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Liu Z, Feng Q, Sun P, Lu Y, Yang M, Zhang X, Jin X, Li Y, Lu SJ, Quan C. Genome-wide DNA methylation drives human embryonic stem cell erythropoiesis by remodeling gene expression dynamics. Epigenomics 2017; 9:1543-1558. [PMID: 29135282 DOI: 10.2217/epi-2017-0039] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
AIM To investigate the role of DNA methylation during erythrocyte production by human embryonic stem cells (hESCs). METHODS We employed an erythroid differentiation model from hESCs, and then tracked the genome-wide DNA methylation maps and gene expression patterns through an Infinium HumanMethylation450K BeadChip and an Ilumina Human HT-12 v4 Expression Beadchip, respectively. RESULTS A negative correlation between DNA methylation and gene expression was substantially enriched during the later differentiation stage and was present in both the promoter and the gene body. Moreover, erythropoietic genes with differentially methylated CpG sites that were primarily enriched in nonisland regions were upregulated, and demethylation of their gene bodies was associated with the presence of enhancers and DNase I hypersensitive sites. Finally, the components of JAK-STAT-NF-κB signaling were DNA hypomethylated and upregulated, which targets the key genes for erythropoiesis. CONCLUSION Erythroid lineage commitment by hESCs requires genome-wide DNA methylation modifications to remodel gene expression dynamics.
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Affiliation(s)
- Zhijing Liu
- Department of Pathology, Qingdao Municipal Hospital, Affiliated with Qingdao University, 1 Jiaozhou Road, Qingdao 266000, Shandong, China
| | - Qiang Feng
- Vcanbio Center for Translational Biotechnology, 21 Strathmore Road, Natick, MA 01760, USA
| | - Pengpeng Sun
- Department of Critical Care Medicine, Qingdao Center Medical Group, Affiliated with Qingdao University, 127 Siliunan Road, Qingdao 266042, Shandong, China
| | - Yan Lu
- Department of Pathology, College of Basic Medical Sciences, Jilin University, 126 Xinmin Avenue, Changchun 130021, China
| | - Minlan Yang
- Department of Pathology, College of Basic Medical Sciences, Jilin University, 126 Xinmin Avenue, Changchun 130021, China
| | - Xiaowei Zhang
- Center for Translational Medicine, Central Hospital of Zibo, Affiliated with Shandong University, 54 Gongqingtuan Road, Zibo 255000, Shandong, China
| | - Xiangshu Jin
- Department of Pathology, College of Basic Medical Sciences, Jilin University, 126 Xinmin Avenue, Changchun 130021, China
| | - Yulin Li
- Department of Pathology, College of Basic Medical Sciences, Jilin University, 126 Xinmin Avenue, Changchun 130021, China
| | - Shi-Jiang Lu
- Vcanbio Center for Translational Biotechnology, 21 Strathmore Road, Natick, MA 01760, USA
| | - Chengshi Quan
- Department of Pathology, College of Basic Medical Sciences, Jilin University, 126 Xinmin Avenue, Changchun 130021, China
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2
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Jung KB, Son YS, Lee H, Jung CR, Kim J, Son MY. Transcriptome dynamics of human pluripotent stem cell-derived contracting cardiomyocytes using an embryoid body model with fetal bovine serum. MOLECULAR BIOSYSTEMS 2017; 13:1565-1574. [DOI: 10.1039/c7mb00174f] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Current cardiomyocyte (CM) differentiation protocols did not promote the sufficient expression of genes involved in oxidative phosphorylation for generating adult-like mature CMs.
