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Banda A, Impomeni O, Singh A, Baloch AR, Hu W, Jaijyan DK. Precision in Action: The Role of Clustered Regularly Interspaced Short Palindromic Repeats/Cas in Gene Therapies. Vaccines (Basel) 2024; 12:636. [PMID: 38932365 PMCID: PMC11209408 DOI: 10.3390/vaccines12060636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2024] [Revised: 05/21/2024] [Accepted: 06/04/2024] [Indexed: 06/28/2024] Open
Abstract
Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)-associated enzyme-CAS holds great promise for treating many uncured human diseases and illnesses by precisely correcting harmful point mutations and disrupting disease-causing genes. The recent Food and Drug Association (FDA) approval of the first CRISPR-based gene therapy for sickle cell anemia marks the beginning of a new era in gene editing. However, delivering CRISPR specifically into diseased cells in vivo is a significant challenge and an area of intense research. The identification of new CRISPR/Cas variants, particularly ultra-compact CAS systems with robust gene editing activities, paves the way for the low-capacity delivery vectors to be used in gene therapies. CRISPR/Cas technology has evolved beyond editing DNA to cover a wide spectrum of functionalities, including RNA targeting, disease diagnosis, transcriptional/epigenetic regulation, chromatin imaging, high-throughput screening, and new disease modeling. CRISPR/Cas can be used to engineer B-cells to produce potent antibodies for more effective vaccines and enhance CAR T-cells for the more precise and efficient targeting of tumor cells. However, CRISPR/Cas technology has challenges, including off-target effects, toxicity, immune responses, and inadequate tissue-specific delivery. Overcoming these challenges necessitates the development of a more effective and specific CRISPR/Cas delivery system. This entails strategically utilizing specific gRNAs in conjunction with robust CRISPR/Cas variants to mitigate off-target effects. This review seeks to delve into the intricacies of the CRISPR/Cas mechanism, explore progress in gene therapies, evaluate gene delivery systems, highlight limitations, outline necessary precautions, and scrutinize the ethical considerations associated with its application.
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Affiliation(s)
- Amrutha Banda
- Department of Biology, The College of New Jersey, Ewing Township, NJ 08618, USA
| | - Olivia Impomeni
- Department of Biology, The College of New Jersey, Ewing Township, NJ 08618, USA
| | - Aparana Singh
- Department of Chemistry, National Institute of Technology Agartala, Agartala 799046, India;
| | - Abdul Rasheed Baloch
- Department of Anatomy and Neurobiology, School of Medicine, Virginia Commonwealth University, Richmond, VA 23284, USA;
| | - Wenhui Hu
- Department of Anatomy and Neurobiology, School of Medicine, Virginia Commonwealth University, Richmond, VA 23284, USA;
| | - Dabbu Kumar Jaijyan
- Department of Anatomy and Neurobiology, School of Medicine, Virginia Commonwealth University, Richmond, VA 23284, USA;
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2
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Doddavarapu B, Lata C, Shah JM. Epigenetic regulation influenced by soil microbiota and nutrients: Paving road to epigenome editing in plants. Biochim Biophys Acta Gen Subj 2024; 1868:130580. [PMID: 38325761 DOI: 10.1016/j.bbagen.2024.130580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 12/25/2023] [Accepted: 02/02/2024] [Indexed: 02/09/2024]
Abstract
Soil is a complex ecosystem that houses microbes and nutrients that are necessary for plant development. Edaphic properties of the soil and environmental conditions influence microbial growth and nutrient accessibility. Various environmental stimuli largely affect the soil microbes and ionic balance, in turn influencing plants. Soil microflora helps decompose organic matter and is involved in mineral uptake. The combination of soil microbes and mineral nutrients notably affects plant growth. Recent advancements have enabled a deeper understanding of plant genetic/molecular regulators. Deficiencies/sufficiencies of soil minerals and microbes also alter plant gene regulation. Gene regulation mediated by epigenetic mechanisms comprises conformational alterations in chromatin structure, DNA/histone modifications, or involvement of small RNAs. Epigenetic regulation is unique due to its potential to inherit without involving alteration of the DNA sequence. Thus, the compilation study of heritable epigenetic changes driven by nutrient imbalances and soil microbes would facilitate understanding this molecular phenomenon in plants. This information can aid in epigenome editing, which has recently emerged as a promising technology for plant non-transgenic/non-mutagenic modification. Potential epigenetic marks induced by biotic and abiotic stresses in plants could be explored as target sites for epigenome editing. This review discusses novel ways of epigenome editing to create epigenome edited plants with desirable and heritable phenotypes. As plants are sessile and in constant exposure to the soil microbiome and nutrients, epigenetic changes induced by these factors could provide more effective, stable and a sustainable molecular solution for crop improvement.
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Affiliation(s)
- Bhavya Doddavarapu
- Department of Plant Science, Central University of Kerala, Kerala, India
| | - Charu Lata
- Inclusive Health & Traditional Knowledge Studies Division, CSIR- National Institute of Science Communication and Policy Research, New Delhi, India
| | - Jasmine M Shah
- Department of Plant Science, Central University of Kerala, Kerala, India.
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3
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Srinivas T, Siqueira E, Guil S. Techniques for investigating lncRNA transcript functions in neurodevelopment. Mol Psychiatry 2024; 29:874-890. [PMID: 38145986 PMCID: PMC11176085 DOI: 10.1038/s41380-023-02377-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 12/05/2023] [Accepted: 12/12/2023] [Indexed: 12/27/2023]
Abstract
Long noncoding RNAs (lncRNAs) are sequences of 200 nucleotides or more that are transcribed from a large portion of the mammalian genome. While hypothesized to have a variety of biological roles, many lncRNAs remain largely functionally uncharacterized due to unique challenges associated with their investigation. For example, some lncRNAs overlap with other genomic loci, are expressed in a cell-type-specific manner, and/or are differentially processed at the post-transcriptional level. The mammalian CNS contains a vast diversity of lncRNAs, and lncRNAs are highly abundant in the mammalian brain. However, interrogating lncRNA function in models of the CNS, particularly in vivo, can be complex and challenging. Here we review the breadth of methods used to investigate lncRNAs in the CNS, their merits, and the understanding they can provide with respect to neurodevelopment and pathophysiology. We discuss remaining challenges in the field and provide recommendations to assay lncRNAs based on current methods.
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Affiliation(s)
- Tara Srinivas
- Josep Carreras Leukaemia Research Institute (IJC), 08916, Badalona, Barcelona, Catalonia, Spain
| | - Edilene Siqueira
- Josep Carreras Leukaemia Research Institute (IJC), 08916, Badalona, Barcelona, Catalonia, Spain
| | - Sonia Guil
- Josep Carreras Leukaemia Research Institute (IJC), 08916, Badalona, Barcelona, Catalonia, Spain.
- Germans Trias i Pujol Health Science Research Institute, 08916, Badalona, Barcelona, Catalonia, Spain.
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4
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Alavijeh NS, Serrano A, Peters MS, Wölper C, Schrader T. Design and Synthesis of Artificial Nucleobases for Sequence-Selective DNA Recognition within the Major Groove. Chem Asian J 2023; 18:e202300637. [PMID: 37616375 DOI: 10.1002/asia.202300637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 08/23/2023] [Indexed: 08/26/2023]
Abstract
We present the design and synthesis of artificial specific nucleobases, each one recognizing a single base pair within the major groove of duplex DNA. Computational calculations indicate that PNAs modified with these nucleobases enable the formation of highly stable triple helices with no sequence restrictions through multiple hydrogen bonding and π⋅⋅⋅π stacking interactions, without significantly widening the DNA double helix. New synthetic routes were developed to the structures of these fused heterocycles which have rarely been described in the literature. NMR titration experiments indicate specific hydrogen bonding at the Hoogsteen sites. The new building blocks allow the construction of four PNA monomers for each canonic base pair and their covalent connection to PNA oligomers. These can be designed complementary to any given DNA sequence. With high efficiency and relative simplicity of operation, the described methodologies and strategies hence form the basis for a new supramolecular ligand system targeting double-stranded DNA without strand invasion.
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Affiliation(s)
- Nahid S Alavijeh
- Department of Chemistry, University of Duisburg-Essen, Universitätsstrasse 7, 45117, Essen, Germany
| | - Alvaro Serrano
- Department of Chemistry, University of Duisburg-Essen, Universitätsstrasse 7, 45117, Essen, Germany
| | - Max S Peters
- Department of Chemistry, University of Duisburg-Essen, Universitätsstrasse 7, 45117, Essen, Germany
| | - Christoph Wölper
- Department of Chemistry, University of Duisburg-Essen, Universitätsstrasse 7, 45117, Essen, Germany
| | - Thomas Schrader
- Department of Chemistry, University of Duisburg-Essen, Universitätsstrasse 7, 45117, Essen, Germany
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5
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Hua Z, Xu K, Xiao W, Shu C, Li N, Li K, Gu H, Zhu Z, Zhang L, Ren H, Zeng Q, Yin Y, Bi Y. Dual single guide RNAs-mediating deletion of mature myostatin peptide results in concomitant muscle fibre hyperplasia and adipocyte hypotrophy in pigs. Biochem Biophys Res Commun 2023; 673:145-152. [PMID: 37390747 DOI: 10.1016/j.bbrc.2023.06.053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 05/25/2023] [Accepted: 06/15/2023] [Indexed: 07/02/2023]
Abstract
Myostatin (MSTN) is a major gene target for skeletal muscle overgrowth in animals. We hypothesized that deletion of the entire mature peptide encoded by MSTN in pigs would knock out its bioactive form and accordingly stimulate skeletal muscle overgrowth. Thus, we engineered two pairs of single-guide RNAs (sgRNAs) to target exons 1 and 3 of MSTN in primary fetal fibroblasts of Taoyuan black pigs. We found that sgRNAs targeting exon 3, which encodes the mature peptide, had higher biallelic null mutation efficiency than those targeting exon 1. Somatic cell nuclear transfer was conducted using the exon 3 mutation cells as donor cells to generate five cloned MSTN null piglets (MSTN-/-). Growth testing revealed that both the growth rate and average daily weight gain of MST-/- pigs were greater than those of wild-type (MSTN+/+) pigs. Slaughter data demonstrated that the lean ratio of MSTN-/- pigs was 11.3% higher (P < 0.01) while the back-fat thickness was 17.33% lower (P < 0.01) than those of MSTN+/+ pigs. Haematoxylin-eosin staining indicated that the increased leanness of MSTN-/- pigs resulted from muscle fibre hyperplasia rather than hypertrophy.HE staining showed markedly decreased adipocyte size in MSTN-/- pigs. We also critically examined the off-target and random integration by resequencing, which showed that the founder MSTN-/- pigs contained no non-target mutations or exogenous plasmid elements. This study is the first to report the successful knock out of the mature MSTN peptide using dual sgRNA-mediated deletion, leading to the most prominent alteration of meat production traits in pigs published thus far. This new strategy is expected to have a wide impact on genetic improvements in food animals.
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Affiliation(s)
- Zaidong Hua
- Hubei Key Laboratory of Animal Embryo Engineering and Molecular Breeding, Hubei Academy of Agricultural Sciences, Wuhan, Hubei Province, China
| | - Kang Xu
- Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan Province, China
| | - Wei Xiao
- Hubei Key Laboratory of Animal Embryo Engineering and Molecular Breeding, Hubei Academy of Agricultural Sciences, Wuhan, Hubei Province, China
| | - Chang Shu
- Hubei Key Laboratory of Animal Embryo Engineering and Molecular Breeding, Hubei Academy of Agricultural Sciences, Wuhan, Hubei Province, China
| | - Nana Li
- Hubei Key Laboratory of Animal Embryo Engineering and Molecular Breeding, Hubei Academy of Agricultural Sciences, Wuhan, Hubei Province, China
| | - Kaiqiang Li
- Hubei Key Laboratory of Animal Embryo Engineering and Molecular Breeding, Hubei Academy of Agricultural Sciences, Wuhan, Hubei Province, China
| | - Hao Gu
- Hubei Key Laboratory of Animal Embryo Engineering and Molecular Breeding, Hubei Academy of Agricultural Sciences, Wuhan, Hubei Province, China
| | - Zhe Zhu
- Hubei Key Laboratory of Animal Embryo Engineering and Molecular Breeding, Hubei Academy of Agricultural Sciences, Wuhan, Hubei Province, China
| | - Liping Zhang
- Hubei Key Laboratory of Animal Embryo Engineering and Molecular Breeding, Hubei Academy of Agricultural Sciences, Wuhan, Hubei Province, China
| | - Hongyan Ren
- Hubei Key Laboratory of Animal Embryo Engineering and Molecular Breeding, Hubei Academy of Agricultural Sciences, Wuhan, Hubei Province, China
| | - Qinghua Zeng
- Hunan Chuweixiang Agriculture and Animal Husbandry Co., Ltd, Changsha, China
| | - Yulong Yin
- Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan Province, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Province, China.
| | - Yanzhen Bi
- Hubei Key Laboratory of Animal Embryo Engineering and Molecular Breeding, Hubei Academy of Agricultural Sciences, Wuhan, Hubei Province, China.
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6
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Hu Z, Sun A, Yang J, Naz G, Sun G, Li Z, Gogo Liu JJ, Zhang S, Zhang X. Regulation of the CRISPR-Cas12a system by methylation and demethylation of guide RNA. Chem Sci 2023; 14:5945-5955. [PMID: 37293662 PMCID: PMC10246701 DOI: 10.1039/d3sc00629h] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 05/08/2023] [Indexed: 06/10/2023] Open
Abstract
Chemical modifications of CRISPR-Cas nucleases help decrease off-target editing and expand the biomedical applications of CRISPR-based gene manipulation tools. Here, we found that epigenetic modifications of guide RNA, such as m6A and m1A methylation, can effectively inhibit both the cis- and trans-DNA cleavage activities of CRISPR-Cas12a. The underlying mechanism is that methylations destabilize the secondary and tertiary structure of gRNA which prevents the assembly of the Cas12a-gRNA nuclease complex, leading to decreased DNA targeting ability. A minimum of three adenine methylated nucleotides are required to completely inhibit the nuclease activity. We also demonstrate that these effects are reversible through the demethylation of gRNA by demethylases. This strategy has been used in the regulation of gene expression, demethylase imaging in living cells and controllable gene editing. The results demonstrate that the methylation-deactivated and demethylase-activated strategy is a promising tool for regulation of the CRISPR-Cas12a system.
