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Programmable Molecular Scissors: Applications of a New Tool for Genome Editing in Biotech. MOLECULAR THERAPY-NUCLEIC ACIDS 2018; 14:212-238. [PMID: 30641475 PMCID: PMC6330515 DOI: 10.1016/j.omtn.2018.11.016] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Revised: 11/23/2018] [Accepted: 11/23/2018] [Indexed: 01/04/2023]
Abstract
Targeted genome editing is an advanced technique that enables precise modification of the nucleic acid sequences in a genome. Genome editing is typically performed using tools, such as molecular scissors, to cut a defined location in a specific gene. Genome editing has impacted various fields of biotechnology, such as agriculture; biopharmaceutical production; studies on the structure, regulation, and function of the genome; and the creation of transgenic organisms and cell lines. Although genome editing is used frequently, it has several limitations. Here, we provide an overview of well-studied genome-editing nucleases, including single-stranded oligodeoxynucleotides (ssODNs), transcription activator-like effector nucleases (TALENs), zinc-finger nucleases (ZFNs), and CRISPR-Cas9 RNA-guided nucleases (CRISPR-Cas9). To this end, we describe the progress toward editable nuclease-based therapies and discuss the minimization of off-target mutagenesis. Future prospects of this challenging scientific field are also discussed.
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2
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Huang Y, Wan J, Guo Y, Zhu S, Wang Y, Wang L, Guo Q, Lu Y, Wang Z. Transcriptome Analysis of Induced Pluripotent Stem Cell (iPSC)-derived Pancreatic β-like Cell Differentiation. Cell Transplant 2018; 26:1380-1391. [PMID: 28901190 PMCID: PMC5680972 DOI: 10.1177/0963689717720281] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Diabetes affects millions of people worldwide, and β-cell replacement is one of the promising new strategies for treatment. Induced pluripotent stem cells (iPSCs) can differentiate into any cell type, including pancreatic β cells, providing a potential treatment for diabetes. However, the molecular mechanisms underlying the differentiation of iPSC-derived β cells have not yet been fully elucidated. Here, we generated pancreatic β-like cells from mouse iPSCs using a 3-step protocol and performed deep RNA sequencing to get a transcriptional landscape of iPSC-derived pancreatic β-like cells during the selective differentiation period. We then focused on the differentially expressed genes (DEGs) during the time course of the differentiation period, and these genes underwent Gene Ontology annotation and Kyoto Encyclopedia of Genes and Genomes pathway analysis. In addition, gene-act networks were constructed for these DEGs, and the expression of pivotal genes detected by quantitative real-time polymerase chain reaction was well correlated with RNA sequence (RNA-seq). Overall, our study provides valuable information regarding the transcriptome changes in β cells derived from iPSCs during differentiation, elucidates the biological process and pathways underlying β-cell differentiation, and promotes the identification and functional analysis of potential genes that could be used for improving functional β-cell generation from iPSCs.
