1
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New insights into the epitranscriptomic control of pluripotent stem cell fate. Exp Mol Med 2022; 54:1643-1651. [PMID: 36266446 PMCID: PMC9636187 DOI: 10.1038/s12276-022-00824-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 05/26/2022] [Accepted: 06/01/2022] [Indexed: 12/29/2022] Open
Abstract
Each cell in the human body has a distinguishable fate. Pluripotent stem cells are challenged with a myriad of lineage differentiation options. Defects are more likely to be fatal to stem cells than to somatic cells due to the broad impact of the former on early development. Hence, a detailed understanding of the mechanisms that determine the fate of stem cells is needed. The mechanisms by which human pluripotent stem cells, although not fully equipped with complex chromatin structures or epigenetic regulatory mechanisms, accurately control gene expression and are important to the stem cell field. In this review, we examine the events driving pluripotent stem cell fate and the underlying changes in gene expression during early development. In addition, we highlight the role played by the epitranscriptome in the regulation of gene expression that is necessary for each fate-related event.
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2
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NUCKS1 is a highly modified, chromatin-associated protein involved in a diverse set of biological and pathophysiological processes. Biochem J 2022; 479:1205-1220. [PMID: 35695515 PMCID: PMC10016235 DOI: 10.1042/bcj20220075] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 05/17/2022] [Accepted: 05/26/2022] [Indexed: 11/17/2022]
Abstract
The Nuclear Casein and Cyclin-dependent Kinase Substrate 1 (NUCKS1) protein is highly conserved in vertebrates, predominantly localized to the nucleus and one of the most heavily modified proteins in the human proteome. NUCKS1 expression is high in stem cells and the brain, developmentally regulated in mice and associated with several diverse malignancies in humans, including cancer, metabolic syndrome and Parkinson's disease. NUCKS1 function has been linked to modulating chromatin architecture and transcription, DNA repair and cell cycle regulation. In this review, we summarize and discuss the published information on NUCKS1 and highlight the questions that remain to be addressed to better understand the complex biology of this multifaceted protein.
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3
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Minor Allele Frequencies and Molecular Pathways Differences for SNPs Associated with Amyotrophic Lateral Sclerosis in Subjects Participating in the UKBB and 1000 Genomes Project. J Clin Med 2021; 10:jcm10153394. [PMID: 34362180 PMCID: PMC8348602 DOI: 10.3390/jcm10153394] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 07/12/2021] [Accepted: 07/28/2021] [Indexed: 12/25/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a complex disease with a late onset and is characterized by the progressive loss of muscular and respiratory functions. Although recent studies have partially elucidated ALS's mechanisms, many questions remain such as what the most important molecular pathways involved in ALS are and why there is such a large difference in ALS onset among different populations. In this study, we addressed this issue with a bioinformatics approach, using the United Kingdom Biobank (UKBB) and the European 1000 Genomes Project (1KG) in order to analyze the most ALS-representative single nucleotide polymorphisms (SNPs) that differ for minor allele frequency (MAF) between the United Kingdom population and some European populations including Finnish in Finland, Iberian population in Spain, and Tuscans in Italy. We found 84 SNPs associated with 46 genes that are involved in different pathways including: "Ca2+ activated K+ channels", "cGMP effects", "Nitric oxide stimulates guanylate cyclase", "Proton/oligopeptide cotransporters", and "Signaling by MAPK mutants". In addition, we revealed that 83% of the 84 SNPs can alter transcription factor-motives binding sites of 224 genes implicated in "Regulation of beta-cell development", "Transcription-al regulation by RUNX3", "Transcriptional regulation of pluripotent stem cells", and "FOXO-mediated transcription of cell death genes". In conclusion, the genes and pathways analyzed could explain the cause of the difference of ALS onset.
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4
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Swaidan NT, Salloum-Asfar S, Palangi F, Errafii K, Soliman NH, Aboughalia AT, Wali AHS, Abdulla SA, Emara MM. Identification of potential transcription factors that enhance human iPSC generation. Sci Rep 2020; 10:21950. [PMID: 33319795 PMCID: PMC7738555 DOI: 10.1038/s41598-020-78932-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 11/25/2020] [Indexed: 11/09/2022] Open
Abstract
Although many factors have been identified and used to enhance the iPSC reprogramming process, its efficiency remains quite low. In addition, reprogramming efficacy has been evidenced to be affected by disease mutations that are present in patient samples. In this study, using RNA-seq platform we have identified and validated the differential gene expression of five transcription factors (TFs) (GBX2, NANOGP8, SP8, PEG3, and ZIC1) that were associated with a remarkable increase in the number of iPSC colonies generated from a patient with Parkinson's disease. We have applied different bioinformatics tools (Gene ontology, protein-protein interaction, and signaling pathways analyses) to investigate the possible roles of these TFs in pluripotency and developmental process. Interestingly, GBX2, NANOGP8, SP8, PEG3, and ZIC1 were found to play a role in maintaining pluripotency, regulating self-renewal stages, and interacting with other factors that are involved in pluripotency regulation including OCT4, SOX2, NANOG, and KLF4. Therefore, the TFs identified in this study could be used as additional transcription factors that enhance reprogramming efficiency to boost iPSC generation technology.
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Affiliation(s)
- Nuha T Swaidan
- Neurological Disorders Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Education City, Qatar Foundation (QF), Doha, Qatar
| | - Salam Salloum-Asfar
- Neurological Disorders Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Education City, Qatar Foundation (QF), Doha, Qatar
| | - Freshteh Palangi
- Neurological Disorders Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Education City, Qatar Foundation (QF), Doha, Qatar
| | - Khaoula Errafii
- Genomics Core Facility, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Education City, Qatar Foundation, Doha, Qatar.,College of Health and Life Sciences, Hamad Bin Khalifa University, Education City, Qatar Foundation, Doha, Qatar
| | - Nada H Soliman
- Basic Medical Sciences Department, College of Medicine, QU Health, Qatar University, Doha, Qatar
| | - Ahmed T Aboughalia
- Basic Medical Sciences Department, College of Medicine, QU Health, Qatar University, Doha, Qatar
| | - Abdul Haseeb S Wali
- Basic Medical Sciences Department, College of Medicine, QU Health, Qatar University, Doha, Qatar
| | - Sara A Abdulla
- Neurological Disorders Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Education City, Qatar Foundation (QF), Doha, Qatar.
| | - Mohamed M Emara
- Basic Medical Sciences Department, College of Medicine, QU Health, Qatar University, Doha, Qatar. .,Biomedical and Pharmaceutical Research Unit, QU Health, Qatar University, Doha, Qatar.
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5
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Zhang N, Zhao C, Zhang X, Cui X, Zhao Y, Yang J, Gao X. Growth arrest-specific 2 protein family: Structure and function. Cell Prolif 2020; 54:e12934. [PMID: 33103301 PMCID: PMC7791176 DOI: 10.1111/cpr.12934] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 09/29/2020] [Accepted: 10/03/2020] [Indexed: 12/15/2022] Open
Abstract
Members of the growth arrest–specific 2 (GAS2) protein family consist of a putative actin‐binding (CH) domain and a microtubule‐binding (GAR) domain and are considered miniversions of spectraplakins. There are four members in the GAS2 family, viz. GAS2, GAS2L1, GAS2L2 and GAS2L3. Although GAS2 is defined as a family of growth arrest–specific proteins, the significant differences in the expression patterns, interaction characteristics and biological issues or diseases among the different GAS2 family members have not been systemically reviewed to date. Therefore, we summarized the available evidence on the structures and functions of GAS2 family members. This review facilitates a comprehensive molecular understanding of the involvement of the GAS2 family members in an array of biological processes, including cytoskeleton reorganization, cell cycle, apoptosis and cancer development.
