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Guo M, Chen H, Dong S, Zhang Z, Luo H. CRISPR-Cas gene editing technology and its application prospect in medicinal plants. Chin Med 2022; 17:33. [PMID: 35246186 PMCID: PMC8894546 DOI: 10.1186/s13020-022-00584-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 02/11/2022] [Indexed: 12/26/2022] Open
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR)-Cas gene editing technology has opened a new era of genome interrogation and genome engineering because of its ease operation and high efficiency. An increasing number of plant species have been subjected to site-directed gene editing through this technology. However, the application of CRISPR-Cas technology to medicinal plants is still in the early stages. Here, we review the research history, structural characteristics, working mechanism and the latest derivatives of CRISPR-Cas technology, and discussed their application in medicinal plants for the first time. Furthermore, we creatively put forward the development direction of CRISPR technology applied to medicinal plant gene editing. The aim is to provide a reference for the application of this technology to genome functional studies, synthetic biology, genetic improvement, and germplasm innovation of medicinal plants. CRISPR-Cas is expected to revolutionize medicinal plant biotechnology in the near future.
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Affiliation(s)
- Miaoxian Guo
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Hongyu Chen
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Shuting Dong
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Zheng Zhang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.
| | - Hongmei Luo
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.
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Genome-wide CRISPR knockout screens identify ADAMTSL3 and PTEN genes as suppressors of HCC proliferation and metastasis, respectively. J Cancer Res Clin Oncol 2020; 146:1509-1521. [PMID: 32266537 DOI: 10.1007/s00432-020-03207-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 03/31/2020] [Indexed: 01/03/2023]
Abstract
PURPOSE It is important for hepatocellular carcinoma (HCC) treatment that the targets related to its progression are identified. Clustered regularly interspaced short palindromic repeat (CRISPR)-associated nuclease 9 (Cas9)-based genetic screening is a powerful tool for identifying genes with loss-of-function mutations that are critical for tumour growth and metastasis. METHODS We transduced the human SMMC7721 HCC cell line expressing Cas9 with a human genome-scale CRISPR-Cas9 knockout (GeCKO) lentiviral library A (hGeCKOa) of 65,383 single-guide RNAs (sgRNAs) targeting 19,050 human genes; we then subcutaneously transplanted the transduced cells into nude mice. RESULTS The transduced cells were found to proliferate and metastasize faster than the untransduced cells. Through next-generation sequencing, the genes potentially related to HCC proliferation and metastasis were identified. The sgRNAs targeting the ADAMTSL3 and PTEN genes appeared twice on the list of genes related to HCC proliferation and metastasis, respectively. Analysis based on the data mining of Oncomine revealed that the ADAMTSL3 and PTEN genes were expressed at lower levels in HCC cells than they were in normal liver cells, indicating their tumour-suppressive roles. Downregulation of ADAMTSL3 and PTEN displayed poor overall survival (OS) and predicted poor relapse-free survival (RFS), further supporting their tumour-suppressive roles. Moreover, knocking out either the ADAMTSL3 or PTEN genes promoted either the proliferation or metastasis of HCC cells, respectively. CONCLUSIONS Using both in vitro and in vivo approaches, we described the profound role of the ADAMTSL3 and PTEN genes. This study indicates novel candidate targets for use in HCC treatment and therapy.
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Abstract
Liposomes are one of the most widely investigated carriers for CRISPR/Cas9 delivery. The surface properties of liposomal carriers, including the surface charge, PEGylation, and ligand modification can significantly affect the gene silencing efficiency. Three barriers of systemic CRISPR/Cas9 delivery (long blood circulation, efficient tumor penetration, and efficient cellular uptake/endosomal escape) are analyzed on liposomal carriers with different surface charges, PEGylations, and ligand modifications. Cationic formulations dominate CRISPR/Cas9 delivery and neutral formulations also have good performance while anionic formulations are generally not proper for CRISPR/Cas9 delivery. The PEG dilemma (prolonged blood circulation vs. reduced cellular uptake/endosomal escape) and the side effect of repeated PEGylated formulation (accelerated blood clearance) were discussed. Effects of ligand modification on cationic and neutral formulations were analyzed. Finally, we summarized the achievements in liposomal CRISPR/Cas9 delivery, outlined existing problems, and provided some future perspectives. Liposomes are one of the most widely investigated carriers for CRISPR/Cas9 delivery. The surface properties of liposomal carriers, including the surface charge, PEGylation, and ligand modification can significantly affect the gene silencing efficiency. Three barriers of systemic siRNA delivery (long blood circulation, efficient tumor penetration, and efficient cellular uptake/endosomal escape) are analyzed on liposomal carriers with different surface charges, PEGylations, and ligand modifications. Cationic formulations dominate CRISPR/Cas9 delivery and neutral formulations also have good performance while anionic formulations are generally not proper for CRISPR/Cas9 delivery. The PEG dilemma (prolonged blood circulation vs. reduced cellular uptake/endosomal escape) and the side effect of repeated PEGylated formulation (accelerated blood clearance) were discussed. Effects of ligand modification on cationic and neutral formulations were analyzed. Finally, we summarized the achievements in liposomal CRISPR/Cas9 delivery, outlined existing problems, and provided some future perspectives.