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Affiliation(s)
- Yan Huang
- 1 Department of General Surgery, Affiliated Hospital of Nantong University, Nantong, Jiangsu Province, China
| | - Jian Wan
- 1 Department of General Surgery, Affiliated Hospital of Nantong University, Nantong, Jiangsu Province, China
| | - Yibing Guo
- 2 Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu Province, China
| | - Shajun Zhu
- 1 Department of General Surgery, Affiliated Hospital of Nantong University, Nantong, Jiangsu Province, China
| | - Yao Wang
- 1 Department of General Surgery, Affiliated Hospital of Nantong University, Nantong, Jiangsu Province, China
| | - Lei Wang
- 1 Department of General Surgery, Affiliated Hospital of Nantong University, Nantong, Jiangsu Province, China
| | - Qingsong Guo
- 1 Department of General Surgery, Affiliated Hospital of Nantong University, Nantong, Jiangsu Province, China
| | - Yuhua Lu
- 1 Department of General Surgery, Affiliated Hospital of Nantong University, Nantong, Jiangsu Province, China
| | - Zhiwei Wang
- 1 Department of General Surgery, Affiliated Hospital of Nantong University, Nantong, Jiangsu Province, China
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3
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Wakao S, Kushida Y, Dezawa M. Basic Characteristics of Muse Cells. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1103:13-41. [PMID: 30484222 DOI: 10.1007/978-4-431-56847-6_2] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Multilineage-differentiating stress-enduring (Muse) cells exhibit the core characteristics of pluripotent stem cells, namely, the expression of pluripotency markers and the capacity for trilineage differentiation both in vitro and in vivo and self-renewability. In addition, Muse cells have unique characteristics not observed in other pluripotent stem cells such as embryonic stem cells, control of pluripotency by environmental switch of adherent suspension, symmetric and asymmetric cell division, expression of factors relevant to stress tolerance, and distinctive tissue distribution. Pluripotent stem cells were recently classified into two discrete states, naïve and primed. These two states have multiple functional differences, including their proliferation rate, molecular properties, and growth factor dependency. The properties exhibited by Muse cells are similar to those of primed pluripotent stem cells while with some uniqueness. In this chapter, we provide a comprehensive description of the basic characteristics of Muse cells.
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Affiliation(s)
- Shohei Wakao
- Department of Stem Cell Biology and Histology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Yoshihiro Kushida
- Department of Stem Cell Biology and Histology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Mari Dezawa
- Department of Stem Cell Biology and Histology, Tohoku University Graduate School of Medicine, Sendai, Japan.
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Junqueira Reis LC, Picanço-Castro V, Paes BCMF, Pereira OA, Gerdes Gyuricza I, de Araújo FT, Morato-Marques M, Moreira LF, Costa EDBO, dos Santos TPM, Covas DT, Pereira Carramaschi LDV, Russo EMDS. Induced Pluripotent Stem Cell for the Study and Treatment of Sickle Cell Anemia. Stem Cells Int 2017; 2017:7492914. [PMID: 28814957 PMCID: PMC5549510 DOI: 10.1155/2017/7492914] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 04/05/2017] [Indexed: 12/14/2022] Open
Abstract
Sickle cell anemia (SCA) is a monogenic disease of high mortality, affecting millions of people worldwide. There is no broad, effective, and safe definitive treatment for SCA, so the palliative treatments are the most used. The establishment of an in vitro model allows better understanding of how the disease occurs, besides allowing the development of more effective tests and treatments. In this context, iPSC technology is a powerful tool for basic research and disease modeling, and a promise for finding and screening more effective and safe drugs, besides the possibility of use in regenerative medicine. This work obtained a model for study and treatment of SCA using iPSC. Then, episomal vectors were used for reprogramming peripheral blood mononuclear cells to obtain integration-free iPSC. Cells were collected from patients treated with hydroxyurea and without treatment. The iPSCP Bscd lines were characterized for pluripotent and differentiation potential. The iPSC lines were differentiated into HSC, so that we obtained a dynamic and efficient protocol of CD34+CD45+ cells production. We offer a valuable tool for a better understanding of how SCA occurs, in addition to making possible the development of more effective drugs and treatments and providing better understanding of widely used treatments, such as hydroxyurea.
