada, V5Z 1L3
| | - Adrian Ally
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada, V5Z 1L3
| | - Neil Chahal
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada, V5Z 1L3
| | - Stephanie Menzies
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada, V5Z 1L3
| | - Asim Siddiqui
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada, V5Z 1L3
| | - Robert Holt
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada, V5Z 1L3
| | - Steven Jones
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada, V5Z 1L3
| | - Daniela S Gerhard
- National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - James A Thomson
- Wisconsin National Primate Research Centre and Department of Anatomy, School of Medicine, University of Wisconsin, Madison, Wisconsin 53715, USA
| | - Connie J Eaves
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada, V5Z 1L3
| | - Marco A Marra
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada, V5Z 1L3
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133
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Orwig KE, Ryu BY, Master SR, Phillips BT, Mack M, Avarbock MR, Chodosh L, Brinster RL. Genes involved in post-transcriptional regulation are overrepresented in stem/progenitor spermatogonia of cryptorchid mouse testes. Stem Cells 2008; 26:927-38. [PMID: 18203673 DOI: 10.1634/stemcells.2007-0893] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Gene expression and consequent biological activity of adult tissue stem cells are regulated by signals emanating from the local microenvironment (niche). To gain insights into the molecular regulation of spermatogonial stem cells (SSCs), gene expression was characterized from SSCs isolated from their cognate niches of cryptorchid (stem cell-enriched), wild-type, and busulfan-treated (stem cell-depleted) mouse testes. Quantitative assessment of stem cell activity in each testis model was determined using an in vivo functional assay and correlated with gene expression using Affymetrix MGU74Av2 microarrays and the ChipStat algorithm optimized to detect gene expression from rare cells in complex tissues. We identified 389 stem/progenitor spermatogonia candidate genes, which exhibited significant overlap with genes expressed by embryonic, hematopoietic, and neural stem cells; enriched spermatogonia; and cultured SSCs identified in previous studies. Candidate cell surface markers identified by the microarray may facilitate the isolation and enrichment of stem and/or progenitor spermatogonia. Flow cytometric analyses confirmed the expression of chemokine receptor 2 (Ccr2) and Cd14 on a subpopulation cryptorchid testis cells (alpha6-integrin+, side scatter(lo)) enriched for SSCs. These cell surface molecules may mark progenitor spermatogonia but not SSCs because Ccr2+ and Cd14+ fractions failed to produce spermatogenesis upon transplantation to recipient testes. Functional annotation of candidate genes and subsequent immunohistochemistry revealed that proteins involved in post-transcriptional regulation are overrepresented in cryptorchid testes that are enriched for SSCs. Comparative analyses indicated that this is a recurrent biological theme among stem cells.
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Affiliation(s)
- Kyle E Orwig
- Department of Obstetrics, Gynecology and Reproductive Sciences, Magee-Womens Research Institute, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
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134
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Abstract
The beauty of microarray analysis of gene expression (MAGE) is that it can be used to discover some genes that were previously thought to be unrelated to a physiologic or pathologic event. During the period from 1999 to 2007, applications of MAGE in cancer investigation have shifted from molecular profiling, identifying previously undiscovered cancer types, predicting outcomes of cancer patients, revealing metastasis signatures of solid tumors, to guiding the use of therapeutics. The roles of cancer genomic signatures have evolved through three phases. In the first phase, genomic signatures were described in stored cancer specimens and dubbed as molecular portraits of cancer. When gene expression profiles were carefully correlated with sufficient clinical information of cancer patients, new subgroups of cancers with distinct outcomes were revealed. In studies of the second phase, validation of cancer signatures was emphasized and commonly performed with independent groups of cancer specimens or independent data set. In the third phase, cancer genomic signatures have been further expanded beyond depicting the molecular portrait of cancer to predicting patient outcomes and guiding the use of cancer therapeutics. Cancer genomic signatures have become an essential part of a new generation of cancer clinical trials. It is advocated that, in future clinical trials of cancer therapy, the cancer specimens of each participant should be tested for currently available predictor genomic signatures, so that the most effective treatment with the least adverse effects for each patient can be identified. Then, participants can be triaged to an appropriate study group.
