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Blanch-Asensio A, Grandela C, Brandão KO, de Korte T, Mei H, Ariyurek Y, Yiangou L, Mol MP, van Meer BJ, Kloet SL, Mummery CL, Davis RP. STRAIGHT-IN enables high-throughput targeting of large DNA payloads in human pluripotent stem cells. CELL REPORTS METHODS 2022; 2:100300. [PMID: 36313798 PMCID: PMC9606106 DOI: 10.1016/j.crmeth.2022.100300] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 07/12/2022] [Accepted: 08/31/2022] [Indexed: 04/20/2023]
Abstract
Inserting large DNA payloads (>10 kb) into specific genomic sites of mammalian cells remains challenging. Applications ranging from synthetic biology to evaluating the pathogenicity of disease-associated variants for precision medicine initiatives would greatly benefit from tools that facilitate this process. Here, we merge the strengths of different classes of site-specific recombinases and combine these with CRISPR-Cas9-mediated homologous recombination to develop a strategy for stringent site-specific replacement of genomic fragments at least 50 kb in size in human induced pluripotent stem cells (hiPSCs). We demonstrate the versatility of STRAIGHT-IN (serine and tyrosine recombinase-assisted integration of genes for high-throughput investigation) by (1) inserting various combinations of fluorescent reporters into hiPSCs to assess the excitation-contraction coupling cascade in derivative cardiomyocytes and (2) simultaneously targeting multiple variants associated with inherited cardiac arrhythmic disorders into a pool of hiPSCs. STRAIGHT-IN offers a precise approach to generate genetically matched panels of hiPSC lines efficiently and cost effectively.
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Affiliation(s)
- Albert Blanch-Asensio
- Department of Anatomy and Embryology, Leiden University Medical Center, 2300RC Leiden, the Netherlands
| | - Catarina Grandela
- Department of Anatomy and Embryology, Leiden University Medical Center, 2300RC Leiden, the Netherlands
| | - Karina O. Brandão
- Department of Anatomy and Embryology, Leiden University Medical Center, 2300RC Leiden, the Netherlands
| | - Tessa de Korte
- Department of Anatomy and Embryology, Leiden University Medical Center, 2300RC Leiden, the Netherlands
| | - Hailiang Mei
- Sequencing Analysis Support Core, Leiden University Medical Center, 2333RC Leiden, the Netherlands
| | - Yavuz Ariyurek
- Leiden Genome Technology Center, Leiden University Medical Center, 2333RC Leiden, the Netherlands
| | - Loukia Yiangou
- Department of Anatomy and Embryology, Leiden University Medical Center, 2300RC Leiden, the Netherlands
| | - Mervyn P.H. Mol
- Department of Anatomy and Embryology, Leiden University Medical Center, 2300RC Leiden, the Netherlands
| | - Berend J. van Meer
- Department of Anatomy and Embryology, Leiden University Medical Center, 2300RC Leiden, the Netherlands
| | - Susan L. Kloet
- Leiden Genome Technology Center, Leiden University Medical Center, 2333RC Leiden, the Netherlands
| | - Christine L. Mummery
- Department of Anatomy and Embryology, Leiden University Medical Center, 2300RC Leiden, the Netherlands
- Department of Applied Stem Cell Technologies, University of Twente, 7500AE Enschede, the Netherlands
| | - Richard P. Davis
- Department of Anatomy and Embryology, Leiden University Medical Center, 2300RC Leiden, the Netherlands
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2
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Vessoni AT, Zhang T, Quinet A, Jeong HC, Munroe M, Wood M, Tedone E, Vindigni A, Shay JW, Greenberg RA, Batista LF. Telomere erosion in human pluripotent stem cells leads to ATR-mediated mitotic catastrophe. J Cell Biol 2021; 220:211982. [PMID: 33851958 PMCID: PMC8050844 DOI: 10.1083/jcb.202011014] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 03/03/2021] [Accepted: 03/15/2021] [Indexed: 12/14/2022] Open
Abstract
It is well established that short telomeres activate an ATM-driven DNA damage response that leads to senescence in terminally differentiated cells. However, technical limitations have hampered our understanding of how telomere shortening is signaled in human stem cells. Here, we show that telomere attrition induces ssDNA accumulation (G-strand) at telomeres in human pluripotent stem cells (hPSCs), but not in their differentiated progeny. This led to a unique role for ATR in the response of hPSCs to telomere shortening that culminated in an extended S/G2 cell cycle phase and a longer period of mitosis, which was associated with aneuploidy and mitotic catastrophe. Loss of p53 increased resistance to death, at the expense of increased mitotic abnormalities in hPSCs. Taken together, our data reveal an unexpected dominant role of ATR in hPSCs, combined with unique cell cycle abnormalities and, ultimately, consequences distinct from those observed in their isogenic differentiated counterparts.