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Affiliation(s)
- Kwang Bo Jung
- Stem Cell Research Center
- Korea Research Institute of Bioscience and Biotechnology (KRIBB)
- Daejeon 34141
- Republic of Korea
- Department of Functional Genomics
| | - Ye Seul Son
- Stem Cell Research Center
- Korea Research Institute of Bioscience and Biotechnology (KRIBB)
- Daejeon 34141
- Republic of Korea
- Department of Functional Genomics
| | - Hana Lee
- Stem Cell Research Center
- Korea Research Institute of Bioscience and Biotechnology (KRIBB)
- Daejeon 34141
- Republic of Korea
| | - Cho-Rok Jung
- Stem Cell Research Center
- Korea Research Institute of Bioscience and Biotechnology (KRIBB)
- Daejeon 34141
- Republic of Korea
- Department of Functional Genomics
| | - Janghwan Kim
- Stem Cell Research Center
- Korea Research Institute of Bioscience and Biotechnology (KRIBB)
- Daejeon 34141
- Republic of Korea
- Department of Functional Genomics
| | - Mi-Young Son
- Stem Cell Research Center
- Korea Research Institute of Bioscience and Biotechnology (KRIBB)
- Daejeon 34141
- Republic of Korea
- Department of Functional Genomics
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3
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Chen T, Wang F, Wu M, Wang ZZ. Development of hematopoietic stem and progenitor cells from human pluripotent stem cells. J Cell Biochem 2016; 116:1179-89. [PMID: 25740540 DOI: 10.1002/jcb.25097] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 01/23/2015] [Indexed: 01/04/2023]
Abstract
Human pluripotent stem cells (hPSCs), including human embryonic stem cells (hESCs) and human induced pluripotent stem cells (hiPSCs), provide a new cell source for regenerative medicine, disease modeling, drug discovery, and preclinical toxicity screening. Understanding of the onset and the sequential process of hematopoietic cells from differentiated hPSCs will enable the achievement of personalized medicine and provide an in vitro platform for studying of human hematopoietic development and disease. During embryogenesis, hemogenic endothelial cells, a specified subset of endothelial cells in embryonic endothelium, are the primary source of multipotent hematopoietic stem cells. In this review, we discuss current status in the generation of multipotent hematopoietic stem and progenitor cells from hPSCs via hemogenic endothelial cells. We also review the achievements in direct reprogramming from non-hematopoietic cells to hematopoietic stem and progenitor cells. Further characterization of hematopoietic differentiation in hPSCs will improve our understanding of blood development and expedite the development of hPSC-derived blood products for therapeutic purpose.
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Affiliation(s)
- Tong Chen
- Department of Hematology, Huashan Hospital, Fudan University, Shanghai, China
| | - Fen Wang
- Department of Hematology, Huashan Hospital, Fudan University, Shanghai, China
| | - Mengyao Wu
- Department of Hematology, Huashan Hospital, Fudan University, Shanghai, China
| | - Zack Z Wang
- Division of Hematology, Johns Hopkins University School of Medicine, Baltimore, Maryland, 21205
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4
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Harkness L, Twine NA, Abu Dawud R, Jafari A, Aldahmash A, Wilkins MR, Adjaye J, Kassem M. Molecular characterisation of stromal populations derived from human embryonic stem cells: Similarities to immortalised bone marrow derived stromal stem cells. Bone Rep 2015; 3:32-39. [PMID: 28377964 PMCID: PMC5365211 DOI: 10.1016/j.bonr.2015.07.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/01/2015] [Revised: 06/30/2015] [Accepted: 07/14/2015] [Indexed: 01/22/2023] Open
Abstract
Human bone marrow-derived stromal (skeletal) stem cells (BM-hMSC) are being employed in an increasing number of clinical trials for tissue regeneration. A limiting factor for their clinical use is the inability to obtain sufficient cell numbers. Human embryonic stem cells (hESC) can provide an unlimited source of clinical grade cells for therapy. We have generated MSC-like cells from hESC (called here hESC-stromal) that exhibit surface markers and differentiate to osteoblasts and adipocytes, similar to BM-hMSC. In the present study, we used microarray analysis to compare the molecular phenotype of hESC-stromal and immortalised BM-hMSC cells (hMSC-TERT). Of the 7379 genes expressed above baseline, only 9.3% of genes were differentially expressed between undifferentiated hESC-stromal and BM-hMSC. Following ex vivo osteoblast induction, 665 and 695 genes exhibited ≥ 2-fold change (FC) in hESC-stromal and BM-hMSC, respectively with 172 genes common to both cell types. Functional annotation of significantly changing genes revealed similarities in gene ontology between the two cell types. Interestingly, genes in categories of cell adhesion/motility and epithelial–mesenchymal transition (EMT) were highly enriched in hESC-stromal whereas genes associated with cell cycle processes were enriched in hMSC-TERT. This data suggests that while hESC-stromal cells exhibit a similar molecular phenotype to hMSC-TERT, differences exist that can be explained by ontological differences between these two cell types. hESC-stromal cells can thus be considered as a possible alternative candidate cells for hMSC, to be employed in regenerative medicine protocols. hESC-derived MSC-like cells were compared to immortalised BM-MSC. Comparison was performed using microarrays on non-induced and OB induced cells. Analysis demonstrated close hierarchical relationships and molecular phenotypes. 90.7% of genes were similarly expressed in non-induced cells. 73% of OB induced genes for both cell lines correlated with GO ontology analysis.
