51
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Wilson AA, Ying L, Liesa M, Segeritz CP, Mills JA, Shen SS, Jean J, Lonza GC, Liberti DC, Lang AH, Nazaire J, Gower AC, Müeller FJ, Mehta P, Ordóñez A, Lomas DA, Vallier L, Murphy GJ, Mostoslavsky G, Spira A, Shirihai OS, Ramirez MI, Gadue P, Kotton DN. Emergence of a stage-dependent human liver disease signature with directed differentiation of alpha-1 antitrypsin-deficient iPS cells. Stem Cell Reports 2015; 4:873-85. [PMID: 25843048 PMCID: PMC4437473 DOI: 10.1016/j.stemcr.2015.02.021] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Revised: 02/25/2015] [Accepted: 02/25/2015] [Indexed: 12/14/2022] Open
Abstract
Induced pluripotent stem cells (iPSCs) provide an inexhaustible source of cells for modeling disease and testing drugs. Here we develop a bioinformatic approach to detect differences between the genomic programs of iPSCs derived from diseased versus normal human cohorts as they emerge during in vitro directed differentiation. Using iPSCs generated from a cohort carrying mutations (PiZZ) in the gene responsible for alpha-1 antitrypsin (AAT) deficiency, we find that the global transcriptomes of PiZZ iPSCs diverge from normal controls upon differentiation to hepatic cells. Expression of 135 genes distinguishes PiZZ iPSC-hepatic cells, providing potential clues to liver disease pathogenesis. The disease-specific cells display intracellular accumulation of mutant AAT protein, resulting in increased autophagic flux. Furthermore, we detect beneficial responses to the drug carbamazepine, which further augments autophagic flux, but adverse responses to known hepatotoxic drugs. Our findings support the utility of iPSCs as tools for drug development or prediction of toxicity.
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Affiliation(s)
- Andrew A Wilson
- Center for Regenerative Medicine (CReM) of Boston University and Boston Medical Center, Boston, MA 02118, USA
| | - Lei Ying
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Marc Liesa
- Evans Center for Interdisciplinary Research, Department of Medicine, Mitochondria ARC, Boston University School of Medicine, Boston, MA 02118, USA
| | - Charis-Patricia Segeritz
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, Anne McLaren Laboratory for Regenerative Medicine and Department of Surgery, University of Cambridge, Cambridge CB2 0SZ, UK
| | - Jason A Mills
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Steven S Shen
- Division of Computational Biomedicine and Department of Pathology and Laboratory Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Jyhchang Jean
- Center for Regenerative Medicine (CReM) of Boston University and Boston Medical Center, Boston, MA 02118, USA
| | - Geordie C Lonza
- Center for Regenerative Medicine (CReM) of Boston University and Boston Medical Center, Boston, MA 02118, USA
| | - Derek C Liberti
- Center for Regenerative Medicine (CReM) of Boston University and Boston Medical Center, Boston, MA 02118, USA
| | - Alex H Lang
- Physics Department, Boston University, Boston, MA 02215, USA
| | - Jean Nazaire
- The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Adam C Gower
- Division of Computational Biomedicine and Department of Pathology and Laboratory Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Franz-Josef Müeller
- Zentrum für Integrative Psychiatrie, Universitätsklinikums Schleswig-Holstein, Kiel 24105, Germany
| | - Pankaj Mehta
- Physics Department, Boston University, Boston, MA 02215, USA
| | - Adriana Ordóñez
- Cambridge Institute for Medical Research, Cambridge CB0 2XY, UK
| | - David A Lomas
- Cambridge Institute for Medical Research, Cambridge CB0 2XY, UK
| | - Ludovic Vallier
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, Anne McLaren Laboratory for Regenerative Medicine and Department of Surgery, University of Cambridge, Cambridge CB2 0SZ, UK
| | - George J Murphy
- Center for Regenerative Medicine (CReM) of Boston University and Boston Medical Center, Boston, MA 02118, USA
| | - Gustavo Mostoslavsky
- Center for Regenerative Medicine (CReM) of Boston University and Boston Medical Center, Boston, MA 02118, USA
| | - Avrum Spira
- Division of Computational Biomedicine and Department of Pathology and Laboratory Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Orian S Shirihai
- Evans Center for Interdisciplinary Research, Department of Medicine, Mitochondria ARC, Boston University School of Medicine, Boston, MA 02118, USA
| | - Maria I Ramirez
- The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Paul Gadue
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Darrell N Kotton
- Center for Regenerative Medicine (CReM) of Boston University and Boston Medical Center, Boston, MA 02118, USA.