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Affiliation(s)
- Zhian Hu
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing 30 Xueyuan Road, Haidian District Beijing 100083 P. R. China
- Department of Chemistry, Tsinghua University Beijing 100084 P. R. China
| | - Ao Sun
- Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University Beijing 100084 P. R. China
| | - Jinlei Yang
- Department of Chemistry, Tsinghua University Beijing 100084 P. R. China
| | - Gul Naz
- Department of Chemistry, Tsinghua University Beijing 100084 P. R. China
| | - Gongwei Sun
- Department of Chemistry, Tsinghua University Beijing 100084 P. R. China
| | - Zhengping Li
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing 30 Xueyuan Road, Haidian District Beijing 100083 P. R. China
| | - Jun-Jie Gogo Liu
- Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University Beijing 100084 P. R. China
- Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University Beijing 100084 P. R. China
| | - Sichun Zhang
- Department of Chemistry, Tsinghua University Beijing 100084 P. R. China
| | - Xinrong Zhang
- Department of Chemistry, Tsinghua University Beijing 100084 P. R. China
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7
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Rajendran AP, Ogundana O, Morales LC, Meenakshi Sundaram DN, Kucharski C, Kc R, Uludağ H. Transfection Efficacy and Cellular Uptake of Lipid-Modified Polyethyleneimine Derivatives for Anionic Nanoparticles as Gene Delivery Vectors. ACS APPLIED BIO MATERIALS 2023; 6:1105-1121. [PMID: 36853230 DOI: 10.1021/acsabm.2c00978] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
Abstract
Cationic polyethylenimine (PEI)-based nonviral gene carriers have been desirable to overcome the limitations of viral vectors in gene therapy. A range of PEI derivatives were designed, synthesized, and evaluated for nonviral delivery applications of plasmid DNA (pDNA). Linolenic acid, lauric acid, and oleic acid were covalently conjugated with low-molecular-weight PEI (Mw ∼ 1200 Da) via two different linkers, gallic acid (GA) and p-hydroxybenzoic acid (PHPA), that allows a differential loading of lipids per modified amine (3 vs 1, respectively). 1H NMR spectrum confirmed the expected structure of the conjugates as well as the level of lipid substitution. SYBR Green binding assay performed to investigate the 50% binding concentration (BC50) of lipophilic polymers to pDNA revealed increased BC50 with an increased level of lipid substitution. The particle analysis determined that GA- and PHPA-modified lipopolymers gave pDNA complexes with ∼300 and ∼100 nm in size, respectively. At the polymer/pDNA ratio of 5.0, the ζ-potentials of the complexes were negative (-6.55 to -10.6 mV) unlike the complexes with the native PEI (+11.2 mV). The transfection experiments indicated that the prepared lipopolymers showed higher transfection in attachment-dependent cells than in suspension cells based on the expression of the reporter green fluorescent protein (GFP) gene. When loaded with Cy3-labeled pDNA, the lipopolymers exhibited effective cellular uptake in attachment-dependent cells while the cellular uptake was limited in suspension cells. These results demonstrate the potential of lipid-conjugated PEI via GA and PHPA linkers, which are promising for the modification of anchorage-dependent cells.
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Affiliation(s)
- Amarnath Praphakar Rajendran
- Department of Chemical and Materials Engineering, Faculty of Engineering, University of Alberta, Edmonton, Alberta T6G 1H9, Canada
| | - Oluwanifemi Ogundana
- Department of Chemical and Materials Engineering, Faculty of Engineering, University of Alberta, Edmonton, Alberta T6G 1H9, Canada
| | - Luis Carlos Morales
- Department of Chemical and Materials Engineering, Faculty of Engineering, University of Alberta, Edmonton, Alberta T6G 1H9, Canada
| | | | - Cezary Kucharski
- Department of Chemical and Materials Engineering, Faculty of Engineering, University of Alberta, Edmonton, Alberta T6G 1H9, Canada
| | - Remant Kc
- Department of Chemical and Materials Engineering, Faculty of Engineering, University of Alberta, Edmonton, Alberta T6G 1H9, Canada
| | - Hasan Uludağ
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, Alberta T6G 2H1, Canada
- Department of Biomedical Engineering, University of Alberta, Edmonton, Alberta T6G 2R3, Canada
- Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2R3, Canada
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8
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Sentis A, Hemptinne J, Magro A, Outreman Y. Biological control needs evolutionary perspectives of ecological interactions. Evol Appl 2022; 15:1537-1554. [PMID: 36330295 PMCID: PMC9624075 DOI: 10.1111/eva.13457] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 07/20/2022] [Accepted: 07/26/2022] [Indexed: 05/30/2024] Open
Abstract
While ecological interactions have been identified as determinant for biological control efficiency, the role of evolution remains largely underestimated in biological control programs. With the restrictions on the use of both pesticides and exotic biological control agents (BCAs), the evolutionary optimization of local BCAs becomes central for improving the efficiency and the resilience of biological control. In particular, we need to better account for the natural processes of evolution to fully understand the interactions of pests and BCAs, including in biocontrol strategies integrating human manipulations of evolution (i.e., artificial selection and genetic engineering). In agroecosystems, the evolution of BCAs traits and performance depends on heritable phenotypic variation, trait genetic architecture, selection strength, stochastic processes, and other selective forces. Humans can manipulate these natural processes to increase the likelihood of evolutionary trait improvement, by artificially increasing heritable phenotypic variation, strengthening selection, controlling stochastic processes, or overpassing evolution through genetic engineering. We highlight these facets by reviewing recent studies addressing the importance of natural processes of evolution and human manipulations of these processes in biological control. We then discuss the interactions between the natural processes of evolution occurring in agroecosystems and affecting the artificially improved BCAs after their release. We emphasize that biological control cannot be summarized by interactions between species pairs because pests and biological control agents are entangled in diverse communities and are exposed to a multitude of deterministic and stochastic selective forces that can change rapidly in direction and intensity. We conclude that the combination of different evolutionary approaches can help optimize BCAs to remain efficient under changing environmental conditions and, ultimately, favor agroecosystem sustainability.
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Affiliation(s)
- Arnaud Sentis
- INRAEAix Marseille University, UMR RECOVERAix‐en‐ProvenceFrance
| | - Jean‐Louis Hemptinne
- Laboratoire Évolution et Diversité biologiqueUMR 5174 CNRS/UPS/IRDToulouseFrance
- Université Fédérale de Toulouse Midi‐Pyrénées – ENSFEACastanet‐TolosanFrance
| | - Alexandra Magro
- Laboratoire Évolution et Diversité biologiqueUMR 5174 CNRS/UPS/IRDToulouseFrance
- Université Fédérale de Toulouse Midi‐Pyrénées – ENSFEACastanet‐TolosanFrance
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9
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Jo DH, Bae S, Kim HH, Kim JS, Kim JH. In vivo application of base and prime editing to treat inherited retinal diseases. Prog Retin Eye Res 2022; 94:101132. [PMID: 36241547 DOI: 10.1016/j.preteyeres.2022.101132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 09/19/2022] [Accepted: 09/28/2022] [Indexed: 11/05/2022]
Abstract
Inherited retinal diseases (IRDs) are vision-threatening retinal disorders caused by pathogenic variants of genes related to visual functions. Genomic analyses in patients with IRDs have revealed pathogenic variants which affect vision. However, treatment options for IRDs are limited to nutritional supplements regardless of genetic variants or gene-targeting approaches based on antisense oligonucleotides and adeno-associated virus vectors limited to targeting few genes. Genome editing, particularly that involving clustered regularly interspaced short palindromic repeat (CRISPR)-Cas9 technologies, can correct pathogenic variants and provide additional treatment opportunities. Recently developed base and prime editing platforms based on CRISPR-Cas9 technologies are promising for therapeutic genome editing because they do not employ double-stranded breaks (DSBs), which are associated with P53 activation, large deletions, and chromosomal translocations. Instead, using attached deaminases and reverse transcriptases, base and prime editing efficiently induces specific base substitutions and intended genetic changes (substitutions, deletions, or insertions), respectively, without DSBs. In this review, we will discuss the recent in vivo application of CRISPR-Cas9 technologies, focusing on base and prime editing, in animal models of IRDs.
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Chen Z, Zhang J, Lyu Q, Wang H, Ji X, Yan Z, Chen F, Dahlgren RA, Zhang M. Modular configurations of living biomaterials incorporating nano-based artificial mediators and synthetic biology to improve bioelectrocatalytic performance: A review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 824:153857. [PMID: 35176368 DOI: 10.1016/j.scitotenv.2022.153857] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 01/24/2022] [Accepted: 02/09/2022] [Indexed: 06/14/2023]
Abstract
Currently, the industrial application of bioelectrochemical systems (BESs) that are incubated with natural electrochemically active microbes (EABs) is limited due to inefficient extracellular electron transfer (EET) by natural EABs. Notably, recent studies have identified several novel living biomaterials comprising highly efficient electron transfer systems allowing unparalleled proficiency of energy conversion. Introduction of these biomaterials into BESs could fundamentally increase their utilization for a wide range of applications. This review provides a comprehensive assessment of recent advancements in the design of living biomaterials that can be exploited to enhance bioelectrocatalytic performance. Further, modular configurations of abiotic and biotic components promise a powerful enhancement through integration of nano-based artificial mediators and synthetic biology. Herein, recent advancements in BESs are synthesized and assessed, including heterojunctions between conductive nanomaterials and EABs, in-situ hybrid self-assembly of EABs and nano-sized semiconductors, cytoprotection in biohybrids, synthetic biological modifications of EABs and electroactive biofilms. Since living biomaterials comprise a broad range of disciplines, such as molecular biology, electrochemistry and material sciences, full integration of technological advances applied in an interdisciplinary framework will greatly enhance/advance the utility and novelty of BESs. Overall, emerging fundamental knowledge concerning living biomaterials provides a powerful opportunity to markedly boost EET efficiency and facilitate the industrial application of BESs to meet global sustainability challenges/goals.
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Affiliation(s)
- Zheng Chen
- School of Public Health and Management, Wenzhou Medical University, Wenzhou 325035, People's Republic of China; School of Environmental Science & Engineering, Tan Kah Kee College, Xiamen University, Zhangzhou 363105, People's Republic of China; Fujian Provincial Key Lab of Coastal Basin Environment, Fujian Polytechnic Normal University, Fuqing 350300, People's Republic of China.
| | - Jing Zhang
- School of Environmental Science & Engineering, Tan Kah Kee College, Xiamen University, Zhangzhou 363105, People's Republic of China
| | - Qingyang Lyu
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, People's Republic of China
| | - Honghui Wang
- School of Environmental Science & Engineering, Tan Kah Kee College, Xiamen University, Zhangzhou 363105, People's Republic of China
| | - Xiaoliang Ji
- School of Public Health and Management, Wenzhou Medical University, Wenzhou 325035, People's Republic of China
| | - Zhiying Yan
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, People's Republic of China
| | - Fang Chen
- Fujian Provincial Key Lab of Coastal Basin Environment, Fujian Polytechnic Normal University, Fuqing 350300, People's Republic of China
| | - Randy A Dahlgren
- School of Public Health and Management, Wenzhou Medical University, Wenzhou 325035, People's Republic of China; Department of Land, Air and Water Resources, University of California, Davis, CA 95616, USA
| | - Minghua Zhang
- School of Public Health and Management, Wenzhou Medical University, Wenzhou 325035, People's Republic of China; Department of Land, Air and Water Resources, University of California, Davis, CA 95616, USA
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11
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Shin H, Choi WL, Lim JY, Huh JH. Epigenome editing: targeted manipulation of epigenetic modifications in plants. Genes Genomics 2022; 44:307-315. [PMID: 35000141 DOI: 10.1007/s13258-021-01199-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 11/25/2021] [Indexed: 12/13/2022]
Abstract
BACKGROUND Epigenetic modifications play important roles in diverse cellular processes such as X chromosome inactivation, cell differentiation, development and senescence. DNA methylation and histone modifications are major epigenetic modifications that regulate chromatin structure and gene expression without DNA sequence changes. Epigenetic alterations may induce phenotypic changes stable enough for mitotic or meiotic inheritance. Moreover, the reversibility of epigenetic marks makes the manipulation of chromatin and epigenetic signature an attractive strategy for therapeutic and breeding purposes. Targeted epigenetic manipulation, or epigenome editing, at the gene of interest commonly utilizes specific epigenetic modifiers fused with a targeting module of the conventional genome editing system. OBJECTIVE This review aims to summarize essential epigenetic components and introduce currently available epigenetic mutants and the corresponding epialleles in plants. Furthermore, advances in epigenome editing technology are discussed while proposing its potential application to plant breeding. CONCLUSIONS Epimutations associated with useful traits may provide a valuable resource for crop development. It is important to explore epimutations in a variety of crop species while understanding the fundamental aspects of epigenetic regulation of agronomically important traits such as yield, quality, disease resistance and stress tolerance. In the end, plant breeding programs through epigenome editing may help not only to expand the use of limited genetic resources but also to alleviate consumers' concerns about genetically manipulated crops.
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Affiliation(s)
- Hosub Shin
- Department of Agriculture, Forestry and Bioresources, College of Agriculture and Life Sciences, Seoul National University, 08826, Seoul, South Korea.,Plant Genomics and Breeding Institute, Seoul National University, 08826, Seoul, South Korea
| | - Woo Lee Choi
- Department of Agriculture, Forestry and Bioresources, College of Agriculture and Life Sciences, Seoul National University, 08826, Seoul, South Korea.,Plant Genomics and Breeding Institute, Seoul National University, 08826, Seoul, South Korea
| | - Joo Young Lim
- Department of Agriculture, Forestry and Bioresources, College of Agriculture and Life Sciences, Seoul National University, 08826, Seoul, South Korea
| | - Jin Hoe Huh
- Department of Agriculture, Forestry and Bioresources, College of Agriculture and Life Sciences, Seoul National University, 08826, Seoul, South Korea. .,Plant Genomics and Breeding Institute, Seoul National University, 08826, Seoul, South Korea. .,Research Institute of Agriculture and Life Sciences, Seoul National University, 08826, Seoul, South Korea.
