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Mohamed KA, Kruf S, Büll C. Putting a cap on the glycome: Dissecting human sialyltransferase functions. Carbohydr Res 2024; 544:109242. [PMID: 39167930 DOI: 10.1016/j.carres.2024.109242] [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: 06/03/2024] [Revised: 07/24/2024] [Accepted: 08/13/2024] [Indexed: 08/23/2024]
Abstract
Human glycans are capped with sialic acids and these nine-carbon sugars mediate many of the biological functions and interactions of glycans. Structurally diverse sialic acid caps mark human cells as self and they form the ligands for the Siglec immune receptors and other glycan-binding proteins. Sialic acids enable host interactions with the human microbiome and many human pathogens utilize sialic acids to infect host cells. Alterations in sialic acid-carrying glycans, sialoglycans, can be found in every major human disease including inflammatory conditions and cancer. Twenty sialyltransferase family members in the Golgi apparatus of human cells transfer sialic acids to distinct glycans and glycoconjugates. Sialyltransferases catalyze specific reactions to form unique sialoglycans or they have shared functions where multiple family members generate the same sialoglycan product. Moreover, some sialyltransferases compete for the same glycan substrate, but create different sialic acid caps. The redundant and competing functions make it difficult to understand the individual roles of the human sialyltransferases in biology and to reveal the specific contributions to pathobiological processes. Recent insights hint towards the existence of biosynthetic rules formed by the individual functions of sialyltransferases, their interactions, and cues from the local Golgi environment that coordinate sialoglycan biosynthesis. In this review, we discuss the current structural and functional understanding of the human sialyltransferase family and we review recent technological advances that enable the dissection of individual sialyltransferase activities.
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Affiliation(s)
- Khadra A Mohamed
- Department of Biomolecular Chemistry, Institute for Molecules and Materials, Faculty of Science, Radboud University Nijmegen, Heyendaalseweg 135, 6525AJ, Nijmegen, the Netherlands
| | - Stijn Kruf
- Department of Biomolecular Chemistry, Institute for Molecules and Materials, Faculty of Science, Radboud University Nijmegen, Heyendaalseweg 135, 6525AJ, Nijmegen, the Netherlands
| | - Christian Büll
- Department of Biomolecular Chemistry, Institute for Molecules and Materials, Faculty of Science, Radboud University Nijmegen, Heyendaalseweg 135, 6525AJ, Nijmegen, the Netherlands.
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2
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Buffone A, Hammer DA, Kim SHJ, Anderson NR, Mochida A, Lee DH, Guin S. Not all (cells) who wander are lost: Upstream migration as a pervasive mode of amoeboid cell motility. Front Cell Dev Biol 2023; 11:1291201. [PMID: 38020916 PMCID: PMC10651737 DOI: 10.3389/fcell.2023.1291201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 10/06/2023] [Indexed: 12/01/2023] Open
Abstract
Leukocytes possess the ability to migrate upstream-against the direction of flow-on surfaces of specific chemistry. Upstream migration was first characterized in vitro for T-cells on surfaces comprised of intracellular adhesion molecule-1 (ICAM-1). Upstream migration occurs when the integrin receptor αLβ2 (also known as lymphocyte function-associated antigen-1, or LFA-1) binds to ICAM-1. LFA-1/ICAM-1 interactions are ubiquitous and are widely found in leukocyte trafficking. Upstream migration would be employed after cells come to arrest on the apical surface of the endothelium and might confer an advantage for both trans-endothelial migration and tissue surveillance. It has now been shown that several other motile amoeboid cells which have the responsibility of trafficking from blood vessels into tissues, such as Marginal zone B cells, hematopoietic stem cells, and neutrophils (when macrophage-1 antigen, Mac-1, is blocked), can also migrate upstream on ICAM-1 surfaces. This review will summarize what is known about the basic mechanisms of upstream migration, which cells have displayed this phenomenon, and the possible role of upstream migration in physiology and tissue homeostasis.
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Affiliation(s)
- Alexander Buffone
- Department of Biomedical Engineering, New Jersey Institute of Technology, Newark, NJ, United States
- Chemical and Materials Engineering, New Jersey Institute of Technology, Newark, NJ, United States
| | - Daniel A. Hammer
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, United States
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA, United States
| | - Sarah Hyun Ji Kim
- Department of Medicine, University of California San Diego, La Jolla, CA, United States
| | | | - Ai Mochida
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, United States
| | - Dong-Hun Lee
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA, United States
| | - Subham Guin
- Department of Biomedical Engineering, New Jersey Institute of Technology, Newark, NJ, United States
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3
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Wang SE, Jiang YH. Novel epigenetic molecular therapies for imprinting disorders. Mol Psychiatry 2023; 28:3182-3193. [PMID: 37626134 PMCID: PMC10618104 DOI: 10.1038/s41380-023-02208-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Revised: 07/21/2023] [Accepted: 07/27/2023] [Indexed: 08/27/2023]
Abstract
Genomic imprinting disorders are caused by the disruption of genomic imprinting processes leading to a deficit or increase of an active allele. Their unique molecular mechanisms underlying imprinted genes offer an opportunity to investigate epigenetic-based therapy for reactivation of an inactive allele or reduction of an active allele. Current treatments are based on managing symptoms, not targeting the molecular mechanisms underlying imprinting disorders. Here, we highlight molecular approaches of therapeutic candidates in preclinical and clinical studies for individual imprinting disorders. These include the significant progress of discovery and testing of small molecules, antisense oligonucleotides, and CRISPR mediated genome editing approaches as new therapeutic strategies. We discuss the significant challenges of translating these promising therapies from the preclinical stage to the clinic, especially for genome editing based approaches.