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52
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Thomas SM, Kagan C, Pavlovic BJ, Burnett J, Patterson K, Pritchard JK, Gilad Y. Reprogramming LCLs to iPSCs Results in Recovery of Donor-Specific Gene Expression Signature. PLoS Genet 2015; 11:e1005216. [PMID: 25950834 PMCID: PMC4423863 DOI: 10.1371/journal.pgen.1005216] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Accepted: 04/13/2015] [Indexed: 11/18/2022] Open
Abstract
Renewable in vitro cell cultures, such as lymphoblastoid cell lines (LCLs), have facilitated studies that contributed to our understanding of genetic influence on human traits. However, the degree to which cell lines faithfully maintain differences in donor-specific phenotypes is still debated. We have previously reported that standard cell line maintenance practice results in a loss of donor-specific gene expression signatures in LCLs. An alternative to the LCL model is the induced pluripotent stem cell (iPSC) system, which carries the potential to model tissue-specific physiology through the use of differentiation protocols. Still, existing LCL banks represent an important source of starting material for iPSC generation, and it is possible that the disruptions in gene regulation associated with long-term LCL maintenance could persist through the reprogramming process. To address this concern, we studied the effect of reprogramming mature LCL cultures from six unrelated donors to iPSCs on the ensuing gene expression patterns within and between individuals. We show that the reprogramming process results in a recovery of donor-specific gene regulatory signatures, increasing the number of genes with a detectable donor effect by an order of magnitude. The proportion of variation in gene expression statistically attributed to donor increases from 6.9% in LCLs to 24.5% in iPSCs (P < 10-15). Since environmental contributions are unlikely to be a source of individual variation in our system of highly passaged cultured cell lines, our observations suggest that the effect of genotype on gene regulation is more pronounced in iPSCs than in LCLs. Our findings indicate that iPSCs can be a powerful model system for studies of phenotypic variation across individuals in general, and the genetic association with variation in gene regulation in particular. We further conclude that LCLs are an appropriate starting material for iPSC generation.
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Affiliation(s)
- Samantha M. Thomas
- Department of Human Genetics, The University of Chicago, Chicago, Illinois, United States of America
| | - Courtney Kagan
- Department of Human Genetics, The University of Chicago, Chicago, Illinois, United States of America
| | - Bryan J. Pavlovic
- Department of Human Genetics, The University of Chicago, Chicago, Illinois, United States of America
| | - Jonathan Burnett
- Department of Human Genetics, The University of Chicago, Chicago, Illinois, United States of America
| | - Kristen Patterson
- Department of Human Genetics, The University of Chicago, Chicago, Illinois, United States of America
| | - Jonathan K. Pritchard
- Departments of Genetics and Biology and Howard Hughes Medical Institute, Stanford University, Stanford, California, United States of America
| | - Yoav Gilad
- Department of Human Genetics, The University of Chicago, Chicago, Illinois, United States of America
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53
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Pineault N, Boisjoli GJ. Megakaryopoiesis andex vivodifferentiation of stem cells into megakaryocytes and platelets. ACTA ACUST UNITED AC 2015. [DOI: 10.1111/voxs.12155] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- N. Pineault
- Center for Innovation; Canadian Blood Services; Ottawa ON Canada
- Department of Biochemistry, Microbiology and Immunology; University of Ottawa; Ottawa ON Canada
| | - G. J. Boisjoli
- Center for Innovation; Canadian Blood Services; Ottawa ON Canada