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12
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Nelson JP, Selin CL, Scott CT. Toward Anticipatory Governance of Human Genome Editing: A Critical Review of Scholarly Governance Discourse. JOURNAL OF RESPONSIBLE INNOVATION 2021; 8:382-420. [PMID: 35281674 PMCID: PMC8916747 DOI: 10.1080/23299460.2021.1957579] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 07/14/2021] [Indexed: 05/04/2023]
Abstract
The rapid development of human genome editing (HGE) techniques evokes an urgent need for forward-looking deliberation regarding the aims, processes, and governance of research. The framework of anticipatory governance (AG) may serve this need. This article reviews scholarly discourse about HGE through an AG lens, aiming to identify gaps in discussion and practice and suggest how AG efforts may fill them. Discourse on HGE has insufficiently reckoned with the institutional and systemic contexts, inputs, and implications of HGE work, to the detriment of its ability to prepare for a variety of possible futures and pursue socially desirable ones. More broadly framed and inclusive efforts in foresight and public engagement, focused not only upon the in-principle permissibility of HGE activities but upon the contexts of such work, may permit improved identification of public values relevant to HGE and of actions by which researchers, funders, policymakers, and publics may promote them.
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Affiliation(s)
- John P. Nelson
- School for the Future of Innovation in Society, Arizona State University, 1120 South Cady Mall, Tempe, Arizona 85287-5603
| | - Cynthia L. Selin
- School for the Future of Innovation in Society/Consortium for Science, Policy & Outcomes, Arizona State University, 1120 South Cady Mall, Tempe, Arizona 85287-5603
| | - Christopher T. Scott
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030-3411
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13
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Gabriel CH, Del Olmo M, Zehtabian A, Jäger M, Reischl S, van Dijk H, Ulbricht C, Rakhymzhan A, Korte T, Koller B, Grudziecki A, Maier B, Herrmann A, Niesner R, Zemojtel T, Ewers H, Granada AE, Herzel H, Kramer A. Live-cell imaging of circadian clock protein dynamics in CRISPR-generated knock-in cells. Nat Commun 2021; 12:3796. [PMID: 34145278 PMCID: PMC8213786 DOI: 10.1038/s41467-021-24086-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 05/25/2021] [Indexed: 02/06/2023] Open
Abstract
The cell biology of circadian clocks is still in its infancy. Here, we describe an efficient strategy for generating knock-in reporter cell lines using CRISPR technology that is particularly useful for genes expressed transiently or at low levels, such as those coding for circadian clock proteins. We generated single and double knock-in cells with endogenously expressed PER2 and CRY1 fused to fluorescent proteins allowing us to simultaneously monitor the dynamics of CRY1 and PER2 proteins in live single cells. Both proteins are highly rhythmic in the nucleus of human cells with PER2 showing a much higher amplitude than CRY1. Surprisingly, CRY1 protein is nuclear at all circadian times indicating the absence of circadian gating of nuclear import. Furthermore, in the nucleus of individual cells CRY1 abundance rhythms are phase-delayed (~5 hours), and CRY1 levels are much higher (>5 times) compared to PER2 questioning the current model of the circadian oscillator.
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Affiliation(s)
- Christian H Gabriel
- Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Laboratory of Chronobiology, Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
| | - Marta Del Olmo
- Institute for Theoretical Biology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Amin Zehtabian
- Institute for Chemistry and Biochemistry, Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Marten Jäger
- Berlin Institute of Health (BIH) Core Genomics Facility, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Silke Reischl
- Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Laboratory of Chronobiology, Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
| | - Hannah van Dijk
- Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Laboratory of Chronobiology, Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
| | - Carolin Ulbricht
- Immune Dynamics, Rheumatology and Clinical Immunology, Charité - Universitätsmedizin Berlin, Berlin, Germany
- Immune Dynamics, Deutsches Rheuma-Forschungszentrum (DRFZ), a Leibniz Institute, Berlin, Germany
| | - Asylkhan Rakhymzhan
- Biophysical Analytics, Deutsches Rheuma-Forschungszentrum (DRFZ), a Leibniz Institute, Berlin, Germany
| | - Thomas Korte
- Molecular Biophysics, Department of Biology, Humboldt Universität zu Berlin, Berlin, Germany
| | - Barbara Koller
- Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Laboratory of Chronobiology, Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
| | - Astrid Grudziecki
- Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Laboratory of Chronobiology, Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
| | - Bert Maier
- Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Laboratory of Chronobiology, Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
| | - Andreas Herrmann
- Molecular Biophysics, Department of Biology, Humboldt Universität zu Berlin, Berlin, Germany
| | - Raluca Niesner
- Biophysical Analytics, Deutsches Rheuma-Forschungszentrum (DRFZ), a Leibniz Institute, Berlin, Germany
- Dynamic and Functional in vivo Imaging, Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | - Tomasz Zemojtel
- Berlin Institute of Health (BIH) Core Genomics Facility, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Helge Ewers
- Institute for Chemistry and Biochemistry, Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Adrián E Granada
- Charité Comprehensive Cancer Center, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Hanspeter Herzel
- Institute for Theoretical Biology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Achim Kramer
- Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Laboratory of Chronobiology, Berlin, Germany.
- Berlin Institute of Health (BIH), Berlin, Germany.
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14
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Tarakanchikova YV, Linnik DS, Mashel T, Muslimov AR, Pavlov S, Lepik KV, Zyuzin MV, Sukhorukov GB, Timin AS. Boosting transfection efficiency: A systematic study using layer-by-layer based gene delivery platform. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2021; 126:112161. [PMID: 34082966 DOI: 10.1016/j.msec.2021.112161] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 04/26/2021] [Accepted: 04/28/2021] [Indexed: 12/24/2022]
Abstract
Nowadays, the nanoparticle-based delivery approach is becoming more and more attractive in gene therapy due to its low toxicity and immunogenicity, sufficient packaging capacity, targeting, and straightforward, low-cost, large-scale good manufacturing practice (GMP) production. A number of research works focusing on multilayer structures have explored different factors and parameters that can affect the delivery efficiency of pDNA. However, there are no systematic studies on the performance of these structures for enhanced gene delivery regarding the gene loading methods, the use of additional organic components and cell/particle incubation conditions. Here, we conducted a detailed analysis of different parameters such as (i) strategy for loading pDNA into carriers, (ii) incorporating both pDNA and organic additives within one carrier and (iii) variation of cell/particle incubation conditions, to evaluate their influence on the efficiency of pDNA delivery with multilayer structures consisting of inorganic cores and polymer layers. Our results reveal that an appropriate combination of all these parameters leads to the development of optimized protocols for high transfection efficiency, compared to the non-optimized process (> 70% vs. < 7%), and shows a good safety profile. In conclusion, we provide the proof-of-principle that these multilayer structures with the developed parameters are a promising non-viral platform for an efficient delivery of nucleic acids.
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Affiliation(s)
- Yana V Tarakanchikova
- Peter the Great St. Petersburg Polytechnic University, Polytechnicheskaya, 29, 195251 St. Petersburg, Russian Federation; Nanobiotechnology Laboratory, St. Petersburg Academic University, 194021 St. Petersburg, Russian Federation
| | - Dmitrii S Linnik
- Peter the Great St. Petersburg Polytechnic University, Polytechnicheskaya, 29, 195251 St. Petersburg, Russian Federation
| | - Tatiana Mashel
- Peter the Great St. Petersburg Polytechnic University, Polytechnicheskaya, 29, 195251 St. Petersburg, Russian Federation; Department of Applied Optics, ITMO University, Kronverkskiy pr. 49, 197101 St. Petersburg, Russian Federation
| | - Albert R Muslimov
- Nanobiotechnology Laboratory, St. Petersburg Academic University, 194021 St. Petersburg, Russian Federation
| | - Sergey Pavlov
- Ioffe Institute, Politekhnicheskaya Ulitsa, 26, 194021 St. Petersburg, Russian Federation
| | - Kirill V Lepik
- R.M. Gorbacheva Research Institute for Pediatric Oncology, Hematology and Transplantation, Pavlov University, Lev Tolstoy str., 6/8, 197022 St. Petersburg, Russian Federation
| | - Mikhail V Zyuzin
- Department of Physics and Engineering, ITMO University, Lomonosova 9, 191002 St. Petersburg, Russian Federation
| | - Gleb B Sukhorukov
- Skolkovo Institute of Science and Technology, 143026 Moscow, Russian Federation; School of Engineering and Material Science, Queen Mary University of London, London, United Kingdom.
| | - Alexander S Timin
- Peter the Great St. Petersburg Polytechnic University, Polytechnicheskaya, 29, 195251 St. Petersburg, Russian Federation; National Research Tomsk Polytechnic University, Lenin Avenue, 30, 634050 Tomsk, Russian Federation.
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15
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Kalidasan V, Theva Das K. Is Malaysia Ready for Human Gene Editing: A Regulatory, Biosafety and Biosecurity Perspective. Front Bioeng Biotechnol 2021; 9:649203. [PMID: 33777918 PMCID: PMC7992004 DOI: 10.3389/fbioe.2021.649203] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 02/16/2021] [Indexed: 01/09/2023] Open
Abstract
Gene editing platforms have revolutionized the field of genetics with a direct impact on the public health system. Although there are apparent benefits, it is often accompanied by public debates over its uncertainties and risks. In the Malaysian context, modern biotechnology has raised questions about how to best govern gene editing in regulations, biosafety, and biosecurity. Even though standards and guidelines on stem cell and cell-based therapies have been developed, there are no appropriate legal frameworks available for gene editing yet. Nevertheless, biosafety regulations were established to balance promoting biotechnology and protecting against their potential environmental and human health risks. There is also a need to address the potential of genetically modified organisms (GMOs) as bioweapons. Numerous frameworks from several international organizations may provide valuable input in formulating documents on gene editing. By establishing comprehensive guidelines, legal policies, and standards to tackle the challenges and risks associated with gene editing, Malaysia can successfully apply this modern technology in this country.
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Affiliation(s)
| | - Kumitaa Theva Das
- Infectomics Cluster, Advanced Medical and Dental Institute, Universiti Sains Malaysia, Kepala Batas, Malaysia
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16
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Doroftei B, Ilie OD, Puiu M, Ciobica A, Ilea C. Mini-Review Regarding the Applicability of Genome Editing Techniques Developed for Studying Infertility. Diagnostics (Basel) 2021; 11:diagnostics11020246. [PMID: 33562517 PMCID: PMC7915733 DOI: 10.3390/diagnostics11020246] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 02/01/2021] [Accepted: 02/02/2021] [Indexed: 11/16/2022] Open
Abstract
Infertility is a highly debated topic today. It has been long hypothesized that infertility has an idiopathic cause, but recent studies demonstrated the existence of a genetic substrate. Fortunately, the methods of editing the human genome proven to be revolutionary. Following research conducted, we identified a total of 21 relevant studies; 14 were performed on mice, 5 on zebrafish and 2 on rats. We concluded that over forty-four genes in total are dispensable for fertility in both sexes without affecting host homeostasis. However, there are genes whose loss-of-function induces moderate to severe phenotypic changes in both sexes. There were situations in which the authors reported infertility, exhibited by the experimental model, or other pathologies such as cryptorchidism, cataracts, or reduced motor activity. Overall, zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9 are techniques that offer a wide range of possibilities for studying infertility, even to create mutant variants. It can be concluded that ZFNs, TALENs, and CRISPR/Cas9 are crucial tools in biomedical research.
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Affiliation(s)
- Bogdan Doroftei
- Faculty of Medicine, University of Medicine and Pharmacy “Grigore T. Popa”, University Street, no 16, 700115 Iasi, Romania; (B.D.); (C.I.)
- Clinical Hospital of Obstetrics and Gynecology “Cuza Voda”, Cuza Voda Street, no 34, 700038 Iasi, Romania
- Origyn Fertility Center, Palace Street, no 3C, 700032 Iasi, Romania
| | - Ovidiu-Dumitru Ilie
- Department of Biology, Faculty of Biology, “Alexandru Ioan Cuza” University, Carol I Avenue, no 20A, 700505 Iasi, Romania;
- Correspondence:
| | - Maria Puiu
- Department of Microscopic Morphology, Faculty of Medicine, University of Medicine and Pharmacy “Victor Babeș”, Eftimie Murgu Square, no 2, 300041 Timișoara, Romania;
| | - Alin Ciobica
- Department of Biology, Faculty of Biology, “Alexandru Ioan Cuza” University, Carol I Avenue, no 20A, 700505 Iasi, Romania;
| | - Ciprian Ilea
- Faculty of Medicine, University of Medicine and Pharmacy “Grigore T. Popa”, University Street, no 16, 700115 Iasi, Romania; (B.D.); (C.I.)
- Clinical Hospital of Obstetrics and Gynecology “Cuza Voda”, Cuza Voda Street, no 34, 700038 Iasi, Romania
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17
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Abstract
Three-dimensional organoids have been widely used for developmental and disease modeling. Organoids are derived from both adult and pluripotent stem cells. Various types are available for mimicking almost all major organs and tissues in the mouse and human. While culture protocols for stepwise differentiation and long-term expansion are well established, methods for genetic manipulation in organoids still need further standardization. In this review, we summarized different methods for organoid genetics and provide the pros and cons of each method for designing an optimal strategy.
