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Chen Y, Sun W, Tang H, Li Y, Li C, Wang L, Chen J, Lin W, Li S, Fan Z, Cheng Y, Chen C. Interactions Between Immunomodulatory Biomaterials and Immune Microenvironment: Cues for Immunomodulation Strategies in Tissue Repair. Front Bioeng Biotechnol 2022; 10:820940. [PMID: 35646833 PMCID: PMC9140325 DOI: 10.3389/fbioe.2022.820940] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 01/31/2022] [Indexed: 11/13/2022] Open
Abstract
The foreign body response (FBR) caused by biomaterials can essentially be understood as the interaction between the immune microenvironment and biomaterials, which has severely impeded the application of biomaterials in tissue repair. This concrete interaction occurs via cells and bioactive substances, such as proteins and nucleic acids. These cellular and molecular interactions provide important cues for determining which element to incorporate into immunomodulatory biomaterials (IMBs), and IMBs can thus be endowed with the ability to modulate the FBR and repair damaged tissue. In terms of cellular, IMBs are modified to modulate functions of immune cells, such as macrophages and mast cells. In terms of bioactive substances, proteins and nucleic acids are delivered to influence the immune microenvironment. Meanwhile, IMBs are designed with high affinity for spatial targets and the ability to self-adapt over time, which allows for more efficient and intelligent tissue repair. Hence, IMB may achieve the perfect functional integration in the host, representing a breakthrough in tissue repair and regeneration medicine.
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Affiliation(s)
- Yi Chen
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University, Shanghai, China
| | - Weiyan Sun
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University, Shanghai, China
| | - Hai Tang
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University, Shanghai, China
| | - Yingze Li
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University, Shanghai, China
- Institute for Regenerative Medicine, Institute for Translational Nanomedicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Chen Li
- School of Materials Science and Engineering, Tongji University, Shanghai, China
| | - Long Wang
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University, Shanghai, China
| | - Jiafei Chen
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University, Shanghai, China
| | - Weikang Lin
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University, Shanghai, China
| | - Shenghui Li
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University, Shanghai, China
| | - Ziwen Fan
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University, Shanghai, China
| | - Yu Cheng
- Institute for Regenerative Medicine, Institute for Translational Nanomedicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
- The Institute for Biomedical Engineering and Nano Science, Tongji University School of Medicine, Shanghai, China
| | - Chang Chen
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University, Shanghai, China
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2
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van Essen M, Riepsaame J, Jacob J. CRISPR-Cas Gene Perturbation and Editing in Human Induced Pluripotent Stem Cells. CRISPR J 2021; 4:634-655. [PMID: 34582693 DOI: 10.1089/crispr.2021.0063] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Directing the fates of human pluripotent stem cells (hPSC) to generate a multitude of differentiated cell types allows the study of the genetic regulation of human development and disease. The translational potential of hPSC is maximized by exploiting CRISPR to silence or activate genes with spatial and temporal precision permanently or reversibly. Here, we summarize the increasingly refined and diverse CRISPR toolkit for the latter forms of gene perturbation in hPSC and their downstream applications. We discuss newer methods to install edits efficiently with single nucleotide resolution and describe pooled CRISPR screens as a powerful means of unbiased discovery of genes associated with a phenotype of interest. Last, we discuss the potential of these combined technologies in the treatment of hitherto intractable human diseases and the challenges to their implementation in the clinic.
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Affiliation(s)
- Max van Essen
- Nuffield Department of Clinical Neurosciences, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom; and University of Oxford, Oxford, United Kingdom
| | - Joey Riepsaame
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - John Jacob
- Nuffield Department of Clinical Neurosciences, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom; and University of Oxford, Oxford, United Kingdom
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3
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Fantoni NZ, Brown T, Kellett A. DNA-Targeted Metallodrugs: An Untapped Source of Artificial Gene Editing Technology. Chembiochem 2021; 22:2184-2205. [PMID: 33570813 DOI: 10.1002/cbic.202000838] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Revised: 02/09/2021] [Indexed: 12/20/2022]
Abstract
DNA binding metal complexes are synonymous with anticancer drug discovery. Given the array of structural and chemical reactivity properties available through careful design, metal complexes have been directed to bind nucleic acid structures through covalent or noncovalent binding modes. Several recognition modes - including crosslinking, intercalation, and oxidation - are central to the clinical success of broad-spectrum anticancer metallodrugs. However, recent progress in nucleic acid click chemistry coupled with advancement in our understanding of metal complex-nucleic acid interactions has opened up new avenues in genetic engineering and targeted therapies. Several of these applications are enabled by the hybridisation of oligonucleotide or polyamine probes to discrete metal complexes, which facilitate site-specific reactivity at the nucleic acid interface under the guidance of the probe. This Review focuses on recent advancements in hybrid design and, by way of an introduction to this topic, we provide a detailed overview of nucleic acid structures and metal complex-nucleic acid interactions. Our aim is to provide readers with an insight on the rational design of metal complexes with DNA recognition properties and an understanding of how the sequence-specific targeting of these interactions can be achieved for gene engineering applications.
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Affiliation(s)
- Nicolò Zuin Fantoni
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
| | - Tom Brown
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
| | - Andrew Kellett
- School of Chemical Sciences and National Institute for, Cellular Biotechnology and Nano Research Facility, Dublin City University, Glasnevin, Dublin, 9, Ireland
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4
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Sugai H, Tomita S, Ishihara S, Yoshioka K, Kurita R. Microfluidic Sensing System with a Multichannel Surface Plasmon Resonance Chip: Damage-Free Characterization of Cells by Pattern Recognition. Anal Chem 2020; 92:14939-14946. [PMID: 33112611 DOI: 10.1021/acs.analchem.0c02220] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The development of a versatile sensing strategy for the damage-free characterization of cultured cells is of great importance for both fundamental biological research and industrial applications. Here, we present a pattern-recognition-based cell-sensing approach using a multichannel surface plasmon resonance (SPR) chip. The chip, in which five cysteine derivatives with different structures are immobilized on Au films, is capable of generating five unique SPR sensorgrams for the cell-secreted molecules that are contained in cell culture media. An automatic statistical program was built to acquire kinetic parameters from the SPR sensorgrams and to select optimal parameters as "pattern information" for subsequent multivariate analysis. Our system rapidly (∼10 min) provides the complex information by merely depositing a small amount of cell culture media (∼25 μL) onto the chip, and the amount of information obtained is comparable to that furnished by a combination of conventional laborious biochemical assays. This noninvasive pattern-recognition-based cell-sensing approach could potentially be employed as a versatile tool for characterizing cells.