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Affiliation(s)
- Linda Harkness
- Molecular Endocrinology Laboratory, Odense University Hospital, University of Southern Denmark, Odense, Denmark
| | - Natalie A Twine
- Molecular Endocrinology Laboratory, Odense University Hospital, University of Southern Denmark, Odense, Denmark; NSW Systems Biology Initiative, University of New South Wales, Sydney, NSW, Australia
| | - Raed Abu Dawud
- Molecular Embryology and Aging group, Max-Planck Institute for Molecular Genetics (Department of Vertebrate Genomics), Berlin, Germany; Stem Cell Unit, Department of Anatomy, College of Medicine, King Saud University, Riyadh, Saudi Arabia; Berlin-Brandenburg Center for Regenerative Therapies, Charité-Universitätsmedizin Berlin, Campus Virchow-Klinikum, Berlin, Germany
| | - Abbas Jafari
- Molecular Endocrinology Laboratory, Odense University Hospital, University of Southern Denmark, Odense, Denmark; Danish Stem Cell Centre (DanStem), Institute of Cellular and Molecular Medicine, University of Copenhagen, Denmark
| | - Abdullah Aldahmash
- Molecular Endocrinology Laboratory, Odense University Hospital, University of Southern Denmark, Odense, Denmark; Stem Cell Unit, Department of Anatomy, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Marc R Wilkins
- NSW Systems Biology Initiative, University of New South Wales, Sydney, NSW, Australia
| | - James Adjaye
- Molecular Embryology and Aging group, Max-Planck Institute for Molecular Genetics (Department of Vertebrate Genomics), Berlin, Germany; Stem Cell Unit, Department of Anatomy, College of Medicine, King Saud University, Riyadh, Saudi Arabia; Institute for Stem Cell Research and Regenerative Medicine, Faculty of Medicine, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
| | - Moustapha Kassem
- Molecular Endocrinology Laboratory, Odense University Hospital, University of Southern Denmark, Odense, Denmark; Stem Cell Unit, Department of Anatomy, College of Medicine, King Saud University, Riyadh, Saudi Arabia; Danish Stem Cell Centre (DanStem), Institute of Cellular and Molecular Medicine, University of Copenhagen, Denmark
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5
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Kim JJ, Khalid O, Namazi A, Tu TG, Elie O, Lee C, Kim Y. Discovery of consensus gene signature and intermodular connectivity defining self-renewal of human embryonic stem cells. Stem Cells 2015; 32:1468-79. [PMID: 24519983 DOI: 10.1002/stem.1675] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Revised: 01/17/2014] [Accepted: 01/18/2014] [Indexed: 11/07/2022]
Abstract
Molecular markers defining self-renewing pluripotent embryonic stem cells (ESCs) have been identified by relative comparisons between undifferentiated and differentiated cells. Most of analysis has been done under a specific differentiation condition that may present significantly different molecular changes over others. Therefore, it is currently unclear if there are true consensus markers defining undifferentiated human ESCs (hESCs). To identify a set of key genes consistently altered during differentiation of hESCs regardless of differentiation conditions, we have performed microarray analysis on undifferentiated hESCs (H1 and H9) and differentiated EBs and validated our results using publicly available expression array datasets. We constructed consensus modules by Weighted Gene Coexpression Network Analysis and discovered novel markers that are consistently present in undifferentiated hESCs under various differentiation conditions. We have validated top markers (downregulated: LCK, KLKB1, and SLC7A3; upregulated: RhoJ, Zeb2, and Adam12) upon differentiation. Functional validation analysis of LCK in self-renewal of hESCs using LCK inhibitor or gene silencing with siLCK resulted in a loss of undifferentiation characteristics-morphological change, reduced alkaline phosphatase activity, and pluripotency gene expression, demonstrating a potential functional role of LCK in self-renewal of hESCs. We have designated hESC markers to interactive networks in the genome, identifying possible interacting partners and showing how new markers relate to each other. Furthermore, comparison of these datasets with available datasets from induced pluripotent stem cells (iPSCs) revealed that the level of these newly identified markers was correlated to the establishment of iPSCs, which may imply a potential role of these markers in gaining of cellular potency.
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Affiliation(s)
- Jeffrey J Kim
- Laboratory of Stem Cell and Cancer Epigenetic Research and Dental Research Institute, UCLA, Los Angeles, California, USA
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6
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Mournetas V, Nunes QM, Murray PA, Sanderson CM, Fernig DG. Network based meta-analysis prediction of microenvironmental relays involved in stemness of human embryonic stem cells. PeerJ 2014; 2:e618. [PMID: 25374775 PMCID: PMC4217173 DOI: 10.7717/peerj.618] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Accepted: 09/22/2014] [Indexed: 12/19/2022] Open
Abstract
Background. Human embryonic stem cells (hESCs) are pluripotent cells derived from the inner cell mass of in vitro fertilised blastocysts, which can either be maintained in an undifferentiated state or committed into lineages under determined culture conditions. These cells offer great potential for regenerative medicine, but at present, little is known about the mechanisms that regulate hESC stemness; in particular, the role of cell-cell and cell-extracellular matrix interactions remain relatively unexplored. Methods and Results. In this study we have performed an in silico analysis of cell-microenvironment interactions to identify novel proteins that may be responsible for the maintenance of hESC stemness. A hESC transcriptome of 8,934 mRNAs was assembled using a meta-analysis approach combining the analysis of microarrays and the use of databases for annotation. The STRING database was utilised to construct a protein-protein interaction network focused on extracellular and transcription factor components contained within the assembled transcriptome. This interactome was structurally studied and filtered to identify a short list of 92 candidate proteins, which may regulate hESC stemness. Conclusion. We hypothesise that this list of proteins, either connecting extracellular components with transcriptional networks, or with hub or bottleneck properties, may contain proteins likely to be involved in determining stemness.