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Affiliation(s)
- Luiza Cunha Junqueira Reis
- Pharmaceutical Sciences School of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil
- Blood Center Foundation of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Virgínia Picanço-Castro
- Blood Center Foundation of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Bárbara Cristina Martins Fernandes Paes
- Blood Center Foundation of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil
- Medical School of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Olívia Ambrozini Pereira
- Philosophy, Sciences and Languages School of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil
| | | | | | | | | | | | | | - Dimas Tadeu Covas
- Blood Center Foundation of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil
- Medical School of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil
| | | | - Elisa Maria de Sousa Russo
- Pharmaceutical Sciences School of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil
- Blood Center Foundation of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil
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Lee JH, Laronde S, Collins TJ, Shapovalova Z, Tanasijevic B, McNicol JD, Fiebig-Comyn A, Benoit YD, Lee JB, Mitchell RR, Bhatia M. Lineage-Specific Differentiation Is Influenced by State of Human Pluripotency. Cell Rep 2017; 19:20-35. [DOI: 10.1016/j.celrep.2017.03.036] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Revised: 01/22/2017] [Accepted: 03/10/2017] [Indexed: 12/27/2022] Open
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6
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Integrating Gene Correction in the Reprogramming and Transdifferentiation Processes: A One-Step Strategy to Overcome Stem Cell-Based Gene Therapy Limitations. Stem Cells Int 2016; 2016:2725670. [PMID: 28074097 PMCID: PMC5198186 DOI: 10.1155/2016/2725670] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Revised: 11/09/2016] [Accepted: 11/16/2016] [Indexed: 12/19/2022] Open
Abstract
The recent advent of induced pluripotent stem cells (iPSCs) and gene therapy tools has raised the possibility of autologous cell therapy for rare genetic diseases. However, cellular reprogramming is inefficient in certain diseases such as ataxia telangiectasia, Fanconi anemia, LIG4 syndrome, and fibrodysplasia ossificans progressiva syndrome, owing to interference of the disease-related genes. To overcome these therapeutic limitations, it is necessary to fundamentally correct the abnormal gene during or prior to the reprogramming process. In addition, as genetic etiology of Parkinson's disease, it has been well known that induced neural stem cells (iNSCs) were progressively depleted by LRRK2 gene mutation, LRRK2 (G2019S). Thus, to maintain the induced NSCs directly derived from PD patient cells harboring LRRK2 (G2019S), it would be ideal to simultaneously treat the LRRK2 (G2019S) fibroblast during the process of TD. Therefore, simultaneous reprogramming (or TD) and gene therapy would provide the solution for therapeutic limitation caused by vulnerability of reprogramming or TD, in addition to being suitable for general application to the generation of autologous cell-therapy products for patients with genetic defects, thereby obviating the need for the arduous processes currently required.
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Kim T, Bershteyn M, Wynshaw-Boris A. Chromosome therapy. Correction of large chromosomal aberrations by inducing ring chromosomes in induced pluripotent stem cells (iPSCs). Nucleus 2015; 5:391-5. [PMID: 25482192 DOI: 10.4161/nucl.36300] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The fusion of the short (p) and long (q) arms of a chromosome is referred to as a "ring chromosome." Ring chromosome disorders occur in approximately 1 in 50,000-100,000 patients. Ring chromosomes can result in birth defects, mental disabilities, and growth retardation if additional genes are deleted during the formation of the ring. Due to the severity of these large-scale aberrations affecting multiple contiguous genes, no possible therapeutic strategies for ring chromosome disorders have so far been proposed. Our recent study (Bershteyn et al.) using patient-derived fibroblast lines containing ring chromosomes, found that cellular reprogramming of these fibroblasts into induced pluripotent stem cells (iPSCs) resulted in the cell-autonomous correction of the ring chromosomal aberration via compensatory uniparental disomy (UPD). These observations have important implications for studying the mechanism of chromosomal number control and may lead to the development of effective therapies for other, more common, chromosomal aberrations.