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18
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Mashel TV, Tarakanchikova YV, Muslimov AR, Zyuzin MV, Timin AS, Lepik KV, Fehse B. Overcoming the delivery problem for therapeutic genome editing: Current status and perspective of non-viral methods. Biomaterials 2020; 258:120282. [DOI: 10.1016/j.biomaterials.2020.120282] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 07/22/2020] [Accepted: 08/01/2020] [Indexed: 12/11/2022]
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19
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Bishop RP, Odongo D, Ahmed J, Mwamuye M, Fry LM, Knowles DP, Nanteza A, Lubega G, Gwakisa P, Clausen PH, Obara I. A review of recent research on Theileria parva: Implications for the infection and treatment vaccination method for control of East Coast fever. Transbound Emerg Dis 2020; 67 Suppl 1:56-67. [PMID: 32174044 DOI: 10.1111/tbed.13325] [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: 03/26/2019] [Revised: 07/17/2019] [Accepted: 08/05/2019] [Indexed: 12/29/2022]
Abstract
The infection and treatment (ITM) live vaccination method for control of Theileria parva infection in cattle is increasingly being adopted, particularly in Maasai pastoralist systems. Several studies indicate positive impacts on human livelihoods. Importantly, the first detailed protocol for live vaccine production at scale has recently been published. However, quality control and delivery issues constrain vaccination sustainability and deployment. There is evidence that the distribution of T. parva is spreading from endemic areas in East Africa, North into Southern Sudan and West into Cameroon, probably as a result of anthropogenic movement of cattle. It has also recently been demonstrated that in Kenya, T. parva derived from cape buffalo can 'breakthrough' the immunity induced by ITM. However, in Tanzania, breakthrough has not been reported in areas where cattle co-graze with buffalo. It has been confirmed that buffalo in northern Uganda national parks are not infected with T. parva and R. appendiculatus appears to be absent, raising issues regarding vector distribution. Recently, there have been multiple field population genetic studies using variable number tandem repeat (VNTR) sequences and sequencing of antigen genes encoding targets of CD8+ T-cell responses. The VNTR markers generally reveal high levels of diversity. The antigen gene sequences present within the trivalent Muguga cocktail are relatively conserved among cattle transmissible T. parva populations. By contrast, greater genetic diversity is present in antigen genes from T. parva of buffalo origin. There is also evidence from several studies for transmission of components of stocks present within the Muguga cocktail, into field ticks and cattle following induction of a carrier state by immunization. In the short term, this may increase live vaccine effectiveness, through a more homogeneous challenge, but the long-term consequences are unknown.
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Affiliation(s)
- Richard P Bishop
- Department of Veterinary Microbiology & Pathology, Washington State University, Pullman, WA, USA
| | - David Odongo
- School of Biological Sciences, University of Nairobi, Nairobi, Kenya
| | - Jabbar Ahmed
- Institute for Parasitology and Tropical Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | - Micky Mwamuye
- Institute for Parasitology and Tropical Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | - Lindsay M Fry
- Department of Veterinary Microbiology & Pathology, Washington State University, Pullman, WA, USA.,Animal Disease Research Unit, Agricultural Research Service, US Department of Agriculture, Pullman, WA, USA
| | - Donald P Knowles
- Department of Veterinary Microbiology & Pathology, Washington State University, Pullman, WA, USA
| | - Anne Nanteza
- College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | - George Lubega
- College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | - Paul Gwakisa
- Genome Science Laboratory, College of Veterinary Medicine and Biomedical Sciences, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Peter-Henning Clausen
- Institute for Parasitology and Tropical Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | - Isaiah Obara
- Institute for Parasitology and Tropical Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
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20
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Abstract
In celebration of the 20th anniversary of Nature Reviews Genetics, we asked 12 leading researchers to reflect on the key challenges and opportunities faced by the field of genetics and genomics. Keeping their particular research area in mind, they take stock of the current state of play and emphasize the work that remains to be done over the next few years so that, ultimately, the benefits of genetic and genomic research can be felt by everyone. To celebrate the first 20 years of Nature Reviews Genetics, we asked 12 leading scientists to reflect on the key challenges and opportunities faced by the field of genetics and genomics. Amy L. McGuire is the Leon Jaworski Professor of Biomedical Ethics and Director of the Center for Medical Ethics and Health Policy at Baylor College of Medicine. She has received numerous teaching awards at Baylor College of Medicine, was recognized by the Texas Executive Women as a Woman on the Move in 2016 and was invited to give a TedMed talk titled “There is No Genome for the Human Spirit” in 2014. In 2020, she was elected as a Hastings Center Fellow. Her research focuses on ethical and policy issues related to emerging technologies, with a particular focus on genomic research, personalized medicine and the clinical integration of novel neurotechnologies. Stacey Gabriel is the Senior Director of the Genomics Platform at the Broad Institute since 2012 and has led platform development, execution and operation since its founding. She is Chair of Institute Scientists and serves on the institute’s executive leadership team. She is widely recognized as a leader in genomic technology and project execution. She has led the Broad’s contributions to numerous flagship projects in human genetics, including the International HapMap Project, the 1000 Genomes Project, The Cancer Genome Atlas, the National Heart, Lung, and Blood Institute’s Exome Sequencing Project and the TOPMed programme. She is Principal Investigator of the Broad’s All of Us (AoU) Genomics Center and serves on the AoU Program Steering Committee. Sarah A. Tishkoff is the David and Lyn Silfen University Associate Professor in Genetics and Biology at the University of Pennsylvania, Philadelphia, USA, and holds appointments in the School of Medicine and the School of Arts and Sciences. She is a member of the US National Academy of Sciences and a recipient of an NIH Pioneer Award, a David and Lucile Packard Career Award, a Burroughs/Wellcome Fund Career Award and an American Society of Human Genetics Curt Stern Award. Her work focuses on genomic variation in Africa, human evolutionary history, the genetic basis of adaptation and phenotypic variation in Africa, and the genetic basis of susceptibility to infectious disease in Africa. Ambroise Wonkam is Professor of Medical Genetics, Director of GeneMAP (Genetic Medicine of African Populations Research Centre) and Deputy Dean Research in the Faculty of Health Sciences, University of Cape Town, South Africa. He has successfully led numerous NIH- and Wellcome Trust-funded projects over the past decade to investigate clinical variability in sickle cell disease, hearing impairment genetics and the return of individual findings in genetic research in Africa. He won the competitive Clinical Genetics Society International Award for 2014 from the British Society of Genetic Medicine. He is president of the African Society of Human Genetics. Aravinda Chakravarti is Director of the Center for Human Genetics and Genomics, the Muriel G. and George W. Singer Professor of Neuroscience and Physiology, and Professor of Medicine at New York University School of Medicine. He is an elected member of the US National Academy of Sciences, the US National Academy of Medicine and the Indian National Science Academy. He has been a key participant in the Human Genome Project, the International HapMap Project and the 1000 Genomes Project. His research attempts to understand the molecular basis of multifactorial disease. He was awarded the 2013 William Allan Award by the American Society of Human Genetics and the 2018 Chen Award by the Human Genome Organization. Eileen E. M. Furlong is Head of the Genome Biology Department at the European Molecular Biology Laboratory (EMBL) and a member of the EMBL Directorate. She is an elected member of the European Molecular Biology Organization (EMBO) and the Academia Europaea, and a European Research Council (ERC) advanced investigator. Her group dissects fundamental principles of how the genome is regulated and how it drives cell fate decisions during embryonic development, including how developmental enhancers are organized and function within the 3D nucleus. Her work combines genetics, (single-cell) genomics, imaging and computational approaches to understand these processes. Her research has advanced the development of genomic methods for use in complex multicellular organisms. Barbara Treutlein is Associate Professor of Quantitative Developmental Biology in the Department of Biosystems Science and Engineering of ETH Zurich in Basel, Switzerland. Her group uses and develops single-cell genomics approaches in combination with stem cell-based 2D and 3D culture systems to study how human organs develop and regenerate and how cell fate is regulated. For her work, Barbara has received multiple awards, including the Friedmund Neumann Prize of the Schering Foundation, the Dr. Susan Lim Award for Outstanding Young Investigator of the International Society of Stem Cell Research and the EMBO Young Investigator Award. Alexander Meissner is a scientific member of the Max Planck Society and currently Managing Director of the Max Planck Institute (MPI) for Molecular Genetics in Berlin, Germany. He heads the Department of Genome Regulation and is a visiting scientist in the Department of Stem Cell and Regenerative Biology at Harvard University. Before his move to the MPI, he was a tenured professor at Harvard University and a senior associate member of the Broad Institute, where he co-directed the epigenomics programme. In 2018, he was elected as an EMBO member. His laboratory uses genomic tools to study developmental and disease biology with a particular focus on epigenetic regulation. Howard Y. Chang is the Virginia and D. K. Ludwig Professor of Cancer Genomics at Stanford University and an investigator at the Howard Hughes Medical Institute. He is a physician–scientist who has focused on deciphering the hidden information in the non-coding genome. His laboratory is best known for studies of long non-coding RNAs in gene regulation and development of new epigenomic technologies. He is an elected member of the US National Academy of Sciences, the US National Academy of Medicine, and the American Academy of Arts and Sciences. Núria López-Bigas is ICREA research Professor at the Institute for Research in Biomedicine and Associate Professor at the University Pompeu Fabra. She obtained an ERC Consolidator Grant in 2015 and was elected as an EMBO member in 2016. Her work has been recognized with the prestigious Banc de Sabadell Award for Research in Biomedicine, the Catalan National Award for Young Research Talent and the Career Development Award from the Human Frontier Science Program. Her research focuses on the identification of cancer driver mutations, genes and pathways across tumour types and in understanding the mutational processes that lead to the accumulation of mutations in cancer cells. Eran Segal is Professor in the Department of Computer Science and Applied Mathematics at the Weizmann Institute of Science, heading a multidisciplinary laboratory with extensive experience in machine learning, computational biology and analysis of heterogeneous high-throughput genomic data. His research focuses on the microbiome, nutrition and genetics, and their effect on health and disease and aims to develop personalized medicine based on big data from human cohorts. He has published more than 150 publications and received several awards and honours for his work, including the Overton and the Michael Bruno awards. He was recently elected as an EMBO member and as a member of the Israel Young Academy. Jin-Soo Kim is Director of the Center for Genome Engineering in the Institute for Basic Science in Daejon, South Korea. He has received numerous awards, including the 2017 Asan Award in Medicine, the 2017 Yumin Award in Science and the 2019 Research Excellence Award (Federation of Asian and Oceanian Biochemists and Molecular Biologists). He was featured as one of ten Science Stars of East Asia in Nature (558, 502–510 (2018)) and has been recognized as a highly cited researcher by Clarivate Analytics since 2018. His work focuses on developing tools for genome editing in biomedical research.
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21
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Almeida MJ, Matos A. Designer Nucleases: Gene-Editing Therapies using CCR5 as an Emerging Target in HIV. Curr HIV Res 2020; 17:306-323. [PMID: 31652113 DOI: 10.2174/1570162x17666191025112918] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 10/16/2019] [Accepted: 10/18/2019] [Indexed: 02/08/2023]
Abstract
Acquired Immunodeficiency Syndrome (AIDS), caused by the Human Immunodeficiency Virus (HIV), is a life-threatening disorder that persists worldwide as a severe health problem. Since it was linked with the HIV attachment process, the Chemokine receptor, CCR5, has been at the development leading edge of several gene-based therapies. Given the shortcomings of the current antiretroviral treatment procedure and the non-availability of a licensed vaccine, the aptitude to modify complex genomes with Designer Nucleases has had a noteworthy impact on biotechnology. Over the last years, ZFN, TALEN and CRISPR/Cas9 gene-editing technology have appeared as a promising solution that mimics the naturally occurring CCR5/Δ32 mutation and permanently guarantees the absence of CCR5-expression on the surface of HIV target-cells, leading to a continuous resistance to the virus entry and, ultimately, proving that cellular immunization from infection could be, in fact, a conceivable therapeutic approach to finally achieve the long-awaited functional cure of HIV.
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Affiliation(s)
- Maria João Almeida
- Laboratory of Microbiology, Faculty of Pharmacy, University of Coimbra, Coimbra, Portugal
| | - Ana Matos
- Laboratory of Microbiology, Faculty of Pharmacy, University of Coimbra, Coimbra, Portugal.,Research Centre on Chemical Processes Engineering and Forest Products (CIEPQF), Faculty of Pharmacy, University of Coimbra, Coimbra, Portugal
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22
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Ding M, Tegel H, Sivertsson Å, Hober S, Snijder A, Ormö M, Strömstedt PE, Davies R, Holmberg Schiavone L. Secretome-Based Screening in Target Discovery. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2020; 25:535-551. [PMID: 32425085 PMCID: PMC7309359 DOI: 10.1177/2472555220917113] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 03/02/2020] [Accepted: 03/10/2020] [Indexed: 12/15/2022]
Abstract
Secreted proteins and their cognate plasma membrane receptors regulate human physiology by transducing signals from the extracellular environment into cells resulting in different cellular phenotypes. Systematic use of secretome proteins in assays enables discovery of novel biology and signaling pathways. Several secretome-based phenotypic screening platforms have been described in the literature and shown to facilitate target identification in drug discovery. In this review, we summarize the current status of secretome-based screening. This includes annotation, production, quality control, and sample management of secretome libraries, as well as how secretome libraries have been applied to discover novel target biology using different disease-relevant cell-based assays. A workflow for secretome-based screening is shared based on the AstraZeneca experience. The secretome library offers several advantages compared with other libraries used for target discovery: (1) screening using a secretome library directly identifies the active protein and, in many cases, its cognate receptor, enabling a rapid understanding of the disease pathway and subsequent formation of target hypotheses for drug discovery; (2) the secretome library covers significant areas of biological signaling space, although the size of this library is small; (3) secretome proteins can be added directly to cells without additional manipulation. These factors make the secretome library ideal for testing in physiologically relevant cell types, and therefore it represents an attractive approach to phenotypic target discovery.
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Affiliation(s)
- Mei Ding
- Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Hanna Tegel
- Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH, Royal Institute of Technology, Stockholm, Sweden
| | - Åsa Sivertsson
- Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH, Royal Institute of Technology, Stockholm, Sweden
| | - Sophia Hober
- Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH, Royal Institute of Technology, Stockholm, Sweden
| | - Arjan Snijder
- Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Mats Ormö
- Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Per-Erik Strömstedt
- Mechanistic Biology and Profiling, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Rick Davies
- Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge, UK
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23
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Han HA, Pang JKS, Soh BS. Mitigating off-target effects in CRISPR/Cas9-mediated in vivo gene editing. J Mol Med (Berl) 2020; 98:615-632. [PMID: 32198625 PMCID: PMC7220873 DOI: 10.1007/s00109-020-01893-z] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 01/28/2020] [Accepted: 02/28/2020] [Indexed: 12/11/2022]
Abstract
The rapid advancement of genome editing technologies has opened up new possibilities in the field of medicine. Nuclease-based techniques such as the CRISPR/Cas9 system are now used to target genetically linked disorders that were previously hard-to-treat. The CRISPR/Cas9 gene editing approach wields several advantages over its contemporary editing systems, notably in the ease of component design, implementation and the option of multiplex genome editing. While results from the early phase clinical trials have been encouraging, the small patient population recruited into these trials hinders a conclusive assessment on the safety aspects of the CRISPR/Cas9 therapy. Potential safety concerns include the lack of fidelity in the CRISPR/Cas9 system which may lead to unintended DNA modifications at non-targeted gene loci. This review focuses modifications to the CRISPR/Cas9 components that can mitigate off-target effects in in vitro and preclinical models and its translatability to gene therapy in patient populations.