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Affiliation(s)
| | - Tianpeng Zhang
- Department of Cancer Biology, Penn Center for Genome Integrity, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Annabel Quinet
- Department of Medicine, Washington University in St. Louis, St. Louis, MO
| | - Ho-Chang Jeong
- Department of Medicine, Washington University in St. Louis, St. Louis, MO
| | - Michael Munroe
- Department of Medicine, Washington University in St. Louis, St. Louis, MO
| | - Matthew Wood
- Department of Medicine, Washington University in St. Louis, St. Louis, MO
| | - Enzo Tedone
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX
| | | | - Jerry W. Shay
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX
| | - Roger A. Greenberg
- Department of Cancer Biology, Penn Center for Genome Integrity, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Luis F.Z. Batista
- Department of Medicine, Washington University in St. Louis, St. Louis, MO
- Center of Regenerative Medicine, Washington University in St. Louis, St. Louis, MO
- Correspondence to Luis F.Z. Batista:
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3
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Nilsri N, Jangprasert P, Pawinwongchai J, Israsena N, Rojnuckarin P. Distinct effects of V617F and exon12-mutated JAK2 expressions on erythropoiesis in a human induced pluripotent stem cell (iPSC)-based model. Sci Rep 2021; 11:5255. [PMID: 33664283 PMCID: PMC7933160 DOI: 10.1038/s41598-021-83895-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Accepted: 02/09/2021] [Indexed: 12/15/2022] Open
Abstract
Activating mutations affecting the JAK-STAT signal transduction is the genetic driver of myeloproliferative neoplasms (MPNs) which comprise polycythemia vera (PV), essential thrombocythemia (ET) and myelofibrosis. The JAK2p.V617F mutation can produce both erythrocytosis in PV and thrombocytosis in ET, while JAK2 exon 12 mutations cause only erythrocytosis. We hypothesized that these two mutations activated different intracellular signals. In this study, the induced pluripotent stem cells (iPSCs) were used to model JAK2-mutated MPNs. Normal iPSCs underwent lentiviral transduction to overexpress JAK2p.V617F or JAK2p.N542_E543del (JAK2exon12) under a doxycycline-inducible system. The modified iPSCs were differentiated into erythroid cells. Compared with JAK2V617F-iPSCs, JAK2exon12-iPSCs yielded more total CD71+GlycophorinA+ erythroid cells, displayed more mature morphology and expressed more adult hemoglobin after doxycycline induction. Capillary Western immunoassay revealed significantly higher phospho-STAT1 but lower phospho-STAT3 and lower Phospho-AKT in JAK2exon12-iPSCs compared with those of JAK2V617F-iPSCs in response to erythropoietin. Furthermore, interferon alpha and arsenic trioxide were tested on these modified iPSCs to explore their potentials for MPN therapy. Both agents preferentially inhibited proliferation and promoted apoptosis of the iPSCs expressing mutant JAK2 compared with those without doxycycline induction. In conclusion, the modified iPSC model can be used to investigate the mechanisms and search for new therapy of MPNs.
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Affiliation(s)
- Nungruthai Nilsri
- Doctor of Philosophy Program in Medical Sciences, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Department of Medical Technology, Faculty of Allied Health Sciences, Naresuan University, Phitsanulok, Thailand
| | - Panchalee Jangprasert
- Interdisciplinary Program of Biomedical Sciences, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | | | - Nipan Israsena
- Stem Cell and Cell Therapy Research Unit, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Ponlapat Rojnuckarin
- Research Unit in Translational Hematology, Division of Hematology, Department of Medicine, Faculty of Medicine, Chulalongkorn University and King Chulalongkorn Memorial Hospital, Bangkok, 10330, Thailand.