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135
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Liu D, Lin X, Ghosh D. Semiparametric regression of multidimensional genetic pathway data: least-squares kernel machines and linear mixed models. Biometrics 2007; 63:1079-88. [PMID: 18078480 PMCID: PMC2665800 DOI: 10.1111/j.1541-0420.2007.00799.x] [Citation(s) in RCA: 233] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
We consider a semiparametric regression model that relates a normal outcome to covariates and a genetic pathway, where the covariate effects are modeled parametrically and the pathway effect of multiple gene expressions is modeled parametrically or nonparametrically using least-squares kernel machines (LSKMs). This unified framework allows a flexible function for the joint effect of multiple genes within a pathway by specifying a kernel function and allows for the possibility that each gene expression effect might be nonlinear and the genes within the same pathway are likely to interact with each other in a complicated way. This semiparametric model also makes it possible to test for the overall genetic pathway effect. We show that the LSKM semiparametric regression can be formulated using a linear mixed model. Estimation and inference hence can proceed within the linear mixed model framework using standard mixed model software. Both the regression coefficients of the covariate effects and the LSKM estimator of the genetic pathway effect can be obtained using the best linear unbiased predictor in the corresponding linear mixed model formulation. The smoothing parameter and the kernel parameter can be estimated as variance components using restricted maximum likelihood. A score test is developed to test for the genetic pathway effect. Model/variable selection within the LSKM framework is discussed. The methods are illustrated using a prostate cancer data set and evaluated using simulations.
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Affiliation(s)
- Dawei Liu
- Center for Statistical Sciences, Brown University, Providence, Rhode Island 02912, USA.
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136
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Graham SM, Vass JK, Holyoake TL, Graham GJ. Transcriptional Analysis of Quiescent and Proliferating CD34+ Human Hemopoietic Cells from Normal and Chronic Myeloid Leukemia Sources. Stem Cells 2007; 25:3111-20. [PMID: 17717066 DOI: 10.1634/stemcells.2007-0250] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Quiescent and dividing hemopoietic stem cells (HSC) display marked differences in their ability to move between the peripheral circulation and the bone marrow. Specifically, long-term engraftment potential predominantly resides in the quiescent HSC subfraction, and G-CSF mobilization results in the preferential accumulation of quiescent HSC in the periphery. In contrast, stem cells from chronic myeloid leukemia (CML) patients display a constitutive presence in the circulation. To understand the molecular basis for this, we have used microarray technology to analyze the transcriptional differences between dividing and quiescent, normal, and CML-derived CD34+ cells. Our data show a remarkable transcriptional similarity between normal and CML dividing cells, suggesting that the effects of BCR-ABL on the CD34+ cell transcriptome are more limited than previously thought. In addition, we show that quiescent CML cells are more similar to their dividing counterparts than quiescent normal cells are to theirs. We also show these transcriptional differences to be reflected in the altered proliferative activity of normal and CML CD34+ cells. Of the most interest is that the major class of genes that is more abundant in the quiescent cells compared with the dividing cells encodes members of the chemokine family. We propose a role for chemokines expressed by quiescent HSC in the orchestration of CD34+ cell mobilization. Disclosure of potential conflicts of interest is found at the end of this article.