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Affiliation(s)
- Hiroka Sugai
- Health and Medical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan
| | - Shunsuke Tomita
- Health and Medical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan.,DAILAB, DBT-AIST International Center for Translational and Environmental Research (DAICENTER), National Institute of Advanced Industrial Science and Technology (AIST), Central 5-41, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8565, Japan
| | - Sayaka Ishihara
- Health and Medical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan
| | - Kyoko Yoshioka
- Health and Medical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan
| | - Ryoji Kurita
- Health and Medical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan.,DAILAB, DBT-AIST International Center for Translational and Environmental Research (DAICENTER), National Institute of Advanced Industrial Science and Technology (AIST), Central 5-41, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8565, Japan.,Faculty of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8573, Japan
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5
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Zhou Y, Zhang S, Chen Z, Bao Y, Chen AT, Sheu WC, Liu F, Jiang Z, Zhou J. Targeted Delivery of Secretory Promelittin via Novel Poly(lactone- co-β-amino ester) Nanoparticles for Treatment of Breast Cancer Brain Metastases. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2020; 7:1901866. [PMID: 32154067 PMCID: PMC7055583 DOI: 10.1002/advs.201901866] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 12/18/2019] [Indexed: 05/05/2023]
Abstract
Breast cancer brain metastases (BCBM) is a devastating disease with dismal prognosis. Although chemotherapy is widely used for clinical management of most tumors, it is often ineffective for BCBM. Therefore, alternative approaches for improved treatment of BCBM are in great demand. Here, an innovative gene therapy regimen is reported that is designed for effective treatment of BCBM. First, poly(lactone-co-β-amino ester) nanoparticles that are capable of efficient gene delivery are synthesized and are engineered for targeted delivery to BCBM through surface conjugation of AMD3100, which interacts with CXCR4 enriched in the tumor microenvironment. Next, an artificial gene, proMel, is designed for the expression of secretory promelittin protein, which has limited toxicity on its own but releases cytolytic melittin after activation by MMP-2 accumulated in tumors. It is demonstrated that delivery of the proMel via the AMD3100-conjugated nanoparticles effectively inhibits tumor progression in a BCBM mouse model. This study suggests a new direction to treat BCBM through targeted delivery of promelittin-mediated gene therapy.
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Affiliation(s)
- Yu Zhou
- Department of NeurosurgeryYale UniversityNew HavenCT06511USA
- Department of NeurosurgeryThe Second Xiangya Hospital of Central South UniversityChangshaHunan410011China
| | - Shenqi Zhang
- Department of NeurosurgeryYale UniversityNew HavenCT06511USA
- Department of NeurosurgeryRenmin Hospital of Wuhan UniversityHubei430060China
| | - Zeming Chen
- Department of NeurosurgeryYale UniversityNew HavenCT06511USA
| | - Youmei Bao
- Department of NeurosurgeryYale UniversityNew HavenCT06511USA
| | - Ann T. Chen
- Department of Biomedical EngineeringYale UniversityNew HavenCT06511USA
| | - Wendy C. Sheu
- Department of Biomedical EngineeringYale UniversityNew HavenCT06511USA
| | - Fuyao Liu
- Department of NeurosurgeryYale UniversityNew HavenCT06511USA
| | - Zhaozhong Jiang
- Department of Biomedical EngineeringYale UniversityNew HavenCT06511USA
| | - Jiangbing Zhou
- Department of NeurosurgeryYale UniversityNew HavenCT06511USA
- Department of Biomedical EngineeringYale UniversityNew HavenCT06511USA
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6
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Lowe B, Ottensmeyer MP, Xu C, He Y, Ye Q, Troulis MJ. The Regenerative Applicability of Bioactive Glass and Beta-Tricalcium Phosphate in Bone Tissue Engineering: A Transformation Perspective. J Funct Biomater 2019; 10:E16. [PMID: 30909518 PMCID: PMC6463135 DOI: 10.3390/jfb10010016] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 03/15/2019] [Accepted: 03/15/2019] [Indexed: 12/12/2022] Open
Abstract
The conventional applicability of biomaterials in the field of bone tissue engineering takes into consideration several key parameters to achieve desired results for prospective translational use. Hence, several engineering strategies have been developed to model in the regenerative parameters of different forms of biomaterials, including bioactive glass and β-tricalcium phosphate. This review examines the different ways these two materials are transformed and assembled with other regenerative factors to improve their application for bone tissue engineering. We discuss the role of the engineering strategy used and the regenerative responses and mechanisms associated with them.
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Affiliation(s)
- Baboucarr Lowe
- School of Dentistry, The University of Queensland, Brisbane, Herston 4006, Queensland, Australia.
- Department of Oral and Maxillofacial Surgery, Massachusetts General Hospital and Harvard School of Dental Medicine, Boston, MA 02114, USA.
| | - Mark P Ottensmeyer
- Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.
| | - Chun Xu
- School of Dentistry, The University of Queensland, Brisbane, Herston 4006, Queensland, Australia.
| | - Yan He
- School of Dentistry, The University of Queensland, Brisbane, Herston 4006, Queensland, Australia.
| | - Qingsong Ye
- School of Dentistry, The University of Queensland, Brisbane, Herston 4006, Queensland, Australia.
| | - Maria J Troulis
- Department of Oral and Maxillofacial Surgery, Massachusetts General Hospital and Harvard School of Dental Medicine, Boston, MA 02114, USA.
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7
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Hasegawa Y, Ikeno M, Suzuki N, Nakayama M, Ohara O. Improving the efficiency of gene insertion in a human artificial chromosome vector and its transfer in human-induced pluripotent stem cells. Biol Methods Protoc 2018; 3:bpy013. [PMID: 32161806 PMCID: PMC6994043 DOI: 10.1093/biomethods/bpy013] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 11/15/2018] [Accepted: 11/26/2018] [Indexed: 01/24/2023] Open
Abstract
A human artificial chromosome (HAC) vector has potential to overcome the problems of stable gene expression associated with plasmid, transposon, and virus-based vectors, such as insertional mutagenesis, position effect, uncontrollable copy number, unstable gene expression, and DNA size limitation. The main advantages of the HAC are its episomal nature and ability to accommodate DNA inserts of any size. However, HAC vectors have two disadvantages: low efficiency of gene insertion and lack of reports regarding the successful HAC transfer to human-induced pluripotent stem cells (iPSCs). We here provide the first report of a method for the efficient transfer of HAC to human iPSCs for obtaining reproducible experimental results. Moreover, we achieved a 10% increase in the gene insertion efficiency in the HAC vector using our new site-specific recombination systems VCre/VloxP and SCre/SloxP.