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Affiliation(s)
- Virginie Mournetas
- Department of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool , Liverpool , United Kingdom ; Department of Biochemistry, Institute of Integrative Biology, University of Liverpool , Liverpool , United Kingdom
| | - Quentin M Nunes
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool , Liverpool , United Kingdom ; NIHR Liverpool Pancreas Biomedical Research Unit, Institute of Translational Medicine, University of Liverpool , Liverpool , United Kingdom
| | - Patricia A Murray
- Department of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool , Liverpool , United Kingdom
| | - Christopher M Sanderson
- Department of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool , Liverpool , United Kingdom
| | - David G Fernig
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool , Liverpool , United Kingdom
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7
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Polstyanoy AM, Sheina UI, Eremeev AV, Polstyanaya GN, Svetlakov AV. Isolation of germ-cell precursors from human ovary tissue. ACTA ACUST UNITED AC 2014. [DOI: 10.1134/s1990519x14030109] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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8
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Tedeschi PM, Markert EK, Gounder M, Lin H, Dvorzhinski D, Dolfi SC, Chan LLY, Qiu J, DiPaola RS, Hirshfield KM, Boros LG, Bertino JR, Oltvai ZN, Vazquez A. Contribution of serine, folate and glycine metabolism to the ATP, NADPH and purine requirements of cancer cells. Cell Death Dis 2013; 4:e877. [PMID: 24157871 PMCID: PMC3920946 DOI: 10.1038/cddis.2013.393] [Citation(s) in RCA: 196] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Revised: 08/30/2013] [Accepted: 09/03/2013] [Indexed: 01/02/2023]
Abstract
Recent observations on cancer cell metabolism indicate increased serine synthesis from glucose as a marker of poor prognosis. We have predicted that a fraction of the synthesized serine is routed to a pathway for ATP production. The pathway is composed by reactions from serine synthesis, one-carbon (folate) metabolism and the glycine cleavage system (SOG pathway). Here we show that the SOG pathway is upregulated at the level of gene expression in a subset of human tumors and that its level of expression correlates with gene signatures of cell proliferation and Myc target activation. We have also estimated the SOG pathway metabolic flux in the NCI60 tumor-derived cell lines, using previously reported exchange fluxes and a personalized model of cell metabolism. We find that the estimated rates of reactions in the SOG pathway are highly correlated with the proliferation rates of these cell lines. We also observe that the SOG pathway contributes significantly to the energy requirements of biosynthesis, to the NADPH requirement for fatty acid synthesis and to the synthesis of purines. Finally, when the PC-3 prostate cancer cell line is treated with the antifolate methotrexate, we observe a decrease in the ATP levels, AMP kinase activation and a decrease in ribonucleotides and fatty acids synthesized from [1,2-13C2]-D-glucose as the single tracer. Taken together our results indicate that the SOG pathway activity increases with the rate of cell proliferation and it contributes to the biosynthetic requirements of purines, ATP and NADPH of cancer cells.
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Affiliation(s)
- P M Tedeschi
- 1] Department of Medicine, Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA [2] Department of Pharmacology, Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
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9
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Nouspikel T. Genetic instability in human embryonic stem cells: prospects and caveats. Future Oncol 2013; 9:867-77. [DOI: 10.2217/fon.13.22] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Human embryonic stem cells (hESCs) display a leaky G1/S checkpoint and inefficient nucleotide excision repair activity. Maintenance of genomic stability in these cells mostly relies on the elimination of damaged cells by high rates of apoptosis. However, a subpopulation survives and proliferates actively, bypassing DNA damage by translesion synthesis, a known mutagenic process. Indeed, high levels of damage-induced mutations were observed in hESCs, similar to those in repair-deficient cells. The surviving cells also become more resistant to further damage, leading to a progressive enrichment of cultures in mutant cells. In long-term cultures, hESCs display features characteristic of neoplastic progression, including chromosomal anomalies often similar to those observed in embryo carcinoma. The implication of these facts for stem cell-based therapy and cancer research are discussed.