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Affiliation(s)
- Nan Zhang
- Department of Biochemistry and Molecular Biology, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China.,Key Laboratory of Immune Microenvironment and Disease, Ministry of Education, Key Laboratory of Cellular and Molecular Immunology in Tianjin, Excellent Talent Project, Tianjin Medical University, Tianjin, China
| | - Chunyan Zhao
- Department of Biochemistry and Molecular Biology, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China.,Key Laboratory of Immune Microenvironment and Disease, Ministry of Education, Key Laboratory of Cellular and Molecular Immunology in Tianjin, Excellent Talent Project, Tianjin Medical University, Tianjin, China
| | - Xinxin Zhang
- Department of Biochemistry and Molecular Biology, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China.,Key Laboratory of Immune Microenvironment and Disease, Ministry of Education, Key Laboratory of Cellular and Molecular Immunology in Tianjin, Excellent Talent Project, Tianjin Medical University, Tianjin, China
| | - Xiaoteng Cui
- Department of Biochemistry and Molecular Biology, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China.,Key Laboratory of Immune Microenvironment and Disease, Ministry of Education, Key Laboratory of Cellular and Molecular Immunology in Tianjin, Excellent Talent Project, Tianjin Medical University, Tianjin, China.,Laboratory of Neuro-Oncology, Tianjin Neurological Institute, Department of Neurosurgery, Tianjin Medical University General Hospital and Key Laboratory of Neurotrauma, Variation, and Regeneration, Ministry of Education and Tianjin Municipal Government, Tianjin, China
| | - Yan Zhao
- Department of Biochemistry and Molecular Biology, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China.,Key Laboratory of Immune Microenvironment and Disease, Ministry of Education, Key Laboratory of Cellular and Molecular Immunology in Tianjin, Excellent Talent Project, Tianjin Medical University, Tianjin, China
| | - Jie Yang
- Department of Biochemistry and Molecular Biology, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China.,Key Laboratory of Immune Microenvironment and Disease, Ministry of Education, Key Laboratory of Cellular and Molecular Immunology in Tianjin, Excellent Talent Project, Tianjin Medical University, Tianjin, China
| | - Xingjie Gao
- Department of Biochemistry and Molecular Biology, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China.,Key Laboratory of Immune Microenvironment and Disease, Ministry of Education, Key Laboratory of Cellular and Molecular Immunology in Tianjin, Excellent Talent Project, Tianjin Medical University, Tianjin, China
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6
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Grundt K, Thiede B, Østvold AC. Identification of kinases phosphorylating 13 sites in the nuclear, DNA-binding protein NUCKS. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1865:359-369. [PMID: 28011258 DOI: 10.1016/j.bbapap.2016.12.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 12/05/2016] [Accepted: 12/19/2016] [Indexed: 12/27/2022]
Abstract
NUCKS is a vertebrate specific, nuclear and DNA-binding phospho protein. The protein is highly expressed in rapidly dividing cells, and is overexpressed in a number of cancer tissues. The phosphorylation of NUCKS is cell cycle and DNA-damage regulated, but little is known about the responsible kinases. By utilizing in vitro and in vivo phosphorylation assays using isolated NUCKS as well as synthetic NUCKS-derived peptides in combination with mass spectrometry, phosphopeptide mapping, phosphphoamino acid analyses, phosphospecific antibodies and the use of specific kinase inhibitors, we found that NUCKS is phosphorylated on 11 sites by CK2. At least 7 of the CK2 sites are phosphorylated in vivo. We also found that NUCKS is phosphorylated on two sites by ATM kinase and DNA-PK in vitro, and is phosphorylated in vivo by ATM kinase in γ-irradiated cells. All together, we identified three kinases phosphorylating 13 out of 39 in vivo phosphorylated sites in mammalian NUCKS. The identification of CK2 and PIKK kinases as kinases phosphorylating NUCKS in vivo provide further evidence for the involvement of NUCKS in cell cycle control and DNA repair.
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Affiliation(s)
- Kirsten Grundt
- University of Oslo, Institute of Basic Medical Sciences, Department of Biochemistry, P.O. Box 1112, Blindern N-0317, Oslo, Norway
| | - Bernd Thiede
- University of Oslo, Department of Biosciences, P.O. Box 1066, Blindern N-0316, Oslo, Norway
| | - Anne Carine Østvold
- University of Oslo, Institute of Basic Medical Sciences, Department of Biochemistry, P.O. Box 1112, Blindern N-0317, Oslo, Norway.
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7
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Long non-coding RNA GAS5 controls human embryonic stem cell self-renewal by maintaining NODAL signalling. Nat Commun 2016; 7:13287. [PMID: 27811843 PMCID: PMC5097163 DOI: 10.1038/ncomms13287] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 09/16/2016] [Indexed: 12/18/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are known players in the regulatory circuitry of the self-renewal in human embryonic stem cells (hESCs). However, most hESC-specific lncRNAs remain uncharacterized. Here we demonstrate that growth-arrest-specific transcript 5 (GAS5), a known tumour suppressor and growth arrest-related lncRNA, is highly expressed and directly regulated by pluripotency factors OCT4 and SOX2 in hESCs. Phenotypic analysis shows that GAS5 knockdown significantly impairs hESC self-renewal, but its overexpression significantly promotes hESC self-renewal. Using RNA sequencing and functional analysis, we demonstrate that GAS5 maintains NODAL signalling by protecting NODAL expression from miRNA-mediated degradation. Therefore, we propose that the above pluripotency factors, GAS5 and NODAL form a feed-forward signalling loop that maintains hESC self-renewal. As this regulatory function of GAS5 is stem cell specific, our findings also indicate that the functions of lncRNAs may vary in different cell types due to competing endogenous mechanisms.
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8
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Player A, Oguamanam T, Okanmelu J, Burrell K, Hollomon M. Preliminary characterization of IL32 in basal-like/triple negative compared to other types of breast cell lines and tissues. BMC Res Notes 2014; 7:501. [PMID: 25100201 PMCID: PMC4132244 DOI: 10.1186/1756-0500-7-501] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Accepted: 07/31/2014] [Indexed: 02/08/2023] Open
Abstract
Background Triple negative breast cancer (TNBC) and often basal-like cancers are defined as negative for estrogen receptor, progesterone receptor and Her2 gene expression. Over the past few years an incredible amount of data has been generated defining the molecular characteristics of both cancers. The aim of these studies is to better understand the cancers and identify genes and molecular pathways that might be useful as targeted therapies. In an attempt to contribute to the understanding of basal-like/TNBC, we examined the Gene Expression Omnibus (GEO) public datasets in search of genes that might define basal-like/TNBC. The Il32 gene was identified as a candidate. Findings Analysis of several GEO datasets showed differential expression of IL32 in patient samples previously designated as basal and/or TNBC compared to normal and luminal breast samples. As validation of the GEO results, RNA and protein expression levels were examined using MCF7 and MDA MB231 cell lines and tissue microarrays (TMAs). IL32 gene expression levels were higher in MDA MB231 compared to MCF7. Analysis of TMAs showed 42% of TNBC tissues and 25% of the non-TNBC were positive for IL32, while non-malignant patient samples and all but one hyperplastic tissue sample demonstrated lower levels of IL32 protein expression. Conclusion Data obtained from several publically available GEO datasets showed overexpression of IL32 gene in basal-like/TNBC samples compared to normal and luminal samples. In support of these data, analysis of TMA clinical samples demonstrated a particular pattern of IL32 differential expression. Considered together, these data suggest IL32 is a candidate suitable for further study.