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4
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Tang Z, Chen S, Chen A, He B, Zhou Y, Chai G, Guo F, Huang J. CasPDB: an integrated and annotated database for Cas proteins from bacteria and archaea. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2019; 2019:5549733. [PMID: 31411686 PMCID: PMC6693189 DOI: 10.1093/database/baz093] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 05/01/2019] [Accepted: 06/21/2019] [Indexed: 12/04/2022]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) and associated proteins (Cas) constitute CRISPR–Cas systems, which are antiphage immune systems present in numerous bacterial and most archaeal species. In recent years, CRISPR–Cas systems have been developed into reliable and powerful genome editing tools. Nevertheless, finding similar or better tools from bacteria or archaea remains crucial. This requires the exploration of different CRISPR systems, identification and characterization new Cas proteins. Archives tailored for Cas proteins are urgently needed and necessitate the prediction and grouping of Cas proteins into an information center with all available experimental evidence. Here, we constructed Cas Protein Data Bank (CasPDB), an integrated and annotated online database for Cas proteins from bacteria and archaea. The CasPDB database contains 287 reviewed Cas proteins, 257 745 putative Cas proteins and 3593 Cas operons from 32 023 bacteria species and 1802 archaea species. The database can be freely browsed and searched. The CasPDB web interface also represents all the 3593 putative Cas operons and its components. Among these operons, 328 are members of the type II CRISPR–Cas system.
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Affiliation(s)
- Zhongjie Tang
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 611731, China
| | - ShaoQi Chen
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 611731, China
| | - Ang Chen
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 611731, China
| | - Bifang He
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 611731, China.,School of Medicine, Guizhou University, Guiyang 550025, China
| | - Yuwei Zhou
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 611731, China
| | - Guoshi Chai
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 611731, China
| | - FengBiao Guo
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 611731, China
| | - Jian Huang
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 611731, China
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Ebrahimi S, Teimoori A, Khanbabaei H, Tabasi M. Harnessing CRISPR/Cas 9 System for manipulation of DNA virus genome. Rev Med Virol 2018; 29:e2009. [PMID: 30260068 DOI: 10.1002/rmv.2009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 08/03/2018] [Accepted: 08/07/2018] [Indexed: 12/17/2022]
Abstract
The recent development of the Clustered Regularly Interspaced Palindromic Repeat (CRISPR)/CRISPR-associated protein 9 (Cas9) system, a genome editing system, has many potential applications in virology. The possibility of introducing site specific breaks has provided new possibilities to precisely manipulate viral genomics. Here, we provide diagrams to summarize the steps involved in the process. We also systematically review recent applications of the CRISPR/Cas9 system for manipulation of DNA virus genomics and discuss the therapeutic potential of the system to treat viral diseases.
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Affiliation(s)
- Saeedeh Ebrahimi
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.,Department of Virology, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Ali Teimoori
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.,Department of Virology, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Hashem Khanbabaei
- Medical Physics Department, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Maryam Tabasi
- Department of Virology, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
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Sun D, Guo Z, Liu Y, Zhang Y. Progress and Prospects of CRISPR/Cas Systems in Insects and Other Arthropods. Front Physiol 2017; 8:608. [PMID: 28932198 PMCID: PMC5592444 DOI: 10.3389/fphys.2017.00608] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 08/07/2017] [Indexed: 01/03/2023] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) and the CRISPR-associated gene Cas9 represent an invaluable system for the precise editing of genes in diverse species. The CRISPR/Cas9 system is an adaptive mechanism that enables bacteria and archaeal species to resist invading viruses and phages or plasmids. Compared with zinc finger nucleases and transcription activator-like effector nucleases, the CRISPR/Cas9 system has the advantage of requiring less time and effort. This efficient technology has been used in many species, including diverse arthropods that are relevant to agriculture, forestry, fisheries, and public health; however, there is no review that systematically summarizes its successful application in the editing of both insect and non-insect arthropod genomes. Thus, this paper seeks to provide a comprehensive and impartial overview of the progress of the CRISPR/Cas9 system in different arthropods, reviewing not only fundamental studies related to gene function exploration and experimental optimization but also applied studies in areas such as insect modification and pest control. In addition, we also describe the latest research advances regarding two novel CRISPR/Cas systems (CRISPR/Cpf1 and CRISPR/C2c2) and discuss their future prospects for becoming crucial technologies in arthropods.