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Affiliation(s)
- Taehyun Kim
- a Department of Genetics and Genome Sciences; School of Medicine; Case Western Reserve University School of Medicine; Cleveland, OH USA
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8
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Alexander P, Thomson HAJ, Luff AJ, Lotery AJ. Retinal pigment epithelium transplantation: concepts, challenges, and future prospects. Eye (Lond) 2015; 29:992-1002. [PMID: 26043704 PMCID: PMC4541358 DOI: 10.1038/eye.2015.89] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 04/14/2015] [Indexed: 12/14/2022] Open
Abstract
The retinal pigment epithelium (RPE) is a single layer of cells that supports the light-sensitive photoreceptor cells that are essential for retinal function. Age-related macular degeneration (AMD) is a leading cause of visual impairment, and the primary pathogenic mechanism is thought to arise in the RPE layer. RPE cell structure and function are well understood, the cells are readily sustainable in laboratory culture and, unlike other cell types within the retina, RPE cells do not require synaptic connections to perform their role. These factors, together with the relative ease of outer retinal imaging, make RPE cells an attractive target for cell transplantation compared with other cell types in the retina or central nervous system. Seminal experiments in rats with an inherited RPE dystrophy have demonstrated that RPE transplantation can prevent photoreceptor loss and maintain visual function. This review provides an update on the progress made so far on RPE transplantation in human eyes, outlines potential sources of donor cells, and describes the technical and surgical challenges faced by the transplanting surgeon. Recent advances in the understanding of pluripotent stem cells, combined with novel surgical instrumentation, hold considerable promise, and support the concept of RPE transplantation as a regenerative strategy in AMD.
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Affiliation(s)
- P Alexander
- Clinical Neurosciences Research Group, Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, University Hospital Southampton, Southampton, UK
| | - H A J Thomson
- Clinical Neurosciences Research Group, Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, University Hospital Southampton, Southampton, UK
| | - A J Luff
- Clinical Neurosciences Research Group, Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, University Hospital Southampton, Southampton, UK
| | - A J Lotery
- Clinical Neurosciences Research Group, Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, University Hospital Southampton, Southampton, UK
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9
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Pfaff N, Lachmann N, Ackermann M, Kohlscheen S, Brendel C, Maetzig T, Niemann H, Antoniou MN, Grez M, Schambach A, Cantz T, Moritz T. A ubiquitous chromatin opening element prevents transgene silencing in pluripotent stem cells and their differentiated progeny. Stem Cells 2014; 31:488-99. [PMID: 23307570 DOI: 10.1002/stem.1316] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2012] [Accepted: 12/04/2012] [Indexed: 11/07/2022]
Abstract
Methylation-induced gene silencing represents a major obstacle to efficient transgene expression in pluripotent cells and thereof derived tissues. As ubiquitous chromatin opening elements (UCOE) have been shown to prevent transgene silencing in cell lines and primary hematopoietic cells, we hypothesized a similar activity in pluripotent cells. This concept was investigated in the context of cytidine deaminase (CDD) gene transfer, an approach to render hematopoietic cells resistant to the chemotherapeutic agent Ara-C. When murine induced pluripotent stem cells (iPSC)/embryonic stem cells (ESCs) were transduced with self-inactivating lentiviral vectors using housekeeping (truncated elongation factor 1α; EFS) or viral (spleen focus-forming virus; SFFV) promoters, incorporation of an heterogeneous nuclear ribonucleoproteins A2 B1/chromobox protein homolog 3 locus-derived UCOE (A2UCOE) significantly increased transgene expression and Ara-C resistance and effectively prevented silencing of the SFFV-promoter. The EFS promoter showed relatively stable transgene expression in naïve iPSCs, but rapid transgene silencing was observed upon hematopoietic differentiation. When combined with the A2UCOE, however, the EFS promoter yielded stable transgene expression in 73% ± 6% of CD41(+) hematopoietic progeny, markedly increased CDD expression levels, and significantly enhanced Ara-C resistance in clonogenic cells. Bisulfite sequencing revealed protection from differentiation-induced promoter CpG methylation to be associated with these effects. Similar transgene promoting activities of the A2UCOE were observed during murine neurogenic differentiation, in naïve human pluripotent cells, and during nondirected multilineage differentiation of these cells. Thus, our data provide strong evidence that UCOEs can efficiently prevent transgene silencing in iPS/ESCs and their differentiated progeny and thereby introduce a generalized concept to circumvent differentiation-induced transgene silencing during the generation of advanced iPSC/ESC-based gene and cell therapy products.
