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Nandy K, Babu D, Rani S, Joshi G, Ijee S, George A, Palani D, Premkumar C, Rajesh P, Vijayanand S, David E, Murugesan M, Velayudhan SR. Efficient gene editing in induced pluripotent stem cells enabled by an inducible adenine base editor with tunable expression. Sci Rep 2023; 13:21953. [PMID: 38081875 PMCID: PMC10713686 DOI: 10.1038/s41598-023-42174-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Accepted: 09/06/2023] [Indexed: 12/18/2023] Open
Abstract
The preferred method for disease modeling using induced pluripotent stem cells (iPSCs) is to generate isogenic cell lines by correcting or introducing pathogenic mutations. Base editing enables the precise installation of point mutations at specific genomic locations without the need for deleterious double-strand breaks used in the CRISPR-Cas9 gene editing methods. We created a bulk population of iPSCs that homogeneously express ABE8e adenine base editor enzyme under a doxycycline-inducible expression system at the AAVS1 safe harbor locus. These cells enabled fast, efficient and inducible gene editing at targeted genomic regions, eliminating the need for single-cell cloning and screening to identify those with homozygous mutations. We could achieve multiplex genomic editing by creating homozygous mutations in very high efficiencies at four independent genomic loci simultaneously in AAVS1-iABE8e iPSCs, which is highly challenging with previously described methods. The inducible ABE8e expression system allows editing of the genes of interest within a specific time window, enabling temporal control of gene editing to study the cell or lineage-specific functions of genes and their molecular pathways. In summary, the inducible ABE8e system provides a fast, efficient and versatile gene-editing tool for disease modeling and functional genomic studies.
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Affiliation(s)
- Krittika Nandy
- Center for Stem Cell Research (A Unit of inStem, Bengaluru, India), Christian Medical College, Tamil Nadu, Vellore, 632002, India
- Department of Biotechnology, Thiruvalluvar University, Vellore, Tamil Nadu, 632115, India
| | - Dinesh Babu
- Center for Stem Cell Research (A Unit of inStem, Bengaluru, India), Christian Medical College, Tamil Nadu, Vellore, 632002, India
| | - Sonam Rani
- Center for Stem Cell Research (A Unit of inStem, Bengaluru, India), Christian Medical College, Tamil Nadu, Vellore, 632002, India
- Department of Biotechnology, Thiruvalluvar University, Vellore, Tamil Nadu, 632115, India
| | - Gaurav Joshi
- Department of Haematology, Christian Medical College, Vellore, Tamil Nadu, 632004, India
- Sree Chitra Tirunal Institute for Medical Sciences and Technology, Thiruvananthapuram, Kerala, 695011, India
| | - Smitha Ijee
- Center for Stem Cell Research (A Unit of inStem, Bengaluru, India), Christian Medical College, Tamil Nadu, Vellore, 632002, India
- Department of Biotechnology, Thiruvalluvar University, Vellore, Tamil Nadu, 632115, India
| | - Anila George
- Center for Stem Cell Research (A Unit of inStem, Bengaluru, India), Christian Medical College, Tamil Nadu, Vellore, 632002, India
- Sree Chitra Tirunal Institute for Medical Sciences and Technology, Thiruvananthapuram, Kerala, 695011, India
| | - Dhavapriya Palani
- Center for Stem Cell Research (A Unit of inStem, Bengaluru, India), Christian Medical College, Tamil Nadu, Vellore, 632002, India
| | - Chitra Premkumar
- Center for Stem Cell Research (A Unit of inStem, Bengaluru, India), Christian Medical College, Tamil Nadu, Vellore, 632002, India
| | - Praveena Rajesh
- Center for Stem Cell Research (A Unit of inStem, Bengaluru, India), Christian Medical College, Tamil Nadu, Vellore, 632002, India
| | - S Vijayanand
- Department of Biotechnology, Thiruvalluvar University, Vellore, Tamil Nadu, 632115, India
| | - Ernest David
- Department of Biotechnology, Thiruvalluvar University, Vellore, Tamil Nadu, 632115, India
| | - Mohankumar Murugesan
- Center for Stem Cell Research (A Unit of inStem, Bengaluru, India), Christian Medical College, Tamil Nadu, Vellore, 632002, India
| | - Shaji R Velayudhan
- Center for Stem Cell Research (A Unit of inStem, Bengaluru, India), Christian Medical College, Tamil Nadu, Vellore, 632002, India.
- Department of Haematology, Christian Medical College, Vellore, Tamil Nadu, 632004, India.