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Affiliation(s)
- Audrey Player
- The Department of Biology, Texas Southern University, Houston, Texas 77004, USA.
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9
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Drosos Y, Kouloukoussa M, Ostvold AC, Havaki S, Katsantoni E, Marinos E, Aleporou-Marinou V. Dynamic expression of the vertebrate-specific protein Nucks during rodent embryonic development. Gene Expr Patterns 2013; 14:19-29. [PMID: 24140890 DOI: 10.1016/j.gep.2013.10.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2013] [Revised: 09/23/2013] [Accepted: 10/07/2013] [Indexed: 11/15/2022]
Abstract
The nuclear casein kinase and cyclin-dependent kinase substrate 1 (NUCKS) is a highly phosphorylated nuclear protein that is overexpressed in many types of cancer. The flexibility of NUCKS and its extensive posttranslational modifications indicate that it is multifunctional, and its expression in most cell types suggests a housekeeping function. However, spatiotemporal expression of the Nucks protein during rodent development has not been reported. Thus, we investigated the expression of both the Nucks mRNA and protein during rat and mouse development by immunohistochemistry, in situ hybridization, Western immunoblotting, and reverse-transcription PCR analysis. We also used BLAST analysis against expressed sequence tag databases to determine whether a NUCKS homologue is expressed in invertebrate organisms. We found that Nucks expression increased during the initial stages of embryonic development, and then gradually decreased until birth in all tissues except the nervous tissue and muscle fibers. Interestingly, the expression of Nucks was very strong in migrating neural crest cells at E13.5 and ectoderm-derived tissues. In most tissues analyzed, the levels of Nucks correlated with the levels of Bax and activated caspase-3, which are indicative of apoptosis. Moreover, Nucks was upregulated very early during neuronal apoptosis in vitro. Expression analysis revealed that no transcript with close homology to the Nucks gene was present in invertebrates. The expression of Nucks in both proliferating and quiescent cells and its correlation with Bax levels and apoptosis strongly suggest that Nucks plays complex roles in cell homeostasis. Furthermore, the lack of homology in invertebrate organisms indicates a specific role for Nucks in vertebrate embryogenesis.
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Affiliation(s)
- Yiannis Drosos
- Department of Genetics and Biotechnology, Faculty of Biology, University of Athens, Panepistimioupoli, 15701 Ilissia, Greece.
| | - Mirsini Kouloukoussa
- Laboratory of Histology and Embryology, Medical School, University of Athens, 75 Mikras Asias Str., 11527 Goudi, Greece
| | - Anne Carine Ostvold
- Department of Biochemistry, Institute of Basic Medical Sciences, University of Oslo, PO Box 1112, Blindern, 0317 Oslo, Norway
| | - Sophia Havaki
- Laboratory of Histology and Embryology, Medical School, University of Athens, 75 Mikras Asias Str., 11527 Goudi, Greece
| | - Eleni Katsantoni
- Hematology/Oncology Division, Biomedical Research Foundation, Academy of Athens, 11527 Athens, Greece
| | - Evangelos Marinos
- Laboratory of Histology and Embryology, Medical School, University of Athens, 75 Mikras Asias Str., 11527 Goudi, Greece
| | - Vassiliki Aleporou-Marinou
- Department of Genetics and Biotechnology, Faculty of Biology, University of Athens, Panepistimioupoli, 15701 Ilissia, Greece
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10
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Harvey AJ, Mao S, Lalancette C, Krawetz SA, Brenner CA. Transcriptional differences between rhesus embryonic stem cells generated from in vitro and in vivo derived embryos. PLoS One 2012; 7:e43239. [PMID: 23028448 PMCID: PMC3445581 DOI: 10.1371/journal.pone.0043239] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2012] [Accepted: 07/18/2012] [Indexed: 01/16/2023] Open
Abstract
Numerous studies have focused on the transcriptional signatures that underlie the maintenance of embryonic stem cell (ESC) pluripotency. However, it remains unclear whether ESC retain transcriptional aberrations seen in in vitro cultured embryos. Here we report the first global transcriptional profile comparison between ESC generated from either in vitro cultured or in vivo derived primate embryos by microarray analysis. Genes involved in pluripotency, oxygen regulation and the cell cycle were downregulated in rhesus ESC generated from in vitro cultured embryos (in vitro ESC). Significantly, several gene differences are similarly downregulated in preimplantation embryos cultured in vitro, which have been associated with long term developmental consequences and disease predisposition. This data indicates that prior to derivation, embryo quality may influence the molecular signature of ESC lines, and may differentially impact the physiology of cells prior to or following differentiation.
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Affiliation(s)
- Alexandra J Harvey
- Department of Physiology, Wayne State University, Detroit, Michigan, United States of America.
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11
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Yung S, Ledran M, Moreno-Gimeno I, Conesa A, Montaner D, Dopazo J, Dimmick I, Slater NJ, Marenah L, Real PJ, Paraskevopoulou I, Bisbal V, Burks D, Santibanez-Koref M, Moreno R, Mountford J, Menendez P, Armstrong L, Lako M. Large-scale transcriptional profiling and functional assays reveal important roles for Rho-GTPase signalling and SCL during haematopoietic differentiation of human embryonic stem cells. Hum Mol Genet 2011; 20:4932-46. [PMID: 21937587 DOI: 10.1093/hmg/ddr431] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Understanding the transcriptional cues that direct differentiation of human embryonic stem cells (hESCs) and human-induced pluripotent stem cells to defined and functional cell types is essential for future clinical applications. In this study, we have compared transcriptional profiles of haematopoietic progenitors derived from hESCs at various developmental stages of a feeder- and serum-free differentiation method and show that the largest transcriptional changes occur during the first 4 days of differentiation. Data mining on the basis of molecular function revealed Rho-GTPase signalling as a key regulator of differentiation. Inhibition of this pathway resulted in a significant reduction in the numbers of emerging haematopoietic progenitors throughout the differentiation window, thereby uncovering a previously unappreciated role for Rho-GTPase signalling during human haematopoietic development. Our analysis indicated that SCL was the 11th most upregulated transcript during the first 4 days of the hESC differentiation process. Overexpression of SCL in hESCs promoted differentiation to meso-endodermal lineages, the emergence of haematopoietic and erythro-megakaryocytic progenitors and accelerated erythroid differentiation. Importantly, intrasplenic transplantation of SCL-overexpressing hESC-derived haematopoietic cells enhanced recovery from induced acute anaemia without significant cell engraftment, suggesting a paracrine-mediated effect.
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Affiliation(s)
- Sun Yung
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK
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12
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Xu H, Schaniel C, Lemischka IR, Ma'ayan A. Toward a complete in silico, multi-layered embryonic stem cell regulatory network. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2011; 2:708-33. [PMID: 20890967 DOI: 10.1002/wsbm.93] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Recent efforts in systematically profiling embryonic stem (ES) cells have yielded a wealth of high-throughput data. Complementarily, emerging databases and computational tools facilitate ES cell studies and further pave the way toward the in silico reconstruction of regulatory networks encompassing multiple molecular layers. Here, we briefly survey databases, algorithms, and software tools used to organize and analyze high-throughput experimental data collected to study mammalian cellular systems with a focus on ES cells. The vision of using heterogeneous data to reconstruct a complete multi-layered ES cell regulatory network is discussed. This review also provides an accompanying manually extracted dataset of different types of regulatory interactions from low-throughput experimental ES cell studies available at http://amp.pharm.mssm.edu/iscmid/literature.