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Affiliation(s)
- Thierry Nouspikel
- Institute for Cancer Studies, University of Sheffield, Beech Hill Road, Sheffield, S10 2RX, UK
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10
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Zhu J, Adli M, Zou JY, Verstappen G, Coyne M, Zhang X, Durham T, Miri M, Deshpande V, De Jager PL, Bennett DA, Houmard JA, Muoio DM, Onder TT, Camahort R, Cowan CA, Meissner A, Epstein CB, Shoresh N, Bernstein BE. Genome-wide chromatin state transitions associated with developmental and environmental cues. Cell 2013; 152:642-54. [PMID: 23333102 DOI: 10.1016/j.cell.2012.12.033] [Citation(s) in RCA: 391] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2011] [Revised: 08/30/2012] [Accepted: 12/11/2012] [Indexed: 11/16/2022]
Abstract
Differences in chromatin organization are key to the multiplicity of cell states that arise from a single genetic background, yet the landscapes of in vivo tissues remain largely uncharted. Here, we mapped chromatin genome-wide in a large and diverse collection of human tissues and stem cells. The maps yield unprecedented annotations of functional genomic elements and their regulation across developmental stages, lineages, and cellular environments. They also reveal global features of the epigenome, related to nuclear architecture, that also vary across cellular phenotypes. Specifically, developmental specification is accompanied by progressive chromatin restriction as the default state transitions from dynamic remodeling to generalized compaction. Exposure to serum in vitro triggers a distinct transition that involves de novo establishment of domains with features of constitutive heterochromatin. We describe how these global chromatin state transitions relate to chromosome and nuclear architecture, and discuss their implications for lineage fidelity, cellular senescence, and reprogramming.
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Affiliation(s)
- Jiang Zhu
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
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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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Fang H, Jin W, Yang Y, Jin Y, Zhang J, Wang K. An organogenesis network-based comparative transcriptome analysis for understanding early human development in vivo and in vitro. BMC SYSTEMS BIOLOGY 2011; 5:108. [PMID: 21733158 PMCID: PMC3141417 DOI: 10.1186/1752-0509-5-108] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/04/2011] [Accepted: 07/06/2011] [Indexed: 12/15/2022]
Abstract
Background Integrated networks hold great promise in a variety of contexts. In a recent study, we have combined expression and interaction data to identify a putative network underlying early human organogenesis that contains two modules, the stemness-relevant module (hStemModule) and the differentiation-relevant module (hDiffModule). However, owing to its hypothetical nature, it remains unclear whether this network allows for comparative transcriptome analysis to advance our understanding of early human development, both in vivo and in vitro. Results Based on this integrated network, we here report comparisons with the context-dependent transcriptome data from a variety of sources. By viewing the network and its two modules as gene sets and conducting gene set enrichment analysis, we demonstrate the network's utility as a quantitative monitor of the stem potential versus the differentiation potential. During early human organogenesis, the hStemModule reflects the generality of a gradual loss of the stem potential. The hDiffModule indicates the stage-specific differentiation potential and is therefore not suitable for depicting an extended developmental window. Processing of cultured cells of different types further revealed that the hStemModule is a general indicator that distinguishes different cell types in terms of their stem potential. In contrast, the hDiffModule cannot distinguish between differentiated cells of different types but is able to predict differences in the differentiation potential of pluripotent cells of different origins. We also observed a significant positive correlation between each of these two modules and early embryoid bodies (EBs), which are used as in vitro differentiation models. Despite this, the network-oriented comparisons showed considerable differences between the developing embryos and the EBs that were cultured in vitro over time to try to mimic in vivo processes. Conclusions We strongly recommend the use of these two modules either when pluripotent cell types of different origins are involved or when the comparisons made are constrained to the in vivo embryos during early human organogenesis (and an equivalent in vitro differentiation models). Network-based comparative transcriptome analysis will contribute to an increase in knowledge about human embryogenesis, particularly when only transcriptome data are currently available. These advances will add an extra dimension to network applications.
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Affiliation(s)
- Hai Fang
- State Key Laboratory of Medical Genomics, Sino-French Research Center for Life Sciences and Genomics, Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Ruijin Rd, II, Shanghai 200025, China
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13
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Bahrami SB, Veiseh M, Dunn AA, Boudreau NJ. Temporal changes in Hox gene expression accompany endothelial cell differentiation of embryonic stem cells. Cell Adh Migr 2011; 5:133-41. [PMID: 21200152 DOI: 10.4161/cam.5.2.14373] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
In pluripotent embryonic stem cells (ESCs), expression of the Hox master regulatory transcription factors that play essential roles in organogenesis, angiogenesis, and maintenance of differentiated tissues, is globally suppressed. We investigated whether differentiation of endothelial cells (ECs) from mouse ESCs was accompanied by activation of distinct Hox gene expression profiles. Differentiation was observed within 3 days, as indicated by the appearance of cells expressing specific endothelial marker genes (Flk-1+ /VE-Cadherin+ ). Expression of HoxA3 and HoxD3, which drive adult endothelial cell invasion and angiogenesis, peaked at day 3 and declined thereafter, whereas expression of HoxA5 and HoxD10, which maintain a mature quiescent EC phenotype, was low at day 3, but increased over time. The temporal and reciprocal changes in HoxD3 and HoxA5 expression were accompanied by corresponding changes in expression of established downstream target genes including integrin β3 and Thrombospondin-2. Our results indicate that differentiation and maturation of ECs derived from cultured ESCs mimic changes in Hox gene expression that accompany maturation of immature angiogenic endothelium into differentiated quiescent endothelium in vivo.