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Affiliation(s)
- Yoshinori Hasegawa
- Laboratory of Clinical Omics Research, Department of Applied Genomics, Kazusa DNA Research Institute, Chiba, Japan
| | | | | | - Manabu Nakayama
- Laboratory of Medical Omics Research, Department of Frontier Research and Development, Kazusa DNA Research Institute, Chiba, Japan
| | - Osamu Ohara
- Laboratory of Clinical Omics Research, Department of Applied Genomics, Kazusa DNA Research Institute, Chiba, Japan
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8
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Abstract
Human-induced pluripotent stem cells (hiPSCs) provide a personalized approach to study conditions and diseases including those of the eye that lack appropriate animal models to facilitate the development of novel therapeutics. Corneal disease is one of the most common causes of blindness. Hence, significant efforts are made to develop novel therapeutic approaches including stem cell-derived strategies to replace the diseased or damaged corneal tissues, thus restoring the vision. The use of adult limbal stem cells in the management of corneal conditions has been clinically successful. However, its limited availability and phenotypic plasticity necessitate the need for alternative stem cell sources to manage corneal conditions. Mesenchymal and embryonic stem cell-based approaches are being explored; nevertheless, their limited differentiation potential and ethical concerns have posed a significant hurdle in its clinical use. hiPSCs have emerged to fill these technical and ethical gaps to render clinical utility. In this review, we discuss and summarize protocols that have been devised so far to direct differentiation of human pluripotent stem cells (hPSCs) to different corneal cell phenotypes. With the summarization, our review intends to facilitate an understanding which would allow developing efficient and robust protocols to obtain specific corneal cell phenotype from hPSCs for corneal disease modeling and for the clinics to treat corneal diseases and injury.
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Affiliation(s)
| | - Rohit Shetty
- Cornea and Refractive Surgery, Narayana Nethralaya, Bengaluru, India
| | - Arkasubhra Ghosh
- GROW Research Laboratory, Narayana Nethralaya Foundation, Bengaluru, India
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9
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Wu M, Liu S, Gao Y, Bai H, Machairaki V, Li G, Chen T, Cheng L. Conditional gene knockout and reconstitution in human iPSCs with an inducible Cas9 system. Stem Cell Res 2018; 29:6-14. [DOI: 10.1016/j.scr.2018.03.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 03/02/2018] [Accepted: 03/06/2018] [Indexed: 12/11/2022] Open
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10
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György B, Lööv C, Zaborowski MP, Takeda S, Kleinstiver BP, Commins C, Kastanenka K, Mu D, Volak A, Giedraitis V, Lannfelt L, Maguire CA, Joung JK, Hyman BT, Breakefield XO, Ingelsson M. CRISPR/Cas9 Mediated Disruption of the Swedish APP Allele as a Therapeutic Approach for Early-Onset Alzheimer's Disease. MOLECULAR THERAPY. NUCLEIC ACIDS 2018; 11:429-440. [PMID: 29858078 PMCID: PMC5992788 DOI: 10.1016/j.omtn.2018.03.007] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Revised: 03/08/2018] [Accepted: 03/12/2018] [Indexed: 12/23/2022]
Abstract
The APPswe (Swedish) mutation in the amyloid precursor protein (APP) gene causes dominantly inherited Alzheimer’s disease (AD) as a result of increased β-secretase cleavage of the amyloid-β (Aβ) precursor protein. This leads to abnormally high Aβ levels, not only in brain but also in peripheral tissues of mutation carriers. Here, we selectively disrupted the human mutant APPSW allele using CRISPR. By applying CRISPR/Cas9 from Streptococcus pyogenes, we generated allele-specific deletions of either APPSW or APPWT. As measured by ELISA, conditioned media of targeted patient-derived fibroblasts displayed an approximate 60% reduction in secreted Aβ. Next, coding sequences for the APPSW-specific guide RNA (gRNA) and Cas9 were packaged into separate adeno-associated viral (AAV) vectors. Site-specific indel formation was achieved both in primary neurons isolated from APPSW transgenic mouse embryos (Tg2576) and after co-injection of these vectors into hippocampus of adult mice. Taken together, we here present proof-of-concept data that CRISPR/Cas9 can selectively disrupt the APPSW allele both ex vivo and in vivo—and thereby decrease pathogenic Aβ. Hence, this system may have the potential to be developed as a tool for gene therapy against AD caused by APPswe and other point mutations associated with increased Aβ.
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Affiliation(s)
- Bence György
- Departments of Neurology and Radiology, Massachusetts General Hospital and Center for NeuroDiscovery, Harvard Medical School, Boston, MA, USA; Department of Neurobiology, Harvard Medical School, 220 Longwood Avenue, Boston, MA 02115, USA
| | - Camilla Lööv
- Departments of Neurology and Radiology, Massachusetts General Hospital and Alzheimer's Disease Research Center, Harvard Medical School, Boston, MA, USA
| | - Mikołaj P Zaborowski
- Departments of Neurology and Radiology, Massachusetts General Hospital and Center for NeuroDiscovery, Harvard Medical School, Boston, MA, USA; Department of Gynecology, Obstetrics and Gynecologic Oncology, Division of Gynecologic Oncology, Poznan University of Medical Sciences, 60-535 Poznan, Poland
| | - Shuko Takeda
- Departments of Neurology and Radiology, Massachusetts General Hospital and Alzheimer's Disease Research Center, Harvard Medical School, Boston, MA, USA
| | - Benjamin P Kleinstiver
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, MA, USA; Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA; Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA, USA; Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - Caitlin Commins
- Departments of Neurology and Radiology, Massachusetts General Hospital and Alzheimer's Disease Research Center, Harvard Medical School, Boston, MA, USA
| | - Ksenia Kastanenka
- Departments of Neurology and Radiology, Massachusetts General Hospital and Alzheimer's Disease Research Center, Harvard Medical School, Boston, MA, USA
| | - Dakai Mu
- Departments of Neurology and Radiology, Massachusetts General Hospital and Center for NeuroDiscovery, Harvard Medical School, Boston, MA, USA
| | - Adrienn Volak
- Departments of Neurology and Radiology, Massachusetts General Hospital and Center for NeuroDiscovery, Harvard Medical School, Boston, MA, USA
| | - Vilmantas Giedraitis
- Department of Public Health and Caring Sciences, Geriatrics, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Lars Lannfelt
- Department of Public Health and Caring Sciences, Geriatrics, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Casey A Maguire
- Departments of Neurology and Radiology, Massachusetts General Hospital and Center for NeuroDiscovery, Harvard Medical School, Boston, MA, USA
| | - J Keith Joung
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, MA, USA; Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA; Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA, USA; Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - Bradley T Hyman
- Departments of Neurology and Radiology, Massachusetts General Hospital and Alzheimer's Disease Research Center, Harvard Medical School, Boston, MA, USA
| | - Xandra O Breakefield
- Departments of Neurology and Radiology, Massachusetts General Hospital and Center for NeuroDiscovery, Harvard Medical School, Boston, MA, USA
| | - Martin Ingelsson
- Departments of Neurology and Radiology, Massachusetts General Hospital and Center for NeuroDiscovery, Harvard Medical School, Boston, MA, USA; Department of Public Health and Caring Sciences, Geriatrics, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden.