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Affiliation(s)
- Dan Sun
- Longping Branch, Graduate School of Hunan UniversityChangsha, China.,Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural SciencesBeijing, China
| | - Zhaojiang Guo
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural SciencesBeijing, China
| | - Yong Liu
- Longping Branch, Graduate School of Hunan UniversityChangsha, China
| | - Youjun Zhang
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural SciencesBeijing, China
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7
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Arend MC, Pereira JO, Markoski MM. The CRISPR/Cas9 System and the Possibility of Genomic Edition for Cardiology. Arq Bras Cardiol 2017; 108:81-83. [PMID: 28146210 PMCID: PMC5245852 DOI: 10.5935/abc.20160200] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 10/13/2016] [Indexed: 11/20/2022] Open
Affiliation(s)
- Marcela Corso Arend
- Laboratório de Cardiologia Molecular e Celular, Instituto de Cardiologia, Fundação Universitária de Cardiologia, Porto Alegre, RS, Brazil
| | - Jessica Olivaes Pereira
- Laboratório de Cardiologia Molecular e Celular, Instituto de Cardiologia, Fundação Universitária de Cardiologia, Porto Alegre, RS, Brazil
| | - Melissa Medeiros Markoski
- Laboratório de Cardiologia Molecular e Celular, Instituto de Cardiologia, Fundação Universitária de Cardiologia, Porto Alegre, RS, Brazil
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Santen RJ, Joham A, Fishbein L, Vella KR, Ebeling PR, Gibson-Helm M, Teede H. Career Advancement: Meeting the Challenges Confronting the Next Generation of Endocrinologists and Endocrine Researchers. J Clin Endocrinol Metab 2016; 101:4512-4520. [PMID: 27691051 DOI: 10.1210/jc.2016-3016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
CONTEXT Challenges and opportunities face the next generation (Next-Gen) of endocrine researchers and clinicians, the lifeblood of the field of endocrinology for the future. A symposium jointly sponsored by The Endocrine Society and the Endocrine Society of Australia was convened to discuss approaches to addressing the present and future Next-Gen needs. EVIDENCE ACQUISITION Data collection by literature review, assessment of previously completed questionnaires, commissioning of a new questionnaire, and summarization of symposium discussions were studied. EVIDENCE SYNTHESIS Next-Gen endocrine researchers face diminishing grant funding in inflation-adjusted terms. The average age of individuals being awarded their first independent investigator funding has increased to age 45 years. For clinicians, a workforce gap exists between endocrinologists needed and those currently trained. Clinicians in practice are increasingly becoming employees of integrated hospital systems, resulting in greater time spent on nonclinical issues. Workforce data and published reviews identify challenges specifically related to early career women in endocrinology. Strategies to Address Issues: Recommendations encompassed the areas of grant support for research, mentoring, education, templates for career development, specific programs for Next-Gen members by senior colleagues as outlined in the text, networking, team science, and life/work integration. Endocrine societies focusing on Next-Gen members provide a powerful mechanism to support these critical areas. CONCLUSIONS A concerted effort to empower, train, and support the next generation of clinical endocrinologists and endocrine researchers is necessary to ensure the viability and vibrancy of our discipline and to optimize our contributions to improving health outcomes. Collaborative engagement of endocrine societies globally will be necessary to support our next generation moving forward.