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54
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Kobold S, Guhr A, Kurtz A, Löser P. Human embryonic and induced pluripotent stem cell research trends: complementation and diversification of the field. Stem Cell Reports 2015; 4:914-25. [PMID: 25866160 PMCID: PMC4437486 DOI: 10.1016/j.stemcr.2015.03.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Revised: 03/06/2015] [Accepted: 03/06/2015] [Indexed: 01/06/2023] Open
Abstract
Research in human induced pluripotent stem cells (hiPSCs) is rapidly developing and there are expectations that this research may obviate the need to use human embryonic stem cells (hESCs), the ethics of which has been a subject of controversy for more than 15 years. In this study, we investigated approximately 3,400 original research papers that reported an experimental use of these types of human pluripotent stem cells (hPSCs) and were published from 2008 to 2013. We found that research into both cell types was conducted independently and further expanded, accompanied by a growing intersection of both research fields. Moreover, an in-depth analysis of papers that reported the use of both cell types indicates that hESCs are still being used as a “gold standard,” but in a declining proportion of publications. Instead, the expanding research field is diversifying and hESC and hiPSC lines are increasingly being used in more independent research and application areas. Research in hESCs and hiPSCs has recently expanded, but to different extents Research in hESCs and hiPSCs partially overlaps, but is also diversifying The “gold standard” use of hESCs is relatively declining Only a few hESC lines are predominantly used as a benchmark in hiPSC research
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Affiliation(s)
| | - Anke Guhr
- Robert Koch Institute, D-13353 Berlin, Germany
| | - Andreas Kurtz
- Berlin-Brandenburg Center for Regenerative Therapies, D-13353 Berlin, Germany; Seoul National University, Seoul 151-742, Korea.
| | - Peter Löser
- Robert Koch Institute, D-13353 Berlin, Germany.
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55
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Comparative analysis of human ex vivo-generated platelets vs megakaryocyte-generated platelets in mice: a cautionary tale. Blood 2015; 125:3627-36. [PMID: 25852052 DOI: 10.1182/blood-2014-08-593053] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Accepted: 03/30/2015] [Indexed: 02/06/2023] Open
Abstract
Thrombopoiesis is the process by which megakaryocytes release platelets that circulate as uniform small, disc-shaped anucleate cytoplasmic fragments with critical roles in hemostasis and related biology. The exact mechanism of thrombopoiesis and the maturation pathways of platelets released into the circulation remain incompletely understood. We showed that ex vivo-generated murine megakaryocytes infused into mice release platelets within the pulmonary vasculature. Here we now show that infused human megakaryocytes also release platelets within the lungs of recipient mice. In addition, we observed a population of platelet-like particles (PLPs) in the infusate, which include platelets released during ex vivo growth conditions. By comparing these 2 platelet populations to human donor platelets, we found marked differences: platelets derived from infused megakaryocytes closely resembled infused donor platelets in morphology, size, and function. On the other hand, the PLP was a mixture of nonplatelet cellular fragments and nonuniform-sized, preactivated platelets mostly lacking surface CD42b that were rapidly cleared by macrophages. These data raise a cautionary note for the clinical use of human platelets released under standard ex vivo conditions. In contrast, human platelets released by intrapulmonary-entrapped megakaryocytes appear more physiologic in nature and nearly comparable to donor platelets for clinical application.