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Rathnam C, Chueng STD, Yang L, Lee KB. Advanced Gene Manipulation Methods for Stem Cell Theranostics. Theranostics 2017; 7:2775-2793. [PMID: 28824715 PMCID: PMC5562215 DOI: 10.7150/thno.19443] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 04/18/2017] [Indexed: 12/20/2022] Open
Abstract
In the field of tissue engineering, autologous cell sources are ideal to prevent adverse immune responses; however, stable and reliable cell sources are limited. To acquire more reliable cell sources, the harvesting and differentiation of stem cells from patients is becoming more and more common. To this end, the need to control the fate of these stem cells before transplantation for therapeutic purposes is urgent. Since transcription factors orchestrate all of the gene activities inside of a cell, researchers have developed engineered and synthetic transcription factors to precisely control the fate of stem cells allowing for safer and more effective cell sources. Engineered transcription factors, mutant fusion proteins of naturally occurring proteins, comprise the three main domains of natural transcription factors including DNA binding domains, transcriptional activation domains, and a linker domain. Several key advancements of engineered zinc finger proteins, transcriptional activator-like effectors, and deficient cas9 proteins have revolutionized the field of engineered transcription factors allowing for precise control of gene regulation. Synthetic transcription factors are chemically made transcription factor mimics that use small molecule based moieties to replicate the main functions of natural transcription factors. These include hairpin polyamides, triple helix forming oligonucleotides, and nanoparticle-based methods. Synthetic transcription factors allow for non-viral delivery and greater spatiotemporal control of gene expression. The developments in engineered and synthetic transcription factors have lowered the risk of tumorigenicity and improved differentiation capability of stem cells, as well as facilitated many key discoveries in the fields of cancer and stem cell biology, thus providing a stepping stone to advance regenerative medicine in the clinic for cell replacement therapies.
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12
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Liu Z, Hui Y, Shi L, Chen Z, Xu X, Chi L, Fan B, Fang Y, Liu Y, Ma L, Wang Y, Xiao L, Zhang Q, Jin G, Liu L, Zhang X. Efficient CRISPR/Cas9-Mediated Versatile, Predictable, and Donor-Free Gene Knockout in Human Pluripotent Stem Cells. Stem Cell Reports 2016; 7:496-507. [PMID: 27594587 PMCID: PMC5032288 DOI: 10.1016/j.stemcr.2016.07.021] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Revised: 07/28/2016] [Accepted: 07/28/2016] [Indexed: 11/17/2022] Open
Abstract
Loss-of-function studies in human pluripotent stem cells (hPSCs) require efficient methodologies for lesion of genes of interest. Here, we introduce a donor-free paired gRNA-guided CRISPR/Cas9 knockout strategy (paired-KO) for efficient and rapid gene ablation in hPSCs. Through paired-KO, we succeeded in targeting all genes of interest with high biallelic targeting efficiencies. More importantly, during paired-KO, the cleaved DNA was repaired mostly through direct end joining without insertions/deletions (precise ligation), and thus makes the lesion product predictable. The paired-KO remained highly efficient for one-step targeting of multiple genes and was also efficient for targeting of microRNA, while for long non-coding RNA over 8 kb, cleavage of a short fragment of the core promoter region was sufficient to eradicate downstream gene transcription. This work suggests that the paired-KO strategy is a simple and robust system for loss-of-function studies for both coding and non-coding genes in hPSCs.
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Affiliation(s)
- Zhongliang Liu
- Shanghai Tenth People's Hospital, and Neuroregeneration Key Laboratory of Shanghai Universities, Tongji University School of Medicine, Shanghai 200092, China
| | - Yi Hui
- Department of Anatomy and Neurobiology, the Jiangsu Key Laboratory of Neuroregeneration, Nantong University, 19 Qixiu Road, Nantong, Jiangsu 226001, China
| | - Lei Shi
- College of Animal Science and Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Zhenyu Chen
- Shanghai Tenth People's Hospital, and Neuroregeneration Key Laboratory of Shanghai Universities, Tongji University School of Medicine, Shanghai 200092, China
| | - Xiangjie Xu
- Shanghai Tenth People's Hospital, and Neuroregeneration Key Laboratory of Shanghai Universities, Tongji University School of Medicine, Shanghai 200092, China
| | - Liankai Chi
- Shanghai Tenth People's Hospital, and Neuroregeneration Key Laboratory of Shanghai Universities, Tongji University School of Medicine, Shanghai 200092, China
| | - Beibei Fan
- Shanghai Tenth People's Hospital, and Neuroregeneration Key Laboratory of Shanghai Universities, Tongji University School of Medicine, Shanghai 200092, China
| | - Yujiang Fang
- Shanghai Tenth People's Hospital, and Neuroregeneration Key Laboratory of Shanghai Universities, Tongji University School of Medicine, Shanghai 200092, China
| | - Yang Liu
- Shanghai Tenth People's Hospital, and Neuroregeneration Key Laboratory of Shanghai Universities, Tongji University School of Medicine, Shanghai 200092, China
| | - Lin Ma
- Shanghai Tenth People's Hospital, and Neuroregeneration Key Laboratory of Shanghai Universities, Tongji University School of Medicine, Shanghai 200092, China
| | - Yiran Wang
- Shanghai Tenth People's Hospital, and Neuroregeneration Key Laboratory of Shanghai Universities, Tongji University School of Medicine, Shanghai 200092, China
| | - Lei Xiao
- College of Animal Science and Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Quanbin Zhang
- Shanghai Tenth People's Hospital, and Neuroregeneration Key Laboratory of Shanghai Universities, Tongji University School of Medicine, Shanghai 200092, China
| | - Guohua Jin
- Department of Anatomy and Neurobiology, the Jiangsu Key Laboratory of Neuroregeneration, Nantong University, 19 Qixiu Road, Nantong, Jiangsu 226001, China.
| | - Ling Liu
- Shanghai Tenth People's Hospital, and Neuroregeneration Key Laboratory of Shanghai Universities, Tongji University School of Medicine, Shanghai 200092, China; Tongji University Advanced Institute of Translational Medicine, Tongji University School of Medicine, 1239 Siping Road, Shanghai 200092, China.
| | - Xiaoqing Zhang
- Shanghai Tenth People's Hospital, and Neuroregeneration Key Laboratory of Shanghai Universities, Tongji University School of Medicine, Shanghai 200092, China; Tongji University Advanced Institute of Translational Medicine, Tongji University School of Medicine, 1239 Siping Road, Shanghai 200092, China; The Collaborative Innovation Center for Brain Science, Tongji University, Shanghai 200092, China.