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MESH Headings
- Antigens, CD34/biosynthesis
- Antigens, CD34/genetics
- Cell Cycle/genetics
- Cell Division/genetics
- Cell Proliferation
- Cells, Cultured
- Female
- Gene Expression Profiling/methods
- Hematopoietic Stem Cells/cytology
- Hematopoietic Stem Cells/metabolism
- Hematopoietic Stem Cells/pathology
- Humans
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/metabolism
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/pathology
- Male
- Neoplastic Cells, Circulating/metabolism
- Neoplastic Cells, Circulating/pathology
- Oligonucleotide Array Sequence Analysis/methods
- Resting Phase, Cell Cycle/genetics
- Tumor Cells, Cultured
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Affiliation(s)
- Susan M Graham
- Experimental Haematology, Division of Cancer Sciences, University of Glasgow, Glasgow Royal Infirmary, Glasgow, United Kingdom
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137
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Epigenetics in embryonic stem cells: regulation of pluripotency and differentiation. Cell Tissue Res 2007; 331:23-9. [DOI: 10.1007/s00441-007-0536-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2007] [Accepted: 10/17/2007] [Indexed: 12/12/2022]
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138
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Abstract
In opposition to terminally differentiated cells, stem cells can self-renew and give rise to multiple cell types. Embryonic stem cells retain the ability of the inner cell mass of blastocysts to differentiate into all cell types of the body and have acquired in culture unlimited self-renewal capacity. Somatic stem cells are found in many adult tissues, have an extensive but finite lifespan and can differentiate into a more restricted array of cell types. A growing body of evidence indicates that multi-lineage differentiation ability of stem cells can be defined by the potential for expression of lineage-specification genes. Gene expression, or as emphasized here, potential for gene expression, is largely controlled by epigenetic modifications of DNA and chromatin on genomic regulatory and coding regions. These modifications modulate chromatin organization not only on specific genes but also at the level of the whole nucleus; they can also affect timing of DNA replication. This review highlights how mechanisms by which genes are poised for transcription in undifferentiated stem cells are being uncovered through primarily the mapping of DNA methylation, histone modifications and transcription factor binding throughout the genome. The combinatorial association of epigenetic marks on developmentally regulated and lineage-specifying genes in undifferentiated cells seems to define a pluripotent state.
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Affiliation(s)
- Philippe Collas
- Institute of Basic Medical Sciences, Department of Biochemistry, Faculty of Medicine, University of Oslo, 0317 Oslo, Norway.
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139
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Gormley M, Dampier W, Ertel A, Karacali B, Tozeren A. Prediction potential of candidate biomarker sets identified and validated on gene expression data from multiple datasets. BMC Bioinformatics 2007; 8:415. [PMID: 17963508 PMCID: PMC2211325 DOI: 10.1186/1471-2105-8-415] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2007] [Accepted: 10/26/2007] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Independently derived expression profiles of the same biological condition often have few genes in common. In this study, we created populations of expression profiles from publicly available microarray datasets of cancer (breast, lymphoma and renal) samples linked to clinical information with an iterative machine learning algorithm. ROC curves were used to assess the prediction error of each profile for classification. We compared the prediction error of profiles correlated with molecular phenotype against profiles correlated with relapse-free status. Prediction error of profiles identified with supervised univariate feature selection algorithms were compared to profiles selected randomly from a) all genes on the microarray platform and b) a list of known disease-related genes (a priori selection). We also determined the relevance of expression profiles on test arrays from independent datasets, measured on either the same or different microarray platforms. RESULTS Highly discriminative expression profiles were produced on both simulated gene expression data and expression data from breast cancer and lymphoma datasets on the basis of ER and BCL-6 expression, respectively. Use of relapse-free status to identify profiles for prognosis prediction resulted in poorly discriminative decision rules. Supervised feature selection resulted in more accurate classifications than random or a priori selection, however, the difference in prediction error decreased as the number of features increased. These results held when decision rules were applied across-datasets to samples profiled on the same microarray platform. CONCLUSION Our results show that many gene sets predict molecular phenotypes accurately. Given this, expression profiles identified using different training datasets should be expected to show little agreement. In addition, we demonstrate the difficulty in predicting relapse directly from microarray data using supervised machine learning approaches. These findings are relevant to the use of molecular profiling for the identification of candidate biomarker panels.
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Affiliation(s)
- Michael Gormley
- School of Biomedical Engineering, Drexel University, Philadelphia, PA, USA.
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140
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Cahan P, Rovegno F, Mooney D, Newman JC, Laurent GS, McCaffrey TA. Meta-analysis of microarray results: challenges, opportunities, and recommendations for standardization. Gene 2007; 401:12-8. [PMID: 17651921 PMCID: PMC2111172 DOI: 10.1016/j.gene.2007.06.016] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2007] [Revised: 06/06/2007] [Accepted: 06/12/2007] [Indexed: 12/31/2022]
Abstract
Microarray profiling of gene expression is a powerful tool for discovery, but the ability to manage and compare the resulting data can be problematic. Biological, experimental, and technical variations between studies of the same phenotype/phenomena create substantial differences in results. The application of conventional meta-analysis to raw microarray data is complicated by differences in the type of microarray used, gene nomenclatures, species, and analytical methods. An alternative approach to combining multiple microarray studies is to compare the published gene lists which result from the investigators' analyses of the raw data, as implemented in Lists of Lists Annotated (LOLA: www.lola.gwu.edu) and L2L (depts.washington.edu/l2l/). The present review considers both the potential value and the limitations of databasing and enabling the comparison of results from different microarray studies. Further, a major impediment to cross-study comparisons is the absence of a standard for reporting microarray study results. We propose a reporting standard: standard microarray results template (SMART), which will facilitate the integration of microarray studies.