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Affiliation(s)
- Huilei Xu
- Department of Gene and Cell Medicine and The Black Family Stem Cell Institute, Mount Sinai School of Medicine, New York, NY 10029, USA
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13
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Galán A, Montaner D, Póo ME, Valbuena D, Ruiz V, Aguilar C, Dopazo J, Simón C. Functional genomics of 5- to 8-cell stage human embryos by blastomere single-cell cDNA analysis. PLoS One 2010; 5:e13615. [PMID: 21049019 PMCID: PMC2964308 DOI: 10.1371/journal.pone.0013615] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2010] [Accepted: 10/02/2010] [Indexed: 12/26/2022] Open
Abstract
Blastomere fate and embryonic genome activation (EGA) during human embryonic development are unsolved areas of high scientific and clinical interest. Forty-nine blastomeres from 5- to 8-cell human embryos have been investigated following an efficient single-cell cDNA amplification protocol to provide a template for high-density microarray analysis. The previously described markers, characteristic of Inner Cell Mass (ICM) (n = 120), stemness (n = 190) and Trophectoderm (TE) (n = 45), were analyzed, and a housekeeping pattern of 46 genes was established. All the human blastomeres from the 5- to 8-cell stage embryo displayed a common gene expression pattern corresponding to ICM markers (e.g., DDX3, FOXD3, LEFTY1, MYC, NANOG, POU5F1), stemness (e.g., POU5F1, DNMT3B, GABRB3, SOX2, ZFP42, TERT), and TE markers (e.g., GATA6, EOMES, CDX2, LHCGR). The EGA profile was also investigated between the 5-6- and 8-cell stage embryos, and compared to the blastocyst stage. Known genes (n = 92) such as depleted maternal transcripts (e.g., CCNA1, CCNB1, DPPA2) and embryo-specific activation (e.g., POU5F1, CDH1, DPPA4), as well as novel genes, were confirmed. In summary, the global single-cell cDNA amplification microarray analysis of the 5- to 8-cell stage human embryos reveals that blastomere fate is not committed to ICM or TE. Finally, new EGA features in human embryogenesis are presented.
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Affiliation(s)
- Amparo Galán
- Valencia Node of The National Stem Cell Bank, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain
| | - David Montaner
- Department of Bioinformatics and Genomics, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain
| | - M. Eugenia Póo
- Valencia Node of The National Stem Cell Bank, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain
| | - Diana Valbuena
- Valencia Node of The National Stem Cell Bank, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain
| | - Verónica Ruiz
- Valencia Node of The National Stem Cell Bank, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain
| | - Cristóbal Aguilar
- Valencia Node of The National Stem Cell Bank, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain
| | - Joaquín Dopazo
- Department of Bioinformatics and Genomics, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain
| | - Carlos Simón
- Valencia Node of The National Stem Cell Bank, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain
- Fundación Instituto Valenciano de Infertilidad (FIVI), Instituto Universitario IVI (IUIVI), University of Valencia, Valencia, Spain
- * E-mail:
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14
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Stroncek DF, Jin P, Ren J, Feng J, Castiello L, Civini S, Wang E, Marincola FM, Sabatino M. Quality assessment of cellular therapies: the emerging role of molecular assays. THE KOREAN JOURNAL OF HEMATOLOGY 2010; 45:14-22. [PMID: 21120158 PMCID: PMC2983004 DOI: 10.5045/kjh.2010.45.1.14] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2010] [Revised: 03/09/2010] [Accepted: 03/16/2010] [Indexed: 12/23/2022]
Abstract
Cellular therapies are becoming increasingly important in treating cancer, hematologic malignancies, autoimmune disorders, and damaged tissue. These therapies are becoming more effective and are being used more frequently, but they are also becoming more complex. As a result, quality testing is becoming an increasingly important part of cellular therapy. Cellular therapies should be tested at several points during their production. The starting material, intermediate products and the final product are usually analyzed. Products are evaluated at critical steps in the manufacturing process and at the end of production prior to the release of the product for clinical use. In addition, the donor of the starting biologic material is usually evaluated. The testing of cellular therapies for stability, consistency, comparability and potency is especially challenging. We and others have found that global gene and microRNA expression analysis is useful for comparability testing and will likely be useful for potency, stability and consistency testing. Several examples of the use of gene expression analysis for assessing cellular therapies are presented.
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Affiliation(s)
- David F Stroncek
- Cellular Therapy and Immunogenetics Sections, Department of Transfusion Medicine, Clinical Center, NIH, Bethesda, MD, USA
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King CC. Culture and preparation of human embryonic stem cells for proteomics-based applications. Methods Mol Biol 2010; 584:151-77. [PMID: 19907977 DOI: 10.1007/978-1-60761-369-5_9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
New challenges will arise as research into human embryonic stem (hES) cell differentiation moves from optimization and overcoming technical hurdles to mechanistic considerations. An immediate need will be to culture hES cells in the absence of contaminating feeder layers and allow for the preparation of purified DNA, RNA, and proteins to analyze changes in microRNA levels, gene expression, protein expression, and signal transduction. Purified, uniform populations of hES cells will allow researchers to better explore the biochemical mechanisms by which differentiation occurs.Much recent work has focused upon genetic analysis of different stem cell populations. Expected variabilities between pluripotent hES cells, mesoderm, ectoderm, and definitive endoderm have been observed in microarray profiles (1-7). Interestingly, there also appears to be significant heterogeneity in mRNA expressed in different hES cell lines (8, 9). One approach to better understand how changes in mRNA levels in differentiating stem cells and individual hES cell lines relate to cell function is to study changes in signal transduction and global changes in protein expression. This chapter describes the methods routinely employed to prepare cells for analysis by traditional biochemistry (fractionation and western blotting) and proteomic analysis (2D electrophoresis/mass spectrometry and free-flow isoelectric focusing).
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Affiliation(s)
- Charles C King
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
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Leychkis Y, Munzer SR, Richardson JL. What is stemness? STUDIES IN HISTORY AND PHILOSOPHY OF BIOLOGICAL AND BIOMEDICAL SCIENCES 2009; 40:312-320. [PMID: 19917490 DOI: 10.1016/j.shpsc.2009.09.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
This paper, addressed to both philosophers of science and stem cell biologists, aims to reduce the obscurity of and disagreements over the nature of stemness. The two most prominent current theories of stemness--the entity theory and the state theory--are both biologically and philosophically unsatisfactory. Improved versions of these theories are likely to converge. Philosophers of science can perform a much needed service in clarifying and formulating ways of testing entity and state theories of stemness. To do so, however, philosophers should acquaint themselves with the latest techniques and approaches employed by bench scientists, such as the use of proteomics, genome-wide association studies, and ChIP-on-chip arrays. An overarching theme of this paper is the desirability of bringing closer together the philosophy of science and the practice of scientific research.
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Affiliation(s)
- Yan Leychkis
- Morrison & Foerster LLP, 12531 High Bluff Road, Suite 100, San Diego, CA 92130-2040, USA.