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Affiliation(s)
- Nils Pfaff
- REBIRTH Research Group Reprogramming, Hannover Medical School, Hannover
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10
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Li M, Suzuki K, Kim NY, Liu GH, Izpisua Belmonte JC. A cut above the rest: targeted genome editing technologies in human pluripotent stem cells. J Biol Chem 2013; 289:4594-9. [PMID: 24362028 DOI: 10.1074/jbc.r113.488247] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Human pluripotent stem cells (hPSCs) offer unprecedented opportunities to study cellular differentiation and model human diseases. The ability to precisely modify any genomic sequence holds the key to realizing the full potential of hPSCs. Thanks to the rapid development of novel genome editing technologies driven by the enormous interest in the hPSC field, genome editing in hPSCs has evolved from being a daunting task a few years ago to a routine procedure in most laboratories. Here, we provide an overview of the mainstream genome editing tools, including zinc finger nucleases, transcription activator-like effector nucleases, clustered regularly interspaced short palindromic repeat/CAS9 RNA-guided nucleases, and helper-dependent adenoviral vectors. We discuss the features and limitations of these technologies, as well as how these factors influence the utility of these tools in basic research and therapies.
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Affiliation(s)
- Mo Li
- From the Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, California 92037 and
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11
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Ackermann M, Lachmann N, Hartung S, Eggenschwiler R, Pfaff N, Happle C, Mucci A, Göhring G, Niemann H, Hansen G, Schambach A, Cantz T, Zweigerdt R, Moritz T. Promoter and lineage independent anti-silencing activity of the A2 ubiquitous chromatin opening element for optimized human pluripotent stem cell-based gene therapy. Biomaterials 2013; 35:1531-42. [PMID: 24290698 DOI: 10.1016/j.biomaterials.2013.11.024] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Accepted: 11/07/2013] [Indexed: 12/31/2022]
Abstract
Epigenetic silencing of retroviral transgene expression in pluripotent stem cells (PSC) and their differentiated progeny constitutes a major roadblock for PSC-based gene therapy. As ubiquitous chromatin opening elements (UCOEs) have been successfully employed to stabilize transgene expression in murine hematopoietic and pluripotent stem cells as well as their differentiated progeny, we here investigated UCOE activity in their human counterparts to establish a basis for future clinical application of the element. To this end, we demonstrate profound anti-silencing activity of the A2UCOE in several human iPS and ES cell lines including their progeny obtained upon directed cardiac or hematopoietic differentiation. We also provide evidence for A2UCOE activity in murine iPSC-derived hepatocyte-like cells, thus establishing efficacy of the element in cells of different germ layers. Finally, we investigated combinations of the A2UCOE with viral promoter/enhancer elements again demonstrating profound stabilization of transgene expression. In all these settings the effect of the A2UCOE was associated with strongly reduced promoter DNA-methylation. Thus, our data clearly support the concept of the A2UCOE as a generalized strategy to prevent epigenetic silencing in PSC and their differentiated progeny and strongly favors its application to stabilize transgene expression in PSC-based cell and gene therapy approaches.