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4
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Munroe M, Niero EL, Fok WC, Vessoni AT, Jeong H, Brenner KA, Batista LFZ. Telomere Dysfunction Activates p53 and Represses HNF4α Expression Leading to Impaired Human Hepatocyte Development and Function. Hepatology 2020; 72:1412-1429. [PMID: 32516515 PMCID: PMC7693115 DOI: 10.1002/hep.31414] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 05/04/2020] [Accepted: 05/19/2020] [Indexed: 12/18/2022]
Abstract
BACKGROUND AND AIMS Telomere attrition is a major risk factor for end-stage liver disease. Due to a lack of adequate models and intrinsic difficulties in studying telomerase in physiologically relevant cells, the molecular mechanisms responsible for liver disease in patients with telomere syndromes remain elusive. To circumvent that, we used genome editing to generate isogenic human embryonic stem cells (hESCs) harboring clinically relevant mutations in telomerase and subjected them to an in vitro, stage-specific hepatocyte differentiation protocol that resembles hepatocyte development in vivo. APPROACH AND RESULTS Using this platform, we observed that while telomerase is highly expressed in hESCs, it is quickly silenced, specifically due to telomerase reverse transcriptase component (TERT) down-regulation, immediately after endoderm differentiation and completely absent in in vitro-derived hepatocytes, similar to what is observed in human primary hepatocytes. While endoderm derivation is not impacted by telomere shortening, progressive telomere dysfunction impaired hepatic endoderm formation. Consequently, hepatocyte derivation, as measured by expression of specific hepatic markers as well by albumin expression and secretion, is severely compromised in telomerase mutant cells with short telomeres. Interestingly, this phenotype was not caused by cell death induction or senescence. Rather, telomere shortening prevents the up-regulation and activation of human hepatocyte nuclear factor 4 alpha (HNF4α) in a p53-dependent manner. Both reactivation of telomerase and silencing of p53 rescued hepatocyte formation in telomerase mutants. Likewise, the conditional expression (doxycycline-controlled) of HNF4α, even in cells that retained short telomeres, accrued DNA damage, and exhibited p53 stabilization, successfully restored hepatocyte formation from hESCS. CONCLUSIONS Our data show that telomere dysfunction acts as a major regulator of HNF4α during hepatocyte development, pointing to a target in the treatment of liver disease in telomere-syndrome patients.
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Affiliation(s)
- Michael Munroe
- Department of MedicineWashington University in St. LouisSt. LouisMO
| | | | - Wilson Chun Fok
- Department of MedicineWashington University in St. LouisSt. LouisMO
| | | | - Ho‐Chang Jeong
- Department of MedicineWashington University in St. LouisSt. LouisMO
| | - Kirsten Ann Brenner
- Department of MedicineWashington University in St. LouisSt. LouisMO
- Present address:
Department of Molecular, Cellular, and Developmental BiologyUniversity of MichiganAnn ArborMI
| | - Luis Francisco Zirnberger Batista
- Department of MedicineWashington University in St. LouisSt. LouisMO
- Department of Developmental BiologyWashington University in St. LouisSt. LouisMO
- Center of Regenerative MedicineWashington University in St. LouisSt. LouisMO
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5
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Silencing Trisomy 21 with XIST in Neural Stem Cells Promotes Neuronal Differentiation. Dev Cell 2020; 52:294-308.e3. [PMID: 31978324 DOI: 10.1016/j.devcel.2019.12.015] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 09/23/2019] [Accepted: 12/19/2019] [Indexed: 12/18/2022]
Abstract
The ability of XIST to dosage compensate a trisomic autosome presents unique experimental opportunities and potentially transformative therapeutic prospects. However, it is currently thought that XIST requires the natural context surrounding pluripotency to initiate chromosome silencing. Here, we demonstrate that XIST RNA induced in differentiated neural cells can trigger chromosome-wide silencing of chromosome 21 in Down syndrome patient-derived cells. Use of this tightly controlled system revealed a deficiency in differentiation of trisomic neural stem cells to neurons, correctible by inducing XIST at different stages of neurogenesis. Single-cell transcriptomics and other analyses strongly implicate elevated Notch signaling due to trisomy 21, thereby promoting neural stem cell cycling that delays terminal differentiation. These findings have significance for illuminating the epigenetic plasticity of cells during development, the understanding of how human trisomy 21 effects Down syndrome neurobiology, and the translational potential of XIST, a unique non-coding RNA.
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6
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Posttranscriptional modulation of TERC by PAPD5 inhibition rescues hematopoietic development in dyskeratosis congenita. Blood 2019; 133:1308-1312. [PMID: 30728146 DOI: 10.1182/blood-2018-11-885368] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 01/18/2019] [Indexed: 12/14/2022] Open
Abstract
Reduced levels of TERC, the telomerase RNA component, cause dyskeratosis congenita (DC) in patients harboring mutations in TERC, PARN, NOP10, NHP2, NAF1, or DKC1. Inhibition of the noncanonical poly(A) polymerase PAPD5, or the exosome RNA degradation complex, partially restores TERC levels in immortalized DKC1 mutant cells, but it remains unknown if modulation of posttranscriptional processing of TERC could improve hematopoietic output in DC. We used human embryonic stem cells (hESCs) with a common dyskerin mutation (DKC1_A353V), which have defective telomere maintenance and reduced definitive hematopoietic potential, to understand the effects of reducing EXOSC3 activity, or silencing PAPD5-mediated oligoadenylation, on hematopoietic progenitor specification and function in DC. Reduction of EXOSC3 or PAPD5 levels in DKC1 mutant hESCs led to functional improvements in TERC levels and telomerase activity, with concomitant telomere elongation and reduced levels of DNA damage signaling. Interestingly, the silencing of PAPD5, but not EXOSC3, significantly restored definitive hematopoietic potential in DKC1 mutant cells. Mechanistically, we show that PAPD5 inhibition is sustained in differentiated CD34+ cells, with a concomitant increase in mature, functional, forms of TERC, indicating that regulation of PAPD5 is a potential strategy to reverse hematologic dysfunction in DC patients.