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56
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Genetic heterogeneity of induced pluripotent stem cells: results from 24 clones derived from a single C57BL/6 mouse. PLoS One 2015; 10:e0120585. [PMID: 25799070 PMCID: PMC4370741 DOI: 10.1371/journal.pone.0120585] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Accepted: 01/24/2015] [Indexed: 12/22/2022] Open
Abstract
Induced pluripotent stem cells (iPSCs) have tremendous potential as a tool for disease modeling, drug testing, and other applications. Since the generation of iPSCs "captures" the genetic history of the individual cell that was reprogrammed, iPSC clones (even those derived from the same individual) would be expected to demonstrate genetic heterogeneity. To assess the degree of genetic heterogeneity, and to determine whether some cells are more genetically "fit" for reprogramming, we performed exome sequencing on 24 mouse iPSC clones derived from skin fibroblasts obtained from two different sites of the same 8-week-old C57BL/6J male mouse. While no differences in the coding regions were detected in the two parental fibroblast pools, each clone had a unique genetic signature with a wide range of heterogeneity observed among the individual clones: a total of 383 iPSC variants were validated for the 24 clones (mean 16.0/clone, range 0-45). Since these variants were all present in the vast majority of the cells in each clone (variant allele frequencies of 40-60% for heterozygous variants), they most likely preexisted in the individual cells that were reprogrammed, rather than being acquired during reprogramming or cell passaging. We then tested whether this genetic heterogeneity had functional consequences for hematopoietic development by generating hematopoietic progenitors in vitro and enumerating colony forming units (CFUs). While there was a range of hematopoietic potentials among the 24 clones, only one clone failed to differentiate into hematopoietic cells; however, it was able to form a teratoma, proving its pluripotent nature. Further, no specific association was found between the mutational spectrum and the hematopoietic potential of each iPSC clone. These data clearly highlight the genetic heterogeneity present within individual fibroblasts that is captured by iPSC generation, and suggest that most of the changes are random, and functionally benign.
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57
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Nelakanti RV, Kooreman NG, Wu JC. Teratoma formation: a tool for monitoring pluripotency in stem cell research. CURRENT PROTOCOLS IN STEM CELL BIOLOGY 2015; 32:4A.8.1-4A.8.17. [PMID: 25640819 PMCID: PMC4402211 DOI: 10.1002/9780470151808.sc04a08s32] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
This unit describes protocols for evaluating the pluripotency of embryonic and induced pluripotent stem cells using a teratoma formation assay. Cells are prepared for injection and transplanted into immunodeficient mice at the gastrocnemius muscle, a site well suited for teratoma growth and surgical access. Teratomas that form from the cell transplants are explanted, fixed in paraformaldehyde, and embedded in paraffin. These preserved samples are sectioned, stained, and analyzed. Pluripotency of a cell line is confirmed by whether the teratoma contains tissues derived from each of the embryonic germ layers: endoderm, mesoderm, and ectoderm. Alternatively, explanted and fixed teratomas can be cryopreserved for immunohistochemistry, which allows for more detailed identification of specific tissue types present in the samples.
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Affiliation(s)
- Raman V Nelakanti
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, California
- Departments of Medicine and Radiology (Molecular Imaging Program), Stanford University School of Medicine, Stanford, California
- Institute of Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California
| | - Nigel G Kooreman
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, California
- Departments of Medicine and Radiology (Molecular Imaging Program), Stanford University School of Medicine, Stanford, California
- Institute of Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California
- Department of Vascular Surgery, Leiden University Medical Center, Leiden, The Netherlands
| | - Joseph C Wu
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, California
- Departments of Medicine and Radiology (Molecular Imaging Program), Stanford University School of Medicine, Stanford, California
- Institute of Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California
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58
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Ikonomou L, Kotton DN. Derivation of Endodermal Progenitors From Pluripotent Stem Cells. J Cell Physiol 2015; 230:246-58. [PMID: 25160562 PMCID: PMC4344429 DOI: 10.1002/jcp.24771] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Accepted: 08/22/2014] [Indexed: 01/18/2023]
Abstract
Stem and progenitor cells play important roles in organogenesis during development and in tissue homeostasis and response to injury postnatally. As the regenerative capacity of many human tissues is limited, cell replacement therapies hold great promise for human disease management. Pluripotent stem cells such as embryonic stem (ES) cells and induced pluripotent stem (iPS) cells are prime candidates for the derivation of unlimited quantities of clinically relevant cell types through development of directed differentiation protocols, that is, the recapitulation of developmental milestones in in vitro cell culture. Tissue-specific progenitors, including progenitors of endodermal origin, are important intermediates in such protocols since they give rise to all mature parenchymal cells. In this review, we focus on the in vivo biology of embryonic endodermal progenitors in terms of key transcription factors and signaling pathways. We critically review the emerging literature aiming to apply this basic knowledge to achieve the efficient and reproducible in vitro derivation of endodermal progenitors such as pancreas, liver and lung precursor cells.