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13
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Robust reprogramming of Ataxia-Telangiectasia patient and carrier erythroid cells to induced pluripotent stem cells. Stem Cell Res 2016; 17:296-305. [DOI: 10.1016/j.scr.2016.08.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 07/29/2016] [Accepted: 08/06/2016] [Indexed: 12/18/2022] Open
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14
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Li M, Izpisua Belmonte JC. Looking to the future following 10 years of induced pluripotent stem cell technologies. Nat Protoc 2016; 11:1579-85. [PMID: 27490631 DOI: 10.1038/nprot.2016.108] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 05/19/2016] [Indexed: 12/12/2022]
Abstract
The development of induced pluripotent stem cells (iPSCs) has fundamentally changed our view on developmental cell-fate determination and led to a cascade of technological innovations in regenerative medicine. Here we provide an overview of the progress in the field over the past decade, as well as our perspective on future directions and clinical implications of iPSC technology.
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Affiliation(s)
- Mo Li
- Gene Expression Laboratory, The Salk Institute for Biological Studies, La Jolla, California, USA.,Gene Expression Laboratory, The Salk Institute for Biological Studies, La Jolla, California, USA
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15
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Huang X, Wang Y, Yan W, Smith C, Ye Z, Wang J, Gao Y, Mendelsohn L, Cheng L. Production of Gene-Corrected Adult Beta Globin Protein in Human Erythrocytes Differentiated from Patient iPSCs After Genome Editing of the Sickle Point Mutation. Stem Cells 2016; 33:1470-9. [PMID: 25702619 DOI: 10.1002/stem.1969] [Citation(s) in RCA: 140] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Accepted: 01/14/2015] [Indexed: 12/11/2022]
Abstract
Human induced pluripotent stem cells (iPSCs) and genome editing provide a precise way to generate gene-corrected cells for disease modeling and cell therapies. Human iPSCs generated from sickle cell disease (SCD) patients have a homozygous missense point mutation in the HBB gene encoding adult β-globin proteins, and are used as a model system to improve strategies of human gene therapy. We demonstrate that the CRISPR/Cas9 system designer nuclease is much more efficient in stimulating gene targeting of the endogenous HBB locus near the SCD point mutation in human iPSCs than zinc finger nucleases and TALENs. Using a specific guide RNA and Cas9, we readily corrected one allele of the SCD HBB gene in human iPSCs by homologous recombination with a donor DNA template containing the wild-type HBB DNA and a selection cassette that was subsequently removed to avoid possible interference of HBB transcription and translation. We chose targeted iPSC clones that have one corrected and one disrupted SCD allele for erythroid differentiation assays, using an improved xeno-free and feeder-free culture condition we recently established. Erythrocytes from either the corrected or its parental (uncorrected) iPSC line were generated with similar efficiencies. Currently ∼6%-10% of these differentiated erythrocytes indeed lacked nuclei, characteristic of further matured erythrocytes called reticulocytes. We also detected the 16-kDa β-globin protein expressed from the corrected HBB allele in the erythrocytes differentiated from genome-edited iPSCs. Our results represent a significant step toward the clinical applications of genome editing using patient-derived iPSCs to generate disease-free cells for cell and gene therapies. Stem Cells 2015;33:1470-1479.
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Affiliation(s)
- Xiaosong Huang
- Division of Hematology, Department of Medicine; Institute for Cell Engineering
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16
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Chen X, Zhai Y, Yu D, Cui J, Hu JF, Li W. Valproic Acid Enhances iPSC Induction From Human Bone Marrow-Derived Cells Through the Suppression of Reprogramming-Induced Senescence. J Cell Physiol 2015; 231:1719-27. [PMID: 26620855 DOI: 10.1002/jcp.25270] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 11/23/2015] [Indexed: 01/19/2023]
Abstract
Reprogramming of human somatic cells into pluripotent cells (iPSCs) by defined transcription factors is an extremely inefficient process. Treatment with the histone deacetylase inhibitor valproic acid (VPA) during reprogramming can improve the induction of iPSCs. To examine the specific mechanism underlying the role of VPA in reprogramming, we transfected human bone marrow-derived cells (HSC-J2 and HSC-L1) with lentiviruses carrying defined factors (OCT4, SOX2, KLF4, and c-MYC, OSKM) in the presence of VPA. We found that, OSKM lentiviruses caused significant senescence in transfected cells. Administration of VPA, however, significantly suppressed this reprogramming-induced stress. Notably, VPA treatment improved cell proliferation in the early stages of reprogramming, and this was related to the down-regulation of the activated p16/p21 pathway. In addition, VPA also released the G2/M phase blockade in lentivirus-transfected cells. This study demonstrates a new mechanistic role of the histone deacetylase inhibitor in enhancing the induction of pluripotency. J. Cell. Physiol. 231: 1719-1727, 2016. © 2015 Wiley Periodicals, Inc.
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Affiliation(s)
- Xi Chen
- Stem Cell and Cancer Center, First Affiliated Hospital, Jilin University, Changchun, Jilin, P.R. China.,Stanford University Medical School, Palo Alto Veterans Institute for Research, Palo Alto, California
| | - Yingying Zhai
- Stem Cell and Cancer Center, First Affiliated Hospital, Jilin University, Changchun, Jilin, P.R. China.,Stanford University Medical School, Palo Alto Veterans Institute for Research, Palo Alto, California
| | - Dehai Yu
- Stem Cell and Cancer Center, First Affiliated Hospital, Jilin University, Changchun, Jilin, P.R. China.,Stanford University Medical School, Palo Alto Veterans Institute for Research, Palo Alto, California
| | - Jiuwei Cui
- Stem Cell and Cancer Center, First Affiliated Hospital, Jilin University, Changchun, Jilin, P.R. China
| | - Ji-Fan Hu
- Stem Cell and Cancer Center, First Affiliated Hospital, Jilin University, Changchun, Jilin, P.R. China.,Stanford University Medical School, Palo Alto Veterans Institute for Research, Palo Alto, California
| | - Wei Li
- Stem Cell and Cancer Center, First Affiliated Hospital, Jilin University, Changchun, Jilin, P.R. China
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17
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Chen Y, Cao J, Xiong M, Petersen AJ, Dong Y, Tao Y, Huang CTL, Du Z, Zhang SC. Engineering Human Stem Cell Lines with Inducible Gene Knockout using CRISPR/Cas9. Cell Stem Cell 2015; 17:233-44. [PMID: 26145478 PMCID: PMC4530040 DOI: 10.1016/j.stem.2015.06.001] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Revised: 04/27/2015] [Accepted: 06/04/2015] [Indexed: 12/26/2022]
Abstract
Precise temporal control of gene expression or deletion is critical for elucidating gene function in biological systems. However, the establishment of human pluripotent stem cell (hPSC) lines with inducible gene knockout (iKO) remains challenging. We explored building iKO hPSC lines by combining CRISPR/Cas9-mediated genome editing with the Flp/FRT and Cre/LoxP system. We found that "dual-sgRNA targeting" is essential for biallelic knockin of FRT sequences to flank the exon. We further developed a strategy to simultaneously insert an activity-controllable recombinase-expressing cassette and remove the drug-resistance gene, thus speeding up the generation of iKO hPSC lines. This two-step strategy was used to establish human embryonic stem cell (hESC) and induced pluripotent stem cell (iPSC) lines with iKO of SOX2, PAX6, OTX2, and AGO2, genes that exhibit diverse structural layout and temporal expression patterns. The availability of iKO hPSC lines will substantially transform the way we examine gene function in human cells.