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7
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Bertero A, Yiangou L, Brown S, Ortmann D, Pawlowski M, Vallier L. Conditional Manipulation of Gene Function in Human Cells with Optimized Inducible shRNA. ACTA ACUST UNITED AC 2018; 44:5C.4.1-5C.4.48. [PMID: 29512130 DOI: 10.1002/cpsc.45] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The difficulties involved in conditionally perturbing complex gene expression networks represent major challenges toward defining the mechanisms controlling human development, physiology, and disease. We developed an OPTimized inducible KnockDown (OPTiKD) platform that addresses the limitations of previous approaches by allowing streamlined, tightly-controlled, and potent loss-of-function experiments for both single and multiple genes. The method relies on single-step genetic engineering of the AAVS1 genomic safe harbor with an optimized tetracycline-responsive cassette driving one or more inducible short hairpin RNAs (shRNAs). OPTiKD provides homogeneous, dose-responsive, and reversible gene knockdown. When implemented in human pluripotent stem cells (hPSCs), the approach can be then applied to a broad range of hPSC-derived mature cell lineages that include neurons, cardiomyocytes, and hepatocytes. Generation of OPTiKD hPSCs in commonly used culture conditions is simple (plasmid based), rapid (two weeks), and highly efficient (>95%). Overall, this method facilitates the functional annotation of the human genome in health and disease. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
- Alessandro Bertero
- Wellcome Trust-MRC Stem Cell Institute, Anne McLaren Laboratory, University of Cambridge, Cambridge, United Kingdom
- Department of Surgery, University of Cambridge, Cambridge, United Kingdom
- Department of Pathology, University of Washington, Seattle, Washington
| | - Loukia Yiangou
- Wellcome Trust-MRC Stem Cell Institute, Anne McLaren Laboratory, University of Cambridge, Cambridge, United Kingdom
- Division of Cardiovascular Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Stephanie Brown
- Wellcome Trust-MRC Stem Cell Institute, Anne McLaren Laboratory, University of Cambridge, Cambridge, United Kingdom
- Department of Surgery, University of Cambridge, Cambridge, United Kingdom
| | - Daniel Ortmann
- Wellcome Trust-MRC Stem Cell Institute, Anne McLaren Laboratory, University of Cambridge, Cambridge, United Kingdom
- Department of Surgery, University of Cambridge, Cambridge, United Kingdom
| | - Matthias Pawlowski
- Wellcome Trust-MRC Stem Cell Institute, Anne McLaren Laboratory, University of Cambridge, Cambridge, United Kingdom
- Department of Clinical Neuroscience, University of Cambridge, Cambridge, United Kingdom
| | - Ludovic Vallier
- Wellcome Trust-MRC Stem Cell Institute, Anne McLaren Laboratory, University of Cambridge, Cambridge, United Kingdom
- Department of Surgery, University of Cambridge, Cambridge, United Kingdom
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
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8
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Daneshvar K, Pondick JV, Kim BM, Zhou C, York SR, Macklin JA, Abualteen A, Tan B, Sigova AA, Marcho C, Tremblay KD, Mager J, Choi MY, Mullen AC. DIGIT Is a Conserved Long Noncoding RNA that Regulates GSC Expression to Control Definitive Endoderm Differentiation of Embryonic Stem Cells. Cell Rep 2017; 17:353-365. [PMID: 27705785 DOI: 10.1016/j.celrep.2016.09.017] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Revised: 08/12/2016] [Accepted: 09/03/2016] [Indexed: 02/06/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) exhibit diverse functions, including regulation of development. Here, we combine genome-wide mapping of SMAD3 occupancy with expression analysis to identify lncRNAs induced by activin signaling during endoderm differentiation of human embryonic stem cells (hESCs). We find that DIGIT is divergent to Goosecoid (GSC) and expressed during endoderm differentiation. Deletion of the SMAD3-occupied enhancer proximal to DIGIT inhibits DIGIT and GSC expression and definitive endoderm differentiation. Disruption of the gene encoding DIGIT and depletion of the DIGIT transcript reveal that DIGIT is required for definitive endoderm differentiation. In addition, we identify the mouse ortholog of DIGIT and show that it is expressed during development and promotes definitive endoderm differentiation of mouse ESCs. DIGIT regulates GSC in trans, and activation of endogenous GSC expression is sufficient to rescue definitive endoderm differentiation in DIGIT-deficient hESCs. Our study defines DIGIT as a conserved noncoding developmental regulator of definitive endoderm.