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Affiliation(s)
- Sung Eun Wang
- Department of Genetics, Yale University School of Medicine, 333 Cedar street, New Haven, CT, 06520, USA
| | - Yong-Hui Jiang
- Department of Genetics, Yale University School of Medicine, 333 Cedar street, New Haven, CT, 06520, USA.
- Department of Neuroscience, Yale University School of Medicine, 333 Cedar street, New Haven, CT, 06520, USA.
- Department of Pediatrics, Yale University School of Medicine, 333 Cedar street, New Haven, CT, 06520, USA.
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4
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Bekaert B, Boel A, Cosemans G, De Witte L, Menten B, Heindryckx B. CRISPR/Cas gene editing in the human germline. Semin Cell Dev Biol 2022; 131:93-107. [PMID: 35305903 DOI: 10.1016/j.semcdb.2022.03.012] [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: 11/15/2021] [Revised: 03/08/2022] [Accepted: 03/09/2022] [Indexed: 12/14/2022]
Abstract
The ease and efficacy of CRISPR/Cas9 germline gene editing in animal models paved the way to human germline gene editing (HGGE), by which permanent changes can be introduced into the embryo. Distinct genes can be knocked out to examine their function during embryonic development. Alternatively, specific sequences can be introduced which can be applied to correct disease-causing mutations. To date, it has been shown that the success of HGGE is dependent on various experimental parameters and that various hurdles (i.e. loss-of-heterozygosity and mosaicism) need to be overcome before clinical applications should be considered. Due to the shortage of human germline material and the ethical constraints concerning HGGE, alternative models such as stem cells have been evaluated as well, in terms of their predictive value on the genetic outcome for HGGE approaches. This review will give an overview of the state of the art of HGGE in oocytes and embryos, and its accompanying challenges.
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Affiliation(s)
- B Bekaert
- Ghent-Fertility And Stem cell Team (G-FaST), Department for Reproductive Medicine, Ghent University Hospital, Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - A Boel
- Ghent-Fertility And Stem cell Team (G-FaST), Department for Reproductive Medicine, Ghent University Hospital, Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - G Cosemans
- Ghent-Fertility And Stem cell Team (G-FaST), Department for Reproductive Medicine, Ghent University Hospital, Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - L De Witte
- Center for Medical Genetics Ghent, Ghent University, Department of Biomolecular Medicine, Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - B Menten
- Center for Medical Genetics Ghent, Ghent University, Department of Biomolecular Medicine, Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - B Heindryckx
- Ghent-Fertility And Stem cell Team (G-FaST), Department for Reproductive Medicine, Ghent University Hospital, Corneel Heymanslaan 10, 9000 Ghent, Belgium.
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5
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Shin S, Jang S, Lim D. Small Molecules for Enhancing the Precision and Safety of Genome Editing. Molecules 2022; 27:6266. [PMID: 36234804 PMCID: PMC9573751 DOI: 10.3390/molecules27196266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/17/2022] [Accepted: 09/20/2022] [Indexed: 11/24/2022] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)-based genome-editing technologies have revolutionized biology, biotechnology, and medicine, and have spurred the development of new therapeutic modalities. However, there remain several barriers to the safe use of CRISPR technologies, such as unintended off-target DNA cleavages. Small molecules are important resources to solve these problems, given their facile delivery and fast action to enable temporal control of the CRISPR systems. Here, we provide a comprehensive overview of small molecules that can precisely modulate CRISPR-associated (Cas) nucleases and guide RNAs (gRNAs). We also discuss the small-molecule control of emerging genome editors (e.g., base editors) and anti-CRISPR proteins. These molecules could be used for the precise investigation of biological systems and the development of safer therapeutic modalities.