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Vats P, Kaushik R, Rawat N, Sharma A, Sharma T, Dua D, Singh MK, Palta P, Singla SK, Manik RS, Chauhan MS. Production of Transgenic Handmade Cloned Goat ( Capra hircus) Embryos by Targeted Integration into Rosa 26 Locus Using Transcription Activator-like Effector Nucleases. Cell Reprogram 2021; 23:250-262. [PMID: 34348041 DOI: 10.1089/cell.2021.0011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Transgenic goats are ideal bioreactors for the production of therapeutic proteins in their mammary glands. However, random integration of the transgene within-host genome often culminates in unstable expression and unpredictable phenotypes. Targeting desired genes to a safe locus in the goat genome using advanced targeted genome-editing tools, such as transcription activator-like effector nucleases (TALENs) might assist in overcoming these hurdles. We identified Rosa 26 locus, a safe harbor for transgene integration, on chromosome 22 in the goat genome for the first time. We further demonstrate that TALEN-mediated targeting of GFP gene cassette at Rosa 26 locus exhibited stable and ubiquitous expression of GFP gene in goat fetal fibroblasts (GFFs) and after that, transgenic cloned embryos generated by handmade cloning (HMC). The transfection of GFFs by the TALEN pair resulted in 13.30% indel frequency at the target site. Upon cotransfection with TALEN and donor vectors, four correctly targeted cell colonies were obtained and all of them showed monoallelic gene insertions. The blastocyst rate for transgenic cloned embryos (3.92% ± 1.12%) was significantly (p < 0.05) lower than cloned embryos (7.84% ± 0.68%) used as control. Concomitantly, 2 out of 15 embryos of morulae and blastocyst stage (13.30%) exhibited site-specific integration. In conclusion, the present study demonstrates TALEN-mediated transgene integration at Rosa 26 locus in caprine fetal fibroblasts and the generation of transgenic cloned embryos using HMC.
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Affiliation(s)
- Preeti Vats
- Embryo Biotechnology Laboratory, Animal Biotechnology Centre, ICAR-National Dairy Research Institute, Karnal, India
| | - Ramakant Kaushik
- Embryo Biotechnology Laboratory, Animal Biotechnology Centre, ICAR-National Dairy Research Institute, Karnal, India
| | - Nidhi Rawat
- Embryo Biotechnology Laboratory, Animal Biotechnology Centre, ICAR-National Dairy Research Institute, Karnal, India
| | - Ankur Sharma
- Embryo Biotechnology Laboratory, Animal Biotechnology Centre, ICAR-National Dairy Research Institute, Karnal, India
| | - Tushar Sharma
- Embryo Biotechnology Laboratory, Animal Biotechnology Centre, ICAR-National Dairy Research Institute, Karnal, India
| | - Diksha Dua
- Embryo Biotechnology Laboratory, Animal Biotechnology Centre, ICAR-National Dairy Research Institute, Karnal, India
| | - Manoj Kumar Singh
- Embryo Biotechnology Laboratory, Animal Biotechnology Centre, ICAR-National Dairy Research Institute, Karnal, India
| | - Prabhat Palta
- Embryo Biotechnology Laboratory, Animal Biotechnology Centre, ICAR-National Dairy Research Institute, Karnal, India
| | - Suresh Kumar Singla
- Embryo Biotechnology Laboratory, Animal Biotechnology Centre, ICAR-National Dairy Research Institute, Karnal, India
| | - Radhey Sham Manik
- Embryo Biotechnology Laboratory, Animal Biotechnology Centre, ICAR-National Dairy Research Institute, Karnal, India
| | - Manmohan Singh Chauhan
- Embryo Biotechnology Laboratory, Animal Biotechnology Centre, ICAR-National Dairy Research Institute, Karnal, India
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Sriram S, Kang NY, Subramanian S, Nandi T, Sudhagar S, Xing Q, Tong GJL, Chen AKL, Srijaya TC, Tan P, Loh YH, Chang YT, Sugii S. Novel live cell fluorescent probe for human-induced pluripotent stem cells highlights early reprogramming population. Stem Cell Res Ther 2021; 12:113. [PMID: 33546754 PMCID: PMC7866770 DOI: 10.1186/s13287-021-02171-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 01/15/2021] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Despite recent rapid progress in method development and biological understanding of induced pluripotent stem (iPS) cells, there has been a relative shortage of tools that monitor the early reprogramming process into human iPS cells. METHODS We screened the in-house built fluorescent library compounds that specifically bind human iPS cells. After tertiary screening, the selected probe was analyzed for its ability to detect reprogramming cells in the time-dependent manner using high-content imaging analysis. The probe was compared with conventional dyes in different reprogramming methods, cell types, and cell culture conditions. Cell sorting was performed with the fluorescent probe to analyze the early reprogramming cells for their pluripotent characteristics and genome-wide gene expression signatures by RNA-seq. Finally, the candidate reprogramming factor identified was investigated for its ability to modulate reprogramming efficiency. RESULTS We identified a novel BODIPY-derived fluorescent probe, BDL-E5, which detects live human iPS cells at the early reprogramming stage. BDL-E5 can recognize authentic reprogramming cells around 7 days before iPS colonies are formed and stained positive with conventional pluripotent markers. Cell sorting of reprogrammed cells with BDL-E5 allowed generation of an increased number and higher quality of iPS cells. RNA sequencing analysis of BDL-E5-positive versus negative cells revealed early reprogramming patterns of gene expression, which notably included CREB1. Reprogramming efficiency was significantly increased by overexpression of CREB1 and decreased by knockdown of CREB1. CONCLUSION Collectively, BDL-E5 offers a valuable tool for delineating the early reprogramming pathway and clinically applicable commercial production of human iPS cells.