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Affiliation(s)
- Hua Alexander Han
- Disease Modeling and Therapeutics Laboratory, A*STAR Institute of Molecular and Cell Biology, 61 Biopolis Drive Proteos, Singapore, 138673, Singapore
| | - Jeremy Kah Sheng Pang
- Disease Modeling and Therapeutics Laboratory, A*STAR Institute of Molecular and Cell Biology, 61 Biopolis Drive Proteos, Singapore, 138673, Singapore
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore, 117543, Singapore
| | - Boon-Seng Soh
- Disease Modeling and Therapeutics Laboratory, A*STAR Institute of Molecular and Cell Biology, 61 Biopolis Drive Proteos, Singapore, 138673, Singapore.
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore, 117543, Singapore.
- Key Laboratory for Major Obstetric Disease of Guangdong Province, The Third Affliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China.
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24
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Abstract
Base editing is emerging as a potent new strategy to achieve precise gene editing. By combining different nucleobase deaminases with Cas9 or Cpf1 proteins, several base editors have recently been developed to achieve targeted base conversions in different genomic contexts. Importantly, base editors have been successfully applied in animals, plants, and bacteria to induce precise substitutions at the single-base level with high efficiency. In this review, we summarize recent progress in the development and application of base editors and discuss some of the future directions of the technology.
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Affiliation(s)
- Bei Yang
- 1 Shanghai Institute for Advanced Immunochemical Studies and Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Li Yang
- 2 Chinese Academy of Sciences (CAS) Key Laboratory of Computational Biology, CAS-Max Planck Gesellschaft Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China; Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China.,3 School of Life Science and Technology, ShanghaiTech University, Shanghai, China; Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Jia Chen
- 3 School of Life Science and Technology, ShanghaiTech University, Shanghai, China; Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China.,4 CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
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25
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Hanss Z, Boussaad I, Jarazo J, Schwamborn JC, Krüger R. Quality Control Strategy for CRISPR-Cas9-Based Gene Editing Complicated by a Pseudogene. Front Genet 2020; 10:1297. [PMID: 31998363 PMCID: PMC6961559 DOI: 10.3389/fgene.2019.01297] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2019] [Accepted: 11/25/2019] [Indexed: 12/02/2022] Open
Abstract
CRISPR-Cas9 mediated gene editing in induced pluripotent stem cells became an efficient tool to investigate biological mechanisms underlying genetic-driven diseases while accounting for the respective genetic background. This technique relies on the targeting of a specific nucleotide sequence present in the gene of interest. Therefore, the gene editing of some genes can be complicated by non-coding pseudogenes presenting a high homology of sequence with their respective genes. Among them, GBA is raising special interest because of its implication as the most common genetic risk factor for Parkinson’s disease. In this study, we present an easy-to-use CRISPR-Cas9 gene editing strategy allowing for specific editing of point mutations in a gene without genetic alteration of its pseudogene exemplified by the correction or insertion of the common N370S mutation in GBA. A quality control strategy by combined fluorescence and PCR-based screening allows the early identification of correctly edited clones with unambiguous identification of the status of its pseudogene, GBAP1. Successful gene editing was confirmed by functional validation. Our work presents the first CRISPR-Cas9 based editing of a point mutation in GBA and paves the way for technically demanding gene engineering due to the presence of pseudogenes.
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Affiliation(s)
- Zoé Hanss
- Clinical and Experimental Neuroscience, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Belvaux, Luxembourg
| | - Ibrahim Boussaad
- Clinical and Experimental Neuroscience, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Belvaux, Luxembourg
| | - Javier Jarazo
- Developmental and Cellular Biology, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Belvaux, Luxembourg
| | - Jens C Schwamborn
- Developmental and Cellular Biology, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Belvaux, Luxembourg
| | - Rejko Krüger
- Clinical and Experimental Neuroscience, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Belvaux, Luxembourg.,Parkinson Research Clinic, Centre Hospitalier de Luxembourg (CHL), Luxembourg, Luxembourg.,Transversal Translational Medicine, Luxembourg Institute of Health, Strassen, Luxembourg
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26
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Morisaka H, Yoshimi K, Okuzaki Y, Gee P, Kunihiro Y, Sonpho E, Xu H, Sasakawa N, Naito Y, Nakada S, Yamamoto T, Sano S, Hotta A, Takeda J, Mashimo T. CRISPR-Cas3 induces broad and unidirectional genome editing in human cells. Nat Commun 2019; 10:5302. [PMID: 31811138 PMCID: PMC6897959 DOI: 10.1038/s41467-019-13226-x] [Citation(s) in RCA: 93] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 10/29/2019] [Indexed: 12/21/2022] Open
Abstract
Although single-component Class 2 CRISPR systems, such as type II Cas9 or type V Cas12a (Cpf1), are widely used for genome editing in eukaryotic cells, the application of multi-component Class 1 CRISPR has been less developed. Here we demonstrate that type I-E CRISPR mediates distinct DNA cleavage activity in human cells. Notably, Cas3, which possesses helicase and nuclease activity, predominantly triggered several thousand base pair deletions upstream of the 5'-ARG protospacer adjacent motif (PAM), without prominent off-target activity. This Cas3-mediated directional and broad DNA degradation can be used to introduce functional gene knockouts and knock-ins. As an example of potential therapeutic applications, we show Cas3-mediated exon-skipping of the Duchenne muscular dystrophy (DMD) gene in patient-induced pluripotent stem cells (iPSCs). These findings broaden our understanding of the Class 1 CRISPR system, which may serve as a unique genome editing tool in eukaryotic cells distinct from the Class 2 CRISPR system.
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Affiliation(s)
- Hiroyuki Morisaka
- Department of Genome Biology, Graduate School of Medicine, Osaka University, Osaka, 565-0871, Japan
- Department of Dermatology, Kochi Medical School, Kochi University, Kochi, 783-8505, Japan
| | - Kazuto Yoshimi
- Genome Editing Research and Development Center, Graduate School of Medicine, Osaka University, Osaka, 565-0871, Japan
- Institute of Experimental Animal Sciences, Graduate School of Medicine, Osaka University, Osaka, 565-0871, Japan
- Division of Animal Genetics, Laboratory Animal Research Center, Institute of Medical Science, The University of Tokyo, Tokyo, 108-8639, Japan
| | - Yuya Okuzaki
- Center for iPS Cell Research and Application (CiRA), Department of Clinical Application, Kyoto University, Kyoto, 606-8507, Japan
| | - Peter Gee
- Center for iPS Cell Research and Application (CiRA), Department of Clinical Application, Kyoto University, Kyoto, 606-8507, Japan
| | - Yayoi Kunihiro
- Genome Editing Research and Development Center, Graduate School of Medicine, Osaka University, Osaka, 565-0871, Japan
| | - Ekasit Sonpho
- Institute of Experimental Animal Sciences, Graduate School of Medicine, Osaka University, Osaka, 565-0871, Japan
- Department of Biology, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| | - Huaigeng Xu
- Center for iPS Cell Research and Application (CiRA), Department of Clinical Application, Kyoto University, Kyoto, 606-8507, Japan
| | - Noriko Sasakawa
- Center for iPS Cell Research and Application (CiRA), Department of Clinical Application, Kyoto University, Kyoto, 606-8507, Japan
| | - Yuki Naito
- Database Center for Life Science, Mishima, 411-8540, Japan
- National Institute of Genetics, Mishima, 411-8540, Japan
| | - Shinichiro Nakada
- Institute for Advanced Co-Creation Studies, Osaka University, Osaka, 565-0871, Japan
| | - Takashi Yamamoto
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Higashi-Hiroshima, 739-8526, Japan
| | - Shigetoshi Sano
- Department of Dermatology, Kochi Medical School, Kochi University, Kochi, 783-8505, Japan
| | - Akitsu Hotta
- Center for iPS Cell Research and Application (CiRA), Department of Clinical Application, Kyoto University, Kyoto, 606-8507, Japan.
| | - Junji Takeda
- Department of Genome Biology, Graduate School of Medicine, Osaka University, Osaka, 565-0871, Japan.
- Research Institute for Microbial Diseases, Osaka University, Osaka, 565-0871, Japan.
| | - Tomoji Mashimo
- Genome Editing Research and Development Center, Graduate School of Medicine, Osaka University, Osaka, 565-0871, Japan.
- Institute of Experimental Animal Sciences, Graduate School of Medicine, Osaka University, Osaka, 565-0871, Japan.
- Division of Animal Genetics, Laboratory Animal Research Center, Institute of Medical Science, The University of Tokyo, Tokyo, 108-8639, Japan.
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27
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Disulphide-less crotamine is effective for formation of DNA-peptide complex but is unable to improve bovine embryo transfection. ZYGOTE 2019; 28:72-79. [PMID: 31662126 DOI: 10.1017/s0967199419000716] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
This study aimed to investigate the ability of disulphide-less crotamine (dLCr) to complex DNA and to evaluate whether the DNA-dLCr complex is capable of improving transfection in bovine embryos. Three experiments were performed to: (i) evaluate the formation and stability of the DNA-dLCr complex; (ii) assess the dLCr embryotoxicity by exposure of bovine embryos to dLCr; and (iii) assess the efficiency of bovine embryo transfection after microinjection of the DNA-dLCr complex or green fluorescent protein (GFP) plasmid alone (control). DNA complexation by dLCr after 30 min of incubation at 1:100 and 1:50 proportions presented higher efficiency (P < 0.05) than the two controls: native crotamine (NCr) 1:10 and lipofectamine. There was no difference between DNA-dLCr 1:25 and the controls. The DNA-dLCr complexation was evaluated at different proportions and times. In all, at least half of maximum complexation was achieved within the initial 30 min. No embryotoxicity of dLCr was verified after exposure of in vitro fertilized embryos to different concentrations of the peptide. The effectiveness of dLCr to improve exogenous gene expression was evaluated by microinjection of the DNA-dLCr complex into in vitro fertilized zygotes, followed by verification of both embryo development and GFP expression. From embryos microinjected with DNA only, 4.6% and 2.8% expressed the GFP transgene at day 5 and day 7, respectively. The DNA-dLCr complex did not increase the number of GFP-positive embryos. In conclusion, dLCr forms a complex with DNA and its application in in vitro culture is possible. However, the dLCr peptide sequence should be redesigned to improve GFP expression.
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28
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Quintana-Bustamante O, Fañanas-Baquero S, Orman I, Torres R, Duchateau P, Poirot L, Gouble A, Bueren JA, Segovia JC. Gene editing of PKLR gene in human hematopoietic progenitors through 5' and 3' UTR modified TALEN mRNA. PLoS One 2019; 14:e0223775. [PMID: 31618280 PMCID: PMC6795450 DOI: 10.1371/journal.pone.0223775] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Accepted: 09/27/2019] [Indexed: 12/14/2022] Open
Abstract
Pyruvate Kinase Deficiency (PKD) is a rare erythroid metabolic disease caused by mutations in the PKLR gene, which encodes the erythroid specific Pyruvate Kinase enzyme. Erythrocytes from PKD patients show an energetic imbalance and are susceptible to hemolysis. Gene editing of hematopoietic stem cells (HSCs) would provide a therapeutic benefit and improve safety of gene therapy approaches to treat PKD patients. In previous studies, we established a gene editing protocol that corrected the PKD phenotype of PKD-iPSC lines through a TALEN mediated homologous recombination strategy. With the goal of moving toward more clinically relevant stem cells, we aim at editing the PKLR gene in primary human hematopoietic progenitors and hematopoietic stem cells (HPSCs). After nucleofection of the gene editing tools and selection with puromycin, up to 96% colony forming units showed precise integration. However, a low yield of gene edited HPSCs was associated to the procedure. To reduce toxicity while increasing efficacy, we worked on i) optimizing gene editing tools and ii) defining optimal expansion and selection times. Different versions of specific nucleases (TALEN and CRISPR-Cas9) were compared. TALEN mRNAs with 5’ and 3’ added motifs to increase RNA stability were the most efficient nucleases to obtain high gene editing frequency and low toxicity. Shortening ex vivo manipulation did not reduce the efficiency of homologous recombination and preserved the hematopoietic progenitor potential of the nucleofected HPSCs. Lastly, a very low level of gene edited HPSCs were detected after engraftment in immunodeficient (NSG) mice. Overall, we showed that gene editing of the PKLR gene in HPSCs is feasible, although further improvements must to be done before the clinical use of the gene editing to correct PKD.