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Affiliation(s)
- Mania Ackermann
- Reprogramming and Gene Therapy Group, REBIRTH Cluster of Excellence, Hannover Medical School, Hannover, Lower Saxony 30625, Germany; Institute of Experimental Hematology, Hannover Medical School, Hannover, Lower Saxony 30625, Germany
| | - Nico Lachmann
- Reprogramming and Gene Therapy Group, REBIRTH Cluster of Excellence, Hannover Medical School, Hannover, Lower Saxony 30625, Germany; Institute of Experimental Hematology, Hannover Medical School, Hannover, Lower Saxony 30625, Germany
| | - Susann Hartung
- Leibniz Research Laboratories for Biotechnology and Artificial Organs (LEBAO), Department of Cardiothoracic, Transplantation and Vascular Surgery, Hannover Medical School, Hannover, Lower Saxony 30625, Germany
| | - Reto Eggenschwiler
- Translational Hepatology and Stem Cell Biology, REBIRTH Cluster of Excellence, Hannover Medical School, Hannover, Lower Saxony 30625, Germany
| | - Nils Pfaff
- Reprogramming and Gene Therapy Group, REBIRTH Cluster of Excellence, Hannover Medical School, Hannover, Lower Saxony 30625, Germany; Institute of Experimental Hematology, Hannover Medical School, Hannover, Lower Saxony 30625, Germany
| | - Christine Happle
- Department of Pediatrics, Hannover Medical School, Hannover, Lower Saxony 30625, Germany; Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Member of the Center for Lung Research (DZL), Hannover Medical School, Hannover, Lower Saxony 30625, Germany
| | - Adele Mucci
- Reprogramming and Gene Therapy Group, REBIRTH Cluster of Excellence, Hannover Medical School, Hannover, Lower Saxony 30625, Germany
| | - Gudrun Göhring
- Institute of Cell and Molecular Pathology, Hannover Medical School, Hannover, Lower Saxony 30625, Germany
| | - Heiner Niemann
- Institute of Farm Animal Genetics, Friedrich-Löffler-Institut, Mariensee/Neustadt, Lower Saxony 31535, Germany
| | - Gesine Hansen
- Department of Pediatrics, Hannover Medical School, Hannover, Lower Saxony 30625, Germany; Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Member of the Center for Lung Research (DZL), Hannover Medical School, Hannover, Lower Saxony 30625, Germany
| | - Axel Schambach
- Institute of Experimental Hematology, Hannover Medical School, Hannover, Lower Saxony 30625, Germany; Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Tobias Cantz
- Translational Hepatology and Stem Cell Biology, REBIRTH Cluster of Excellence, Hannover Medical School, Hannover, Lower Saxony 30625, Germany
| | - Robert Zweigerdt
- Leibniz Research Laboratories for Biotechnology and Artificial Organs (LEBAO), Department of Cardiothoracic, Transplantation and Vascular Surgery, Hannover Medical School, Hannover, Lower Saxony 30625, Germany
| | - Thomas Moritz
- Reprogramming and Gene Therapy Group, REBIRTH Cluster of Excellence, Hannover Medical School, Hannover, Lower Saxony 30625, Germany; Institute of Experimental Hematology, Hannover Medical School, Hannover, Lower Saxony 30625, Germany.
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12
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Hematopoietic specification from human pluripotent stem cells: current advances and challenges toward de novo generation of hematopoietic stem cells. Blood 2013; 122:4035-46. [PMID: 24124087 DOI: 10.1182/blood-2013-07-474825] [Citation(s) in RCA: 95] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Significant advances in cellular reprogramming technologies and hematopoietic differentiation from human pluripotent stem cells (hPSCs) have already enabled the routine production of multiple lineages of blood cells in vitro and opened novel opportunities to study hematopoietic development, model genetic blood diseases, and manufacture immunologically matched cells for transfusion and cancer immunotherapy. However, the generation of hematopoietic cells with robust and sustained multilineage engraftment has not been achieved. Here, we highlight the recent advances in understanding the molecular and cellular pathways leading to blood development from hPSCs and discuss potential approaches that can be taken to facilitate the development of technologies for de novo production of hematopoietic stem cells.