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Affiliation(s)
- Kaveh Daneshvar
- Gastrointestinal Unit, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Joshua V Pondick
- Gastrointestinal Unit, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Byeong-Moo Kim
- Gastrointestinal Unit, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Chan Zhou
- Gastrointestinal Unit, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Samuel R York
- Gastrointestinal Unit, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Jillian A Macklin
- Gastrointestinal Unit, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Ameed Abualteen
- Gastrointestinal Unit, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Bo Tan
- Gastrointestinal Unit, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; School of Fundamental Medical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510405, China
| | - Alla A Sigova
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Chelsea Marcho
- Department of Veterinary and Animal Sciences, University of Massachusetts at Amherst, Amherst, MA 01003, USA
| | - Kimberly D Tremblay
- Department of Veterinary and Animal Sciences, University of Massachusetts at Amherst, Amherst, MA 01003, USA
| | - Jesse Mager
- Department of Veterinary and Animal Sciences, University of Massachusetts at Amherst, Amherst, MA 01003, USA
| | - Michael Y Choi
- Gastrointestinal Unit, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Alan C Mullen
- Gastrointestinal Unit, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA.
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9
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Dai X, Chen X, Fang Q, Li J, Bai Z. Inducible CRISPR genome-editing tool: classifications and future trends. Crit Rev Biotechnol 2017; 38:573-586. [DOI: 10.1080/07388551.2017.1378999] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Xiaofeng Dai
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Xiao Chen
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Qiuwu Fang
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Jia Li
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Zhonghu Bai
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
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10
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Pineda M, Moghadam F, Ebrahimkhani MR, Kiani S. Engineered CRISPR Systems for Next Generation Gene Therapies. ACS Synth Biol 2017; 6:1614-1626. [PMID: 28558198 DOI: 10.1021/acssynbio.7b00011] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
An ideal in vivo gene therapy platform provides safe, reprogrammable, and precise strategies which modulate cell and tissue gene regulatory networks with a high temporal and spatial resolution. Clustered regularly interspaced short palindromic repeats (CRISPR), a bacterial adoptive immune system, and its CRISPR-associated protein 9 (Cas9), have gained attention for the ability to target and modify DNA sequences on demand with unprecedented flexibility and precision. The precision and programmability of Cas9 is derived from its complexation with a guide-RNA (gRNA) that is complementary to a desired genomic sequence. CRISPR systems open-up widespread applications including genetic disease modeling, functional screens, and synthetic gene regulation. The plausibility of in vivo genetic engineering using CRISPR has garnered significant traction as a next generation in vivo therapeutic. However, there are hurdles that need to be addressed before CRISPR-based strategies are fully implemented. Some key issues center on the controllability of the CRISPR platform, including minimizing genomic-off target effects and maximizing in vivo gene editing efficiency, in vivo cellular delivery, and spatial-temporal regulation. The modifiable components of CRISPR systems: Cas9 protein, gRNA, delivery platform, and the form of CRISPR system delivered (DNA, RNA, or ribonucleoprotein) have recently been engineered independently to design a better genome engineering toolbox. This review focuses on evaluating CRISPR potential as a next generation in vivo gene therapy platform and discusses bioengineering advancements that can address challenges associated with clinical translation of this emerging technology.