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Affiliation(s)
- Sandhya Sriram
- Fat Metabolism and Stem Cell Group, Singapore Bioimaging Consortium, A*STAR, 11 Biopolis Way, Singapore, 138667, Singapore
| | - Nam-Young Kang
- Laboratory of Bioimaging Probe Development, Singapore Bioimaging Consortium, A*STAR, 11 Biopolis Way, Singapore, 138667, Singapore.,Department of Creative IT Engineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
| | - Subha Subramanian
- Fat Metabolism and Stem Cell Group, Singapore Bioimaging Consortium, A*STAR, 11 Biopolis Way, Singapore, 138667, Singapore
| | - Tannistha Nandi
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, 60 Biopolis Street, Genome #02-01, Singapore, 138672, Singapore
| | - Samydurai Sudhagar
- Genome Institute of Singapore, 60 Biopolis Street, Genome, #02-01, Singapore, 138672, Singapore
| | - Qiaorui Xing
- Epigenetics and Cell Fates Laboratory, Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore, 138673, Singapore.,School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Gerine Jin-Ling Tong
- Bioprocessing Technology Institute, A*STAR, 20 Biopolis Way, #06-01 Centros, Singapore, 138668, Singapore
| | - Allen Kuan-Liang Chen
- Bioprocessing Technology Institute, A*STAR, 20 Biopolis Way, #06-01 Centros, Singapore, 138668, Singapore
| | | | - Patrick Tan
- Genome Institute of Singapore, 60 Biopolis Street, Genome, #02-01, Singapore, 138672, Singapore.,Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore.,SingHealth/Duke-NUS Institute of Precision Medicine, Singapore, 168752, Singapore
| | - Yuin-Han Loh
- Epigenetics and Cell Fates Laboratory, Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore, 138673, Singapore.,Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore, 117543, Singapore
| | - Young-Tae Chang
- Laboratory of Bioimaging Probe Development, Singapore Bioimaging Consortium, A*STAR, 11 Biopolis Way, Singapore, 138667, Singapore.,Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore, 117543, Singapore.,Department of Chemistry, POSTECH, Pohang, Gyeongbuk, 37673, Republic of Korea.,Center for Self-assembly and Complexity, Institute for Basic Science (IBS), Pohang, 37673, Republic of Korea
| | - Shigeki Sugii
- Fat Metabolism and Stem Cell Group, Singapore Bioimaging Consortium, A*STAR, 11 Biopolis Way, Singapore, 138667, Singapore. .,Cardiovascular and Metabolic Disorders Program, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore. .,Institute of Bioengineering and Nanotechnology, A*STAR, 31 Biopolis Way, Singapore, 138669, Singapore.
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Pang LK, Pena M, Zhao R, Lee DF. Modeling of osteosarcoma with induced pluripotent stem cells. Stem Cell Res 2020; 49:102006. [PMID: 33022533 DOI: 10.1016/j.scr.2020.102006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 06/18/2020] [Accepted: 09/14/2020] [Indexed: 12/29/2022] Open
Abstract
Osteosarcoma is the most common type of bone cancer. Osteosarcoma is commonly associated with TP53 inactivation (around 95% of cases) and RB1 inactivation (around 28% of cases). With the discovery of reprogramming factors to induce pluripotency even in terminally differentiated cells, induced pluripotent stem cells (iPSCs) have emerged as a promising disease model. iPSC-based disease modeling uniquely recapitulates disease phenotypes and can support discoveries into disease etiology and is used extensively today to study a variety of diseases, including cancers. This paper focuses on iPSC-based modeling of Li-Fraumeni syndrome (LFS), an autosomal dominant disorder commonly associated with TP53 mutation and high osteosarcoma incidence. As iPSCs are increasingly utilized as a platform for cancer modeling, the experimental approaches that we discuss here may serve as a guide for future studies.
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Affiliation(s)
- Lon Kai Pang
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA; Rice University, Houston, TX 77005, USA
| | - Mezthly Pena
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA; Rice University, Houston, TX 77005, USA
| | - Ruiying Zhao
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Dung-Fang Lee
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA; The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA; Center for Stem Cell and Regenerative Medicine, The Brown Foundation Institute of Molecular Medicine for the Prevention of Human Diseases, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA; Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA.