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Affiliation(s)
- Laertis Ikonomou
- Center for Regenerative Medicine, Boston University and Boston
Medical Center, Boston, MA, USA
- Boston University Pulmonary Center, Boston University School of
Medicine, Boston, MA, USA
| | - Darrell N. Kotton
- Center for Regenerative Medicine, Boston University and Boston
Medical Center, Boston, MA, USA
- Boston University Pulmonary Center, Boston University School of
Medicine, Boston, MA, USA
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59
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Byrska-Bishop M, VanDorn D, Campbell AE, Betensky M, Arca PR, Yao Y, Gadue P, Costa FF, Nemiroff RL, Blobel GA, French DL, Hardison RC, Weiss MJ, Chou ST. Pluripotent stem cells reveal erythroid-specific activities of the GATA1 N-terminus. J Clin Invest 2015; 125:993-1005. [PMID: 25621499 DOI: 10.1172/jci75714] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Accepted: 12/15/2014] [Indexed: 01/13/2023] Open
Abstract
Germline GATA1 mutations that result in the production of an amino-truncated protein termed GATA1s (where s indicates short) cause congenital hypoplastic anemia. In patients with trisomy 21, similar somatic GATA1s-producing mutations promote transient myeloproliferative disease and acute megakaryoblastic leukemia. Here, we demonstrate that induced pluripotent stem cells (iPSCs) from patients with GATA1-truncating mutations exhibit impaired erythroid potential, but enhanced megakaryopoiesis and myelopoiesis, recapitulating the major phenotypes of the associated diseases. Similarly, in developmentally arrested GATA1-deficient murine megakaryocyte-erythroid progenitors derived from murine embryonic stem cells (ESCs), expression of GATA1s promoted megakaryopoiesis, but not erythropoiesis. Transcriptome analysis revealed a selective deficiency in the ability of GATA1s to activate erythroid-specific genes within populations of hematopoietic progenitors. Although its DNA-binding domain was intact, chromatin immunoprecipitation studies showed that GATA1s binding at specific erythroid regulatory regions was impaired, while binding at many nonerythroid sites, including megakaryocytic and myeloid target genes, was normal. Together, these observations indicate that lineage-specific GATA1 cofactor associations are essential for normal chromatin occupancy and provide mechanistic insights into how GATA1s mutations cause human disease. More broadly, our studies underscore the value of ESCs and iPSCs to recapitulate and study disease phenotypes.