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Tahara H, Sato M, Thurin M, Wang E, Butterfield LH, Disis ML, Fox BA, Lee PP, Khleif SN, Wigginton JM, Ambs S, Akutsu Y, Chaussabel D, Doki Y, Eremin O, Fridman WH, Hirohashi Y, Imai K, Jacobson J, Jinushi M, Kanamoto A, Kashani-Sabet M, Kato K, Kawakami Y, Kirkwood JM, Kleen TO, Lehmann PV, Liotta L, Lotze MT, Maio M, Malyguine A, Masucci G, Matsubara H, Mayrand-Chung S, Nakamura K, Nishikawa H, Palucka AK, Petricoin EF, Pos Z, Ribas A, Rivoltini L, Sato N, Shiku H, Slingluff CL, Streicher H, Stroncek DF, Takeuchi H, Toyota M, Wada H, Wu X, Wulfkuhle J, Yaguchi T, Zeskind B, Zhao Y, Zocca MB, Marincola FM. Emerging concepts in biomarker discovery; the US-Japan Workshop on Immunological Molecular Markers in Oncology. J Transl Med 2009; 7:45. [PMID: 19534815 PMCID: PMC2724494 DOI: 10.1186/1479-5876-7-45] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2009] [Accepted: 06/17/2009] [Indexed: 02/08/2023] Open
Abstract
Supported by the Office of International Affairs, National Cancer Institute (NCI), the "US-Japan Workshop on Immunological Biomarkers in Oncology" was held in March 2009. The workshop was related to a task force launched by the International Society for the Biological Therapy of Cancer (iSBTc) and the United States Food and Drug Administration (FDA) to identify strategies for biomarker discovery and validation in the field of biotherapy. The effort will culminate on October 28th 2009 in the "iSBTc-FDA-NCI Workshop on Prognostic and Predictive Immunologic Biomarkers in Cancer", which will be held in Washington DC in association with the Annual Meeting. The purposes of the US-Japan workshop were a) to discuss novel approaches to enhance the discovery of predictive and/or prognostic markers in cancer immunotherapy; b) to define the state of the science in biomarker discovery and validation. The participation of Japanese and US scientists provided the opportunity to identify shared or discordant themes across the distinct immune genetic background and the diverse prevalence of disease between the two Nations. Converging concepts were identified: enhanced knowledge of interferon-related pathways was found to be central to the understanding of immune-mediated tissue-specific destruction (TSD) of which tumor rejection is a representative facet. Although the expression of interferon-stimulated genes (ISGs) likely mediates the inflammatory process leading to tumor rejection, it is insufficient by itself and the associated mechanisms need to be identified. It is likely that adaptive immune responses play a broader role in tumor rejection than those strictly related to their antigen-specificity; likely, their primary role is to trigger an acute and tissue-specific inflammatory response at the tumor site that leads to rejection upon recruitment of additional innate and adaptive immune mechanisms. Other candidate systemic and/or tissue-specific biomarkers were recognized that might be added to the list of known entities applicable in immunotherapy trials. The need for a systematic approach to biomarker discovery that takes advantage of powerful high-throughput technologies was recognized; it was clear from the current state of the science that immunotherapy is still in a discovery phase and only a few of the current biomarkers warrant extensive validation. It was, finally, clear that, while current technologies have almost limitless potential, inadequate study design, limited standardization and cross-validation among laboratories and suboptimal comparability of data remain major road blocks. The institution of an interactive consortium for high throughput molecular monitoring of clinical trials with voluntary participation might provide cost-effective solutions.
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Affiliation(s)
- Hideaki Tahara
- Department of Surgery and Bioengineering, Advanced Clinical Research Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Marimo Sato
- Department of Surgery and Bioengineering, Advanced Clinical Research Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Magdalena Thurin
- Cancer Diagnosis Program, National Cancer Institute (NCI), National Institutes of Health (NIH), Rockville, Maryland, 20852, USA
| | - Ena Wang
- Infectious Disease and Immunogenetics Section (IDIS), Department of Transfusion Medicine, Clinical Center and Center for Human Immunology (CHI), NIH, Bethesda, Maryland, 20892, USA
| | - Lisa H Butterfield
- Departments of Medicine, Surgery and Immunology, Division of Hematology Oncology, University of Pittsburgh Cancer Institute, Pittsburgh, Pennsylvania, 15213, USA
| | - Mary L Disis
- Tumor Vaccine Group, Center for Translational Medicine in Women's Health, University of Washington, Seattle, Washington, 98195, USA
| | - Bernard A Fox
- Earle A Chiles Research Institute, Robert W Franz Research Center, Providence Portland Medical Center, and Department of Molecular Microbiology and Immunology, Oregon Health and Science University, Portland, Oregon, 97213, USA
| | - Peter P Lee
- Department of Medicine, Division of Hematology, Stanford University, Stanford, California, 94305, USA
| | - Samir N Khleif
- Cancer Vaccine Section, NCI, NIH, Bethesda, Maryland, 20892, USA
| | - Jon M Wigginton
- Discovery Medicine-Oncology, Bristol-Myers Squibb Inc., Princeton, New Jersey, USA
| | - Stefan Ambs
- Laboratory of Human Carcinogenesis, Center of Cancer Research, NCI, NIH, Bethesda, Maryland, 20892, USA
| | - Yasunori Akutsu
- Department of Frontier Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Damien Chaussabel
- Baylor Institute for Immunology Research and Baylor Research Institute, Dallas, Texas, 75204, USA
| | - Yuichiro Doki
- Department of Surgery, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Oleg Eremin
- Section of Surgery, Biomedical Research Unit, Nottingham Digestive Disease Centre, University of Nottingham, NG7 2UH, UK
| | - Wolf Hervé Fridman
- Centre de la Reserche des Cordeliers, INSERM, Paris Descarte University, 75270 Paris, France
| | | | - Kohzoh Imai
- Sapporo Medical University, School of Medicine, Sapporo, Japan
| | - James Jacobson
- Cancer Diagnosis Program, National Cancer Institute (NCI), National Institutes of Health (NIH), Rockville, Maryland, 20852, USA
| | - Masahisa Jinushi
- Department of Surgery and Bioengineering, Advanced Clinical Research Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Akira Kanamoto
- Department of Surgery and Bioengineering, Advanced Clinical Research Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | | | - Kazunori Kato
- Department of Molecular Medicine, Sapporo Medical University, School of Medicine, Sapporo, Japan
| | - Yutaka Kawakami
- Division of Cellular Signaling, Institute for Advanced Medical Research, Keio University School of Medicine, Tokyo, Japan
| | - John M Kirkwood
- Departments of Medicine, Surgery and Immunology, Division of Hematology Oncology, University of Pittsburgh Cancer Institute, Pittsburgh, Pennsylvania, 15213, USA
| | - Thomas O Kleen
- Cellular Technology Ltd, Shaker Heights, Ohio, 44122, USA
| | - Paul V Lehmann
- Cellular Technology Ltd, Shaker Heights, Ohio, 44122, USA
| | - Lance Liotta
- Department of Molecular Pathology and Microbiology, Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, Virginia, 10900, USA
| | - Michael T Lotze
- Illman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania, 15213, USA
| | - Michele Maio
- Medical Oncology and Immunotherapy, Department. of Oncology, University, Hospital of Siena, Istituto Toscano Tumori, Siena, Italy
- Cancer Bioimmunotherapy Unit, Department of Medical Oncology, Centro di Riferimento Oncologico, IRCCS, Aviano, 53100, Italy
| | - Anatoli Malyguine
- Laboratory of Cell Mediated Immunity, SAIC-Frederick, Inc. NCI-Frederick, Frederick, Maryland, 21702, USA
| | - Giuseppe Masucci
- Department of Oncology-Pathology, Karolinska Institute, Stockholm, 171 76, Sweden
| | - Hisahiro Matsubara
- Department of Frontier Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Shawmarie Mayrand-Chung
- The Biomarkers Consortium (BC), Public-Private Partnership Program, Office of the Director, NIH, Bethesda, Maryland, 20892, USA
| | - Kiminori Nakamura
- Department of Molecular Medicine, Sapporo Medical University, School of Medicine, Sapporo, Japan
| | - Hiroyoshi Nishikawa
- Department of Cancer Vaccine, Department of Immuno-gene Therapy, Mie University Graduate School of Medicine, Mie, Japan
| | - A Karolina Palucka
- Baylor Institute for Immunology Research and Baylor Research Institute, Dallas, Texas, 75204, USA
| | - Emanuel F Petricoin
- Department of Molecular Pathology and Microbiology, Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, Virginia, 10900, USA
| | - Zoltan Pos
- Infectious Disease and Immunogenetics Section (IDIS), Department of Transfusion Medicine, Clinical Center and Center for Human Immunology (CHI), NIH, Bethesda, Maryland, 20892, USA
| | - Antoni Ribas
- Department of Medicine, Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, California, 90095, USA