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Affiliation(s)
- Oscar Quintana-Bustamante
- Division of Hematopoietic Innovative Therapies, Centro de Investigaciones Energéticas Medioambientales y Tecnológicas/Centro de Investigación Biomédica en Red de Enfermedades Raras (CIEMAT/CIBERER), Madrid, Spain
- Instituto de Investigación Sanitaria Fundación Jiménez Díaz (IIS-FJD, UAM), Madrid, Spain
- * E-mail:
| | - Sara Fañanas-Baquero
- Division of Hematopoietic Innovative Therapies, Centro de Investigaciones Energéticas Medioambientales y Tecnológicas/Centro de Investigación Biomédica en Red de Enfermedades Raras (CIEMAT/CIBERER), Madrid, Spain
- Instituto de Investigación Sanitaria Fundación Jiménez Díaz (IIS-FJD, UAM), Madrid, Spain
| | - Israel Orman
- Division of Hematopoietic Innovative Therapies, Centro de Investigaciones Energéticas Medioambientales y Tecnológicas/Centro de Investigación Biomédica en Red de Enfermedades Raras (CIEMAT/CIBERER), Madrid, Spain
- Instituto de Investigación Sanitaria Fundación Jiménez Díaz (IIS-FJD, UAM), Madrid, Spain
| | - Raul Torres
- Centro Nacional de Investigaciones Oncológicas (CNIO), Madrid, Spain
- Instituto Josep Carreras, Barcelona, Spain
| | | | | | | | - Juan A. Bueren
- Division of Hematopoietic Innovative Therapies, Centro de Investigaciones Energéticas Medioambientales y Tecnológicas/Centro de Investigación Biomédica en Red de Enfermedades Raras (CIEMAT/CIBERER), Madrid, Spain
- Instituto de Investigación Sanitaria Fundación Jiménez Díaz (IIS-FJD, UAM), Madrid, Spain
| | - Jose C. Segovia
- Division of Hematopoietic Innovative Therapies, Centro de Investigaciones Energéticas Medioambientales y Tecnológicas/Centro de Investigación Biomédica en Red de Enfermedades Raras (CIEMAT/CIBERER), Madrid, Spain
- Instituto de Investigación Sanitaria Fundación Jiménez Díaz (IIS-FJD, UAM), Madrid, Spain
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29
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Sinatti VVC, Gonçalves CAX, Romão-Dumaresq AS. Identification of metabolites identical and similar to drugs as candidates for metabolic engineering. J Biotechnol 2019; 302:67-76. [PMID: 31254549 DOI: 10.1016/j.jbiotec.2019.06.303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 04/20/2019] [Accepted: 06/25/2019] [Indexed: 11/18/2022]
Abstract
Natural compounds and derivatives play an essential role in the pharmaceutical industry, however, the difficulty in resynthesizing natural products or isolate them from the native host, often limit their availability, elevate costs and slow down the pharmaceutical manufacturing process. In this context, application of synthetic biology could enable the efficient production of large amounts of drugs or drug precursors in heterologous microorganisms aiming to accelerate the entire manufacturing process. Considering this perspective, here we developed a pipeline to automatically search for metabolites available in the metabolic space that are structurally similar to worldwide approved drugs. This pipeline involved the in silico screening of metabolites from a metabolic pathway meta-database using both Tanimoto coefficients based on Daylight like fingerprints and Maximum Common Substructure algorithm. The method was successfully applied to identify metabolites sharing essential scaffolds with one or more drugs as potential candidates for metabolic engineering. Three of these metabolites (Festuclavine, Scopolamine, and Baccatin III) were identified as similar to many drugs like Cabergoline, Oxitropium, Paclitaxel and had their metabolic pathways computationally mapped for their production in Saccharomyces cerevisiae with our proprietary pathway design software. These compounds are examples of new opportunities for the application of synthetic biology in pharmaceutical production.
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Affiliation(s)
- Vanessa V C Sinatti
- SENAI Innovation Institute for Biosynthetics, Technology Center for Chemical and Textile Industry, Rio de Janeiro, Brazil.
| | - Carlos Alberto X Gonçalves
- SENAI Innovation Institute for Biosynthetics, Technology Center for Chemical and Textile Industry, Rio de Janeiro, Brazil
| | - Aline S Romão-Dumaresq
- SENAI Innovation Institute for Biosynthetics, Technology Center for Chemical and Textile Industry, Rio de Janeiro, Brazil
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30
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Konno M, Taniguchi M, Ishii H. Significant epitranscriptomes in heterogeneous cancer. Cancer Sci 2019; 110:2318-2327. [PMID: 31187550 PMCID: PMC6676114 DOI: 10.1111/cas.14095] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 06/03/2019] [Accepted: 06/05/2019] [Indexed: 02/06/2023] Open
Abstract
Precision medicine places significant emphasis on techniques for the identification of DNA mutations and gene expression by deep sequencing of gene panels to obtain medical data. However, other diverse information that is not easily readable using bioinformatics, including RNA modifications, has emerged as a novel diagnostic and innovative therapy owing to its multifunctional aspects. It is suggested that this breakthrough innovation might open new avenues for the elucidation of uncharacterized cancer cellular functions to develop more precise medical applications. The functional characteristics and regulatory mechanisms of RNA modifications, ie, the epitranscriptome (ETR), which reflects RNA metabolism, remains unclear, mainly due to detection methods being limited. Recent studies have revealed that N6‐methyl adenosine, the most common modification in mRNA in eukaryotes, is affected in various types of cancer and, in some cases, cancer stem cells, but also affects cellular responses to viral infections. The ETR can control cancer cell fate through mRNA splicing, stability, nuclear export, and translation. Here we report on the recent progress of ETR detection methods, and biological findings regarding the significance of ETR in cancer precision medicine.
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Affiliation(s)
- Masamitsu Konno
- Department of Frontier Science for Cancer and Chemotherapy, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Masateru Taniguchi
- The Institute of Scientific and Industrial Research, Osaka University, Osaka, Japan
| | - Hideshi Ishii
- Department of Medical Data Science, Graduate School of Medicine, Osaka University, Osaka, Japan
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31
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Ormond KE, Bombard Y, Bonham VL, Hoffman-Andrews L, Howard H, Isasi R, Musunuru K, Riggan KA, Michie M, Allyse M. The clinical application of gene editing: ethical and social issues. Per Med 2019; 16:337-350. [DOI: 10.2217/pme-2018-0155] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Gene-editing techniques have progressed rapidly in the past 5 years. There are already ongoing human somatic gene-editing clinical trials for multiple diseases. And there has been one purported scenario of human germline gene editing in late 2018. In this paper, we will review the current state of the technology, discuss the ethical and social issues that surround the various forms of gene editing, as well as review emerging stakeholder data from professionals, the ‘general public’ and individuals and families dealing with genetic diseases potentially treatable by gene editing.
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Affiliation(s)
- Kelly E Ormond
- Department of Genetics & Stanford Center for Biomedical Ethics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Yvonne Bombard
- Institute of Health Policy, Management & Evaluation, University of Toronto; Li Ka Shing Knowledge Institute of St Michael’s Hospital, Toronto, ON, Canada
- Li Ka Shing Knowledge Institute of St Michael’s Hospital, Toronto, ON, Canada
| | - Vence L Bonham
- Social & Behavioral Research Branch, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Lily Hoffman-Andrews
- Penn Center for Inherited Cardiac Disease, Penn Medicine, Philadelphia, PA 19104, USA
| | - Heidi Howard
- Centre for Research Ethics & Bioethics, Uppsala University, Uppsala, Sweden
- Society & Ethics Research, Connecting Science, Wellcome Genome Campus, Cambridge, UK
| | - Rosario Isasi
- Dr J T Macdonald Foundation Department of Human Genetics, Institute of Bioethics & Health Policy, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Kiran Musunuru
- Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, PA 19104, USA
| | - Kirsten A Riggan
- Biomedical Ethics Research Program, Mayo Clinic, Rochester, MN 55905, USA
| | - Marsha Michie
- Department of Bioethics, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Megan Allyse
- Biomedical Ethics Research Program & Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA
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32
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Aksoz M, Albayrak E, Aslan GS, Turan RD, Alyazici LY, Siyah P, Tuysuz EC, Canikyan S, Yucel D, Meric N, Gulbas Z, Sahin F, Kocabas F. c-Myc Inhibitor 10074-G5 Induces Murine and Human Hematopoietic Stem and Progenitor Cell Expansion and HDR Modulator Rad51 Expression. Curr Cancer Drug Targets 2019; 19:479-494. [DOI: 10.2174/1568009618666180905100608] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2017] [Revised: 04/24/2018] [Accepted: 08/25/2018] [Indexed: 12/29/2022]
Abstract
Background:c-Myc plays a major role in the maintenance of glycolytic metabolism and hematopoietic stem cell (HSC) quiescence.Objective:Targeting modulators of HSC quiescence and metabolism could lead to HSC cell cycle entry with concomitant expansion.Methods and Results:Here we show that c-Myc inhibitor 10074-G5 treatment leads to 2-fold increase in murine LSKCD34low HSC compartment post 7 days. In addition, c-Myc inhibition increases CD34+ and CD133+ human HSC number. c-Myc inhibition leads to downregulation of glycolytic and cyclindependent kinase inhibitor (CDKI) gene expression ex vivo and in vivo. In addition, c-Myc inhibition upregulates major HDR modulator Rad51 expression in hematopoietic cells. Besides, c-Myc inhibition does not alter proliferation kinetics of endothelial cells, fibroblasts or adipose-derived mesenchymal stem cells, however, it limits bone marrow derived mesenchymal stem cell proliferation. We further demonstrate that a cocktail of c-Myc inhibitor 10074-G5 along with tauroursodeoxycholic acid (TUDCA) and i-NOS inhibitor L-NIL provides a robust HSC maintenance and expansion ex vivo as evident by induction of all stem cell antigens analyzed. Intriguingly, the cocktail of c-Myc inhibitor 10074-G5, TUDCA and L-NIL improves HDR related gene expression.Conclusion:These findings provide tools to improve ex vivo HSC maintenance and expansion, autologous HSC transplantation and gene editing through modulation of HSC glycolytic and HDR pathways.
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Affiliation(s)
- Merve Aksoz
- Regenerative Biology Research Laboratory, Department of Genetics and Bioengineering, Faculty of Engineering, Yeditepe University, Istanbul, Turkey
| | - Esra Albayrak
- Regenerative Biology Research Laboratory, Department of Genetics and Bioengineering, Faculty of Engineering, Yeditepe University, Istanbul, Turkey
| | - Galip Servet Aslan
- Regenerative Biology Research Laboratory, Department of Genetics and Bioengineering, Faculty of Engineering, Yeditepe University, Istanbul, Turkey
| | - Raife Dilek Turan
- Regenerative Biology Research Laboratory, Department of Genetics and Bioengineering, Faculty of Engineering, Yeditepe University, Istanbul, Turkey
| | - Lamia Yazgi Alyazici
- Regenerative Biology Research Laboratory, Department of Genetics and Bioengineering, Faculty of Engineering, Yeditepe University, Istanbul, Turkey
| | - Pınar Siyah
- Regenerative Biology Research Laboratory, Department of Genetics and Bioengineering, Faculty of Engineering, Yeditepe University, Istanbul, Turkey
| | - Emre Can Tuysuz
- Biotechnology Program, Graduate School of Natural and Applied Sciences, Yeditepe University, 34755, Istanbul, Turkey
| | - Serli Canikyan
- Onkim Stem Cell Technologies, Istanbul Technical University - KOSGEB, Istanbul, Turkey
| | - Dogacan Yucel
- Faculty of Medicine, University of Minnesota, Minneapolis, MN, United States
| | - Neslihan Meric
- Regenerative Biology Research Laboratory, Department of Genetics and Bioengineering, Faculty of Engineering, Yeditepe University, Istanbul, Turkey
| | - Zafer Gulbas
- Bone Marrow Transplantation Center, Anadolu Medical Center, Kocaeli, Turkey
| | - Fikrettin Sahin
- Regenerative Biology Research Laboratory, Department of Genetics and Bioengineering, Faculty of Engineering, Yeditepe University, Istanbul, Turkey
| | - Fatih Kocabas
- Regenerative Biology Research Laboratory, Department of Genetics and Bioengineering, Faculty of Engineering, Yeditepe University, Istanbul, Turkey
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Unexpected genomic rearrangements at targeted loci associated with CRISPR/Cas9-mediated knock-in. Sci Rep 2019; 9:3486. [PMID: 30837594 PMCID: PMC6401152 DOI: 10.1038/s41598-019-40181-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 12/20/2018] [Indexed: 12/26/2022] Open
Abstract
The CRISPR/Cas9 gene editing tool enables accessible and efficient modifications which (re)ignited molecular research in certain species. However, targeted integration of large DNA fragments using CRISPR/Cas9 can still be challenging in numerous models. To systematically compare CRISPR/Cas9’s efficiency to classical homologous recombination (cHR) for insertion of large DNA fragments, we thoroughly performed and analyzed 221 experiments targeting 128 loci in mouse ES cells. Although both technologies proved efficient, CRISPR/Cas9 yielded significantly more positive clones as detected by overlapping PCRs. It also induced unexpected rearrangements around the targeted site, ultimately rendering CRISPR/Cas9 less efficient than cHR for the production of fully validated clones. These data show that CRISPR/Cas9-mediated recombination can induce complex long-range modifications at targeted loci, thus emphasizing the need for thorough characterization of any genetically modified material obtained through CRISPR-mediated gene editing before further functional studies or therapeutic use.
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Anuar ND, Kurscheid S, Field M, Zhang L, Rebar E, Gregory P, Buchou T, Bowles J, Koopman P, Tremethick DJ, Soboleva TA. Gene editing of the multi-copy H2A.B gene and its importance for fertility. Genome Biol 2019; 20:23. [PMID: 30704500 PMCID: PMC6357441 DOI: 10.1186/s13059-019-1633-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2018] [Accepted: 01/16/2019] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Altering the biochemical makeup of chromatin by the incorporation of histone variants during development represents a key mechanism in regulating gene expression. The histone variant H2A.B, H2A.B.3 in mice, appeared late in evolution and is most highly expressed in the testis. In the mouse, it is encoded by three different genes. H2A.B expression is spatially and temporally regulated during spermatogenesis being most highly expressed in the haploid round spermatid stage. Active genes gain H2A.B where it directly interacts with polymerase II and RNA processing factors within splicing speckles. However, the importance of H2A.B for gene expression and fertility are unknown. RESULTS Here, we report the first mouse knockout of this histone variant and its effects on fertility, nuclear organization, and gene expression. In view of the controversy related to the generation of off-target mutations by gene editing approaches, we test the specificity of TALENs by disrupting the H2A.B multi-copy gene family using only one pair of TALENs. We show that TALENs do display a high level of specificity since no off-target mutations are detected by bioinformatics analyses of exome sequences obtained from three consecutive generations of knockout mice and by Sanger DNA sequencing. Male H2A.B.3 knockout mice are subfertile and display an increase in the proportion of abnormal sperm and clogged seminiferous tubules. Significantly, a loss of proper RNA Pol II targeting to distinct transcription-splicing territories and changes to pre-mRNA splicing are observed. CONCLUSION We have produced the first H2A.B knockout mouse using the TALEN approach.