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5
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Lungova V, Chen X, Wang Z, Kendziorski C, Thibeault SL. Human induced pluripotent stem cell-derived vocal fold mucosa mimics development and responses to smoke exposure. Nat Commun 2019; 10:4161. [PMID: 31551422 PMCID: PMC6760204 DOI: 10.1038/s41467-019-12069-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Accepted: 08/15/2019] [Indexed: 01/27/2023] Open
Abstract
Development of treatments for vocal dysphonia has been inhibited by lack of human vocal fold (VF) mucosa models because of difficulty in procuring VF epithelial cells, epithelial cells' limited proliferative capacity and absence of cell lines. Here we report development of engineered VF mucosae from hiPSC, transfected via TALEN constructs for green fluorescent protein, that mimic development of VF epithelial cells in utero. Modulation of FGF signaling achieves stratified squamous epithelium from definitive and anterior foregut derived cultures. Robust culturing of these cells on collagen-fibroblast constructs produces three-dimensional models comparable to in vivo VF mucosa. Furthermore, we demonstrate mucosal inflammation upon exposure of these constructs to 5% cigarette smoke extract. Upregulation of pro-inflammatory genes in epithelium and fibroblasts leads to aberrant VF mucosa remodeling. Collectively, our results demonstrate that hiPSC-derived VF mucosa is a versatile tool for future investigation of genetic and molecular mechanisms underlying epithelium-fibroblasts interactions in health and disease.
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Affiliation(s)
- Vlasta Lungova
- Department of Surgery, University of Wisconsin Madison, Wisconsin Institute for Medical Research, Madison, WI, USA
| | - Xia Chen
- Department of Surgery, University of Wisconsin Madison, Wisconsin Institute for Medical Research, Madison, WI, USA
| | - Ziyue Wang
- Department of Biostatistics & Medical Informatics, University of Wisconsin Madison, Madison, WI, USA
| | - Christina Kendziorski
- Department of Biostatistics & Medical Informatics, University of Wisconsin Madison, Madison, WI, USA
| | - Susan L Thibeault
- Department of Surgery, University of Wisconsin Madison, Wisconsin Institute for Medical Research, Madison, WI, USA.
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6
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Lee J, Bayarsaikhan D, Arivazhagan R, Park H, Lim B, Gwak P, Jeong GB, Lee J, Byun K, Lee B. CRISPR/Cas9 Edited sRAGE-MSCs Protect Neuronal Death in Parkinsons Disease Model. Int J Stem Cells 2019; 12:114-124. [PMID: 30836725 PMCID: PMC6457706 DOI: 10.15283/ijsc18110] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 12/21/2018] [Accepted: 12/23/2018] [Indexed: 12/23/2022] Open
Abstract
Background and Objectives Parkinsons disease (PD) is a fatal and progressive degenerative disease of the nervous system. Until recently, its promising treatment and underlying mechanisms for neuronal death are poorly understood. This study was investigated to identify the molecular mechanism of neuronal death in the substantia nigra and corpus striatum of PD. Methods The soluble RAGE (sRAGE) secreting Umbilical Cord Blood-derived Mesenchymal Stem Cell (UCB-MSC) was generated by gene editing method using clustered regularly interspaced short palindromic repeats/CRISPR associated protein 9 (CRISPR/Cas9). These cells were transplanted into Corpus Striatum of rotenone-induced PD animal models then behavioral test, morphological analysis, and immunohistochemical experiments were performed to determine the neuronal cell death and recovery of movement. Results The neuronal cell death in Corpus Striatum and Substantia Nigra was dramatically reduced and the movement was improved after sRAGE secreting UCB-MSC treatment in PD mice by inhibition of RAGE in neuronal cells. Conclusions We suggest that sRAGE secreting UCB-MSC based therapeutic approach could be a potential treatment strategy for neurodegenerative disease including PD.