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Affiliation(s)
- Siyoon Shin
- School of Biopharmaceutical and Medical Sciences, Sungshin University, Seoul 01133, Korea
- Department of Next-Generation Applied Science, Sungshin University, Seoul 01133, Korea
| | - Seeun Jang
- School of Biopharmaceutical and Medical Sciences, Sungshin University, Seoul 01133, Korea
- Department of Next-Generation Applied Science, Sungshin University, Seoul 01133, Korea
| | - Donghyun Lim
- School of Biopharmaceutical and Medical Sciences, Sungshin University, Seoul 01133, Korea
- Department of Next-Generation Applied Science, Sungshin University, Seoul 01133, Korea
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6
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Torriano S, Baulier E, Garcia Diaz A, Corneo B, Farber DB. CRISPR-AsCas12a Efficiently Corrects a GPR143 Intronic Mutation in Induced Pluripotent Stem Cells from an Ocular Albinism Patient. CRISPR J 2022; 5:457-471. [PMID: 35686978 PMCID: PMC9233509 DOI: 10.1089/crispr.2021.0110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Mutations in the GPR143 gene cause X-linked ocular albinism type 1 (OA1), a disease that severely impairs vision. We recently generated induced pluripotent stem cells (iPSCs) from skin fibroblasts of an OA1 patient carrying a point mutation in intron 7 of GPR143. This mutation activates a new splice site causing the incorporation of a pseudoexon. In this study, we present a high-performance CRISPR-Cas ribonucleoprotein strategy to permanently correct the GPR143 mutation in these patient-derived iPSCs. Interestingly, the two single-guide RNAs available for SpCas9 did not allow the cleavage of the target region. In contrast, the cleavage achieved with the CRISPR-AsCas12a system promoted homology-directed repair at a high rate. The CRISPR-AsCas12a-mediated correction did not alter iPSC pluripotency or genetic stability, nor did it result in off-target events. Moreover, we highlight that the disruption of the pathological splice site caused by CRISPR-AsCas12a-mediated insertions/deletions also rescued the normal splicing of GPR143 and its expression level.
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Affiliation(s)
- Simona Torriano
- Department of Ophthalmology, UCLA School of Medicine, Jules Stein Eye Institute, Los Angeles, California, USA
| | - Edouard Baulier
- Department of Ophthalmology, UCLA School of Medicine, Jules Stein Eye Institute, Los Angeles, California, USA
| | - Alejandro Garcia Diaz
- Stem Cell Core, Columbia Stem Cell Initiative, Columbia University Irving Medical Center, New York, New York, USA
| | - Barbara Corneo
- Stem Cell Core, Columbia Stem Cell Initiative, Columbia University Irving Medical Center, New York, New York, USA
| | - Debora B Farber
- Department of Ophthalmology, UCLA School of Medicine, Jules Stein Eye Institute, Los Angeles, California, USA.,Molecular Biology Institute and UCLA, Los Angeles, California, USA.,Brain Research Institute, UCLA, Los Angeles, California, USA
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7
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Kelkar A, Groth T, Neelamegham S. Forward Genetic Screens of Human Glycosylation Pathways Using the GlycoGene CRISPR Library. Curr Protoc 2022; 2:e402. [PMID: 35427438 PMCID: PMC9467456 DOI: 10.1002/cpz1.402] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
CRISPR-Cas9-based forward genetic screens represent a powerful discovery platform to uncover genes regulating specific biological processes. This article describes a method for utilizing a freely available GlycoGene CRISPR library to knock out any gene participating in human glycosylation in arbitrary cell types. The end product is a stable GlycoGene CRISPR knockout cell library, where each cell contains one or more sgRNA and lacks corresponding function. The cell library can be screened using various lectin/antibody reagents. It can also be applied in functional assays to establish glycan structure-glycogene-glycopathway relationships. This is a powerful systems glycobiology strategy for dissecting glycosylation pathways and processes. © 2022 Wiley Periodicals LLC. Basic Protocol 1: Scale-up and NGS validation of the GlycoGene CRISPR plasmid library Basic Protocol 2: Preparation of a GlycoGene CRISPR lentivirus pool and an isogenic cell line stably expressing Cas9 nuclease Basic Protocol 3: Preparation of a GlycoGene CRISPR cell library, self-inactivation of Cas9, and library validation by NGS Basic Protocol 4: Enrichment of lectin-binding or non-binding cells and related multiplex NGS data acquisition Basic Protocol 5: Bioinformatics pathway analysis.
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Affiliation(s)
- Anju Kelkar
- 906 Furnas Hall, University at Buffalo, State University of New York, Buffalo, New York
| | - Theodore Groth
- 906 Furnas Hall, University at Buffalo, State University of New York, Buffalo, New York
| | - Sriram Neelamegham
- 906 Furnas Hall, University at Buffalo, State University of New York, Buffalo, New York
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8
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Khajanchi N, Saha K. Controlling CRISPR with small molecule regulation for somatic cell genome editing. Mol Ther 2022; 30:17-31. [PMID: 34174442 PMCID: PMC8753294 DOI: 10.1016/j.ymthe.2021.06.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 05/26/2021] [Accepted: 06/21/2021] [Indexed: 01/07/2023] Open
Abstract
Biomedical research has been revolutionized by the introduction of many CRISPR-Cas systems that induce programmable edits to nearly any gene in the human genome. Nuclease-based CRISPR-Cas editors can produce on-target genomic changes but can also generate unwanted genotoxicity and adverse events, in part by cleaving non-targeted sites in the genome. Additional translational challenges for in vivo somatic cell editing include limited packaging capacity of viral vectors and host immune responses. Altogether, these challenges motivate recent efforts to control the expression and activity of different Cas systems in vivo. Current strategies utilize small molecules, light, magnetism, and temperature to conditionally control Cas systems through various activation, inhibition, or degradation mechanisms. This review focuses on small molecules that can be incorporated as regulatory switches to control Cas genome editors. Additional development of CRISPR-Cas-based therapeutic approaches with small molecule regulation have high potential to increase editing efficiency with less adverse effects for somatic cell genome editing strategies in vivo.