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Affiliation(s)
- Nur Diana Anuar
- The John Curtin School of Medical Research, The Australian National University, Canberra, ACT, 2601, Australia
| | - Sebastian Kurscheid
- The John Curtin School of Medical Research, The Australian National University, Canberra, ACT, 2601, Australia.,Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Matt Field
- The John Curtin School of Medical Research, The Australian National University, Canberra, ACT, 2601, Australia.,Present Address: James Cook University, PO Box 6811, Cairns, QLD, 4870, Australia.,Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Lei Zhang
- Sangamo Therapeutics, 501 Canal Blvd, Richmond, CA, 94804, USA
| | - Edward Rebar
- Sangamo Therapeutics, 501 Canal Blvd, Richmond, CA, 94804, USA
| | - Philip Gregory
- Sangamo Therapeutics, 501 Canal Blvd, Richmond, CA, 94804, USA.,Present Address: bluebird bio, 60 Binney St, Cambridge, MA, 02142, USA
| | - Thierry Buchou
- CNRS UMR 5309, Inserm U1209, Universite' Grenoble Alpes, Institute for Advanced Biosciences, 38700, Grenoble, France
| | - Josephine Bowles
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Peter Koopman
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - David J Tremethick
- The John Curtin School of Medical Research, The Australian National University, Canberra, ACT, 2601, Australia.
| | - Tatiana A Soboleva
- The John Curtin School of Medical Research, The Australian National University, Canberra, ACT, 2601, Australia.
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Liang Z, Chen K, Yan Y, Zhang Y, Gao C. Genotyping genome-edited mutations in plants using CRISPR ribonucleoprotein complexes. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:2053-2062. [PMID: 29723918 PMCID: PMC6230946 DOI: 10.1111/pbi.12938] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Revised: 04/03/2018] [Accepted: 04/05/2018] [Indexed: 05/04/2023]
Abstract
Despite the great achievements in genome editing, accurately detecting mutations induced by sequence-specific nucleases is still a challenge in plants, especially in polyploidy plants. An efficient detection method is particularly vital when the mutation frequency is low or when a large population needs to be screened. Here, we applied purified CRISPR ribonucleoprotein complexes to cleave PCR products for genome-edited mutation detection in hexaploid wheat and diploid rice. We show that this mutation detection method is more sensitive than Sanger sequencing and more applicable than PCR/RE method without the requirement for restriction enzyme site. We also demonstrate that this detection method is especially useful for genome editing in wheat, because target sites are often surrounded by single nucleotide polymorphisms. Using this screening method, we were also able to detect foreign DNA-free tagw2 mutations induced by purified TALEN protein. Finally, we show that partial base editing mutations can also be detected using high-fidelity SpCas9 variants or FnCpf1. The PCR/RNP method is low-cost and widely applicable for rapid detection of genome-edited mutation in plants.
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Affiliation(s)
- Zhen Liang
- State Key Laboratory of Plant Cell and Chromosome EngineeringCenter for Genome EditingInstitute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Kunling Chen
- State Key Laboratory of Plant Cell and Chromosome EngineeringCenter for Genome EditingInstitute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
| | - Yan Yan
- State Key Laboratory of Plant Cell and Chromosome EngineeringCenter for Genome EditingInstitute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
| | - Yi Zhang
- Key Laboratory of Plant Stress ResearchCollege of Life ScienceShandong Normal UniversityJinanChina
| | - Caixia Gao
- State Key Laboratory of Plant Cell and Chromosome EngineeringCenter for Genome EditingInstitute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
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Abstract
While research in gene editing technology has been active since the 1990s, recent advances in CRISPR ease of use have sparked significant enthusiasm in the biomedical community. Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) gene editing has the potential to shape the therapeutic landscape of genetically-defined diseases, with key players such as CRISPR Therapeutics, Intellia, and Editas leading the way in β-thalassemia and sickle cell disease. In coming years, clinical development of CRISPR technology promises to change how we think about monogenic and polygenic diseases, though data is still in its infancy. While concerns regarding safety and administration of CRISPR persist and researchers are still seeking to better understand its effect on the body's ability to recognize and repair damaged DNA, the applications for personalized medicine are exciting and wide-ranging. This review examines potential applications of CRISPR for human therapeutics, with a private sector focus detailing anticipated clinical advances and evolving challenges along the way.
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Affiliation(s)
- Andrew Hong
- Axiom Life Science, 17 Hulfish St. Suite 240, Princeton, NJ 08540, U.S.A..
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37
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Long-Term Effects of In Vivo Genome Editing in the Mouse Retina Using Campylobacter jejuni Cas9 Expressed via Adeno-Associated Virus. Mol Ther 2018; 27:130-136. [PMID: 30470629 DOI: 10.1016/j.ymthe.2018.10.009] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 10/08/2018] [Accepted: 10/11/2018] [Indexed: 12/26/2022] Open
Abstract
Genome editing with CRISPR systems provides an unprecedented opportunity to modulate cellular responses in pathological conditions by inactivating undruggable targets, such as transcription factors. Previously, we demonstrated that the smallest Cas9 ortholog characterized to date, from Campylobacter jejuni (CjCas9) targeted to Hif1a and delivered in an adeno-associated virus (AAV) vector, effectively suppressed pathological choroidal neovascularization in the mouse retina. Before implementation of CjCas9 as an in vivo therapeutic modality, it is essential to investigate the long-term effects of target gene disruption via AAV-mediated delivery of CjCas9 in vivo. In this study, histologic and electroretinographic analyses demonstrated that CjCas9 targeted to Hif1a did not induce any definite toxicity in the retina, although the target gene was mutated with a frequency ranging from 45% to 79% in retinal or retinal pigment epithelial cells. Importantly, at 14 months after injection, no indels were detected at potential off-target sites identified using Digenome-seq and Cas-OFFinder, suggesting that long-term expression of CjCas9 does not aggravate off-target effects. Taken together, our results show that intravitreal injection of AAV encoding CjCas9 targeted to Hif1a effectively induced and maintained mutations in retinal tissues for more than 1 year and did not affect retinal histologic integrity or functions.
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Batista AC, Pacheco LG. Detecting pathogens with Zinc-Finger, TALE and CRISPR- based programmable nucleic acid binding proteins. J Microbiol Methods 2018; 152:98-104. [DOI: 10.1016/j.mimet.2018.07.024] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 07/16/2018] [Accepted: 07/31/2018] [Indexed: 12/26/2022]
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Perkons NR, Sheth R, Ackerman D, Chen J, Saleh K, Hunt SJ, Nadolski GJ, Shi J, Gade TP. The Implications of CRISPR-Cas9 Genome Editing for IR. J Vasc Interv Radiol 2018; 29:1264-1267.e1. [PMID: 30146193 DOI: 10.1016/j.jvir.2018.02.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 02/23/2018] [Accepted: 02/23/2018] [Indexed: 11/28/2022] Open
Affiliation(s)
- Nicholas R Perkons
- Department of Radiology, Perelman School of Medicine at the University of Pennsylvania, 452 BRB II/III, 421 Curie Blvd., Philadelphia, PA 19104-6160; Penn Image-Guided Interventions Laboratory, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Rahul Sheth
- Department of Radiology, MD Anderson Cancer Center, Houston, Texas
| | - Daniel Ackerman
- Department of Radiology, Perelman School of Medicine at the University of Pennsylvania, 452 BRB II/III, 421 Curie Blvd., Philadelphia, PA 19104-6160; Penn Image-Guided Interventions Laboratory, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania
| | - James Chen
- Department of Radiology, Perelman School of Medicine at the University of Pennsylvania, 452 BRB II/III, 421 Curie Blvd., Philadelphia, PA 19104-6160; Penn Image-Guided Interventions Laboratory, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Kamiel Saleh
- Department of Radiology, Perelman School of Medicine at the University of Pennsylvania, 452 BRB II/III, 421 Curie Blvd., Philadelphia, PA 19104-6160; Penn Image-Guided Interventions Laboratory, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Stephen J Hunt
- Department of Radiology, Perelman School of Medicine at the University of Pennsylvania, 452 BRB II/III, 421 Curie Blvd., Philadelphia, PA 19104-6160; Penn Image-Guided Interventions Laboratory, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Gregory J Nadolski
- Department of Radiology, Perelman School of Medicine at the University of Pennsylvania, 452 BRB II/III, 421 Curie Blvd., Philadelphia, PA 19104-6160; Penn Image-Guided Interventions Laboratory, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Junwei Shi
- Department of Cancer Biology, Perelman School of Medicine at the University of Pennsylvania, 452 BRB II/III, 421 Curie Blvd., Philadelphia, PA 19104-6160
| | - Terence P Gade
- Department of Radiology, Perelman School of Medicine at the University of Pennsylvania, 452 BRB II/III, 421 Curie Blvd., Philadelphia, PA 19104-6160; Department of Cancer Biology, Perelman School of Medicine at the University of Pennsylvania, 452 BRB II/III, 421 Curie Blvd., Philadelphia, PA 19104-6160; Penn Image-Guided Interventions Laboratory, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania.
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Karlgren M, Simoff I, Keiser M, Oswald S, Artursson P. CRISPR-Cas9: A New Addition to the Drug Metabolism and Disposition Tool Box. Drug Metab Dispos 2018; 46:1776-1786. [PMID: 30126863 DOI: 10.1124/dmd.118.082842] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 08/03/2018] [Indexed: 02/06/2023] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR associated protein 9 (Cas9), i.e., CRISPR-Cas9, has been extensively used as a gene-editing technology during recent years. Unlike earlier technologies for gene editing or gene knockdown, such as zinc finger nucleases and RNA interference, CRISPR-Cas9 is comparably easy to use, affordable, and versatile. Recently, CRISPR-Cas9 has been applied in studies of drug absorption, distribution, metabolism, and excretion (ADME) and for ADME model generation. To date, about 50 papers have been published describing in vitro or in vivo CRISPR-Cas9 gene editing of ADME and ADME-related genes. Twenty of these papers describe gene editing of clinically relevant genes, such as ATP-binding cassette drug transporters and cytochrome P450 drug-metabolizing enzymes. With CRISPR-Cas9, the ADME tool box has been substantially expanded. This new technology allows us to develop better and more predictive in vitro and in vivo ADME models and map previously underexplored ADME genes and gene families. In this mini-review, we give an overview of the CRISPR-Cas9 technology and summarize recent applications of CRISPR-Cas9 within the ADME field. We also speculate about future applications of CRISPR-Cas9 in ADME research.
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Affiliation(s)
- M Karlgren
- Department of Pharmacy (M.Ka., P.A.), Uppsala University Drug Optimization and Pharmaceutical Profiling Platform, Department of Pharmacy (I.S.), and Science for Life Laboratory (P.A.), Uppsala University, Uppsala, Sweden; and Department of Clinical Pharmacology, Center of Drug Absorption and Transport, University Medicine of Greifswald, Germany (M.Ke., S.O.)
| | - I Simoff
- Department of Pharmacy (M.Ka., P.A.), Uppsala University Drug Optimization and Pharmaceutical Profiling Platform, Department of Pharmacy (I.S.), and Science for Life Laboratory (P.A.), Uppsala University, Uppsala, Sweden; and Department of Clinical Pharmacology, Center of Drug Absorption and Transport, University Medicine of Greifswald, Germany (M.Ke., S.O.)
| | - M Keiser
- Department of Pharmacy (M.Ka., P.A.), Uppsala University Drug Optimization and Pharmaceutical Profiling Platform, Department of Pharmacy (I.S.), and Science for Life Laboratory (P.A.), Uppsala University, Uppsala, Sweden; and Department of Clinical Pharmacology, Center of Drug Absorption and Transport, University Medicine of Greifswald, Germany (M.Ke., S.O.)
| | - S Oswald
- Department of Pharmacy (M.Ka., P.A.), Uppsala University Drug Optimization and Pharmaceutical Profiling Platform, Department of Pharmacy (I.S.), and Science for Life Laboratory (P.A.), Uppsala University, Uppsala, Sweden; and Department of Clinical Pharmacology, Center of Drug Absorption and Transport, University Medicine of Greifswald, Germany (M.Ke., S.O.)
| | - P Artursson
- Department of Pharmacy (M.Ka., P.A.), Uppsala University Drug Optimization and Pharmaceutical Profiling Platform, Department of Pharmacy (I.S.), and Science for Life Laboratory (P.A.), Uppsala University, Uppsala, Sweden; and Department of Clinical Pharmacology, Center of Drug Absorption and Transport, University Medicine of Greifswald, Germany (M.Ke., S.O.)
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Varshney RK, Thudi M, Pandey MK, Tardieu F, Ojiewo C, Vadez V, Whitbread AM, Siddique KHM, Nguyen HT, Carberry PS, Bergvinson D. Accelerating genetic gains in legumes for the development of prosperous smallholder agriculture: integrating genomics, phenotyping, systems modelling and agronomy. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:3293-3312. [PMID: 29514298 DOI: 10.1093/jxb/ery088] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 02/22/2018] [Indexed: 05/23/2023]
Abstract
Grain legumes form an important component of the human diet, provide feed for livestock, and replenish soil fertility through biological nitrogen fixation. Globally, the demand for food legumes is increasing as they complement cereals in protein requirements and possess a high percentage of digestible protein. Climate change has enhanced the frequency and intensity of drought stress, posing serious production constraints, especially in rainfed regions where most legumes are produced. Genetic improvement of legumes, like other crops, is mostly based on pedigree and performance-based selection over the past half century. To achieve faster genetic gains in legumes in rainfed conditions, this review proposes the integration of modern genomics approaches, high throughput phenomics, and simulation modelling in support of crop improvement that leads to improved varieties that perform with appropriate agronomy. Selection intensity, generation interval, and improved operational efficiencies in breeding are expected to further enhance the genetic gain in experimental plots. Improved seed access to farmers, combined with appropriate agronomic packages in farmers' fields, will deliver higher genetic gains. Enhanced genetic gains, including not only productivity but also nutritional and market traits, will increase the profitability of farming and the availability of affordable nutritious food especially in developing countries.