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Affiliation(s)
- Jaesuk Lee
- Center for Genomics and Proteomics & Stem Cell Core Facility, Lee Gil Ya Cancer and Diabetes Institute, Gachon University, Incheon, Korea
| | - Delger Bayarsaikhan
- Center for Genomics and Proteomics & Stem Cell Core Facility, Lee Gil Ya Cancer and Diabetes Institute, Gachon University, Incheon, Korea
| | - Roshini Arivazhagan
- Center for Genomics and Proteomics & Stem Cell Core Facility, Lee Gil Ya Cancer and Diabetes Institute, Gachon University, Incheon, Korea
| | - Hyejung Park
- Center for Genomics and Proteomics & Stem Cell Core Facility, Lee Gil Ya Cancer and Diabetes Institute, Gachon University, Incheon, Korea
| | - Byungyoon Lim
- Center for Genomics and Proteomics & Stem Cell Core Facility, Lee Gil Ya Cancer and Diabetes Institute, Gachon University, Incheon, Korea
| | - Peter Gwak
- Center for Genomics and Proteomics & Stem Cell Core Facility, Lee Gil Ya Cancer and Diabetes Institute, Gachon University, Incheon, Korea
| | - Goo-Bo Jeong
- Center for Genomics and Proteomics & Stem Cell Core Facility, Lee Gil Ya Cancer and Diabetes Institute, Gachon University, Incheon, Korea.,Department of Anatomy & Cell Biology, Graduate School of Medicine, Gachon University, Incheon, Korea
| | - Jaewon Lee
- Department of Aquatic Life Medicine, Pukyong National University, Busan, Korea
| | - Kyunghee Byun
- Center for Genomics and Proteomics & Stem Cell Core Facility, Lee Gil Ya Cancer and Diabetes Institute, Gachon University, Incheon, Korea.,Department of Anatomy & Cell Biology, Graduate School of Medicine, Gachon University, Incheon, Korea
| | - Bonghee Lee
- Center for Genomics and Proteomics & Stem Cell Core Facility, Lee Gil Ya Cancer and Diabetes Institute, Gachon University, Incheon, Korea.,Department of Anatomy & Cell Biology, Graduate School of Medicine, Gachon University, Incheon, Korea
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Eguizabal C, Aran B, Chuva de Sousa Lopes SM, Geens M, Heindryckx B, Panula S, Popovic M, Vassena R, Veiga A. Two decades of embryonic stem cells: a historical overview. Hum Reprod Open 2019; 2019:hoy024. [PMID: 30895264 PMCID: PMC6396646 DOI: 10.1093/hropen/hoy024] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 12/10/2018] [Indexed: 12/12/2022] Open
Abstract
STUDY QUESTION How did the field of stem cell research develop in the years following the derivation of the first human embryonic stem cell (hESC) line? SUMMARY ANSWER Supported by the increasing number of clinical trials to date, significant technological advances in the past two decades have brought us ever closer to clinical therapies derived from pluripotent cells. WHAT IS KNOWN ALREADY Since their discovery 20 years ago, the use of human pluripotent stem cells has progressed tremendously from bench to bedside. Here, we provide a concise review of the main keystones of this journey and focus on ongoing clinical trials, while indicating the most relevant future research directions. STUDY DESIGN, SIZE, DURATION This is a historical narrative, including relevant publications in the field of pluripotent stem cells (PSC) derivation and differentiation, recounted both through scholarly research of published evidence and interviews of six pioneers who participated in some of the most relevant discoveries in the field. PARTICIPANTS/MATERIALS, SETTING, METHODS The authors all contributed by researching the literature and agreed upon body of works. Portions of the interviews of the field pioneers have been integrated into the review and have also been included in full for advanced reader interest. MAIN RESULTS AND THE ROLE OF CHANCE The stem cell field is ever expanding. We find that in the 20 years since the derivation of the first hESC lines, several relevant developments have shaped the pluripotent cell field, from the discovery of different states of pluripotency, the derivation of induced PSC, the refinement of differentiation protocols with several clinical trials underway, as well as the recent development of organoids. The challenge for the years to come will be to validate and refine PSCs for clinical use, from the production of highly defined cell populations in clinical grade conditions to the possibility of creating replacement organoids for functional, if not anatomical, function restoration. LIMITATIONS, REASONS FOR CAUTION This is a non-systematic review of current literature. Some references may have escaped the experts’ analysis due to the exceedingly diverse nature of the field. As the field of regenerative medicine is rapidly advancing, some of the most recent developments may have not been captured entirely. WIDER IMPLICATIONS OF THE FINDINGS The multi-disciplinary nature and tremendous potential of the stem cell field has important implications for basic as well as translational research. Recounting these activities will serve to provide an in-depth overview of the field, fostering a further understanding of human stem cell and developmental biology. The comprehensive overview of clinical trials and expert opinions included in this narrative may serve as a valuable scientific resource, supporting future efforts in translational approaches. STUDY FUNDING/COMPETING INTEREST(S) ESHRE provided funding for the authors’ on-site meeting and discussion during the preparation of this manuscript. S.M.C.S.L. is funded by the European Research Council Consolidator (ERC-CoG-725722-OVOGROWTH). M.P. is supported by the Special Research Fund, Bijzonder Onderzoeksfonds (BOF01D08114). M.G. is supported by the Methusalem grant of Vrije Universiteit Brussel, in the name of Prof. Karen Sermon and by Innovation by Science and Technology in Flanders (IWT, Project Number: 150042). A.V. and B.A. are supported by the Plataforma de Proteomica, Genotipado y Líneas Celulares (PT1770019/0015) (PRB3), Instituto de Salud Carlos III. Research grant to B.H. by the Research Foundation—Flanders (FWO) (FWO.KAN.2016.0005.01 and FWO.Project G051516N). There are no conflicts of interest to declare. TRIAL REGISTRATION NUMBER Not applicable. ESHRE Pages are not externally peer reviewed. This article has been approved by the Executive Committee of ESHRE.