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Affiliation(s)
- Namita Khajanchi
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Krishanu Saha
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA; Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, USA.
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9
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Evaluation of two in vitro assays for tumorigenicity assessment of CRISPR-Cas9 genome-edited cells. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2021; 23:241-253. [PMID: 34703845 PMCID: PMC8505356 DOI: 10.1016/j.omtm.2021.09.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 09/03/2021] [Indexed: 12/26/2022]
Abstract
Off-target editing is one of the main safety concerns for the use of CRISPR-Cas9 genome editing in gene therapy. These unwanted modifications could lead to malignant transformation, which renders tumorigenicity assessment of gene therapy products indispensable. In this study, we established two in vitro transformation assays, the soft agar colony-forming assay (SACF) and the growth in low attachment assay (GILA) as alternative methods for tumorigenicity evaluation of genome-edited cells. Using a CRISPR-Cas9-based approach to transform immortalized MCF10A cells, we identified PTPN12, a known tumor suppressor, as a valid positive control in GILA and SACF. Next, we measured the limit of detection for both assays and proved that SACF is more sensitive than GILA (0.8% versus 3.1% transformed cells). We further validated SACF and GILA by identifying a set of positive and negative controls and by testing the suitability of another cell line (THLE-2). Moreover, in contrast to SACF and GILA, an in vivo tumorigenicity study failed to detect the known tumorigenic potential of PTPN12 deletion, demonstrating the relevance of GILA and SACF in tumorigenicity testing. In conclusion, SACF and GILA are both attractive and valuable additions to preclinical safety assessment of gene therapy products.
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10
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Wagner DL, Peter L, Schmueck-Henneresse M. Cas9-directed immune tolerance in humans-a model to evaluate regulatory T cells in gene therapy? Gene Ther 2021; 28:549-559. [PMID: 33574580 PMCID: PMC8455332 DOI: 10.1038/s41434-021-00232-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 01/20/2021] [Indexed: 01/31/2023]
Abstract
The dichotomic nature of the adaptive immune response governs the outcome of clinical gene therapy. On the one hand, neutralizing antibodies and cytotoxic T cells can have a dramatic impact on the efficacy and safety of human gene therapies. On the other hand, regulatory T cells (Treg) can promote tolerance toward transgenes thereby enabling long-term benefits of in vivo gene therapy after a single administration. Pre-existing antibodies and T cell immunity has been a major obstacle for in vivo gene therapies with viral vectors. As CRISPR-Cas9 gene editing advances toward the clinics, the technology's inherent immunogenicity must be addressed in order to guide clinical treatment decisions. This review summarizes the recent evidence on Cas9-specific immunity in humans-including early results from clinical trials-and discusses the risks for in vivo gene therapies. Finally, we focus on solutions and highlight the potential role of Cas9-specific Treg cells to promote immune tolerance. As a "beneficial alliance" beyond Cas9-immunity, antigen-specific Treg cells may serve as a living and targeted immunosuppressant to increase safety and efficacy of gene therapy.
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Affiliation(s)
- Dimitrios Laurin Wagner
- Berlin Institute of Health (BIH)-Center for Regenerative Therapies (B-CRT), Charité-Universitätsmedizin Berlin, Berlin, Germany
- Berlin Center for Advanced Therapies (BeCAT), Charité-Universitätsmedizin Berlin, Berlin, Germany
- Institute of Transfusion Medicine, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Lena Peter
- Berlin Institute of Health (BIH)-Center for Regenerative Therapies (B-CRT), Charité-Universitätsmedizin Berlin, Berlin, Germany
- Einstein Center for Regenerative Therapies, Charité-Universitätsmedizin Berlin, 13353, Berlin, Germany
| | - Michael Schmueck-Henneresse
- Berlin Institute of Health (BIH)-Center for Regenerative Therapies (B-CRT), Charité-Universitätsmedizin Berlin, Berlin, Germany.
- Berlin Center for Advanced Therapies (BeCAT), Charité-Universitätsmedizin Berlin, Berlin, Germany.