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60
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Kamat V, Paluru P, Myint M, French DL, Gadue P, Diamond SL. MicroRNA screen of human embryonic stem cell differentiation reveals miR-105 as an enhancer of megakaryopoiesis from adult CD34+ cells. Stem Cells 2014; 32:1337-46. [PMID: 24446170 DOI: 10.1002/stem.1640] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Accepted: 12/03/2013] [Indexed: 12/19/2022]
Abstract
MicroRNAs (miRNAs) can control stem cell differentiation by targeting mRNAs. Using 96-well plate electroporation, we screened 466 human miRNA mimics by four-color flow cytometry to explore differentiation of common myeloid progenitors (CMP) derived from human embryonic stem cells (hESCs). The transfected cells were then cultured in a cytokine cocktail that supported multiple hematopoietic lineages. At 4-5 days post-transfection, flow cytometry of erythroid (CD235(+)CD41(-)), megakaryocyte (CD41(+)CD42(+)), and myeloid (CD18(+)CD235(-)) lineages revealed miR-105 as a novel enhancer of megakaryocyte production during in vitro primitive hematopoiesis. In hESC-derived CMPs, miR-105 caused a sixfold enhancement in megakaryocyte production. miR-513a, miR-571, and miR-195 were found to be less potent megakaryocyte enhancers. We confirmed the relevance of miR-105 in adult megakaryopoiesis by demonstrating increased megakaryocyte yield and megakaryocyte colony forming potential in human adult CD34(+) cells derived from peripheral blood. In addition, adult CD34(+) cells express endogenous miR-105 during megakaryocyte differentiation. siRNA knockdown of the hematopoietic transcription factor c-Myb caused a similar enhancement of megakaryocyte production as miR-105. Finally, a luciferase/c-Myb-3'UTR construct and Western blot analysis demonstrated that the hematopoietic transcription factor c-Myb mRNA was a target of miR-105. We report a novel hESC-based miR screening platform and demonstrate that miR-105 is an enhancer of megakaryopoiesis in both primitive and definitive hematopoiesis.
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Affiliation(s)
- Viraj Kamat
- Institute for Medicine and Engineering, Department of Chemical and Biomolecular Engineering, 1024 Vagelos Research Laboratory, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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61
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Level of RUNX1 activity is critical for leukemic predisposition but not for thrombocytopenia. Blood 2014; 125:930-40. [PMID: 25490895 DOI: 10.1182/blood-2014-06-585513] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
To explore how RUNX1 mutations predispose to leukemia, we generated induced pluripotent stem cells (iPSCs) from 2 pedigrees with germline RUNX1 mutations. The first, carrying a missense R174Q mutation, which acts as a dominant-negative mutant, is associated with thrombocytopenia and leukemia, and the second, carrying a monoallelic gene deletion inducing a haploinsufficiency, presents only as thrombocytopenia. Hematopoietic differentiation of these iPSC clones demonstrated profound defects in erythropoiesis and megakaryopoiesis and deregulated expression of RUNX1 targets. iPSC clones from patients with the R174Q mutation specifically generated an increased amount of granulomonocytes, a phenotype reproduced by an 80% RUNX1 knockdown in the H9 human embryonic stem cell line, and a genomic instability. This phenotype, found only with a lower dosage of RUNX1, may account for development of leukemia in patients. Altogether, RUNX1 dosage could explain the differential phenotype according to RUNX1 mutations, with a haploinsufficiency leading to thrombocytopenia alone in a majority of cases whereas a more complete gene deletion predisposes to leukemia.
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62
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Cancer-like epigenetic derangements of human pluripotent stem cells and their impact on applications in regeneration and repair. Curr Opin Genet Dev 2014; 28:43-9. [PMID: 25461449 DOI: 10.1016/j.gde.2014.09.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Revised: 09/12/2014] [Accepted: 09/14/2014] [Indexed: 01/27/2023]
Abstract
A growing body of work has raised concern that many human pluripotent stem cell (hPSC) lines possess tumorigenic potential following differentiation to clinically relevant lineages. In this review, we highlight recent work characterizing the spectrum of cancer-like epigenetic derangements in human embryonic stem cells (hESC) and human induced pluripotent stem cells (hiPSC) that are associated with reprogramming errors or prolonged culture that may contribute to such tumorigenicity. These aberrations include cancer-like promoter DNA hypermethylation and histone marks associated with pluripotency, as well as aberrant X-chromosome regulation. We also feature recent work that suggests optimized high-fidelity reprogramming derivation methods can minimize cancer-associated epigenetic aberrations in hPSC, and thus ultimately improve the ultimate clinical utility of hiPSC in regenerative medicine.