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Affiliation(s)
- Patrick Cahan
- Department of Internal Medicine, Washington University, St. Louis, MO 63110, USA
| | - Felicia Rovegno
- The George Washington University Medical Center, Department of Biochemistry and Molecular Biology & The Catherine Birch McCormick Genomics Center
| | - Denise Mooney
- The George Washington University Medical Center, Department of Biochemistry and Molecular Biology & The Catherine Birch McCormick Genomics Center
| | - John C. Newman
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Georges St. Laurent
- The George Washington University Medical Center, Department of Biochemistry and Molecular Biology & The Catherine Birch McCormick Genomics Center
| | - Timothy A. McCaffrey
- The George Washington University Medical Center, Department of Biochemistry and Molecular Biology & The Catherine Birch McCormick Genomics Center
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141
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Abstract
Peter Nowell and David Hungerford's discovery of the Philadelphia chromosome facilitated many critical studies that have led to a paradigm shift in our understanding of cancer as a disease of stem cells. This Review focuses on the application of these concepts to investigation of the role of stem cells in prostate cancer initiation and progression. Major strides in the development of in vitro and in vivo assays have enabled identification and characterization of prostate stem cells as well as functional evaluation of the tumorigenic effects of prostate cancer-related genetic alterations.
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Affiliation(s)
- Devon A. Lawson
- Department of Microbiology, Immunology and Molecular Genetics, and
Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, and
Howard Hughes Medical Institute, UCLA, Los Angeles, California, USA
| | - Owen N. Witte
- Department of Microbiology, Immunology and Molecular Genetics, and
Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, and
Howard Hughes Medical Institute, UCLA, Los Angeles, California, USA
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142
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Stanton LW, Bakre MM. Genomic and proteomic characterization of embryonic stem cells. Curr Opin Chem Biol 2007; 11:399-404. [PMID: 17646122 DOI: 10.1016/j.cbpa.2007.05.029] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2007] [Accepted: 05/24/2007] [Indexed: 11/28/2022]
Abstract
Stem cell biology, like all areas of cell biology, has been significantly affected by the arrival of the genomics era. The rendering of the human and mouse genome sequences and the development of attendant technologies have made it possible to comprehensively explore embryonic stem cell biology at the molecular level. Recently, there has been emphasis on global characterization of the transcriptome, epigenome, and proteome of embryonic stem cells. These omic evaluations of embryonic stem cells are leading to improved methods for cell-based therapies and are advancing our basic understanding of early embryonic development.
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Affiliation(s)
- Lawrence W Stanton
- Stem Cell and Developmental Biology Program, Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672, Singapore.
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143
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Yap DYL, Smith DK, Zhang XW, Hill J. Using biomarker signature patterns for an mRNA molecular diagnostic of mouse embryonic stem cell differentiation state. BMC Genomics 2007; 8:210. [PMID: 17605829 PMCID: PMC1931595 DOI: 10.1186/1471-2164-8-210] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2006] [Accepted: 07/03/2007] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND The pluripotency and self-renewal capabilities, which define the "stemness" state, of mouse embryonic stem (ES) cells, are usually investigated by functional assays or quantitative measurements of the expression levels of known ES cell markers. Strong correlations between these expression levels and functional assays, particularly at the early stage of cell differentiation, have usually not been observed. An effective molecular diagnostic to properly identify the differentiation state of mouse ES cells, prior to further experimentation, is needed. RESULTS A novel molecular pattern recognition procedure has been developed to diagnose the differentiation state of ES cells. This is based on mRNA transcript levels of genes differentially expressed between ES cells and their differentiating progeny. Large publicly available ES cell data sets from various platforms were used to develop and test the diagnostic model. Signature patterns consisting of five gene expression levels achieved high accuracy at determining the cell state (sensitivity and specificity > 97%). CONCLUSION The effective ES cell state diagnostic scheme described here can be implemented easily to assist researchers in identifying the differentiation state of their cultures. It also provides a step towards standardization of experiments relying on cells being in the stem cell or differentiating state.