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Affiliation(s)
- Richard J Santen
- Division of Endocrinology and Metabolism (R.J.S.), University of Virginia Health Sciences System, Charlottesville, Virginia 22908; Monash Centre for Health Research and Implementation (A.J., M.G.-H., H.T.), School of Public Health and Preventive Medicine, and Department of Medicine (P.R.E.), School of Clinical Sciences, Monash University, Clayton, Victoria 3168, Australia; Department of Medicine (L.F.), Divisions of Endocrinology, Metabolism, and Diabetes and Bioinformatics and Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045; Department of Medicine (K.R.V.), Division of Endocrinology, Diabetes, and Metabolism, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215
| | - Anju Joham
- Division of Endocrinology and Metabolism (R.J.S.), University of Virginia Health Sciences System, Charlottesville, Virginia 22908; Monash Centre for Health Research and Implementation (A.J., M.G.-H., H.T.), School of Public Health and Preventive Medicine, and Department of Medicine (P.R.E.), School of Clinical Sciences, Monash University, Clayton, Victoria 3168, Australia; Department of Medicine (L.F.), Divisions of Endocrinology, Metabolism, and Diabetes and Bioinformatics and Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045; Department of Medicine (K.R.V.), Division of Endocrinology, Diabetes, and Metabolism, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215
| | - Lauren Fishbein
- Division of Endocrinology and Metabolism (R.J.S.), University of Virginia Health Sciences System, Charlottesville, Virginia 22908; Monash Centre for Health Research and Implementation (A.J., M.G.-H., H.T.), School of Public Health and Preventive Medicine, and Department of Medicine (P.R.E.), School of Clinical Sciences, Monash University, Clayton, Victoria 3168, Australia; Department of Medicine (L.F.), Divisions of Endocrinology, Metabolism, and Diabetes and Bioinformatics and Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045; Department of Medicine (K.R.V.), Division of Endocrinology, Diabetes, and Metabolism, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215
| | - Kristen R Vella
- Division of Endocrinology and Metabolism (R.J.S.), University of Virginia Health Sciences System, Charlottesville, Virginia 22908; Monash Centre for Health Research and Implementation (A.J., M.G.-H., H.T.), School of Public Health and Preventive Medicine, and Department of Medicine (P.R.E.), School of Clinical Sciences, Monash University, Clayton, Victoria 3168, Australia; Department of Medicine (L.F.), Divisions of Endocrinology, Metabolism, and Diabetes and Bioinformatics and Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045; Department of Medicine (K.R.V.), Division of Endocrinology, Diabetes, and Metabolism, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215
| | - Peter R Ebeling
- Division of Endocrinology and Metabolism (R.J.S.), University of Virginia Health Sciences System, Charlottesville, Virginia 22908; Monash Centre for Health Research and Implementation (A.J., M.G.-H., H.T.), School of Public Health and Preventive Medicine, and Department of Medicine (P.R.E.), School of Clinical Sciences, Monash University, Clayton, Victoria 3168, Australia; Department of Medicine (L.F.), Divisions of Endocrinology, Metabolism, and Diabetes and Bioinformatics and Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045; Department of Medicine (K.R.V.), Division of Endocrinology, Diabetes, and Metabolism, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215
| | - Melanie Gibson-Helm
- Division of Endocrinology and Metabolism (R.J.S.), University of Virginia Health Sciences System, Charlottesville, Virginia 22908; Monash Centre for Health Research and Implementation (A.J., M.G.-H., H.T.), School of Public Health and Preventive Medicine, and Department of Medicine (P.R.E.), School of Clinical Sciences, Monash University, Clayton, Victoria 3168, Australia; Department of Medicine (L.F.), Divisions of Endocrinology, Metabolism, and Diabetes and Bioinformatics and Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045; Department of Medicine (K.R.V.), Division of Endocrinology, Diabetes, and Metabolism, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215
| | - Helena Teede
- Division of Endocrinology and Metabolism (R.J.S.), University of Virginia Health Sciences System, Charlottesville, Virginia 22908; Monash Centre for Health Research and Implementation (A.J., M.G.-H., H.T.), School of Public Health and Preventive Medicine, and Department of Medicine (P.R.E.), School of Clinical Sciences, Monash University, Clayton, Victoria 3168, Australia; Department of Medicine (L.F.), Divisions of Endocrinology, Metabolism, and Diabetes and Bioinformatics and Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045; Department of Medicine (K.R.V.), Division of Endocrinology, Diabetes, and Metabolism, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215
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Lossouarn J, Dupont S, Gorlas A, Mercier C, Bienvenu N, Marguet E, Forterre P, Geslin C. An abyssal mobilome: viruses, plasmids and vesicles from deep-sea hydrothermal vents. Res Microbiol 2015; 166:742-52. [DOI: 10.1016/j.resmic.2015.04.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Revised: 04/08/2015] [Accepted: 04/09/2015] [Indexed: 01/11/2023]