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Affiliation(s)
- Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Mahendar Thudi
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Manish K Pandey
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Francois Tardieu
- French National Institute for Agricultural Research (INRA), Monpellier, France
| | - Chris Ojiewo
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Nairobi, Kenya
| | - Vincent Vadez
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- Institut de recherche pour le développement (IRD), Montpellier, France
| | - Anthony M Whitbread
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | | | | | - Peter S Carberry
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - David Bergvinson
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
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42
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Affiliation(s)
- Ianis G Matsoukas
- Faculty of Health and Wellbeing, School of Sport and Biomedical Sciences, University of Bolton, Bolton, United Kingdom
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43
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Medicinal Application of Synthetic Biology. Synth Biol (Oxf) 2018. [DOI: 10.1007/978-981-10-8693-9_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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Choi K. Advances towards Controlling Meiotic Recombination for Plant Breeding. Mol Cells 2017; 40:814-822. [PMID: 29179262 PMCID: PMC5712510 DOI: 10.14348/molcells.2017.0171] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Revised: 11/10/2017] [Accepted: 11/17/2017] [Indexed: 12/28/2022] Open
Abstract
Meiotic homologous recombination generates new combinations of preexisting genetic variation and is a crucial process in plant breeding. Within the last decade, our understanding of plant meiotic recombination and genome diversity has advanced considerably. Innovation in DNA sequencing technology has led to the exploration of high-resolution genetic and epigenetic information in plant genomes, which has helped to accelerate plant breeding practices via high-throughput genotyping, and linkage and association mapping. In addition, great advances toward understanding the genetic and epigenetic control mechanisms of meiotic recombination have enabled the expansion of breeding programs and the unlocking of genetic diversity that can be used for crop improvement. This review highlights the recent literature on plant meiotic recombination and discusses the translation of this knowledge to the manipulation of meiotic recombination frequency and location with regards to crop plant breeding.
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Affiliation(s)
- Kyuha Choi
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673,
Korea
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45
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Gene Editing and CRISPR Therapeutics: Strategies Taught by Cell and Gene Therapy. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2017. [PMID: 29150002 DOI: 10.1016/bs.pmbts.2017.08.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register]
Abstract
A few years ago, we assisted in the demonstration for the first time of the revolutionary idea of a type of adaptive-immune system in the bacteria kingdom. This system, named CRISPR, and variants engineered in the lab, have been demonstrated as functional with extremely high frequency and fidelity in almost all eukaryotic cells studied to date. The capabilities of this RNA-guided nuclease have added to the interest that was announced with the advent of previous technologies for genome editing tools, such as ZFN and TALEN. The capabilities exhibited by these gene editors, opens up a novel scenario that indicates the promise of a next-generation medicine based on precision and personalized objectives, mostly due to the change in the paradigm regarding gene-surgery. This has certainly attracted, like never before, the attention of the biotech business and investor community. This chapter offers a brief overview of some of the factors that have contributed to a rapid entry into the biotech and pharmaceutical company's pipeline, focusing on how cell and gene therapies (CGT), collectively known as advanced therapies, have become the driving forces toward the therapeutic uses of gene editing technology. The sum of all those efforts for more than 30years has contributed to the new paradigm of considering genes as medicines.
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46
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Adair PR, Kim YC, Zhang AH, Yoon J, Scott DW. Human Tregs Made Antigen Specific by Gene Modification: The Power to Treat Autoimmunity and Antidrug Antibodies with Precision. Front Immunol 2017; 8:1117. [PMID: 28983300 PMCID: PMC5613123 DOI: 10.3389/fimmu.2017.01117] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 08/25/2017] [Indexed: 11/17/2022] Open
Abstract
Human regulatory CD4+ T cells (Tregs) are potent immunosuppressive lymphocytes responsible for immune tolerance and homeostasis. Since the seminal reports identifying Tregs, vast research has been channeled into understanding their genesis, signature molecular markers, mechanisms of suppression, and role in disease. This research has opened the doors for Tregs as a potential therapeutic for diseases and disorders such as multiple sclerosis, type I diabetes, transplantation, and immune responses to protein therapeutics, like factor VIII. Seminal clinical trials have used polyclonal Tregs, but the frequency of antigen-specific Tregs among polyclonal populations is low, and polyclonal Tregs may risk non-specific immunosuppression. Antigen-specific Treg therapy, which uses genetically modified Tregs expressing receptors specific for target antigens, greatly mitigates this risk. Building on the principles of T-cell receptor cloning, chimeric antigen receptors (CARs), and a novel CAR derivative, called B-cell antibody receptors, our lab has developed different types of antigen-specific Tregs. This review discusses the current research and optimization of gene-modified antigen-specific human Tregs in our lab in several disease models. The preparations and considerations for clinical use of such Tregs also are discussed.
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Affiliation(s)
- Patrick R Adair
- Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Yong Chan Kim
- Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Ai-Hong Zhang
- Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Jeongheon Yoon
- Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - David W Scott
- Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
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Mittal R, Nguyen D, Patel AP, Debs LH, Mittal J, Yan D, Eshraghi AA, Van De Water TR, Liu XZ. Recent Advancements in the Regeneration of Auditory Hair Cells and Hearing Restoration. Front Mol Neurosci 2017; 10:236. [PMID: 28824370 PMCID: PMC5534485 DOI: 10.3389/fnmol.2017.00236] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 07/11/2017] [Indexed: 12/18/2022] Open
Abstract
Neurosensory responses of hearing and balance are mediated by receptors in specialized neuroepithelial sensory cells. Any disruption of the biochemical and molecular pathways that facilitate these responses can result in severe deficits, including hearing loss and vestibular dysfunction. Hearing is affected by both environmental and genetic factors, with impairment of auditory function being the most common neurosensory disorder affecting 1 in 500 newborns, as well as having an impact on the majority of elderly population. Damage to auditory sensory cells is not reversible, and if sufficient damage and cell death have taken place, the resultant deficit may lead to permanent deafness. Cochlear implants are considered to be one of the most successful and consistent treatments for deaf patients, but only offer limited recovery at the expense of loss of residual hearing. Recently there has been an increased interest in the auditory research community to explore the regeneration of mammalian auditory hair cells and restoration of their function. In this review article, we examine a variety of recent therapies, including genetic, stem cell and molecular therapies as well as discussing progress being made in genome editing strategies as applied to the restoration of hearing function.
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Affiliation(s)
- Rahul Mittal
- Department of Otolaryngology, University of Miami Miller School of MedicineMiami, FL, United States
| | - Desiree Nguyen
- Department of Otolaryngology, University of Miami Miller School of MedicineMiami, FL, United States
| | - Amit P. Patel
- Department of Otolaryngology, University of Miami Miller School of MedicineMiami, FL, United States
| | - Luca H. Debs
- Department of Otolaryngology, University of Miami Miller School of MedicineMiami, FL, United States
| | - Jeenu Mittal
- Department of Otolaryngology, University of Miami Miller School of MedicineMiami, FL, United States
| | - Denise Yan
- Department of Otolaryngology, University of Miami Miller School of MedicineMiami, FL, United States
| | - Adrien A. Eshraghi
- Department of Otolaryngology, University of Miami Miller School of MedicineMiami, FL, United States
| | - Thomas R. Van De Water
- Department of Otolaryngology, University of Miami Miller School of MedicineMiami, FL, United States
| | - Xue Z. Liu
- Department of Otolaryngology, University of Miami Miller School of MedicineMiami, FL, United States
- Department of Otolaryngology, Xiangya Hospital, Central South UniversityChangsha, China
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Abstract
As eukaryotes, filamentous fungi share many features with humans, and they produce numerous active metabolites, some of which are toxic. Traditional genetic approaches are generally inefficient, but the clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 system that has been widely used for basic research on bacteria, mammals and plants offers a simple, fast, versatile technology for systemic research on filamentous fungi. In this review, we summarized the current knowledge on Cas9 and its variants, various selective markers used to screen positive clones, different ways used to detect off-target mutations, and different approaches used to express and transform the CRISPR complex. We also highlight several methods that improve the nuclease specificity and efficiency, and discuss current and potential applications of CRISPR/Cas9 system in filamentous fungi for pathogenesis decoding, confirmation of the gene and pathway, bioenergy process, drug discovery, and chromatin dynamics. We also describe how the synthetic gene circuit of CRISPR/Cas9 systems has been used in the response to various complex environmental signals to redirect metabolite flux and ensure continuous metabolite biosynthesis.
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Affiliation(s)
- Huaxiang Deng
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, People's Republic of China
| | - Ruijie Gao
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, People's Republic of China
| | - Xiangru Liao
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, People's Republic of China.
| | - Yujie Cai
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, People's Republic of China.
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49
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Rádis-Baptista G, Campelo IS, Morlighem JÉRL, Melo LM, Freitas VJF. Cell-penetrating peptides (CPPs): From delivery of nucleic acids and antigens to transduction of engineered nucleases for application in transgenesis. J Biotechnol 2017; 252:15-26. [PMID: 28479163 DOI: 10.1016/j.jbiotec.2017.05.002] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 04/22/2017] [Accepted: 05/03/2017] [Indexed: 01/13/2023]
Abstract
Cell-penetrating peptides (CPPs) have been studied for their capacity to translocate across the lipid membrane of several cell types. In membrane translocation, these peptides can remarkably transport biologically active hydrophilic molecules, such as pharmaceuticals, nucleic acids (DNA and RNA) and even high-molecular-weight proteins, Fig. 3 into the cell cytoplasm and organelles. The development of CPPs as transduction agents includes the modification of gene and protein expression, the reprogramming and differentiation of induced pluripotent stem cells and the preparation of cellular vaccines. A relatively recent field of CPP application is the transduction of plasmid DNA vectors and CPP-fusion proteins to modify genomes and introduce new traits in cells and organisms. CPP-mediated transduction of components for genome editing is an advantageous alternative to viral DNA vectors. Engineered site-specific nucleases, such as Cre recombinase, ZFN, TALENs and CRISPR associated protein (Cas), have been coupled to CPPs, and the fused proteins have been used to permeate targeted cells and tissues. The functionally active fusion CPP-nucleases subsequently home to the nucleus, incise genomic DNA at specific sites and induce repair and recombination. This review has the objective of discussing CPPs and elucidating the prospective use of CPP-mediated transduction technology, particularly in genome modification and transgenesis.
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Affiliation(s)
- Gandhi Rádis-Baptista
- Laboratory of Biochemistry and Biotechnology, Institute for Marine Science, Federal University of Ceará, Fortaleza-CE, 60.165-081, Brazil.
| | - Iana S Campelo
- Laboratory of Physiology and Control of Reproduction, Faculty of Veterinary, State University of Ceará, Fortaleza-CE, 60.714-903, Brazil
| | - Jean-Étienne R L Morlighem
- Laboratory of Biochemistry and Biotechnology, Institute for Marine Science, Federal University of Ceará, Fortaleza-CE, 60.165-081, Brazil; Northeast Biotechnology Network (RENORBIO), Post-graduation program in Biotechnology, Federal University of Ceará, Fortaleza, CE, 60.455-900, Brazil
| | - Luciana M Melo
- Laboratory of Physiology and Control of Reproduction, Faculty of Veterinary, State University of Ceará, Fortaleza-CE, 60.714-903, Brazil
| | - Vicente J F Freitas
- Laboratory of Physiology and Control of Reproduction, Faculty of Veterinary, State University of Ceará, Fortaleza-CE, 60.714-903, Brazil.
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50
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Vervoort Y, Linares AG, Roncoroni M, Liu C, Steensels J, Verstrepen KJ. High-throughput system-wide engineering and screening for microbial biotechnology. Curr Opin Biotechnol 2017; 46:120-125. [PMID: 28346890 DOI: 10.1016/j.copbio.2017.02.011] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Revised: 02/06/2017] [Accepted: 02/07/2017] [Indexed: 01/08/2023]
Abstract
Genetic engineering and screening of large number of cells or populations is a crucial bottleneck in today's systems biology and applied (micro)biology. Instead of using standard methods in bottles, flasks or 96-well plates, scientists are increasingly relying on high-throughput strategies that miniaturize their experiments to the nanoliter and picoliter scale and the single-cell level. In this review, we summarize different high-throughput system-wide genome engineering and screening strategies for microbes. More specifically, we will emphasize the use of multiplex automated genome evolution (MAGE) and CRISPR/Cas systems for high-throughput genome engineering and the application of (lab-on-chip) nanoreactors for high-throughput single-cell or population screening.
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Affiliation(s)
- Yannick Vervoort
- Laboratory for Systems Biology, VIB Center for Microbiology, Gaston Geenslaan 1, B-3001 Leuven, Belgium; Laboratory for Genetics and Genomics, KU Leuven, Gaston Geenslaan 1, B-3001 Leuven, Belgium; Imec Life Science Technologies, Kapeldreef 75, B-3001 Leuven, Belgium
| | - Alicia Gutiérrez Linares
- Laboratory for Systems Biology, VIB Center for Microbiology, Gaston Geenslaan 1, B-3001 Leuven, Belgium; Laboratory for Genetics and Genomics, KU Leuven, Gaston Geenslaan 1, B-3001 Leuven, Belgium
| | - Miguel Roncoroni
- Laboratory for Systems Biology, VIB Center for Microbiology, Gaston Geenslaan 1, B-3001 Leuven, Belgium; Laboratory for Genetics and Genomics, KU Leuven, Gaston Geenslaan 1, B-3001 Leuven, Belgium
| | - Chengxun Liu
- Imec Life Science Technologies, Kapeldreef 75, B-3001 Leuven, Belgium
| | - Jan Steensels
- Laboratory for Systems Biology, VIB Center for Microbiology, Gaston Geenslaan 1, B-3001 Leuven, Belgium; Laboratory for Genetics and Genomics, KU Leuven, Gaston Geenslaan 1, B-3001 Leuven, Belgium
| | - Kevin J Verstrepen
- Laboratory for Systems Biology, VIB Center for Microbiology, Gaston Geenslaan 1, B-3001 Leuven, Belgium; Laboratory for Genetics and Genomics, KU Leuven, Gaston Geenslaan 1, B-3001 Leuven, Belgium.
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