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Affiliation(s)
- Michael Pineda
- School
of Biological and Health Systems Engineering, Arizona State University, Tempe, Arizona 85281, United States
| | - Farzaneh Moghadam
- School
of Biological and Health Systems Engineering, Arizona State University, Tempe, Arizona 85281, United States
| | - Mo R. Ebrahimkhani
- School
of Biological and Health Systems Engineering, Arizona State University, Tempe, Arizona 85281, United States
- Center for Regenerative
Medicine, Mayo Clinic, Phoenix, Arizona 85054, United States
| | - Samira Kiani
- School
of Biological and Health Systems Engineering, Arizona State University, Tempe, Arizona 85281, United States
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11
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p53 Mediates Failure of Human Definitive Hematopoiesis in Dyskeratosis Congenita. Stem Cell Reports 2017; 9:409-418. [PMID: 28757166 PMCID: PMC5550027 DOI: 10.1016/j.stemcr.2017.06.015] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 06/27/2017] [Accepted: 06/27/2017] [Indexed: 12/23/2022] Open
Abstract
Dyskeratosis congenita (DC) is a bone marrow failure syndrome associated with telomere dysfunction. The progression and molecular determinants of hematopoietic failure in DC remain poorly understood. Here, we use the directed differentiation of human embryonic stem cells harboring clinically relevant mutations in telomerase to understand the consequences of DC-associated mutations on the primitive and definitive hematopoietic programs. Interestingly, telomere shortening does not broadly impair hematopoiesis, as primitive hematopoiesis is not impaired in DC cells. In contrast, while phenotypic definitive hemogenic endothelium is specified, the endothelial-to-hematopoietic transition is impaired in cells with shortened telomeres. This failure is caused by DNA damage accrual and is mediated by p53 stabilization. These observations indicate that detrimental effects of telomere shortening in the hematopoietic system are specific to the definitive hematopoietic lineages. This work illustrates how telomere dysfunction impairs hematopoietic development and creates a robust platform for therapeutic discovery for treatment of DC patients. CRISPR/Cas9 was used to generate different DC-associated mutations in hESCs Telomere shortening specifically impairs definitive hematopoietic specification Genetic instability and p53 activation regulate hematopoietic specification in DC In vitro hematopoietic failure resembles phenotypes of aplastic anemia in DC
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12
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Creamer JP, Dege C, Ren Q, Ho JTK, Valentine MC, Druley TE, Sturgeon CM. Human definitive hematopoietic specification from pluripotent stem cells is regulated by mesodermal expression of CDX4. Blood 2017; 129:2988-2992. [PMID: 28408465 PMCID: PMC5454336 DOI: 10.1182/blood-2016-11-749382] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2016] [Accepted: 04/08/2017] [Indexed: 12/15/2022] Open
Abstract
The generation of hematopoietic stem cells from human pluripotent stem cells (hPSCs) is a major goal for regenerative medicine. Achieving this goal is complicated by our incomplete understanding of the mechanism regulating definitive hematopoietic specification. We used our stage-specific hPSC differentiation method to obtain and identify, via CD235a expression, mesoderm harboring exclusively primitive or definitive hematopoietic potential to understand the genetic regulation of definitive hematopoietic specification. Whole-transcriptome gene expression analyses on WNT-dependent KDR+CD235a- definitive hematopoietic mesoderm and WNT-independent KDR+CD235a+ primitive hematopoietic mesoderm revealed strong CDX gene expression within definitive hematopoietic mesoderm. Temporal expression analyses revealed that CDX4 was expressed exclusively within definitive hematopoietic KDR+CD235a- mesoderm in a WNT- and fibroblast growth factor-dependent manner. We found that exogenous CDX4 expression exclusively during mesoderm specification resulted in a >90% repression in primitive hematopoietic potential, but conferred fivefold greater definitive hematopoietic potential, similar to that observed following WNT stimulation. In contrast, CDX4 knockout hPSCs had intact primitive hematopoietic potential, but exhibited a fivefold decrease in multilineage definitive hematopoietic potential. Taken together, these findings indicate that CDX4 is a critical transcription factor in the regulation of human definitive hematopoietic specification, and provides a mechanistic basis for WNT-mediated definitive hematopoietic specification from hPSCs.
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Affiliation(s)
| | | | - Qihao Ren
- Division of Hematology, Department of Medicine
| | | | | | | | - Christopher M Sturgeon
- Division of Hematology, Department of Medicine
- Department of Developmental Biology, Washington University in St. Louis, St. Louis, MO
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LiPS-A3S, a human genomic site for robust expression of inserted transgenes. MOLECULAR THERAPY-NUCLEIC ACIDS 2016; 5:e394. [PMID: 27898090 PMCID: PMC5155331 DOI: 10.1038/mtna.2016.99] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2016] [Accepted: 10/06/2016] [Indexed: 01/14/2023]
Abstract
Transgenesis of human pluripotent stem cells (hPSCs) can enable and empower a variety of studies in stem cell research, including lineage tracing and functional genetics studies. While in recent years much progress has been made in the development of tools for gene targeting, little attention has been given to the identification of sites in the human genome where transgenes can be inserted and reliably expressed. In order to find human genomic sites capable of supporting long-term and high-level transgene expression in hPSCs, we performed a lentiviral screen in human induced pluripotent stem cells (iPSCs). We isolated 40 iPSC clones each harboring a single vector copy and characterized the level of transgene expression afforded by each unique integration site. We selected one clone, LiPS-A3 with an integration site in chromosome 15 maintaining robust expression without silencing and demonstrate that different transgenes can be inserted therein rapidly and efficiently through recombinase-mediated cassette exchange (RMCE). The LiPS-A3 line can greatly facilitate the insertion of reporter and other genes in hPSCs. Targeting transgenes in the LiPS-A3S genomic locus can find broad applications in stem cell research and possibly cell and gene therapy.