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10
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Silencing and overexpression of human blood group antigens in transfusion: Paving the way for the next steps. Blood Rev 2015; 29:163-9. [DOI: 10.1016/j.blre.2014.10.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Accepted: 10/23/2014] [Indexed: 01/25/2023]
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Kanherkar RR, Bhatia-Dey N, Makarev E, Csoka AB. Cellular reprogramming for understanding and treating human disease. Front Cell Dev Biol 2014; 2:67. [PMID: 25429365 PMCID: PMC4228919 DOI: 10.3389/fcell.2014.00067] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Accepted: 10/27/2014] [Indexed: 12/15/2022] Open
Abstract
In the last two decades we have witnessed a paradigm shift in our understanding of cells so radical that it has rewritten the rules of biology. The study of cellular reprogramming has gone from little more than a hypothesis, to applied bioengineering, with the creation of a variety of important cell types. By way of metaphor, we can compare the discovery of reprogramming with the archeological discovery of the Rosetta stone. This stone slab made possible the initial decipherment of Egyptian hieroglyphics because it allowed us to see this language in a way that was previously impossible. We propose that cellular reprogramming will have an equally profound impact on understanding and curing human disease, because it allows us to perceive and study molecular biological processes such as differentiation, epigenetics, and chromatin in ways that were likewise previously impossible. Stem cells could be called “cellular Rosetta stones” because they allow also us to perceive the connections between development, disease, cancer, aging, and regeneration in novel ways. Here we present a comprehensive historical review of stem cells and cellular reprogramming, and illustrate the developing synergy between many previously unconnected fields. We show how stem cells can be used to create in vitro models of human disease and provide examples of how reprogramming is being used to study and treat such diverse diseases as cancer, aging, and accelerated aging syndromes, infectious diseases such as AIDS, and epigenetic diseases such as polycystic ovary syndrome. While the technology of reprogramming is being developed and refined there have also been significant ongoing developments in other complementary technologies such as gene editing, progenitor cell production, and tissue engineering. These technologies are the foundations of what is becoming a fully-functional field of regenerative medicine and are converging to a point that will allow us to treat almost any disease.
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Affiliation(s)
- Riya R Kanherkar
- Epigenetics Laboratory, Department of Anatomy, Howard University Washington, DC, USA
| | - Naina Bhatia-Dey
- Epigenetics Laboratory, Department of Anatomy, Howard University Washington, DC, USA
| | - Evgeny Makarev
- InSilico Medicine, Emerging Technology Center, Johns Hopkins University Eastern Baltimore, MD, USA
| | - Antonei B Csoka
- Epigenetics Laboratory, Department of Anatomy, Howard University Washington, DC, USA
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Doorschodt B, Teubner A, Kobayashi E, Tolba R. Promising future for the transgenic rat in transplantation research. Transplant Rev (Orlando) 2014; 28:155-62. [DOI: 10.1016/j.trre.2014.05.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2014] [Revised: 04/02/2014] [Accepted: 05/20/2014] [Indexed: 01/17/2023]
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13
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RNAi for silencing drug resistance in microbes toward development of nanoantibiotics. J Control Release 2014; 189:150-7. [DOI: 10.1016/j.jconrel.2014.06.054] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Revised: 06/25/2014] [Accepted: 06/25/2014] [Indexed: 01/01/2023]
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Abstract
Small non-coding RNA (ncRNA) therapeutics make use of small ncRNA effectors for desired therapeutic purposes that are essentially short (10–20 kD) RNA segments. These small ncRNA effectors are potentially tremendously powerful therapeutic agents, but are typically unable to reach disease target cells in vivo without the assistance of a delivery system or vector. The main focus of this review is the use of lipid-based nanoparticles (LNPs) for the functional delivery of small ncRNA effectors in vivo. LNPs appear to be amongst the most effective delivery systems currently available for this purpose. Moreover, studies on LNP-mediated delivery in vivo are leading to the emergence of useful biophysical parameters and physical organic chemistry rules that provide a framework for understanding LNP-mediated in vivo delivery behaviors and outcomes. These same parameters and rules should also suggest ways and means to develop next generations of LNPs with genuine utility and long-term clinical viability.