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Affiliation(s)
- S Bahram Bahrami
- Department of Surgery; University of California-San Francisco, CA, USA
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14
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Zhang B, Chen B, Wu T, Xuan Z, Zhu X, Chen R. Estimating developmental states of tumors and normal tissues using a linear time-ordered model. BMC Bioinformatics 2011; 12:53. [PMID: 21310084 PMCID: PMC3223864 DOI: 10.1186/1471-2105-12-53] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2010] [Accepted: 02/11/2011] [Indexed: 11/18/2022] Open
Abstract
Background Tumor cells are considered to have an aberrant cell state, and some evidence indicates different development states appearing in the tumorigenesis. Embryonic development and stem cell differentiation are ordered processes in which the sequence of events over time is highly conserved. The "cancer attractor" concept integrates normal developmental processes and tumorigenesis into a high-dimensional "cell state space", and provides a reasonable explanation of the relationship between these two biological processes from theoretical viewpoint. However, it is hard to describe such relationship by using existed experimental data; moreover, the measurement of different development states is also difficult. Results Here, by applying a novel time-ordered linear model based on a co-bisector which represents the joint direction of a series of vectors, we described the trajectories of development process by a line and showed different developmental states of tumor cells from developmental timescale perspective in a cell state space. This model was used to transform time-course developmental expression profiles of human ESCs, normal mouse liver, ovary and lung tissue into "cell developmental state lines". Then these cell state lines were applied to observe the developmental states of different tumors and their corresponding normal samples. Mouse liver and ovarian tumors showed different similarity to early development stage. Similarly, human glioma cells and ovarian tumors became developmentally "younger". Conclusions The time-ordered linear model captured linear projected development trajectories in a cell state space. Meanwhile it also reflected the change tendency of gene expression over time from the developmental timescale perspective, and our finding indicated different development states during tumorigenesis processes in different tissues.
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Affiliation(s)
- Bo Zhang
- Laboratory of Bioinformatics and Noncoding RNA, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, PR China
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Zhang B, Chen B, Wu T, Tan Y, Qiu S, Xuan Z, Zhu X, Chen R. Estimating the quality of reprogrammed cells using ES cell differentiation expression patterns. PLoS One 2011; 6:e15336. [PMID: 21283513 PMCID: PMC3023460 DOI: 10.1371/journal.pone.0015336] [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: 09/19/2010] [Accepted: 11/07/2010] [Indexed: 02/02/2023] Open
Abstract
Somatic cells can be reprogrammed to a pluripotent state by over-expression of defined factors, and pluripotency has been confirmed by the tetraploid complementation assay. However, especially in human cells, estimating the quality of Induced Pluripotent Stem Cell(iPSC) is still difficult. Here, we present a novel supervised method for the assessment of the quality of iPSCs by estimating the gene expression profile using a 2-D “Differentiation-index coordinate”, which consists of two “developing lines” that reflects the directions of ES cell differentiation and the changes of cell states during differentiation. By applying a novel liner model to describe the differentiation trajectory, we transformed the ES cell differentiation time-course expression profiles to linear “developing lines”; and use these lines to construct the 2-D “Differentiation-index coordinate” of mouse and human. We compared the published gene expression profiles of iPSCs, ESCs and fibroblasts in mouse and human “Differentiation-index coordinate”. Moreover, we defined the Distance index to indicate the qualities of iPS cells, which based on the projection distance of iPSCs-ESCs and iPSCs-fibroblasts. The results indicated that the “Differentiation-index coordinate” can distinguish differentiation states of the different cells types. Furthermore, by applying this method to the analysis of expression profiles in the tetraploid complementation assay, we showed that the Distance index which reflected spatial distributions correlated the pluripotency of iPSCs. We also analyzed the significantly changed gene sets of “developing lines”. The results suggest that the method presented here is not only suitable for the estimation of the quality of iPS cells based on expression profiles, but also is a new approach to analyze time-resolved experimental data.