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11
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Groth T, Gunawan R, Neelamegham S. A systems-based framework to computationally describe putative transcription factors and signaling pathways regulating glycan biosynthesis. Beilstein J Org Chem 2021; 17:1712-1724. [PMID: 34367349 PMCID: PMC8313979 DOI: 10.3762/bjoc.17.119] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 07/12/2021] [Indexed: 01/05/2023] Open
Abstract
Glycosylation is a common posttranslational modification, and glycan biosynthesis is regulated by a set of glycogenes. The role of transcription factors (TFs) in regulating the glycogenes and related glycosylation pathways is largely unknown. In this work, we performed data mining of TF–glycogene relationships from the Cistrome Cancer database (DB), which integrates chromatin immunoprecipitation sequencing (ChIP-Seq) and RNA-Seq data to constitute regulatory relationships. In total, we observed 22,654 potentially significant TF–glycogene relationships, which include interactions involving 526 unique TFs and 341 glycogenes that span 29 the Cancer Genome Atlas (TCGA) cancer types. Here, TF–glycogene interactions appeared in clusters or so-called communities, suggesting that changes in single TF expression during both health and disease may affect multiple carbohydrate structures. Upon applying the Fisher’s exact test along with glycogene pathway classification, we identified TFs that may specifically regulate the biosynthesis of individual glycan types. Integration with Reactome DB knowledge provided an avenue to relate cell-signaling pathways to TFs and cellular glycosylation state. Whereas analysis results are presented for all 29 cancer types, specific focus is placed on human luminal and basal breast cancer disease progression. Overall, the article presents a computational approach to describe TF–glycogene relationships, the starting point for experimental system-wide validation.
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Affiliation(s)
- Theodore Groth
- Chemical and Biological Engineering, University at Buffalo, State University of New York, Buffalo, NY 14260, USA
| | - Rudiyanto Gunawan
- Chemical and Biological Engineering, University at Buffalo, State University of New York, Buffalo, NY 14260, USA
| | - Sriram Neelamegham
- Chemical and Biological Engineering, University at Buffalo, State University of New York, Buffalo, NY 14260, USA.,Biomedical Engineering, University at Buffalo, State University of New York, Buffalo, NY 14260, USA.,Medicine, University at Buffalo, State University of New York, Buffalo, NY 14260, USA
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12
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A new mouse SNP genotyping assay for speed congenics: combining flexibility, affordability, and power. BMC Genomics 2021; 22:378. [PMID: 34030629 PMCID: PMC8142480 DOI: 10.1186/s12864-021-07698-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 05/10/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Speed congenics is an important tool for creating congenic mice to investigate gene functions, but current SNP genotyping methods for speed congenics are expensive. These methods usually rely on chip or array technologies, and a different assay must be developed for each backcross strain combination. "Next generation" high throughput DNA sequencing technologies have the potential to decrease cost and increase flexibility and power of speed congenics, but thus far have not been utilized for this purpose. RESULTS We took advantage of the power of high throughput sequencing technologies to develop a cost-effective, high-density SNP genotyping assay that can be used across many combinations of backcross strains. The assay surveys 1640 genome-wide SNPs known to be polymorphic across > 100 mouse strains, with an expected average of 549 ± 136 SD diagnostic SNPs between each pair of strains. We demonstrated that the assay has a high density of diagnostic SNPs for backcrossing the BALB/c strain into the C57BL/6J strain (807-819 SNPs), and a sufficient density of diagnostic SNPs for backcrossing the closely related substrains C57BL/6N and C57BL/6J (123-139 SNPs). Furthermore, the assay can easily be modified to include additional diagnostic SNPs for backcrossing other closely related substrains. We also developed a bioinformatic pipeline for SNP genotyping and calculating the percentage of alleles that match the backcross recipient strain for each sample; this information can be used to guide the selection of individuals for the next backcross, and to assess whether individuals have become congenic. We demonstrated the effectiveness of the assay and bioinformatic pipeline with a backcross experiment of BALB/c-IL4/IL13 into C57BL/6J; after six generations of backcrosses, offspring were up to 99.8% congenic. CONCLUSIONS The SNP genotyping assay and bioinformatic pipeline developed here present a valuable tool for increasing the power and decreasing the cost of many studies that depend on speed congenics. The assay is highly flexible and can be used for combinations of strains that are commonly used for speed congenics. The assay could also be used for other techniques including QTL mapping, standard F2 crosses, ancestry analysis, and forensics.
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13
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Mukhopadhyay S, Bhutia SK. Trends in CRISPR-Cas9 technology application in cancer. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2021; 178:175-192. [PMID: 33685596 DOI: 10.1016/bs.pmbts.2020.12.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The evolution of the CRISPR-Cas9 technology in cancer research has tremendous potential to shape the future of oncology. Although this gene-editing tool's pre-clinical progress is into its nascent stage, there are many unanswered questions regarding health benefits and therapy precision using CRISPR. The application of CRISPR is highly specific, economically sustainable, and is a high throughput technique, but on the other hand, its application involves measured risk of countering the toxic immune response of Cas protein, off-target effects, limitation of delivering the edited cells back into cancer patients. The current chapter highlights the possibilities and perils of the present-day CRISPR engineering in cancer that should highlight CRISPR translation to therapy.
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Affiliation(s)
- Subhadip Mukhopadhyay
- Department of Radiation Oncology, Laura and Isaac Perlmutter Cancer Center, NYU Medical School, New York, NY, United States.
| | - Sujit Kumar Bhutia
- Department of Life Science, National Institute of Technology, Rourkela, Odisha, India.