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15
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The molecular basis of bacterial-insect symbiosis. J Mol Biol 2014; 426:3830-7. [PMID: 24735869 DOI: 10.1016/j.jmb.2014.04.005] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Revised: 04/02/2014] [Accepted: 04/08/2014] [Indexed: 12/12/2022]
Abstract
Insects provide experimentally tractable and cost-effective model systems to investigate the molecular basis of animal-bacterial interactions. Recent research is revealing the central role of the insect innate immune system, especially anti-microbial peptides and reactive oxygen species, in regulating the abundance and composition of the microbiota in various insects, including Drosophila and the mosquitoes Aedes and Anopheles. Interactions between the immune system and microbiota are, however, bidirectional with evidence that members of the resident microbiota can promote immune function, conferring resistance to pathogens and parasites by both activation of immune effectors and production of toxins. Antagonistic and mutualistic interactions among bacteria have also been implicated as determinants of the microbiota composition, including exclusion of pathogens, but the molecular mechanisms are largely unknown. Some bacteria are crucial for insect nutrition, through provisioning of specific nutrients (e.g., B vitamins, essential amino acids) and modulation of the insect nutritional sensing and signaling pathways (e.g., insulin signaling) that regulate nutrient allocation, especially to lipid and other energy reserves. A key challenge for future research is to identify the molecular interaction between specific bacterial effectors and animal receptors, as well as to determine how these interactions translate into microbiota-dependent signaling, metabolism, and immune function in the host.
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CRISPR-based technologies: prokaryotic defense weapons repurposed. Trends Genet 2014; 30:111-8. [PMID: 24555991 DOI: 10.1016/j.tig.2014.01.003] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Revised: 01/16/2014] [Accepted: 01/17/2014] [Indexed: 12/18/2022]
Abstract
To combat potentially deadly viral infections, prokaryotic microbes enlist small RNA-based adaptive immune systems (CRISPR-Cas systems) that protect through sequence-specific recognition and targeted destruction of viral nucleic acids (either DNA or RNA depending on the system). Here, we summarize rapid progress made in redirecting the nuclease activities of these microbial immune systems to bind and cleave DNA or RNA targets of choice, by reprogramming the small guide RNAs of the various CRISPR-Cas complexes. These studies have demonstrated the potential of Type II CRISPR-Cas systems both as efficient and versatile genome-editing tools and as potent and specific regulators of gene expression in a broad range of cell types (including human) and organisms. Progress is also being made in developing a Type III RNA-targeting CRISPR-Cas system as a novel gene knockdown platform to investigate gene function and modulate gene expression for metabolic engineering in microbes.
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Wood DO, Wood RR, Tucker AM. Genetic systems for studying obligate intracellular pathogens: an update. Curr Opin Microbiol 2013; 17:11-6. [PMID: 24581687 DOI: 10.1016/j.mib.2013.10.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Revised: 10/23/2013] [Accepted: 10/29/2013] [Indexed: 11/18/2022]
Abstract
Rapid advancements in the genetic manipulation of obligate intracellular bacterial pathogens have been made over the past two years. In this paper we attempt to summarize the work published since 2011 that documents these exciting accomplishments. Although each genus comprising this diverse group of pathogens poses unique problems, requiring modifications of established techniques and the introduction of new tools, all appear amenable to genetic analysis. Significantly, the field is moving forward from a focus on the identification and development of genetic techniques to their application in addressing crucial questions related to mechanisms of bacterial pathogenicity and the requirements of obligate intracellular growth.
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Affiliation(s)
- David O Wood
- Laboratory of Molecular Biology, Department of Microbiology and Immunology, College of Medicine, University of South Alabama, 501 Aubrey Green Drive, Mobile, AL 36688-0002, United States.
| | - Raphael R Wood
- Laboratory of Molecular Biology, Department of Microbiology and Immunology, College of Medicine, University of South Alabama, 501 Aubrey Green Drive, Mobile, AL 36688-0002, United States
| | - Aimee M Tucker
- Laboratory of Molecular Biology, Department of Microbiology and Immunology, College of Medicine, University of South Alabama, 501 Aubrey Green Drive, Mobile, AL 36688-0002, United States
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Delihas N. Editorial on the Special Issue: Regulation by non-coding RNAs. Int J Mol Sci 2013; 14:21960-4. [PMID: 24201126 PMCID: PMC3856044 DOI: 10.3390/ijms141121960] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2013] [Accepted: 10/31/2013] [Indexed: 12/13/2022] Open
Abstract
This Special Issue of IJMS is devoted to regulation by non-coding RNAs and contains both original research and review articles. An attempt is made to provide an up-to-date analysis of this very fast moving field and cover regulatory roles of both microRNAs and long non-coding RNAs. Multifaceted functions of these RNAs in normal cellular processes, as well as in disease progression, are highlighted.
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Affiliation(s)
- Nicholas Delihas
- Department of Molecular Genetics and Microbiology, School of Medicine, Stony Brook University, Stony Brook, NY 11794-5222 USA.
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