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Affiliation(s)
- Daniel YL Yap
- Bioinformatics Institute, 30 Biopolis Street, #07-01, Matrix, 138671, Singapore
| | - David K Smith
- Department of Biochemistry, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, Pokfulam, Hong Kong SAR, China
| | - Xue W Zhang
- College of Light Industry and Food Sciences, South China University of Technology, Guangzhou, Guangdong, China
| | - Jeffrey Hill
- Bioinformatics Institute, 30 Biopolis Street, #07-01, Matrix, 138671, Singapore
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144
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Roma G, Cobellis G, Claudiani P, Maione F, Cruz P, Tripoli G, Sardiello M, Peluso I, Stupka E. A novel view of the transcriptome revealed from gene trapping in mouse embryonic stem cells. Genome Res 2007; 17:1051-60. [PMID: 17540781 PMCID: PMC1899116 DOI: 10.1101/gr.5720807] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2006] [Accepted: 02/12/2007] [Indexed: 11/24/2022]
Abstract
Embryonic stem (ES) cells are pluripotent cell lines with the capacity of self-renewal and the ability to differentiate into specific cell types. We performed the first genome-wide analysis of the mouse ES cell transcriptome using approximately 250,000 gene trap sequence tags deposited in public databases. We unveiled >8000 novel transcripts, mostly non-coding, and >1000 novel alternative and often tissue-specific exons of known genes. Experimental verification of the expression of these genes and exons by RT-PCR yielded a 70% validation rate. A novel non-coding transcript within the set studied showed a highly specific pattern of expression by in situ hybridization. Our analysis also shows that the genome presents gene trapping hotspots, which correspond to 383 known and 87 novel genes. These "hypertrapped" genes show minimal overlap with previously published expression profiles of ES cells; however, we prove by real-time PCR that they are highly expressed in this cell type, thus potentially contributing to the phenotype of ES cells. Although gene trapping was initially devised as an insertional mutagenesis technique, our study demonstrates its impact on the discovery of a substantial and unprecedented portion of the transcriptome.
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Affiliation(s)
- Guglielmo Roma
- Telethon Institute of Genetics and Medicine (TIGEM), 80131 Napoli, Italy
| | - Gilda Cobellis
- Telethon Institute of Genetics and Medicine (TIGEM), 80131 Napoli, Italy
- Dipartimento di Patologia Generale, Seconda Universita’ di Napoli, 80100 Napoli, Italy
| | - Pamela Claudiani
- Telethon Institute of Genetics and Medicine (TIGEM), 80131 Napoli, Italy
| | - Francesco Maione
- Telethon Institute of Genetics and Medicine (TIGEM), 80131 Napoli, Italy
| | - Pedro Cruz
- Telethon Institute of Genetics and Medicine (TIGEM), 80131 Napoli, Italy
| | - Gaetano Tripoli
- Telethon Institute of Genetics and Medicine (TIGEM), 80131 Napoli, Italy
| | - Marco Sardiello
- Telethon Institute of Genetics and Medicine (TIGEM), 80131 Napoli, Italy
| | - Ivana Peluso
- Telethon Institute of Genetics and Medicine (TIGEM), 80131 Napoli, Italy
| | - Elia Stupka
- Telethon Institute of Genetics and Medicine (TIGEM), 80131 Napoli, Italy
- CBM S.c.r.l., Area Science Park, Basovizza- SS14, Km 163,5 Trieste, 34012 Italy
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145
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Tiede S, Kloepper JE, Bodò E, Tiwari S, Kruse C, Paus R. Hair follicle stem cells: walking the maze. Eur J Cell Biol 2007; 86:355-76. [PMID: 17576022 DOI: 10.1016/j.ejcb.2007.03.006] [Citation(s) in RCA: 125] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2006] [Revised: 03/20/2007] [Accepted: 03/21/2007] [Indexed: 12/17/2022] Open
Abstract
The discovery of epithelial stem cells (eSCs) in the bulge region of the outer root sheath of hair follicles in mice and man has encouraged research into utilizing the hair follicle as a therapeutic source of stem cells (SCs) for regenerative medicine, and has called attention to the hair follicle as a highly instructive model system for SC biology. Under physiological circumstances, bulge eSCs serve as cell pool for the cyclic regeneration of the anagen hair bulb, while they can also regenerate the sebaceous gland and the epidermis after injury. More recently, melanocyte SCs, nestin+, mesenchymal and additional, as yet ill-defined "stem cell" populations, have also been identified in or immediately adjacent to the hair follicle epithelium, including in the specialized hair follicle mesenchyme (connective tissue sheath), which is crucial to wound healing. Thus the hair follicle and its adjacent tissue environment contain unipotent, multipotent, and possibly even pluripotent SC populations of different developmental origin. It provides an ideal model system for the study of central issues in SC biology such as plasticity and SC niches, and for the identification of reliable, specific SC markers, which distinguish them from their immediate progeny (e.g. transient amplifying cells). The current review attempts to provide some guidance in this growing maze of hair follicle-associated SCs and their progeny, critically reviews potential or claimed hair follicle SC markers, highlights related differences between murine and human hair follicles, and defines major unanswered questions in this rapidly advancing field.