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14
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Narimatsu Y, Büll C, Chen YH, Wandall HH, Yang Z, Clausen H. Genetic glycoengineering in mammalian cells. J Biol Chem 2021; 296:100448. [PMID: 33617880 PMCID: PMC8042171 DOI: 10.1016/j.jbc.2021.100448] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 02/17/2021] [Accepted: 02/18/2021] [Indexed: 02/06/2023] Open
Abstract
Advances in nuclease-based gene-editing technologies have enabled precise, stable, and systematic genetic engineering of glycosylation capacities in mammalian cells, opening up a plethora of opportunities for studying the glycome and exploiting glycans in biomedicine. Glycoengineering using chemical, enzymatic, and genetic approaches has a long history, and precise gene editing provides a nearly unlimited playground for stable engineering of glycosylation in mammalian cells to explore and dissect the glycome and its many biological functions. Genetic engineering of glycosylation in cells also brings studies of the glycome to the single cell level and opens up wider use and integration of data in traditional omics workflows in cell biology. The last few years have seen new applications of glycoengineering in mammalian cells with perspectives for wider use in basic and applied glycosciences, and these have already led to discoveries of functions of glycans and improved designs of glycoprotein therapeutics. Here, we review the current state of the art of genetic glycoengineering in mammalian cells and highlight emerging opportunities.
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Affiliation(s)
- Yoshiki Narimatsu
- Department of Cellular and Molecular Medicine, Faculty of Health Sciences, Copenhagen Center for Glycomics, University of Copenhagen, Copenhagen, Denmark; GlycoDisplay ApS, Copenhagen, Denmark.
| | - Christian Büll
- Department of Cellular and Molecular Medicine, Faculty of Health Sciences, Copenhagen Center for Glycomics, University of Copenhagen, Copenhagen, Denmark.
| | | | - Hans H Wandall
- Department of Cellular and Molecular Medicine, Faculty of Health Sciences, Copenhagen Center for Glycomics, University of Copenhagen, Copenhagen, Denmark
| | - Zhang Yang
- Department of Cellular and Molecular Medicine, Faculty of Health Sciences, Copenhagen Center for Glycomics, University of Copenhagen, Copenhagen, Denmark; GlycoDisplay ApS, Copenhagen, Denmark
| | - Henrik Clausen
- Department of Cellular and Molecular Medicine, Faculty of Health Sciences, Copenhagen Center for Glycomics, University of Copenhagen, Copenhagen, Denmark.
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15
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Modell AE, Siriwardena SU, Shoba VM, Li X, Choudhary A. Chemical and optical control of CRISPR-associated nucleases. Curr Opin Chem Biol 2020; 60:113-121. [PMID: 33253976 DOI: 10.1016/j.cbpa.2020.10.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 10/10/2020] [Accepted: 10/12/2020] [Indexed: 02/06/2023]
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR)-Cas system of bacteria has furnished programmable nucleases (e.g., Cas9) that are transforming the field of genome editing with applications in basic and biomedical research, biotechnology, and agriculture. However, broader real-world applications of Cas9 require precision control of its activity over dose, time, and space as off-target effects, embryonic mosaicism, chromosomal translocations, and genotoxicity have been observed with elevated and/or prolonged nuclease activity. Here, we review chemical and optical methods for precision control of Cas9's activity.
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Affiliation(s)
- Ashley E Modell
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA; Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA
| | - Sachini U Siriwardena
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA; Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA
| | - Veronika M Shoba
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA; Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA
| | - Xing Li
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA; Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA
| | - Amit Choudhary
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA; Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA; Divisions of Renal Medicine and Engineering, Brigham and Women's Hospital, Boston, MA, 02115, USA.
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16
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Kostyushev D, Kostyusheva A, Brezgin S, Smirnov V, Volchkova E, Lukashev A, Chulanov V. Gene Editing by Extracellular Vesicles. Int J Mol Sci 2020; 21:E7362. [PMID: 33028045 PMCID: PMC7582630 DOI: 10.3390/ijms21197362] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 09/23/2020] [Accepted: 10/03/2020] [Indexed: 12/12/2022] Open
Abstract
CRISPR/Cas technologies have advanced dramatically in recent years. Many different systems with new properties have been characterized and a plethora of hybrid CRISPR/Cas systems able to modify the epigenome, regulate transcription, and correct mutations in DNA and RNA have been devised. However, practical application of CRISPR/Cas systems is severely limited by the lack of effective delivery tools. In this review, recent advances in developing vehicles for the delivery of CRISPR/Cas in the form of ribonucleoprotein complexes are outlined. Most importantly, we emphasize the use of extracellular vesicles (EVs) for CRISPR/Cas delivery and describe their unique properties: biocompatibility, safety, capacity for rational design, and ability to cross biological barriers. Available molecular tools that enable loading of desired protein and/or RNA cargo into the vesicles in a controllable manner and shape the surface of EVs for targeted delivery into specific tissues (e.g., using targeting ligands, peptides, or nanobodies) are discussed. Opportunities for both endogenous (intracellular production of CRISPR/Cas) and exogenous (post-production) loading of EVs are presented.