| | - Licia Rivoltini
- Unit of Immunotherapy of Human Tumors, IRCCS Foundation, Istituto Nazionale Tumori, Milan, 20100, Italy
| | - Noriyuki Sato
- Department of Pathology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Hiroshi Shiku
- Department of Cancer Vaccine, Department of Immuno-gene Therapy, Mie University Graduate School of Medicine, Mie, Japan
| | - Craig L Slingluff
- Department of Surgery, Division of Surgical Oncology, University of Virginia School of Medicine, Charlottesville, Virginia, 22908, USA
| | - Howard Streicher
- Cancer Therapy Evaluation Program, DCTD, NCI, NIH, Rockville, Maryland, 20892, USA
| | - David F Stroncek
- Cell Therapy Section (CTS), Department of Transfusion Medicine, Clinical Center, NIH, Bethesda, Maryland, 20892, USA
| | - Hiroya Takeuchi
- Department of Surgery, Keio University School of Medicine, Tokyo, Japan
| | - Minoru Toyota
- Department of Biochemistry, Sapporo Medical University, School of Medicine, Sapporo, Japan
| | - Hisashi Wada
- Department of Surgery, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Xifeng Wu
- Department of Epidemiology, University of Texas, MD Anderson Cancer Center, Houston, Texas, 77030, USA
| | - Julia Wulfkuhle
- Department of Molecular Pathology and Microbiology, Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, Virginia, 10900, USA
| | - Tomonori Yaguchi
- Division of Cellular Signaling, Institute for Advanced Medical Research, Keio University School of Medicine, Tokyo, Japan
| | | | - Yingdong Zhao
- Biometric Research Branch, NCI, NIH, Bethesda, Maryland, 20892, USA
| | | | - Francesco M Marincola
- Infectious Disease and Immunogenetics Section (IDIS), Department of Transfusion Medicine, Clinical Center and Center for Human Immunology (CHI), NIH, Bethesda, Maryland, 20892, USA
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van de Geijn GJM, Hersmus R, Looijenga LHJ. Recent developments in testicular germ cell tumor research. ACTA ACUST UNITED AC 2009; 87:96-113. [DOI: 10.1002/bdrc.20140] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Yamanaka factors critically regulate the developmental signaling network in mouse embryonic stem cells. Cell Res 2008; 18:1177-89. [DOI: 10.1038/cr.2008.309] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
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Player A, Wang Y, Rao M, Kawasaki E. Gene expression analysis of RNA purified from embryonic stem cells and embryoid body-derived cells using a high-throughput microarray platform. CURRENT PROTOCOLS IN STEM CELL BIOLOGY 2008; Chapter 1:Unit 1B.2. [PMID: 18785160 DOI: 10.1002/9780470151808.sc01b02s2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
In this unit, starting with purified RNA, experimental protocols for performing microarray expression analysis of embryonic stem cell lines compared to their corresponding differentiated embryocidal bodies are described. Methods for data analysis are suggested, with the goal of determining which genes are differentially expressed between the preparations. As an example, the use of the Affymetrix microarray expression platform is described, but alternative experimental options for analysis of RNA transcript levels are also summarized. This unit suggests quality control metrics, summarizes the critical parameters necessary for obtaining reproducible experimental results, and outlines quantitative PCR methods for validating microarray results.
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Vinoth KJ, Heng BC, Poonepalli A, Banerjee B, Balakrishnan L, Lu K, Hande MP, Cao T. Human embryonic stem cells may display higher resistance to genotoxic stress as compared to primary explanted somatic cells. Stem Cells Dev 2008; 17:599-607. [PMID: 18498216 DOI: 10.1089/scd.2007.0088] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The use of human embryonic stem (hES) cells in genotoxicity screening can potentially overcome the deficiencies associated with using immortalized cell lines, primary explanted somatic cells, and live animal models. Hence this study sought to compare the responses of hES cells and primary explanted somatic cells (IMR-90 cells, human fetal lung fibroblasts) to genotoxic stress, to evaluate whether hES cells can accurately reflect the normal physiology of human somatic cells. The effects of mitomycin C (MMC) on the chromosomal stability of hESC and IMR-90 was assayed and compared by fluorescence in situ hybridization (FISH) with telomere-specific peptide nucleic acid and multicolor (m) FISH techniques. The results showed that, the percentage of aberrant cells increased from 6% in the untreated control to 57.5% at the higher dose of 0.06 microg/ml MMC (9.6-fold increase) group in the case of IMR-90 cells, whereas hES cells displayed a corresponding increase from 6% to 28% (4.6-fold increase). Telomere FISH ascertained that the main types of damage induced by MMC are chromosomal breaks and the loss of telomeric signals. No fusions were observed in all samples analyzed. This was further confirmed by mFISH, which showed that fusions and translocations were not the type of aberration induced by MMC, with no such aberrations being observed in all samples analyzed. Hence, hES cells of the H1 line are apparently more resistant to MMC-induced DNA damage, as compared to the IMR-90 cells. These results highlight possible intrinsic differences in response to damaging agents between hES cells and normal somatic cells.
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Bellido-Martín L, de Frutos PG. Vitamin K-dependent actions of Gas6. VITAMINS AND HORMONES 2008; 78:185-209. [PMID: 18374195 DOI: 10.1016/s0083-6729(07)00009-x] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Gas6 (growth arrest-specific gene 6) is the last addition to the family of plasma vitamin K-dependent proteins. Gas6 was cloned and characterized in 1993 and found to be similar to the plasma anticoagulant protein S. Soon after it was recognized as a growth factor-like molecule, as it interacted with receptor tyrosine kinases (RTKs) of the TAM family; Tyro3, Axl, and MerTK. Since then, the role of Gas6, protein S, and the TAM receptors has been found to be important in inflammation, hemostasis, and cancer, making this system an interesting target in biomedicine. Gas6 employs a unique mechanism of action, interacting through its vitamin K-dependent Gla module with phosphatidylserine-containing membranes and through its carboxy-terminal LG domains with the TAM membrane receptors. The fact that these proteins are affected by anti-vitamin K therapy is discussed in detail.
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Affiliation(s)
- Lola Bellido-Martín
- Department of Cell Death and Proliferation, Institute for Biomedical Research of Barcelona, IIBB-CSIC-IDIBAPS, Barcelona 08036, Spain
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23
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Shin JW, Jin P, Fan Y, Slezak S, David-Ocampo V, Khuu HM, Read EJ, Wang E, Marincola FM, Stroncek DF. Evaluation of gene expression profiles of immature dendritic cells prepared from peripheral blood mononuclear cells. Transfusion 2008; 48:647-57. [PMID: 18282241 DOI: 10.1111/j.1537-2995.2007.01615.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
BACKGROUND Dendritic cells (DCs) generated ex vivo from peripheral blood monocytes or mobilized CD34+ cells and intended for clinical immunotherapy are typically characterized by morphologic, phenotypic, and functional assays. Assay results are highly dependent on conditions used to prepare the cells, so there is no standard assay battery for clinical DC products. This study evaluated gene expression profiling for characterization of immature DCs prepared from monocytes that had been elutriated from normal donor peripheral blood mononuclear cells (PBMNCs) immediately after collection or after storage at 4 degrees C for 48 hours. STUDY DESIGN AND METHODS RNA was isolated from fresh and 48-hour-stored PBMNCs, elutriated monocytes, elutriated lymphocytes, and immature DCs from five healthy subjects and was analyzed with a cDNA gene expression microarray with 17,500 genes. RESULTS Unsupervised hierarchical clustering separated the 40 products into four groups: one with all 10 immature DCs, one with all 10 elutriated lymphocytes, one with 7 PBMNCs, and one with 10 elutriated monocytes and 3 PBMNCs. Within each of the four groups, however, fresh and stored products, or products derived from fresh or stored products, clustered together. Comparison of genes differentially expressed by fresh versus stored products (paired t tests, p < 0.005) found 273 genes that differed between fresh and stored PBMCs, 429 between lymphocytes elutriated from fresh versus stored PBMNCs, 711 between monocytes elutriated from fresh versus stored PBMNCs, and 3 between immature DCs prepared from monocytes elutriated from fresh versus stored PBMCs. CONCLUSIONS This study demonstrates the potential utility of gene expression profiling for characterization of cell therapy products.