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Affiliation(s)
- C Eguizabal
- Cell Therapy and Stem Cell Group, Basque Center for Blood Transfusion and Human Tissues, Barrio Labeaga S/N, Galdakao, Spain
| | - B Aran
- Barcelona Stem Cell Bank, Centre of Regenerative Medicine in Barcelona, Barcelona, Spain
| | - S M Chuva de Sousa Lopes
- Department of Anatomy and Embryology, Leiden University Medical Center, Einthovenweg 20, Leiden, The Netherlands.,Ghent Fertility and Stem cell Team (G-FaST), Department for Reproductive Medicine, Ghent University Hospital, Ghent, Belgium
| | - M Geens
- Research Group Reproduction and Genetics, Vrije Univeristeit Brussel, Laarbeeklaan 103, Jette (Brussels), Belgium
| | - B Heindryckx
- Ghent Fertility and Stem cell Team (G-FaST), Department for Reproductive Medicine, Ghent University Hospital, Ghent, Belgium
| | - S Panula
- Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden
| | - M Popovic
- Ghent Fertility and Stem cell Team (G-FaST), Department for Reproductive Medicine, Ghent University Hospital, Ghent, Belgium
| | | | - A Veiga
- Barcelona Stem Cell Bank, Centre of Regenerative Medicine in Barcelona, Barcelona, Spain.,Dexeus Mujer, Hospital Universitari Dexeus, Barcelona, Spain
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8
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Apáti Á, Varga N, Berecz T, Erdei Z, Homolya L, Sarkadi B. Application of human pluripotent stem cells and pluripotent stem cell-derived cellular models for assessing drug toxicity. Expert Opin Drug Metab Toxicol 2018; 15:61-75. [PMID: 30526128 DOI: 10.1080/17425255.2019.1558207] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Introduction: Human pluripotent stem cells (hPSCs) are capable of differentiating into all types of cells in the body and so provide suitable toxicology screening systems even for hard-to-obtain human tissues. Since hPSCs can also be generated from differentiated cells and current gene editing technologies allow targeted genome modifications, hPSCs can be applied for drug toxicity screening both in normal and disease-specific models. Targeted hPSC differentiation is still a challenge but cardiac, neuronal or liver cells, and complex cellular models are already available for practical applications. Areas covered: The authors review new gene-editing and cell-biology technologies to generate sensitive toxicity screening systems based on hPSCs. Then the authors present the use of undifferentiated hPSCs for examining embryonic toxicity and discuss drug screening possibilities in hPSC-derived models. The authors focus on the application of human cardiomyocytes, hepatocytes, and neural cultures in toxicity testing, and discuss the recent possibilities for drug screening in a 'body-on-a-chip' model system. Expert opinion: hPSCs and their genetically engineered derivatives provide new possibilities to investigate drug toxicity in human tissues. The key issues in this regard are still the selection and generation of proper model systems, and the interpretation of the results in understanding in vivo drug effects.
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Affiliation(s)
- Ágota Apáti
- a Institute of Enzymology , Research Centre for Natural Sciences , Budapest , Hungary
| | - Nóra Varga
- a Institute of Enzymology , Research Centre for Natural Sciences , Budapest , Hungary
| | - Tünde Berecz
- a Institute of Enzymology , Research Centre for Natural Sciences , Budapest , Hungary
| | - Zsuzsa Erdei
- a Institute of Enzymology , Research Centre for Natural Sciences , Budapest , Hungary
| | - László Homolya
- a Institute of Enzymology , Research Centre for Natural Sciences , Budapest , Hungary
| | - Balázs Sarkadi
- a Institute of Enzymology , Research Centre for Natural Sciences , Budapest , Hungary
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9
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Liu M, Tu J, Gingold JA, Kong CSL, Lee DF. Cancer in a dish: progress using stem cells as a platform for cancer research. Am J Cancer Res 2018; 8:944-954. [PMID: 30034933 PMCID: PMC6048395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 05/18/2018] [Indexed: 06/08/2023] Open
Abstract
Cancer models derived from patient specimens poorly reflect early-stage cancer development because cancer cells acquire numerous additional molecular alterations before the disease is clinically detectable. Earlier studies have used differentiated cells derived from induced pluripotent cancer cells (iPCCs) to partially mirror cancer disease phenotype, but the highly heterogeneous nature of cancer cells as well as difficulties with reprogramming cancer cells has limited the application of this technique. An alternative approach to modeling cancer in a dish entails reprogramming adult differentiated cells from patients with cancer syndromes to pluripotent stem cells (PSCs), followed by directed differentiation of those PSCs. A directed reprogramming and differentiation strategy has the potential to recapitulate cancer progression and capture the earliest molecular alterations that underlie cancer initiation. The reprogrammed cells share patient-specific genetic and epigenetic traits, offering a new platform to develop personalized therapy for cancer patients. In this review, we will provide an overview of available reprogramming methods of cancer cells and describe how cancer-derived stem cells have been used to characterize effects of defined molecular alterations in specific cell types. We also describe the "disease in a dish" model developed to study genetic cancer syndromes. These approaches highlight recent contributions of stem cell technology to the cancer biology realm.