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63
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Tan Y, Ooi S, Wang L. Immunogenicity and tumorigenicity of pluripotent stem cells and their derivatives: genetic and epigenetic perspectives. Curr Stem Cell Res Ther 2014; 9:63-72. [PMID: 24160683 PMCID: PMC3873036 DOI: 10.2174/1574888x113086660068] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2013] [Revised: 10/19/2013] [Accepted: 10/22/2013] [Indexed: 12/18/2022]
Abstract
One aim of stem cell-based therapy is to utilize pluripotent stem cells (PSCs) as a supplementary source of cells
to repair or replace tissues or organs that have ceased to function due to severe tissue damage. However, PSC-based therapy
requires extensive research to ascertain if PSC derivatives are functional without the risk of tumorigenicity, and also
do not engender severe immune rejection that threatens graft survival and function. Recently, the suitability of induced
pluripotent stem cells applied for patient-tailored cell therapy has been questioned since the discovery of several genetic
and epigenetic aberrations during the reprogramming process. Hence, it is crucial to understand the effect of these abnormalities
on the immunogenicity and survival of PSC grafts. As induced PSC-based therapy represents a hallmark for the
potential solution to prevent and arrest immune rejection, this review also summarizes several up-to-date key findings in
the field.
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Affiliation(s)
| | | | - Lisheng Wang
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa K1H8M5, Canada.
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64
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Tiyaboonchai A, Mac H, Shamsedeen R, Mills JA, Kishore S, French DL, Gadue P. Utilization of the AAVS1 safe harbor locus for hematopoietic specific transgene expression and gene knockdown in human ES cells. Stem Cell Res 2014; 12:630-7. [PMID: 24631742 DOI: 10.1016/j.scr.2014.02.004] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Revised: 02/05/2014] [Accepted: 02/12/2014] [Indexed: 12/21/2022] Open
Abstract
Human pluripotent stem cells offer a powerful system to study human biology and disease. Here, we report a system to both express transgenes specifically in ES cell derived hematopoietic cells and knockdown gene expression stably throughout the differentiation of ES cells. We characterize a CD43 promoter construct that when inserted into the AAVS1 "safe harbor" locus utilizing a zinc finger nuclease specifically drives GFP expression in hematopoietic cells derived from a transgenic ES cell line and faithfully recapitulates endogenous CD43 expression. In addition, using the same gene targeting strategy we demonstrate that constitutive expression of short hairpin RNAs within a microRNA backbone can suppress expression of PU.1, an important regulator of myeloid cell development. We show that PU.1 knockdown cell lines display an inhibition in myeloid cell formation and skewing towards erythroid development. Overall, we have generated a powerful system to track hematopoietic development from pluripotent stem cells and study gene function through hematopoietic specific gene expression and constitutive gene knockdown.
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Affiliation(s)
- Amita Tiyaboonchai
- School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, USA; Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Helen Mac
- Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Razveen Shamsedeen
- Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Jason A Mills
- Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Siddarth Kishore
- Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Deborah L French
- Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA; Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Paul Gadue
- Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA; Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.
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65
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Abstract
This chapter describes a two-dimensional "monolayer" system for differentiating human pluripotent stem cells (PSCs) into "primitive" hematopoietic progenitor cells (HPCs) resembling those produced in vivo by the early embryonic yolk sac. This experimental system utilizes defined conditions without serum or feeder cells. Cytokines are added sequentially to stimulate the formation of mesoderm and its subsequent patterning to hematopoietic progenitors. The HPCs produced by this protocol have multi-lineage potential (erythroid, megakaryocyte, and myeloid) and can be isolated as a homogeneous population for use in standard hematopoietic studies including liquid expansion to mature lineages and colony assays. In addition, the HPCs can be cryopreserved for distribution or analysis at later times. The HPCs generated by this protocol have been used successfully to better define intrinsic variation in hematopoietic potential between different PSC lines and to model human hematopoietic diseases using patient-derived induced pluripotent stem cells.