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Affiliation(s)
- Jeong Won Shin
- Department of Transfusion Medicine, NIH Clinical Center, National Institutes of Health, Bethesda, Maryland 20892-1184, USA
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Winkler DA. Network models in drug discovery and regenerative medicine. BIOTECHNOLOGY ANNUAL REVIEW 2008; 14:143-70. [PMID: 18606362 DOI: 10.1016/s1387-2656(08)00005-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Network motifs and modelling paradigms are attracting increasing attention as modelling tools in drug design and development, and in regenerative medicine. There is a gradual but inexorable convergence between these hitherto disparate disciplines. This review summarizes some very recent work in these areas, leading to an understanding of the complementary roles networks play and factors driving this convergence: network paradigms can be excellent ways of modelling and understanding drug molecules and their action, an understanding of the robustness and vulnerabilities of biological targets may improve the efficacy of drug design and discovery, drug design has an increasingly large role to play in directing stem cell properties, stem cell regulatory networks can be modelled in useful ways using network models at a reasonable level of scale, and the network tools of drug design are also very useful for the design of biomaterials used in regenerative medicine.
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Affiliation(s)
- David A Winkler
- CSIRO Molecular and Health Technologies, Clayton 3168, Australia.
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Langton S, Gudas LJ. CYP26A1 knockout embryonic stem cells exhibit reduced differentiation and growth arrest in response to retinoic acid. Dev Biol 2007; 315:331-54. [PMID: 18241852 DOI: 10.1016/j.ydbio.2007.12.021] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2007] [Revised: 12/13/2007] [Accepted: 12/17/2007] [Indexed: 01/08/2023]
Abstract
CYP26A1, a cytochrome P450 enzyme, metabolizes all-trans-retinoic acid (RA) into polar metabolites, e.g. 4-oxo-RA and 4-OH-RA. To determine if altering RA metabolism affects embryonic stem (ES) cell differentiation, we disrupted both alleles of Cyp26a1 by homologous recombination. CYP26a1(-/-) ES cells had a 11.0+/-3.2-fold higher intracellular RA concentration than Wt ES cells after RA treatment for 48 h. RA-treated CYP26A1(-/-) ES cells exhibited 2-3 fold higher mRNA levels of Hoxa1, a primary RA target gene, than Wt ES cells. Despite increased intracellular RA levels, CYP26a1(-/-) ES cells were more resistant than Wt ES cells to RA-induced proliferation arrest. Transcripts for parietal endodermal differentiation markers, including laminin, J6(Hsp 47), and J31(SPARC, osteonectin) were expressed at lower levels in RA-treated CYP26a1(-/-) ES cells, indicating that the lack of CYP26A1 activity inhibits RA-associated differentiation. Microarray analyses revealed that RA-treated CYP26A1(-/-) ES cells exhibited lower mRNA levels than Wt ES cells for genes involved in differentiation, particularly in neural (Epha4, Pmp22, Nrp1, Gap43, Ndn) and smooth muscle differentiation (Madh3, Nrp1, Tagln Calponin, Caldesmon1). In contrast, genes involved in the stress response (e.g. Tlr2, Stk2, Fcgr2b, Bnip3, Pdk1) were expressed at higher levels in CYP26A1(-/-) than in Wt ES cells without RA. Collectively, our results show that CYP26A1 activity regulates intracellular RA levels, cell proliferation, transcriptional regulation of primary RA target genes, and ES cell differentiation to parietal endoderm.
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Affiliation(s)
- Simne Langton
- Department of Pharmacology, Weill Cornell Medical College, 1300 York Avenue, Rm. E-409, New York, NY 10021, USA
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Jin VX, O’Geen H, Iyengar S, Green R, Farnham PJ. Identification of an OCT4 and SRY regulatory module using integrated computational and experimental genomics approaches. Genome Res 2007; 17:807-17. [PMID: 17567999 PMCID: PMC1891340 DOI: 10.1101/gr.6006107] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
ChIP-chip studies have revealed that many in vivo binding sites have a weak match to the consensus sequence for the transcription factor being analyzed. Possible explanations for these observations include (1) the in vitro-derived consensus site does not represent the in vivo binding site and/or (2) the factor is recruited to a weak binding site via interaction with another protein. To address these possibilities, we developed an approach (ChIPMotifs) that incorporates a bootstrap resampling method to statistically infer the optimal cutoff threshold for a position weight matrix (PWM) of a motif identified from ChIP-chip data by ab initio motif discovery programs. Using OCT4 ChIP-chip data and the ChIPMotifs approach, we first developed a refined OCT4 PWM. We then used the refined PWM and a ChIPModules approach to identify transcription factors colocalizing with OCT4 in Ntera2 testicular embryonal carcinoma cells. We found that the consensus binding site for SRY, a transcription factor critical for testis development, colocalizes with the OCT4 PWM. To further characterize the relationship between OCT4 and SRY, we performed ChIP-chip experiments with human promoter microarrays, and found that 49% of the top approximately 1000 OCT4 target promoters were also bound by SRY. This analysis represents the first identification of SRY target promoters. Interestingly, we determined that promoters bound by OCT4 and SRY, but not those bound by SRY alone, were also bound by the transcriptional repressor KAP1. Our studies not only validate the ChIPMotifs and ChIPModules combinatorial approach but also identify a possible new regulatory partner of OCT4.
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Affiliation(s)
- Victor X. Jin
- Department of Pharmacology and the Genome Center, University of California–Davis, Davis, California 95616, USA
| | - Henriette O’Geen
- Department of Pharmacology and the Genome Center, University of California–Davis, Davis, California 95616, USA
| | - Sushma Iyengar
- Department of Pharmacology and the Genome Center, University of California–Davis, Davis, California 95616, USA
| | - Roland Green
- NimbleGen Systems, Inc., Madison, Wisconsin 53711, USA
| | - Peggy J. Farnham
- Department of Pharmacology and the Genome Center, University of California–Davis, Davis, California 95616, USA
- Corresponding author.E-mail ; fax (530) 754-9658
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Stroncek DF, Jin P, Wang E, Jett B. Potency analysis of cellular therapies: the emerging role of molecular assays. J Transl Med 2007; 5:24. [PMID: 17537259 PMCID: PMC1891278 DOI: 10.1186/1479-5876-5-24] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2007] [Accepted: 05/30/2007] [Indexed: 12/22/2022] Open
Abstract
Potency testing is an important part of the evaluation of cellular therapy products. Potency assays are quantitative measures of a product-specific biological activity that is linked to a relevant biological property and, ideally, a product's in vivo mechanism of action. Both in vivo and in vitro assays can be used for potency testing. Since there is often a limited period of time between the completion of production and the release from the laboratory for administration to the patient, in vitro assays such are flow cytometry, ELISA, and cytotoxicity are typically used. Better potency assays are needed to assess the complex and multiple functions of cellular therapy products, some of which are not well understood. Gene expression profiling using microarray technology has been widely and effectively used to assess changes of cells in response to stimuli and to classify cancers. Preliminary studies have shown that the expression of noncoding microRNA which play an important role in cellular development, differentiation, metabolism and signal transduction can distinguish different types of stem cells and leukocytes. Both gene and microRNA expression profiling have the potential to be important tools for testing the potency of cellular therapies. Potency testing, the complexities associated with potency testing of cellular therapies, and the potential role of gene and microRNA expression microarrays in potency testing of cellular therapies is discussed.