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Affiliation(s)
- Stephan Tiede
- Department of Dermatology, University Hospital Schleswig-Holstein, University of Lübeck, Ratzeburger Allee 160, D-23538 Lübeck, Germany
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146
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Xue HH, Bollenbacher-Reilley J, Wu Z, Spolski R, Jing X, Zhang YC, McCoy JP, Leonard WJ. The transcription factor GABP is a critical regulator of B lymphocyte development. Immunity 2007; 26:421-31. [PMID: 17442597 DOI: 10.1016/j.immuni.2007.03.010] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2006] [Revised: 01/09/2007] [Accepted: 03/16/2007] [Indexed: 12/19/2022]
Abstract
GA binding protein (GABP) is a ubiquitously expressed Ets-family transcription factor that critically regulates the expression of the interleukin-7 receptor alpha chain (IL-7Ralpha) in T cells, whereas it is dispensable for IL-7Ralpha expression in fetal liver B cells. Here we showed that deficiency of GABPalpha, the DNA-binding subunit of GABP, resulted in profoundly defective B cell development and a compromised humoral immune response, in addition to thymic developmental defects. Furthermore, the expression of Pax5 and Pax5 target genes such as Cd79a was greatly diminished in GABPalpha-deficient B cell progenitors, pro-B, and mature B cells. GABP could bind to the regulatory regions of Pax5 and Cd79a in vivo. Thus, GABP is a key regulator of B cell development, maturation, and function.
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Affiliation(s)
- Hai-Hui Xue
- Laboratory of Molecular Immunology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892-1674, USA
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147
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Walker E, Ohishi M, Davey RE, Zhang W, Cassar PA, Tanaka TS, Der SD, Morris Q, Hughes TR, Zandstra PW, Stanford WL. Prediction and Testing of Novel Transcriptional Networks Regulating Embryonic Stem Cell Self-Renewal and Commitment. Cell Stem Cell 2007; 1:71-86. [PMID: 18371337 DOI: 10.1016/j.stem.2007.04.002] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2006] [Revised: 03/16/2007] [Accepted: 04/19/2007] [Indexed: 01/07/2023]
Affiliation(s)
- Emily Walker
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, 164 College Street, Toronto, ON, M5S 3G9, Canada
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148
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Thybaud V, Le Fevre AC, Boitier E. Application of toxicogenomics to genetic toxicology risk assessment. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2007; 48:369-79. [PMID: 17567850 DOI: 10.1002/em.20304] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Based on the assumption that compounds having similar toxic modes of action induce specific gene expression changes, the toxicity of unknown compounds can be predicted after comparison of their molecular fingerprints with those obtained with compounds of known toxicity. These predictive models will therefore rely on the characterization of marker genes. Toxicogenomics (TGX) also provides mechanistic insight into the mode of toxicity, and can therefore be used as an adjunct to the standard battery of genotoxicity tests. Promising results, highlighting the ability of TGX to differentiate genotoxic from non-genotoxic carcinogens, as well as DNA-reactive from non-DNA reactive genotoxins, have been reported. Additional data suggested the possibility of ranking genotoxins according to the nature of their interactions with DNA. This new approach could contribute to the improvement of risk assessment. TGX could be applied as a follow-up testing strategy in case of positive in vitro genotoxicity findings, and could contribute to improve our ability to identify the molecular mechanism of action and to possibly better assess dose-response curves. TGX has been found to be less sensitive than the standard genotoxicity end-points, probably because it measures the whole cell population response, when compared with standard tests designed to detect rare events in a small number of cells. Further validation will be needed (1) to better link the profiles obtained with TGX to the established genotoxicity end-points, (2) to improve the gene annotation tools, and (3) to standardise study design and data analysis and to better evaluate the impact of variability between platforms and bioinformatics approaches.