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Affiliation(s)
- Yuejun Chen
- Waisman Center, University of Wisconsin, Madison, WI 53705, USA.
| | - Jingyuan Cao
- Waisman Center, University of Wisconsin, Madison, WI 53705, USA
| | - Man Xiong
- Waisman Center, University of Wisconsin, Madison, WI 53705, USA; Institute of Pediatrics, Children's Hospital, Fudan University, 399 Wanyuan Road, Shanghai 201102, China
| | | | - Yi Dong
- Waisman Center, University of Wisconsin, Madison, WI 53705, USA
| | - Yunlong Tao
- Waisman Center, University of Wisconsin, Madison, WI 53705, USA
| | | | - Zhongwei Du
- Waisman Center, University of Wisconsin, Madison, WI 53705, USA
| | - Su-Chun Zhang
- Waisman Center, University of Wisconsin, Madison, WI 53705, USA; Neuroscience Training Program, University of Wisconsin, Madison, WI 53705, USA; Department of Neuroscience, School of Medicine and Public Health, University of Wisconsin, Madison, WI 53705, USA; Department of Neurology, School of Medicine and Public Health, University of Wisconsin, Madison, WI 53705, USA.
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18
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Ornoy A, Reece EA, Pavlinkova G, Kappen C, Miller RK. Effect of maternal diabetes on the embryo, fetus, and children: congenital anomalies, genetic and epigenetic changes and developmental outcomes. ACTA ACUST UNITED AC 2015; 105:53-72. [PMID: 25783684 DOI: 10.1002/bdrc.21090] [Citation(s) in RCA: 169] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
INTRODUCTION Pregestational and gestational diabetes mellitus (PGDM; GDM) are significant health concerns because they are associated with an increased rate of malformations and maternal health complications. METHODS We reviewed the data that help us to understand the effects of diabetes in pregnancy. RESULTS Diabetic embryopathy can affect any developing organ system, but cardiovascular and neural tube defects are among the most frequent anomalies. Other complications include preeclampsia, preterm delivery, fetal growth abnormalities, and perinatal mortality. Neurodevelopmental studies on offspring of mothers with diabetes demonstrated increased rate of Gross and Fine motor abnormalities, of Attention Deficit Hyperactivity Disorder, learning difficulties, and possibly also Autism Spectrum Disorder. The mechanisms underlying the effects of maternal hyperglycemia on the developing fetus may involve increased oxidative stress, hypoxia, apoptosis, and epigenetic changes. Evidence for epigenetic changes are the following: not all progeny are affected and not to the same extent; maternal diet may influence pregnancy outcomes; and maternal diabetes alters embryonic transcriptional profiles and increases the variation between transcriptomic profiles as a result of altered gene regulation. Research in animal models has revealed that maternal hyperglycemia is a teratogen, and has helped uncover potential therapeutic targets which, when blocked, can mitigate or ameliorate the negative effects of diabetes on the developing fetus. CONCLUSIONS Tight metabolic control, surveillance, and labor management remain the cornerstone of care for pregnant women with diabetes, but advances in the field indicate that new treatments to protect the mother and baby are not far from becoming clinical realities.
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Affiliation(s)
- Asher Ornoy
- Department of Medical Neurobiology, Laboratory of Teratology, Hebrew University Hadassah Medical School, Jerusalem, Israel
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19
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Kusuma S, Smith Q, Facklam A, Gerecht S. Micropattern size-dependent endothelial differentiation from a human induced pluripotent stem cell line. J Tissue Eng Regen Med 2015; 11:855-861. [PMID: 25641688 DOI: 10.1002/term.1985] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Revised: 11/13/2014] [Accepted: 12/09/2014] [Indexed: 01/02/2023]
Abstract
The multifaceted extracellular milieu presents biochemical and biophysical stimuli that influence stem cell differentiation. Two-dimensional (2D) micropatterned substrates allow the presentation of these cues in spatially defined geometries that have been demonstrated to guide stem cell fate decisions. Leveraging stem cells to reconstruct microvasculature, made up of an inner lining of endothelial cells (ECs) supported by pericytes, is critical to tissue-engineering advances; thus, methods to improve endothelial differentiation efficiency are vital to these efforts. In this study, we examine the hypothesis that the diameter of micropatterned islands influences endothelial differentiation from human induced pluripotent stem cells (hiPSCs). Comparing island diameters of 80, 140, 225 and 500 µm, we found that co-cultures of control ECs and pericytes did not yield variable ratios of cell types; however, when hiPSCs were differentiated toward a bicellular population of ECs and pericytes on these varying micropattern feature sizes, we found that smaller islands promoted EC differentiation efficiency, yielding a derived population composed of 70% ECs, which exhibited a greater sprouting propensity. Differentiation on the largest feature size exhibited a smaller EC yield, similar to that on non-patterned substrates. Taken together, these data demonstrate that micropatterned islands of varying diameters can be used to modulate EC differentiation efficiency. Copyright © 2015 John Wiley & Sons, Ltd.