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Affiliation(s)
- David F Stroncek
- Department of Transfusion Medicine, Clinical Center, National Institutes of Health, Bethesda MD, 20892, USA
| | - Ping Jin
- Department of Transfusion Medicine, Clinical Center, National Institutes of Health, Bethesda MD, 20892, USA
| | - Ena Wang
- Department of Transfusion Medicine, Clinical Center, National Institutes of Health, Bethesda MD, 20892, USA
| | - Betsy Jett
- Department of Transfusion Medicine, Clinical Center, National Institutes of Health, Bethesda MD, 20892, USA
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28
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Abstract
Gene expression analyses of stem cells (SCs) will help to uncover or further define signaling pathways and molecular mechanisms involved in the maintenance of self-renewal, pluripotency, and/or multipotency. In recent years, proteomic approaches have produced a wealth of data identifying proteins and mechanisms involved in SC proliferation and differentiation. Although many proteomics techniques have been developed and improved in peptide and protein separation, as well as mass spectrometry, several important issues, including sample heterogeneity, post-translational modifications, protein-protein interaction, and high-throughput quantification of hydrophobic and low-abundance proteins, still remain to be addressed and require further technical optimization. This review summarizes the methodologies used and the information gathered with proteome analyses of SCs, and it discusses biological and technical challenges for proteomic study of SCs. Disclosure of potential conflicts of interest is found at the end of this article.
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29
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Sharova LV, Sharov AA, Piao Y, Shaik N, Sullivan T, Stewart CL, Hogan BL, Ko MS. Global gene expression profiling reveals similarities and differences among mouse pluripotent stem cells of different origins and strains. Dev Biol 2007; 307:446-59. [PMID: 17560561 PMCID: PMC2000702 DOI: 10.1016/j.ydbio.2007.05.004] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2006] [Revised: 05/01/2007] [Accepted: 05/04/2007] [Indexed: 10/23/2022]
Abstract
Pluripotent stem cell lines with similar phenotypes can be derived from both blastocysts (embryonic stem cells, ESC) and primordial germ cells (embryonic germ cells, EGC). Here, we present a compendium DNA microarray analysis of multiple mouse ESCs and EGCs from different genetic backgrounds (strains 129 and C57BL/6) cultured under standard conditions and in differentiation-promoting conditions by the withdrawal of Leukemia Inhibitory Factor (LIF) or treatment with retinoic acid (RA). All pluripotent cell lines showed similar gene expression patterns, which separated them clearly from other tissue stem cells with lower developmental potency. Differences between pluripotent lines derived from different sources (ESC vs. EGC) were smaller than differences between lines derived from different mouse strains (129 vs. C57BL/6). Even in the differentiation-promoting conditions, these pluripotent cells showed the same general trends of gene expression changes regardless of their origin and genetic background. These data indicate that ESCs and EGCs are indistinguishable based on global gene expression patterns alone. On the other hand, a detailed comparison between a group of ESC lines and a group of EGC lines identified 20 signature genes whose average expression levels were consistently higher in ESC lines, and 84 signature genes whose average expression levels were consistently higher in EGC lines, irrespective of mouse strains. Similar analysis identified 250 signature genes whose average expression levels were consistently higher in a group of 129 cell lines, and 337 signature genes whose average expression levels were consistently higher in a group of C57BL/6 cell lines. Although none of the genes was exclusively expressed in either ESCs versus EGCs or 129 versus C57BL/6, in combination these signature genes provide a reliable separation and identification of each cell type. Differentiation-promoting conditions also revealed some minor differences between the cell lines. For example, in the presence of RA, EGCs showed a lower expression of muscle- and cardiac-related genes and a higher expression of gonad-related genes than ESCs. Taken together, the results provide a rich source of information about the similarities and differences between ESCs and EGCs as well as 129 lines and C57BL/6 lines. Such information will be crucial to our understanding of pluripotent stem cells. The results also underscore the importance of studying multiple cell lines from different strains when making comparisons based on gene expression analysis.
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Affiliation(s)
- Lioudmila V. Sharova
- Laboratory of Genetics, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Alexei A. Sharov
- Laboratory of Genetics, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Yulan Piao
- Laboratory of Genetics, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Nabeebi Shaik
- Laboratory of Genetics, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Terry Sullivan
- Cancer and Developmental Biology Laboratory, National Cancer Institute, NIH, Frederick, MD 21702, USA
| | - Colin L. Stewart
- Cancer and Developmental Biology Laboratory, National Cancer Institute, NIH, Frederick, MD 21702, USA
| | - Brigid L.M. Hogan
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Minoru S.H. Ko
- Laboratory of Genetics, National Institute on Aging, NIH, Baltimore, MD 21224, USA
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30
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Assou S, Le Carrour T, Tondeur S, Ström S, Gabelle A, Marty S, Nadal L, Pantesco V, Réme T, Hugnot JP, Gasca S, Hovatta O, Hamamah S, Klein B, De Vos J. A meta-analysis of human embryonic stem cells transcriptome integrated into a web-based expression atlas. Stem Cells 2007; 25:961-73. [PMID: 17204602 PMCID: PMC1906587 DOI: 10.1634/stemcells.2006-0352] [Citation(s) in RCA: 274] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Microarray technology provides a unique opportunity to examine gene expression patterns in human embryonic stem cells (hESCs). We performed a meta-analysis of 38 original studies reporting on the transcriptome of hESCs. We determined that 1,076 genes were found to be overexpressed in hESCs by at least three studies when compared to differentiated cell types, thus composing a "consensus hESC gene list." Only one gene was reported by all studies: the homeodomain transcription factor POU5F1/OCT3/4. The list comprised other genes critical for pluripotency such as the transcription factors NANOG and SOX2, and the growth factors TDGF1/CRIPTO and Galanin. We show that CD24 and SEMA6A, two cell surface protein-coding genes from the top of the consensus hESC gene list, display a strong and specific membrane protein expression on hESCs. Moreover, CD24 labeling permits the purification by flow cytometry of hESCs cocultured on human fibroblasts. The consensus hESC gene list also included the FZD7 WNT receptor, the G protein-coupled receptor GPR19, and the HELLS helicase, which could play an important role in hESCs biology. Conversely, we identified 783 genes downregulated in hESCs and reported in at least three studies. This "consensus differentiation gene list" included the IL6ST/GP130 LIF receptor. We created an online hESC expression atlas, http://amazonia.montp.inserm.fr, to provide an easy access to this public transcriptome dataset. Expression histograms comparing hESCs to a broad collection of fetal and adult tissues can be retrieved with this web tool for more than 15,000 genes.
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Affiliation(s)
- Said Assou
- Centre Hospitalier Universitaire de Montpellier, Institute for Research in Biotherapy, Hôpital Saint-Eloi, 80 Avenue Augustin Fliche, 34295 Montpellier Cedex 5, France.
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