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Affiliation(s)
- Dmitry Kostyushev
- National Medical Research Center of Tuberculosis and Infectious Diseases, Ministry of Health, 127994 Moscow, Russia; (A.K.); (S.B.); (V.C.)
| | - Anastasiya Kostyusheva
- National Medical Research Center of Tuberculosis and Infectious Diseases, Ministry of Health, 127994 Moscow, Russia; (A.K.); (S.B.); (V.C.)
| | - Sergey Brezgin
- National Medical Research Center of Tuberculosis and Infectious Diseases, Ministry of Health, 127994 Moscow, Russia; (A.K.); (S.B.); (V.C.)
- Institute of Immunology, Federal Medical Biological Agency, 115522 Moscow, Russia;
| | - Valery Smirnov
- Institute of Immunology, Federal Medical Biological Agency, 115522 Moscow, Russia;
- Sechenov First Moscow State Medical University, 119146 Moscow, Russia; (E.V.); (A.L.)
| | - Elena Volchkova
- Sechenov First Moscow State Medical University, 119146 Moscow, Russia; (E.V.); (A.L.)
| | - Alexander Lukashev
- Sechenov First Moscow State Medical University, 119146 Moscow, Russia; (E.V.); (A.L.)
| | - Vladimir Chulanov
- National Medical Research Center of Tuberculosis and Infectious Diseases, Ministry of Health, 127994 Moscow, Russia; (A.K.); (S.B.); (V.C.)
- Sechenov First Moscow State Medical University, 119146 Moscow, Russia; (E.V.); (A.L.)
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17
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Vu A, McCray PB. New Directions in Pulmonary Gene Therapy. Hum Gene Ther 2020; 31:921-939. [PMID: 32814451 PMCID: PMC7495918 DOI: 10.1089/hum.2020.166] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 08/19/2020] [Indexed: 12/12/2022] Open
Abstract
The lung has long been a target for gene therapy, yet efficient delivery and phenotypic disease correction has remained challenging. Although there have been significant advancements in gene therapies of other organs, including the development of several ex vivo therapies, in vivo therapeutics of the lung have been slower to transition to the clinic. Within the past few years, the field has witnessed an explosion in the development of new gene addition and gene editing strategies for the treatment of monogenic disorders. In this review, we will summarize current developments in gene therapy for cystic fibrosis, alpha-1 antitrypsin deficiency, and surfactant protein deficiencies. We will explore the different gene addition and gene editing strategies under investigation and review the challenges of delivery to the lung.
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Affiliation(s)
- Amber Vu
- Stead Family Department of Pediatrics, Center for Gene Therapy, The University of Iowa, Iowa City, Iowa, USA
| | - Paul B. McCray
- Stead Family Department of Pediatrics, Center for Gene Therapy, The University of Iowa, Iowa City, Iowa, USA
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18
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Da Silva Sanchez A, Paunovska K, Cristian A, Dahlman JE. Treating Cystic Fibrosis with mRNA and CRISPR. Hum Gene Ther 2020; 31:940-955. [PMID: 32799680 PMCID: PMC7495921 DOI: 10.1089/hum.2020.137] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 08/13/2020] [Indexed: 12/16/2022] Open
Abstract
Less than 20% of the protein coding genome is thought to be targetable using small molecules. mRNA therapies are not limited in the same way since in theory, they can silence or edit any gene by encoding CRISPR nucleases, or alternatively, produce any missing protein. Yet not all mRNA therapies are equally likely to succeed. Over the past several years, an increasing number of clinical trials with siRNA- and antisense oligonucleotide-based drugs have revealed three key concepts that will likely extend to mRNA therapies delivered by nonviral systems. First, scientists have come to understand that some genes make better targets for RNA therapies than others. Second, scientists have learned that the type and position of chemical modifications made to an RNA drug can alter its therapeutic window, toxicity, and bioavailability. Third, scientists have found that safe and targeted drug delivery vehicles are required to ferry mRNA therapies into diseased cells. In this study, we apply these learnings to cystic fibrosis (CF). We also describe lessons learned from a subset of CF gene therapies that have already been tested in patients. Finally, we highlight the scientific advances that are still required for nonviral mRNA- or CRISPR-based drugs to treat CF successfully in patients.