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Affiliation(s)
- Véronique Thybaud
- Drug Safety Evaluation, Sanofi Aventis R&D, Vitry sur Seine, France.
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149
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Galan-Caridad JM, Harel S, Arenzana TL, Hou ZE, Doetsch FK, Mirny LA, Reizis B. Zfx controls the self-renewal of embryonic and hematopoietic stem cells. Cell 2007; 129:345-57. [PMID: 17448993 PMCID: PMC1899089 DOI: 10.1016/j.cell.2007.03.014] [Citation(s) in RCA: 189] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2006] [Revised: 10/21/2006] [Accepted: 03/02/2007] [Indexed: 01/09/2023]
Abstract
Stem cells (SC) exhibit a unique capacity for self-renewal in an undifferentiated state. It is unclear whether the self-renewal of pluripotent embryonic SC (ESC) and of tissue-specific adult SC such as hematopoietic SC (HSC) is controlled by common mechanisms. The deletion of transcription factor Zfx impaired the self-renewal but not the differentiation capacity of murine ESC; conversely, Zfx overexpression facilitated ESC self-renewal by opposing differentiation. Furthermore, Zfx deletion abolished the maintenance of adult HSC but did not affect erythromyeloid progenitors or fetal HSC. Zfx-deficient ESC and HSC showed increased apoptosis and SC-specific upregulation of stress-inducible genes. Zfx directly activated common target genes in ESC and HSC, as well as ESC-specific target genes including ESC self-renewal regulators Tbx3 and Tcl1. These studies identify Zfx as a shared transcriptional regulator of ESC and HSC, suggesting a common genetic basis of self-renewal in embryonic and adult SC.
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Affiliation(s)
- Jose M. Galan-Caridad
- Department of Microbiology, Columbia University Medical Center, New York, NY, 10032, USA
| | - Sivan Harel
- Department of Microbiology, Columbia University Medical Center, New York, NY, 10032, USA
| | - Teresita L. Arenzana
- Department of Microbiology, Columbia University Medical Center, New York, NY, 10032, USA
| | - Z. Esther Hou
- Department of Microbiology, Columbia University Medical Center, New York, NY, 10032, USA
| | - Fiona K. Doetsch
- Department of Pathology, Columbia University Medical Center, New York, NY, 10032, USA
| | - Leonid A. Mirny
- Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Boris Reizis
- Department of Microbiology, Columbia University Medical Center, New York, NY, 10032, USA
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150
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Abstract
Pluripotent stem cells, similar to more restricted stem cells, are able to both self-renew and generate differentiated progeny. Although this dual functionality has been much studied, the search for molecular signatures of 'stemness' and pluripotency is only now beginning to gather momentum. While the focus of much of this work has been on the transcriptional features of embryonic stem cells, recent studies have indicated the importance of unique epigenetic profiles that keep key developmental genes 'poised' in a repressed but activatable state. Determining how these epigenetic features relate to the transcriptional signatures of ES cells, and whether they are also important in other types of stem cell, is a key challenge for the future.
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Affiliation(s)
- Mikhail Spivakov
- Lymphocyte Development Group, MRC Clinical Sciences Centre, Imperial College School of Medicine, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
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