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Affiliation(s)
- Sravanti Kusuma
- Department of Chemical and Biomolecular Engineering, Johns Hopkins Physical Sciences, Oncology Center and Institute for NanoBioTechnology, Baltimore, MD, USA.,Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Quinton Smith
- Department of Chemical and Biomolecular Engineering, Johns Hopkins Physical Sciences, Oncology Center and Institute for NanoBioTechnology, Baltimore, MD, USA
| | - Amanda Facklam
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Sharon Gerecht
- Department of Chemical and Biomolecular Engineering, Johns Hopkins Physical Sciences, Oncology Center and Institute for NanoBioTechnology, Baltimore, MD, USA.,Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, MD, USA
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20
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Maimets T. Induced Pluripotency for the Study of Disease Mechanisms and Cell Therapy. Rare Dis 2015. [DOI: 10.1007/978-94-017-9214-1_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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21
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Qian K, Huang CTL, Huang CL, Chen H, Blackbourn LW, Chen Y, Cao J, Yao L, Sauvey C, Du Z, Zhang SC. A simple and efficient system for regulating gene expression in human pluripotent stem cells and derivatives. Stem Cells 2014; 32:1230-8. [PMID: 24497442 DOI: 10.1002/stem.1653] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Accepted: 01/06/2014] [Indexed: 12/19/2022]
Abstract
Regulatable transgene expression in human pluripotent stem cells (hPSCs) and their progenies is often necessary to dissect gene function in a temporal and spatial manner. However, hPSC lines with inducible transgene expression, especially in differentiated progenies, have not been established due to silencing of randomly inserted genes during stem cell expansion and/or differentiation. Here, we report the use of transcription activator-like effector nucleases-mediated targeting to AAVS1 site to generate versatile conditional hPSC lines. Transgene (both green fluorescent protein and a functional gene) expression in hPSCs and their derivatives was not only sustained but also tightly regulated in response to doxycycline both in vitro and in vivo. We modified the donor construct so that any gene of interest can be readily inserted to produce hPSC lines with conditional transgene expression. This technology will substantially improve the way we study human stem cells.
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Affiliation(s)
- Kun Qian
- Reproductive Medicine Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China; Waisman Center, School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin, USA
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22
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Zhang T, Price JC, Nouri-Nigjeh E, Li J, Hellerstein MK, Qu J, Ghaemmaghami S. Kinetics of precursor labeling in stable isotope labeling in cell cultures (SILAC) experiments. Anal Chem 2014; 86:11334-41. [PMID: 25301408 DOI: 10.1021/ac503067a] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Recent advances in mass spectrometry have enabled proteome-wide analyses of cellular protein turnover. These studies have been greatly propelled by the development of stable isotope labeling in cell cultures (SILAC), a set of standardized protocols, reagents aimed at quantifying the incorporation of (15)N/(13)C labeled amino acids into proteins. In dynamic SILAC experiments, the degree of isotope incorporation in proteins is measured over time and used to determine turnover kinetics. However, the kinetics of isotope incorporation in proteins can potentially be influenced not only by their intracellular turnover but also by amino acid uptake, recycling and aminoacyl-tRNA synthesis. To assess the influence of these processes in dynamic SILAC experiments, we have measured the kinetics of isotopic enrichment within intracellular free amino acid and aminoacyl-tRNA precursor pools in dividing and division-arrested neuroblastoma cells following the introduction of extracellular (15)N labeled amino acids. We show that the total flux of extracellular amino acids into cells greatly exceeds that of intracellular amino acid recycling and synthesis. Furthermore, in comparison to internal sources, external amino acids are preferentially utilized as substrates for aminoacyl-tRNA precursors for protein synthesis. As a result, in dynamic SILAC experiments conducted in culture, the aminoacyl-tRNA precursor pool is near completely labeled in a few hours and protein turnover is the limiting factor in establishing the labeling kinetics of most proteins.
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Affiliation(s)
- Tian Zhang
- Department of Biology, University of Rochester , Rochester, New York 14627, United States
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23
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Oliveira PH, da Silva CL, Cabral JM. Concise Review: Genomic Instability in Human Stem Cells: Current Status and Future Challenges. Stem Cells 2014; 32:2824-32. [DOI: 10.1002/stem.1796] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Revised: 06/03/2014] [Accepted: 06/09/2014] [Indexed: 12/26/2022]
Affiliation(s)
- Pedro H. Oliveira
- Institut Pasteur; Microbial Evolutionary Genomics, Département Génomes et Génétique; Paris France
- CNRS; UMR3525 Paris France
| | - Cláudia Lobato da Silva
- Institute for Biotechnology and Bioengineering, Department of Bioengineering; Instituto Superior Técnico, Universidade de Lisboa; Lisboa Portugal
| | - Joaquim M.S. Cabral
- Institute for Biotechnology and Bioengineering, Department of Bioengineering; Instituto Superior Técnico, Universidade de Lisboa; Lisboa Portugal
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24
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Choi KA, Hwang I, Park HS, Oh SI, Kang S, Hong S. Stem cell therapy and cellular engineering for treatment of neuronal dysfunction in Huntington's disease. Biotechnol J 2014; 9:882-94. [PMID: 24827816 DOI: 10.1002/biot.201300560] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2013] [Revised: 02/25/2014] [Accepted: 03/27/2014] [Indexed: 01/09/2023]
Abstract
Huntington's disease (HD) is a fatal inherited neurodegenerative disorder characterized by progressive loss of neurons in the striatum, a sub-cortical region of the forebrain. The sub-cortical region of the forebrain is associated with the control of movement and behavior, thus HD initially presents with coordination difficulty and cognitive decline. Recent reprogramming technologies, including induced pluripotent stem cells (iPSCs) and induced neural stem cells (iNSCs), have created opportunities to understand the pathological cascades that underlie HD and to develop new treatments for this currently incurable neurological disease. The ultimate objectives of stem cell-based therapies for HD are to replace lost neurons and to prevent neuronal dysfunction and death. In this review, we examine the current understanding of the molecular and pathological mechanisms involved in HD. We discuss disease modeling with HD-iPSCs derived from the somatic cells of patients, which could provide an invaluable platform for understanding HD pathogenesis. We speculate about the benefits and drawbacks of using iNSCs as an alternative stem cell source for HD treatment. Finally, we discuss cell culture and engineering systems that promote the directed differentiation of pluripotent stem cell-derived NSCs into a striatal DARPP32(+) GABAergic MSN phenotype for HD. In conclusion, this review summarizes the potentials of cell reprogramming and engineering technologies relevant to the development of cell-based therapies for HD.