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Affiliation(s)
- Mo Liu
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at HoustonHouston, TX 77030, USA
| | - Jian Tu
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at HoustonHouston, TX 77030, USA
- Department of Musculoskeletal Oncology, The First Affiliated Hospital of Sun Yat-sen UniversityGuangzhou 510080, PR China
| | - Julian A Gingold
- Women’s Health Institute, Cleveland Clinic FoundationCleveland, OH 44195, USA
| | - Celine Shuet Lin Kong
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at HoustonHouston, TX 77030, USA
| | - Dung-Fang Lee
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at HoustonHouston, TX 77030, USA
- The University of Texas MD Anderson Cancer Center UT Health Graduate School of Biomedical SciencesHouston, TX 77030, USA
- Center for Stem Cell and Regenerative Medicine, The Brown Foundation Institute of Molecular Medicine for The Prevention of Human Diseases, The University of Texas Health Science Center at HoustonHouston, TX 77030, USA
- Center for Precision Health, School of Biomedical Informatics and School of Public Health, The University of Texas Health Science Center at HoustonHouston, TX 77030, USA
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Hendriks WT, Warren CR, Cowan CA. Genome Editing in Human Pluripotent Stem Cells: Approaches, Pitfalls, and Solutions. Cell Stem Cell 2016; 18:53-65. [PMID: 26748756 DOI: 10.1016/j.stem.2015.12.002] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Human pluripotent stem cells (hPSCs) with knockout or mutant alleles can be generated using custom-engineered nucleases. Transcription activator-like effector nucleases (TALENs) and clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 nucleases are the most commonly employed technologies for editing hPSC genomes. In this Protocol Review, we provide a brief overview of custom-engineered nucleases in the context of gene editing in hPSCs with a focus on the application of TALENs and CRISPR/Cas9. We will highlight the advantages and disadvantages of each method and discuss theoretical and technical considerations for experimental design.
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Affiliation(s)
- William T Hendriks
- The Collaborative Center for X-Linked Dystonia Parkinsonism, Department of Neurology, Massachusetts General Hospital, Charlestown, MA 02129, USA; Harvard Brain Science Initiative, Harvard Medical School, Boston, MA 02114, USA
| | - Curtis R Warren
- Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA
| | - Chad A Cowan
- Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA; Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA.
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Abstract
The elucidation of cancer pathogenesis has been hindered by limited access to patient samples, tumor heterogeneity and the lack of reliable model organisms. Characterized by their ability to self-renew indefinitely and differentiate into all cell lineages of an organism, pluripotent stem cells (PSCs), including embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs), provide a powerful and unlimited source to generate differentiated cells that can be used to study disease biology, facilitate drug discovery and development, and provide key insights for developing personalized therapies. This article reviews the recent developments and technologies converting PSCs into clinically relevant model systems for cancer research.
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Affiliation(s)
- Julian Gingold
- Women's Health Institute, Cleveland Clinic Foundation, Cleveland, OH 44195, USA
| | - Ruoji Zhou
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA; The University of Texas Graduate School of Biomedical Sciences at Houston, Houston, TX 77030, USA
| | - Ihor R Lemischka
- Department of Developmental and Regenerative Biology, Department of Pharmacology and System Therapeutics, The Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Dung-Fang Lee
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA; The University of Texas Graduate School of Biomedical Sciences at Houston, Houston, TX 77030, USA; Center for Stem Cell and Regenerative Medicine, The Brown Foundation Institute of Molecular Medicine for the Prevention of Human Diseases, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
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12
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Hendriks WT, Jiang X, Daheron L, Cowan CA. TALEN- and CRISPR/Cas9-Mediated Gene Editing in Human Pluripotent Stem Cells Using Lipid-Based Transfection. ACTA ACUST UNITED AC 2015; 34:5B.3.1-5B.3.25. [PMID: 26237572 DOI: 10.1002/9780470151808.sc05b03s34] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Using custom-engineered nuclease-mediated genome editing, such as Transcription Activator-Like Effector Nucleases (TALENs) and Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) RNA-guided Cas9 nucleases, human pluripotent stem cell (hPSC) lines with knockout or mutant alleles can be generated and differentiated into various cell types. This strategy of genome engineering in hPSCs will prove invaluable for studying human biology and disease. Here, we provide a detailed protocol for design and construction of TALEN and CRISPR vectors, testing of their nuclease activity, and delivery of TALEN or CRISPR vectors into hPSCs. In addition, we describe the use of single-stranded oligodeoxynucleotides (ssODNs) to introduce or repair point mutations. Next, we describe the identification of edited hPSC clones without antibiotic selection, including their clonal selection, genotyping, and expansion for downstream applications.