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Kao T, Labonne T, Niclis JC, Chaurasia R, Lokmic Z, Qian E, Bruveris FF, Howden SE, Motazedian A, Schiesser JV, Costa M, Sourris K, Ng E, Anderson D, Giudice A, Farlie P, Cheung M, Lamande SR, Penington AJ, Parish CL, Thomson LH, Rafii A, Elliott DA, Elefanty AG, Stanley EG. GAPTrap: A Simple Expression System for Pluripotent Stem Cells and Their Derivatives. Stem Cell Reports 2016; 7:518-526. [PMID: 27594589 PMCID: PMC5032031 DOI: 10.1016/j.stemcr.2016.07.015] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Revised: 07/15/2016] [Accepted: 07/16/2016] [Indexed: 01/30/2023] Open
Abstract
The ability to reliably express fluorescent reporters or other genes of interest is important for using human pluripotent stem cells (hPSCs) as a platform for investigating cell fates and gene function. We describe a simple expression system, designated GAPTrap (GT), in which reporter genes, including GFP, mCherry, mTagBFP2, luc2, Gluc, and lacZ are inserted into the GAPDH locus in hPSCs. Independent clones harboring variations of the GT vectors expressed remarkably consistent levels of the reporter gene. Differentiation experiments showed that reporter expression was reliably maintained in hematopoietic cells, cardiac mesoderm, definitive endoderm, and ventral midbrain dopaminergic neurons. Similarly, analysis of teratomas derived from GT-lacZ hPSCs showed that β-galactosidase expression was maintained in a spectrum of cell types representing derivatives of the three germ layers. Thus, the GAPTrap vectors represent a robust and straightforward tagging system that enables indelible labeling of PSCs and their differentiated derivatives. GAPTrap vector system targets transgenes to the ubiquitously expressed GAPDH locus Targeting transgenes to the GAPDH locus yields reliable transgene expression Transgenes at this locus are robustly expressed in differentiated cells Generation of GAPTrap targeted human PSC lines is simple and efficient
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Affiliation(s)
- Tim Kao
- Murdoch Childrens Research Institute, Flemington Road, Parkville, VIC 3052, Australia; Department of Paediatrics, University of Melbourne, Parkville, VIC 3050, Australia
| | - Tanya Labonne
- Murdoch Childrens Research Institute, Flemington Road, Parkville, VIC 3052, Australia
| | - Jonathan C Niclis
- The Florey Institute of Neuroscience and Mental Health, Melbourne University, Parkville, VIC 3052, Australia
| | - Ritu Chaurasia
- Department of Paediatrics, University of Melbourne, Parkville, VIC 3050, Australia
| | - Zerina Lokmic
- Murdoch Childrens Research Institute, Flemington Road, Parkville, VIC 3052, Australia
| | - Elizabeth Qian
- Murdoch Childrens Research Institute, Flemington Road, Parkville, VIC 3052, Australia; Department of Paediatrics, University of Melbourne, Parkville, VIC 3050, Australia
| | - Freya F Bruveris
- Murdoch Childrens Research Institute, Flemington Road, Parkville, VIC 3052, Australia; Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC 3800, Australia
| | - Sara E Howden
- Murdoch Childrens Research Institute, Flemington Road, Parkville, VIC 3052, Australia; Department of Paediatrics, University of Melbourne, Parkville, VIC 3050, Australia
| | - Ali Motazedian
- Murdoch Childrens Research Institute, Flemington Road, Parkville, VIC 3052, Australia; Department of Paediatrics, University of Melbourne, Parkville, VIC 3050, Australia
| | - Jacqueline V Schiesser
- Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC 3800, Australia; Division of Developmental Biology, Cincinnati Children's Hospital Medical Centre, Cincinnati, OH 45229, USA
| | - Magdaline Costa
- Australian Centre for Blood Diseases, Monash University, The Alfred Centre, Melbourne, VIC 3004, Australia
| | - Koula Sourris
- Murdoch Childrens Research Institute, Flemington Road, Parkville, VIC 3052, Australia
| | - Elizabeth Ng
- Murdoch Childrens Research Institute, Flemington Road, Parkville, VIC 3052, Australia
| | - David Anderson
- Murdoch Childrens Research Institute, Flemington Road, Parkville, VIC 3052, Australia
| | - Antonietta Giudice
- Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC 3800, Australia
| | - Peter Farlie
- Murdoch Childrens Research Institute, Flemington Road, Parkville, VIC 3052, Australia; Department of Paediatrics, University of Melbourne, Parkville, VIC 3050, Australia
| | - Michael Cheung
- Murdoch Childrens Research Institute, Flemington Road, Parkville, VIC 3052, Australia; Department of Paediatrics, University of Melbourne, Parkville, VIC 3050, Australia; Department of Cardiology, The Royal Children's Hospital, Parkville, VIC 3052, Australia
| | - Shireen R Lamande
- Murdoch Childrens Research Institute, Flemington Road, Parkville, VIC 3052, Australia; Department of Paediatrics, University of Melbourne, Parkville, VIC 3050, Australia
| | - Anthony J Penington