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Affiliation(s)
- Kyung-Ah Choi
- School of Biosystem and Biomedical Science, College of Health Science, Korea University, Seoul, Republic of Korea; Department of Chemistry, College of Science, Korea University, Seoul, Republic of Korea
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25
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Kusuma S, Gerecht S. Recent progress in the use of induced pluripotent stem cells in vascular regeneration. Expert Rev Cardiovasc Ther 2014; 11:661-3. [PMID: 23750673 DOI: 10.1586/erc.13.54] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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26
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Ben-David U. Flowing through the CRISPR-CAScade: Will genome editing boost cell therapies? MOLECULAR AND CELLULAR THERAPIES 2013; 1:3. [PMID: 26056569 PMCID: PMC4448953 DOI: 10.1186/2052-8426-1-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Accepted: 09/30/2013] [Indexed: 11/11/2022]
Abstract
Recent years have seen great advancements in genome editing technologies, allowing for efficient and specific targeting of DNA sequences into the genome. In parallel, advancements in stem cell research, and especially the ability to induce pluripotency in somatic cells, have brought stem cell-derived therapies closer to the clinic. In this commentary, I envision how groundbreaking genome editing technologies will influence stem cell biology research, paving the way to regenerative medicine with genetically engineered cells.
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Affiliation(s)
- Uri Ben-David
- Stem Cell Unit, Department of Genetics, Silberman Institute of Life Sciences, The Hebrew University, Jerusalem, 91904 Israel
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27
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Ben-David U. Flowing through the CRISPR-CAScade: Will genome editing boost cell therapies? MOLECULAR AND CELLULAR THERAPIES 2013; 1:3. [PMID: 26056569 PMCID: PMC4448953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Accepted: 09/30/2013] [Indexed: 11/21/2023]
Abstract
Recent years have seen great advancements in genome editing technologies, allowing for efficient and specific targeting of DNA sequences into the genome. In parallel, advancements in stem cell research, and especially the ability to induce pluripotency in somatic cells, have brought stem cell-derived therapies closer to the clinic. In this commentary, I envision how groundbreaking genome editing technologies will influence stem cell biology research, paving the way to regenerative medicine with genetically engineered cells.
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Affiliation(s)
- Uri Ben-David
- Stem Cell Unit, Department of Genetics, Silberman Institute of Life Sciences, The Hebrew University, Jerusalem, 91904 Israel
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28
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Wang Y, Cheng L, Gerecht S. Efficient and scalable expansion of human pluripotent stem cells under clinically compliant settings: a view in 2013. Ann Biomed Eng 2013; 42:1357-72. [PMID: 24132657 DOI: 10.1007/s10439-013-0921-4] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Accepted: 10/02/2013] [Indexed: 12/20/2022]
Abstract
Human pluripotent stem cells (hPSCs) hold great promise for revolutionizing regenerative medicine for their potential applications in disease modeling, drug discovery, and cellular therapy. Many their applications require robust and scalable expansion of hPSCs, even under settings compliant to good clinical practices. Rapid evolution of media and substrates provided safer and more defined culture conditions for long-term expansion of undifferentiated hPSCs in either adhesion or suspension. With well-designed automatic systems or fully controlled bioreactors, production of a clinically relevant quantity of hPSCs could be achieved in the near future. The goal is to find a scalable, xeno-free, chemically defined, and economic culture system for clinical-grade expansion of hPSCs that complies the requirements of current good manufacturing practices. This review provides an updated overview of the current development and challenges on the way to accomplish this goal, including discussions on basic principles for bioprocess design, serum-free media, extracellular matric or synthesized substrate, microcarrier- or cell aggregate-based suspension culture, and scalability and practicality of equipment.
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Affiliation(s)
- Ying Wang
- Department of Chemical and Biomolecular Engineering and Institute for NanoBioTechnology, The Johns Hopkins University, 3400 N. Charles St., Baltimore, MD, 21218, USA
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29
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Han C, Gu H, Wang J, Lu W, Mei Y, Wu M. Regulation ofL-Threonine Dehydrogenase in Somatic Cell Reprogramming. Stem Cells 2013; 31:953-65. [DOI: 10.1002/stem.1335] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2012] [Accepted: 12/21/2012] [Indexed: 12/22/2022]
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30
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Steliou K, Boosalis MS, Perrine SP, Sangerman J, Faller DV. Butyrate histone deacetylase inhibitors. Biores Open Access 2013; 1:192-8. [PMID: 23514803 PMCID: PMC3559235 DOI: 10.1089/biores.2012.0223] [Citation(s) in RCA: 113] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
In addition to being a part of the metabolic fatty acid fuel cycle, butyrate is also capable of inducing growth arrest in a variety of normal cell types and senescence-like phenotypes in gynecological cancer cells, inhibiting DNA synthesis and cell growth in colonic tumor cell lines, suppressing hTERT mRNA expression and telomerase activity in human prostate cancer cells, and inducing stem cell differentiation and apoptosis by DNA fragmentation. It regulates gene expression by inhibiting histone deacetylases (HDACs), enhances memory recovery and formation in mice, stimulates neurogenesis in the ischemic brain, promotes osteoblast formation, selectively blocks cell replication in transformed cells (compared to healthy cells), and can prevent and treat diet-induced obesity and insulin resistance in mouse models of obesity, as well as stimulate fetal hemoglobin expression in individuals with hematologic diseases such as the thalassemias and sickle-cell disease, in addition to a multitude of other biochemical effects in vivo. However, efforts to exploit the potential of butyrate in the clinical treatment of cancer and other medical disorders are thwarted by its poor pharmacological properties (short half-life and first-pass hepatic clearance) and the multigram doses needed to achieve therapeutic concentrations in vivo. Herein, we review some of the methods used to overcome these difficulties with an emphasis on HDAC inhibition.
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Affiliation(s)
- Kosta Steliou
- PhenoMatriX, Inc. , Boston, Massachusetts. ; Cancer Research Center, Boston University School of Medicine , Boston, Massachusetts
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31
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Promise and challenges of human iPSC-based hematologic disease modeling and treatment. Int J Hematol 2012; 95:601-9. [PMID: 22619021 DOI: 10.1007/s12185-012-1095-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2012] [Accepted: 05/07/2012] [Indexed: 12/30/2022]
Abstract
Postnatal hematopoietic stem cells (HSCs) from umbilical cord blood and adult marrow/blood have been successfully used for treating various human diseases in the past several decades. However, the availability of optimal numbers of HSCs from autologous patients or allogeneic donors with adequate match remains a great barrier to improve and extend HSC and marrow transplantation to more needing patients. In addition, the inability to expand functional human HSCs to sufficient quantity in the laboratory has hindered our research and understanding of human HSCs and hematopoiesis. Recent development in reprogramming technology has provided patient-specific pluripotent stem cells (iPSCs) as a powerful enabling tool for modeling disease and developing therapeutics. Studies have demonstrated the potential of human iPSCs, which can be expanded exponentially and amenable for genome engineering, for using in modeling both inherited and acquired blood diseases. Proof-of-principle studies have also shown the feasibility of iPSCs in gene and cell therapy. Here, we review the recent development in iPSC-based blood disease modeling, and discuss the unsolved issues and challenges in this new and promising field.
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