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66
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Watanabe A, Amano N, Tokunaga Y, Poolsap U, Yamanaka S. Evaluation of safety of induced pluripotent stem cells by genome integrity. Inflamm Regen 2014. [DOI: 10.2492/inflammregen.34.087] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
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Paluru P, Hudock KM, Cheng X, Mills JA, Ying L, Galvão AM, Lu L, Tiyaboonchai A, Sim X, Sullivan SK, French DL, Gadue P. The negative impact of Wnt signaling on megakaryocyte and primitive erythroid progenitors derived from human embryonic stem cells. Stem Cell Res 2013; 12:441-51. [PMID: 24412757 DOI: 10.1016/j.scr.2013.12.003] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Revised: 12/06/2013] [Accepted: 12/07/2013] [Indexed: 01/17/2023] Open
Abstract
The Wnt gene family consists of structurally related genes encoding secreted signaling molecules that have been implicated in many developmental processes, including regulation of cell fate and patterning during embryogenesis. Previously, we found that Wnt signaling is required for primitive or yolk sac-derived-erythropoiesis using the murine embryonic stem cell (ESC) system. Here, we examine the effect of Wnt signaling on the formation of early hematopoietic progenitors derived from human ESCs. The first hematopoietic progenitor cells in the human ESC system express the pan-hematopoietic marker CD41 and the erythrocyte marker, glycophorin A or CD235. We have developed a novel serum-free, feeder-free, adherent differentiation system that can efficiently generate large numbers of CD41+CD235+ cells. We demonstrate that this cell population contains progenitors not just for primitive erythroid and megakaryocyte cells but for the myeloid lineage as well and term this population the primitive common myeloid progenitor (CMP). Treatment of mesoderm-specified cells with Wnt3a led to a loss of hematopoietic colony-forming ability while the inhibition of canonical Wnt signaling with DKK1 led to an increase in the number of primitive CMPs. Canonical Wnt signaling also inhibits the expansion and/or survival of primitive erythrocytes and megakaryocytes, but not myeloid cells, derived from this progenitor population. These findings are in contrast to the role of Wnt signaling during mouse ESC differentiation and demonstrate the importance of the human ESC system in studying species-specific differences in development.
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Affiliation(s)
- Prasuna Paluru
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA; Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Kristin M Hudock
- Division of Pulmonary, Allergy & Critical Care Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Xin Cheng
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA; Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Jason A Mills
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA; Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Lei Ying
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA; Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Aline M Galvão
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA; Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Lin Lu
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA; Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Amita Tiyaboonchai
- Department of Pathology and Laboratory Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Xiuli Sim
- Department of Pathology and Laboratory Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | | | - Deborah L French
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA; Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, USA; Department of Pathology and Laboratory Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Paul Gadue
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA; Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, USA; Department of Pathology and Laboratory Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA, USA.
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68
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High-level transgene expression in induced pluripotent stem cell-derived megakaryocytes: correction of Glanzmann thrombasthenia. Blood 2013; 123:753-7. [PMID: 24335497 DOI: 10.1182/blood-2013-10-530725] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Megakaryocyte-specific transgene expression in patient-derived induced pluripotent stem cells (iPSCs) offers a new approach to study and potentially treat disorders affecting megakaryocytes and platelets. By using a Gp1ba promoter, we developed a strategy for achieving a high level of protein expression in human megakaryocytes. The feasibility of this approach was demonstrated in iPSCs derived from two patients with Glanzmann thrombasthenia (GT), an inherited platelet disorder caused by mutations in integrin αIIbβ3. Hemizygous insertion of Gp1ba promoter-driven human αIIb complementary DNA into the AAVS1 locus of iPSCs led to high αIIb messenger RNA and protein expression and correction of surface αIIbβ3 in megakaryocytes. Agonist stimulation of these cells displayed recovery of integrin αIIbβ3 activation. Our findings demonstrate a novel approach to studying human megakaryocyte biology as well as functional correction of the GT defect, offering a potential therapeutic strategy for patients with diseases that affect platelet function.
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