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Affiliation(s)
- Bo Zhang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, People's Republic of China
- Graduate University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Beibei Chen
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, People's Republic of China
- Graduate University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Tao Wu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Yuliang Tan
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, People's Republic of China
- Graduate University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Shuang Qiu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, People's Republic of China
- Graduate University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Zhenyu Xuan
- Department of Molecular and Cell Biology, Center for Systems Biology, University of Texas at Dallas, Richardson, Texas, United States of America
| | - Xiaopeng Zhu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, People's Republic of China
- * E-mail: (XZ); (RC)
| | - Runsheng Chen
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, People's Republic of China
- * E-mail: (XZ); (RC)
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Power KA, Fitzgerald KT, Gallagher WM. Examination of cell–host–biomaterial interactions via high-throughput technologies: A re-appraisal. Biomaterials 2010; 31:6667-74. [DOI: 10.1016/j.biomaterials.2010.05.029] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2010] [Accepted: 05/17/2010] [Indexed: 01/08/2023]
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Choi JH, Ryu YS, Kim KH, Lee YR, Cha KW, Han IS, Kwon BS. In vitro development of a hemangioblast from a human embryonic stem cell, SNUhES#3. Life Sci 2009; 85:39-45. [DOI: 10.1016/j.lfs.2009.04.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2008] [Revised: 04/01/2009] [Accepted: 04/18/2009] [Indexed: 11/26/2022]
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Mariappan D, Niemann R, Gajewski M, Winkler J, Chen S, Choorapoikayil S, Bitzer M, Schulz H, Hescheler J, Sachinidis A. Somitovasculin, a novel endothelial-specific transcript involved in the vasculature development. Arterioscler Thromb Vasc Biol 2009; 29:1823-9. [PMID: 19542019 DOI: 10.1161/atvbaha.109.190751] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
OBJECTIVE We recently isolated and characterized endothelial-like CD31(+) cells derived from mouse embryonic stem (mES) cells and identified their transcriptome. The main objective of this study was to determine the functional relevance of the transcripts of unknown function (TUF) for vasculature development. METHODS AND RESULTS We selected 2 TUFs of more than 27 to study their role for blood vessel development in zebrafish. Morpholino (MO) knockdown of the zebrafish orthologs of the first TUF (TUF1, mouse cDNA BC022623) showed disruption of the intersegmental vessels (ISV) at 2 days postfertilization as observed by live imaging of fli:EGFP-transgenic embryos. The morphants showed abnormal blood circulation, but no effect on hematopoiesis was observed as demonstrated by gata-1 in situ hybridizations. Because knockdown of TUF1 resulted in disruption of the ISV patterning we named the TUF1 somitovasculin. TUF2 has been identified as cDNA clone BC020535. The MO knockdown of TUF2 resulted in a phenotype with an enlarged heart and the embryos lacked circulation completely. CONCLUSIONS We have shown the participation of a novel transcript (named somitovasculin) in circulatory vessel development. The combination of expression profiling in differentiating mES cells and the zebrafish model has the potential for rapid identification and functional characterization of TUFs.
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Affiliation(s)
- Devi Mariappan
- University of Cologne, Center of Physiology and Pathophysiology, Institute of Neurophysiology, Cologne, Germany
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Ren J, Jin P, Wang E, Marincola FM, Stroncek DF. MicroRNA and gene expression patterns in the differentiation of human embryonic stem cells. J Transl Med 2009; 7:20. [PMID: 19309508 PMCID: PMC2669448 DOI: 10.1186/1479-5876-7-20] [Citation(s) in RCA: 140] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2009] [Accepted: 03/23/2009] [Indexed: 12/26/2022] Open
Abstract
Background The unique features of human embryonic stem (hES) cells make them the best candidate resource for both cell replacement therapy and development research. However, the molecular mechanisms responsible for the simultaneous maintenance of their self-renewal properties and undifferentiated state remain unclear. Non-coding microRNAs (miRNA) which regulate mRNA cleavage and inhibit encoded protein translation exhibit temporal or tissue-specific expression patterns and they play an important role in development timing. Results In this study, we analyzed miRNA and gene expression profiles among samples from 3 hES cell lines (H9, I6 and BG01v), differentiated embryoid bodies (EB) derived from H9 cells at different time points, and 5 adult cell types including Human Microvascular Endothelial Cells (HMVEC), Human Umbilical Vein Endothelial Cells (HUVEC), Umbilical Artery Smooth Muscle Cells (UASMC), Normal Human Astrocytes (NHA), and Lung Fibroblasts (LFB). This analysis rendered 104 miRNAs and 776 genes differentially expressed among the three cell types. Selected differentially expressed miRNAs and genes were further validated and confirmed by quantitative real-time-PCR (qRT-PCR). Especially, members of the miR-302 cluster on chromosome 4 and miR-520 cluster on chromosome 19 were highly expressed in undifferentiated hES cells. MiRNAs in these two clusters displayed similar expression levels. The members of these two clusters share a consensus 7-mer seed sequence and their targeted genes had overlapping functions. Among the targeted genes, genes with chromatin structure modification function are enriched suggesting a role in the maintenance of chromatin structure. We also found that the expression level of members of the two clusters, miR-520b and miR-302c, were negatively correlated with their targeted genes based on gene expression analysis Conclusion We identified the expression patterns of miRNAs and gene transcripts in the undifferentiation of human embryonic stem cells; among the miRNAs that are highly expressed in undifferentiated embryonic stem cells, the miR-520 cluster may be closely involved in hES cell function and its relevance to chromatin structure warrants further study.