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Affiliation(s)
- William T Hendriks
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Xin Jiang
- Harvard University, Department of Stem Cell and Regenerative Biology and Harvard Stem Cell Institute, Cambridge, Massachusetts
| | - Laurence Daheron
- Harvard University, Department of Stem Cell and Regenerative Biology and Harvard Stem Cell Institute, Cambridge, Massachusetts
| | - Chad A Cowan
- Harvard University, Department of Stem Cell and Regenerative Biology and Harvard Stem Cell Institute, Cambridge, Massachusetts
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, Massachusetts
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Pei Y, Sierra G, Sivapatham R, Swistowski A, Rao MS, Zeng X. A platform for rapid generation of single and multiplexed reporters in human iPSC lines. Sci Rep 2015; 5:9205. [PMID: 25777362 PMCID: PMC4361878 DOI: 10.1038/srep09205] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Accepted: 02/25/2015] [Indexed: 12/20/2022] Open
Abstract
Induced pluripotent stem cells (iPSC) are important tools for drug discovery assays and toxicology screens. In this manuscript, we design high efficiency TALEN and ZFN to target two safe harbor sites on chromosome 13 and 19 in a widely available and well-characterized integration-free iPSC line. We show that these sites can be targeted in multiple iPSC lines to generate reporter systems while retaining pluripotent characteristics. We extend this concept to making lineage reporters using a C-terminal targeting strategy to endogenous genes that express in a lineage-specific fashion. Furthermore, we demonstrate that we can develop a master cell line strategy and then use a Cre-recombinase induced cassette exchange strategy to rapidly exchange reporter cassettes to develop new reporter lines in the same isogenic background at high efficiency. Equally important we show that this recombination strategy allows targeting at progenitor cell stages, further increasing the utility of the platform system. The results in concert provide a novel platform for rapidly developing custom single or dual reporter systems for screening assays.
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Affiliation(s)
- Ying Pei
- Buck Institute for Age Research, Novato, CA
| | | | | | | | | | - Xianmin Zeng
- 1] Buck Institute for Age Research, Novato, CA [2] XCell Science, Novato, CA
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Cerbini T, Luo Y, Rao MS, Zou J. Transfection, selection, and colony-picking of human induced pluripotent stem cells TALEN-targeted with a GFP gene into the AAVS1 safe harbor. J Vis Exp 2015. [PMID: 25741760 DOI: 10.3791/52504] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Targeted transgene addition can provide persistent gene expression while circumventing the gene silencing and insertional mutagenesis caused by viral vector mediated random integration. This protocol describes a universal and efficient transgene targeted addition platform in human iPSCs based on utilization of validated open-source TALENs and a gene-trap-like donor to deliver transgenes into a safe harbor locus. Importantly, effective gene editing is rate-limited by the delivery efficiency of gene editing vectors. Therefore, this protocol first focuses on preparation of iPSCs for transfection to achieve high nuclear delivery efficiency. When iPSCs are dissociated into single cells using a gentle-cell dissociation reagent and transfected using an optimized program, >50% cells can be induced to take up the large gene editing vectors. Because the AAVS1 locus is located in the intron of an active gene (PPP1R12C), a splicing acceptor (SA)-linked puromycin resistant gene (PAC) was used to select targeted iPSCs while excluding random integration-only and untransfected cells. This strategy greatly increases the chance of obtaining targeted clones, and can be used in other active gene targeting experiments as well. Two weeks after puromycin selection at the dose adjusted for the specific iPSC line, clones are ready to be picked by manual dissection of large, isolated colonies into smaller pieces that are transferred to fresh medium in a smaller well for further expansion and genetic and functional screening. One can follow this protocol to readily obtain multiple GFP reporter iPSC lines that are useful for in vivo and in vitro imaging and cell isolation.
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Affiliation(s)
- Trevor Cerbini
- National Institute of Arthritis, Musculoskeletal and Skin Diseases, National Institutes of Health
| | - Yongquan Luo
- National Institute of Arthritis, Musculoskeletal and Skin Diseases, National Institutes of Health
| | | | - Jizhong Zou
- National Institute of Arthritis, Musculoskeletal and Skin Diseases, National Institutes of Health;
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