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Folmes CD, Arrell DK, Zlatkovic-Lindor J, Martinez-Fernandez A, Perez-Terzic C, Nelson TJ, Terzic A. Metabolome and metaboproteome remodeling in nuclear reprogramming. Cell Cycle 2013; 12:2355-65. [PMID: 23839047 DOI: 10.4161/cc.25509] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Nuclear reprogramming resets differentiated tissue to generate induced pluripotent stem (iPS) cells. While genomic attributes underlying reacquisition of the embryonic-like state have been delineated, less is known regarding the metabolic dynamics underscoring induction of pluripotency. Metabolomic profiling of fibroblasts vs. iPS cells demonstrated nuclear reprogramming-associated induction of glycolysis, realized through augmented utilization of glucose and accumulation of lactate. Real-time assessment unmasked downregulated mitochondrial reserve capacity and ATP turnover correlating with pluripotent induction. Reduction in oxygen consumption and acceleration of extracellular acidification rates represent high-throughput markers of the transition from oxidative to glycolytic metabolism, characterizing stemness acquisition. The bioenergetic transition was supported by proteome remodeling, whereby 441 proteins were altered between fibroblasts and derived iPS cells. Systems analysis revealed overrepresented canonical pathways and interactome-associated biological processes predicting differential metabolic behavior in response to reprogramming stimuli, including upregulation of glycolysis, purine, arginine, proline, ribonucleoside and ribonucleotide metabolism, and biopolymer and macromolecular catabolism, with concomitant downregulation of oxidative phosphorylation, phosphate metabolism regulation, and precursor biosynthesis processes, prioritizing the impact of energy metabolism within the hierarchy of nuclear reprogramming. Thus, metabolome and metaboproteome remodeling is integral for induction of pluripotency, expanding on the genetic and epigenetic requirements for cell fate manipulation.
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Affiliation(s)
- Clifford Dl Folmes
- Center for Regenerative Medicine and Marriott Heart Disease Research Program; Division of Cardiovascular Diseases; Departments of Medicine, Molecular Pharmacology and Experimental Therapeutics, and Medical Genetics; Mayo Clinic; Rochester, MN USA
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14
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Li M, Liu GH, Izpisua Belmonte JC. Navigating the epigenetic landscape of pluripotent stem cells. Nat Rev Mol Cell Biol 2012; 13:524-35. [PMID: 22820889 DOI: 10.1038/nrm3393] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Pluripotent stem cells, which include embryonic stem cells and induced pluripotent stem cells, use a complex network of genetic and epigenetic pathways to maintain a delicate balance between self-renewal and multilineage differentiation. Recently developed high-throughput genomic tools greatly facilitate the study of epigenetic regulation in pluripotent stem cells. Increasing evidence suggests the existence of extensive crosstalk among epigenetic pathways that modify DNA, histones and nucleosomes. Novel methods of mapping higher-order chromatin structure and chromatin-nuclear matrix interactions also provide the first insight into the three-dimensional organization of the genome and a framework in which existing genomic data of epigenetic regulation can be integrated to discover new rules of gene regulation.
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Affiliation(s)
- Mo Li
- Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, California 92037, USA
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15
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miRNAs involved in the generation, maintenance, and differentiation of pluripotent cells. J Mol Med (Berl) 2012; 90:747-52. [PMID: 22684238 DOI: 10.1007/s00109-012-0922-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2012] [Revised: 05/04/2012] [Accepted: 05/24/2012] [Indexed: 12/24/2022]
Abstract
With the groundbreaking work of Takahashi and Yamanaka, induced pluripotent stem cells (iPSCs) have taken the stage of international stem cell research as a novel source of pluripotent cells and an alternative to embryonic stem cells (ESCs). Apart from their enormous potential as a starting source for the generation of patient-specific cell therapy products, iPSCs also highlight the power of artificially modulating transcriptional networks to induce dramatic changes of cell specification. Since small non-coding RNAs play important roles in the modulation and fine-tuning of transcriptional networks, microRNAs also exhibit important functions in directing cell fate decisions. In this review, we will discuss the role of microRNAs in pluripotent stem cells and their impact on the induction of pluripotency during reprogramming of somatic cells.