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Affiliation(s)
- Jiaqiang Ren
- Department of Transfusion Medicine, Clinical Center, National Institute of Health, 9000 Rockville Pike, Bethesda, Maryland 20892, USA
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Abstract
Stem cells have emerged as the starting material of choice for bioprocesses to produce cells and tissues to treat degenerative, genetic, and immunological disease. Translating the biological properties and potential of stem cells into therapies will require overcoming significant cell-manufacturing and regulatory challenges. Bioprocess engineering fundamentals, including bioreactor design and process control, need to be combined with cellular systems biology principles to guide the development of next-generation technologies capable of producing cell-based products in a safe, robust, and cost-effective manner. The step-wise implementation of these bioengineering strategies will enhance cell therapy product quality and safety, expediting clinical development.
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Abstract
The shortage of organ donors for regenerative medicine has stimulated research on stem cells as a potential resource for cell-based therapy. Stem cells have been used widely for regenerative medicine applications. The development of innovative methods to generate stem cells from different sources suggests that there may be new alternatives for cell-based therapies. Here, we provide an overview of human embryonic stem cells (hES) and the methods for obtaining these cells and other broadly multipotent or pluripotent cell types. These methods include somatic cell nuclear transfer, single cell embryo biopsy, arrested embryos, altered nuclear transfer, and reprogramming somatic cells. We also discuss the use of amniotic-fluid derived stem cells (AFS) for potential patient-specific therapies.
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Hipp JA, Hipp JD, Yoo JJ, Atala A, Andersson KE. Microarray analysis of bladder smooth muscle from patients with myelomeningocele. BJU Int 2008; 102:741-6. [DOI: 10.1111/j.1464-410x.2008.07606.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Nikolova-Krstevski V, Bhasin M, Otu HH, Libermann T, Oettgen P. Gene expression analysis of embryonic stem cells expressing VE-cadherin (CD144) during endothelial differentiation. BMC Genomics 2008; 9:240. [PMID: 18498633 PMCID: PMC2440556 DOI: 10.1186/1471-2164-9-240] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2007] [Accepted: 05/22/2008] [Indexed: 11/11/2022] Open
Abstract
Background Endothelial differentiation occurs during normal vascular development in the developing embryo. This process is recapitulated in the adult when endothelial progenitor cells are generated in the bone marrow and can contribute to vascular repair or angiogenesis at sites of vascular injury or ischemia. The molecular mechanisms of endothelial differentiation remain incompletely understood. Novel approaches are needed to identify the factors that regulate endothelial differentiation. Methods Mouse embryonic stem (ES) cells were used to further define the molecular mechanisms of endothelial differentiation. By flow cytometry a population of VEGF-R2 positive cells was identified as early as 2.5 days after differentiation of ES cells, and a subset of VEGF-R2+ cells, that were CD41 positive at 3.5 days. A separate population of VEGF-R2+ stem cells expressing the endothelial-specific marker CD144 (VE-cadherin) was also identified at this same time point. Channels lined by VE-cadherin positive cells developed within the embryoid bodies (EBs) formed by differentiating ES cells. VE-cadherin and CD41 expressing cells differentiate in close proximity to each other within the EBs, supporting the concept of a common origin for cells of hematopoietic and endothelial lineages. Results Microarray analysis of >45,000 transcripts was performed on RNA obtained from cells expressing VEGF-R2+, CD41+, and CD144+ and VEGF-R2-, CD41-, and CD144-. All microarray experiments were performed in duplicate using RNA obtained from independent experiments, for each subset of cells. Expression profiling confirmed the role of several genes involved in hematopoiesis, and identified several putative genes involved in endothelial differentiation. Conclusion The isolation of CD144+ cells during ES cell differentiation from embryoid bodies provides an excellent model system and method for identifying genes that are expressed during endothelial differentiation and that are distinct from hematopoiesis.
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Affiliation(s)
- Vesna Nikolova-Krstevski
- Division of Cardiology, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Institutes of Medicine, Boston, USA.
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