- Murdoch Childrens Research Institute, Flemington Road, Parkville, VIC 3052, Australia; Department of Paediatrics, University of Melbourne, Parkville, VIC 3050, Australia
| | - Clare L Parish
- The Florey Institute of Neuroscience and Mental Health, Melbourne University, Parkville, VIC 3052, Australia
| | - Lachlan H Thomson
- The Florey Institute of Neuroscience and Mental Health, Melbourne University, Parkville, VIC 3052, Australia
| | - Arash Rafii
- Stem Cell and Microenvironment Laboratory, Weill Cornell Medical College in Qatar, Qatar Foundation, Education City, Doha, Qatar; Department of Genetic Medicine, Weill Cornell Medical College, New York, NY 10065-4896, USA
| | - David A Elliott
- Murdoch Childrens Research Institute, Flemington Road, Parkville, VIC 3052, Australia; School of Biosciences, University of Melbourne, Parkville, VIC 3050, Australia
| | - Andrew G Elefanty
- Murdoch Childrens Research Institute, Flemington Road, Parkville, VIC 3052, Australia; Department of Paediatrics, University of Melbourne, Parkville, VIC 3050, Australia; Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC 3800, Australia.
| | - Edouard G Stanley
- Murdoch Childrens Research Institute, Flemington Road, Parkville, VIC 3052, Australia; Department of Paediatrics, University of Melbourne, Parkville, VIC 3050, Australia; Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC 3800, Australia.
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15
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lncRHOXF1, a Long Noncoding RNA from the X Chromosome That Suppresses Viral Response Genes during Development of the Early Human Placenta. Mol Cell Biol 2016; 36:1764-75. [PMID: 27066803 DOI: 10.1128/mcb.01098-15] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 04/07/2016] [Indexed: 11/20/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) can regulate gene expression in a cell-specific fashion during development. Here, we identify a novel lncRNA from the X chromosome that we named lncRHOXF1 and which is abundantly expressed in trophectoderm and primitive endoderm cells of human blastocyst-stage embryos. lncRHOXF1 is a spliced and polyadenylated lncRNA about 1 kb in length that is found in both the nuclear and cytoplasmic compartments of in vitro differentiated human trophectoderm progenitor cells. Gain-of-function experiments in human embryonic stem cells, which normally lack lncRHOXF1 RNA, revealed that lncRHOXF1 reduced proliferation and favored cellular differentiation. lncRHOXF1 knockdown using small interfering RNAs (siRNAs) in human trophectoderm progenitors increased expression of viral response genes, including type I interferon. Sendai virus infection of human trophectoderm progenitor cells increased lncRHOXF1 RNA levels, and siRNA-mediated disruption of lncRHOXF1 during infection reduced the expression of viral response genes leading to higher virus replication. Thus, lncRHOXF1 RNA is the first example of a lncRNA that regulates the host response to viral infections in human placental progenitor cells, and we propose that it functions as a repressor of the viral response during early human development.
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Understanding platelet generation from megakaryocytes: implications for in vitro-derived platelets. Blood 2016; 127:1227-33. [PMID: 26787738 DOI: 10.1182/blood-2015-08-607929] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 09/30/2015] [Indexed: 12/12/2022] Open
Abstract
Platelets are anucleate cytoplasmic discs derived from megakaryocytes that circulate in the blood and have major roles in hemostasis, thrombosis, inflammation, and vascular biology. Platelet transfusions are required to prevent the potentially life-threatening complications of severe thrombocytopenia seen in a variety of medical settings including cancer therapy, trauma, and sepsis. Platelets used in the clinic are currently donor-derived which is associated with concerns over sufficient availability, quality, and complications due to immunologic and/or infectious issues. To overcome our dependence on donor-derived platelets for transfusion, efforts have been made to generate in vitro-based platelets. Work in this area has advanced our understanding of the complex processes that megakaryocytes must undergo to generate platelets both in vivo and in vitro. This knowledge has also defined the challenges that must be overcome to bring in vitro-based platelet manufacturing to a clinical reality. This review will focus on our understanding of committed megakaryocytes and platelet release in vivo and in vitro, and how this knowledge can guide the development of in vitro-derived platelets for clinical application.
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Cellular Engineering and Disease Modeling with Gene-Editing Nucleases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016. [DOI: 10.1007/978-1-4939-3509-3_12] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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