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16
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Clinical Pharmacology & Therapeutics 2011: Year in Review. Clin Pharmacol Ther 2012. [DOI: 10.1038/clpt.2011.353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Pan H, Zhang W, Zhang W, Liu GH. Find and replace: editing human genome in pluripotent stem cells. Protein Cell 2011; 2:950-6. [PMID: 22173708 DOI: 10.1007/s13238-011-1132-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2011] [Accepted: 12/04/2011] [Indexed: 12/14/2022] Open
Abstract
Genetic manipulation of human pluripotent stem cells (hPSCs) provides a powerful tool for modeling diseases and developing future medicine. Recently a number of independent genome-editing techniques were developed, including plasmid, bacterial artificial chromosome, adeno-associated virus vector, zinc finger nuclease, transcription activator-like effecter nuclease, and helper-dependent adenoviral vector. Gene editing has been successfully employed in different aspects of stem cell research such as gene correction, mutation knock-in, and establishment of reporter cell lines (Raya et al., 2009; Howden et al., 2011; Li et al., 2011; Liu et al., 2011b; Papapetrou et al., 2011; Sebastiano et al., 2011; Soldner et al., 2011; Zou et al., 2011a). These techniques combined with the utility of hPSCs will significantly influence the area of regenerative medicine.
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Affiliation(s)
- Huize Pan
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
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Nelson TJ, Terzic A. Induced pluripotent stem cells: an emerging theranostics platform. Clin Pharmacol Ther 2011; 89:648-50. [PMID: 21512525 DOI: 10.1038/clpt.2010.304] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Nuclear reprogramming generates induced pluripotent stem (iPS) cells endowed with the unlimited potential to reconstruct genetically identical tissues. This biomedical tool offers unprecedented opportunities to develop scalable yet personalized cell-based reagents. The emerging platform of regenerative theranostics provides a unique approach to expose mechanisms of disease etiology in the context of dysfunctional cell biology. Resolved molecular dynamics that define and regulate the regenerative capacity of individual stem cells will enable next-generation, patient-specific diagnostic and therapeutic applications.
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Affiliation(s)
- T J Nelson
- Marriott Heart Disease Research Program, Division of Cardiovascular Diseases, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA.
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Liu GH, Suzuki K, Qu J, Sancho-Martinez I, Yi F, Li M, Kumar S, Nivet E, Kim J, Soligalla RD, Dubova I, Goebl A, Plongthongkum N, Fung HL, Zhang K, Loring JF, Laurent LC, Izpisua Belmonte JC. Targeted gene correction of laminopathy-associated LMNA mutations in patient-specific iPSCs. Cell Stem Cell 2011; 8:688-94. [PMID: 21596650 DOI: 10.1016/j.stem.2011.04.019] [Citation(s) in RCA: 189] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2011] [Revised: 04/22/2011] [Accepted: 04/29/2011] [Indexed: 11/25/2022]
Abstract
Combination of stem cell-based approaches with gene-editing technologies represents an attractive strategy for studying human disease and developing therapies. However, gene-editing methodologies described to date for human cells suffer from technical limitations including limited target gene size, low targeting efficiency at transcriptionally inactive loci, and off-target genetic effects that could hamper broad clinical application. To address these limitations, and as a proof of principle, we focused on homologous recombination-based gene correction of multiple mutations on lamin A (LMNA), which are associated with various degenerative diseases. We show that helper-dependent adenoviral vectors (HDAdVs) provide a highly efficient and safe method for correcting mutations in large genomic regions in human induced pluripotent stem cells and can also be effective in adult human mesenchymal stem cells. This type of approach could be used to generate genotype-matched cell lines for disease modeling and drug discovery and potentially also in therapeutics.
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Affiliation(s)
- Guang-Hui Liu
- Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
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A new dimension of clinical pharmacology: induced pluripotent stem cells. Clin Pharmacol Ther 2011; 89:629-32. [PMID: 21512518 DOI: 10.1038/clpt.2011.41] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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