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Affiliation(s)
- Alejandro Da Silva Sanchez
- Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia, USA
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Kalina Paunovska
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Ana Cristian
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - James E. Dahlman
- Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia, USA
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA
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19
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Zhu Y, Groth T, Kelkar A, Zhou Y, Neelamegham S. A GlycoGene CRISPR-Cas9 lentiviral library to study lectin binding and human glycan biosynthesis pathways. Glycobiology 2020; 31:173-180. [PMID: 32776087 DOI: 10.1093/glycob/cwaa074] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 07/27/2020] [Accepted: 07/27/2020] [Indexed: 12/25/2022] Open
Abstract
Glycan biosynthesis on cell surface proteins and lipids is orchestrated by different classes of enzymes and proteins including the following: i. glycosyltransferases that add saccharides; ii. glycosidases that trim glycans; iii. conserved oligomeric golgi complex members that regulate intracellular transport; iv. enzymes aiding the biosynthesis of sugar-nucleotides; and v. sulfotransferases. This manuscript describes a pooled "glycoGene CRISPR" lentiviral library that targets 347 human genes involved in the above processes. Approximately 10 single-guide RNA (sgRNA) are included against each glycogene, with the putative editing site spanning the length of the target. A data analysis scheme is presented in order to determine glycosylation pathways regulating biological processes. As proof of principle, forward genetic screen results are presented to identify penetrating glycogenes that regulate the binding of P-/E-selectin, anti-sialyl Lewis-X monoclonal antibody HECA-452 and selected lectins (phaseolus vulgaris leucoagglutinin, vicia villosa lectin, peanut agglutinin) to HL-60 promyelocytic cells. Besides validating previously established biology, the study identifies three enzymes, PAPSS1, SLC35B2 and TPST2, as key molecules regulating sulfation of the major P-selectin glycoprotein ligand-1 in leukocytes. Approximately 80-90% of the sgRNA used in this study displayed high editing efficiency, and the CRISPR library picked up entire gene sets regulating specific biosynthetic pathways rather than only isolated genes. These data suggest that the glycoGene CRISPR library contains high-efficiency sgRNA. Further, this resource could be useful for the rapid screening of glycosylation-related genes and pathways that control lectin recognition in a variety of contexts.
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Affiliation(s)
- Yuqi Zhu
- Chemical and Biological Engineering, Biomedical Engineering and Medicine, University at Buffalo, State University of New York, Buffalo, NY 14260, USA
| | - Theodore Groth
- Chemical and Biological Engineering, Biomedical Engineering and Medicine, University at Buffalo, State University of New York, Buffalo, NY 14260, USA
| | - Anju Kelkar
- Chemical and Biological Engineering, Biomedical Engineering and Medicine, University at Buffalo, State University of New York, Buffalo, NY 14260, USA
| | - Yusen Zhou
- Chemical and Biological Engineering, Biomedical Engineering and Medicine, University at Buffalo, State University of New York, Buffalo, NY 14260, USA
| | - Sriram Neelamegham
- Chemical and Biological Engineering, Biomedical Engineering and Medicine, University at Buffalo, State University of New York, Buffalo, NY 14260, USA
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20
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Moses C, Hodgetts SI, Nugent F, Ben-Ary G, Park KK, Blancafort P, Harvey AR. Transcriptional repression of PTEN in neural cells using CRISPR/dCas9 epigenetic editing. Sci Rep 2020; 10:11393. [PMID: 32647121 PMCID: PMC7347541 DOI: 10.1038/s41598-020-68257-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 06/19/2020] [Indexed: 12/11/2022] Open
Abstract
After damage to the adult mammalian central nervous system (CNS), surviving neurons have limited capacity to regenerate and restore functional connectivity. Conditional genetic deletion of PTEN results in robust CNS axon regrowth, while PTEN repression with short hairpin RNA (shRNA) improves regeneration but to a lesser extent, likely due to suboptimal PTEN mRNA knockdown using this approach. Here we employed the CRISPR/dCas9 system to repress PTEN transcription in neural cells. We targeted the PTEN proximal promoter and 5' untranslated region with dCas9 fused to the repressor protein Krüppel-associated box (KRAB). dCas9-KRAB delivered in a lentiviral vector with one CRISPR guide RNA (gRNA) achieved potent and specific PTEN repression in human cell line models and neural cells derived from human iPSCs, and induced histone (H)3 methylation and deacetylation at the PTEN promoter. The dCas9-KRAB system outperformed a combination of four shRNAs targeting the PTEN transcript, a construct previously used in CNS injury models. The CRISPR system also worked more effectively than shRNAs for Pten repression in rat neural crest-derived PC-12 cells, and enhanced neurite outgrowth after nerve growth factor stimulation. PTEN silencing with CRISPR/dCas9 epigenetic editing may provide a new option for promoting axon regeneration and functional recovery after CNS trauma.
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Affiliation(s)
- C Moses
- School of Human Sciences, Faculty of Science, The University of Western Australia, 35 Stirling Highway, Perth, WA, 6009, Australia
- Cancer Epigenetics Laboratory, The Harry Perkins Institute of Medical Research, 6 Verdun Street, Nedlands, WA, 6009, Australia
| | - S I Hodgetts
- School of Human Sciences, Faculty of Science, The University of Western Australia, 35 Stirling Highway, Perth, WA, 6009, Australia
- Perron Institute for Neurological and Translational Science, 8 Verdun Street, Nedlands, WA, 6009, Australia
| | - F Nugent
- Cancer Epigenetics Laboratory, The Harry Perkins Institute of Medical Research, 6 Verdun Street, Nedlands, WA, 6009, Australia
- School of Molecular Sciences, Faculty of Science, The University of Western Australia, 35 Stirling Highway, Perth, WA, 6009, Australia
| | - G Ben-Ary
- School of Human Sciences, Faculty of Science, The University of Western Australia, 35 Stirling Highway, Perth, WA, 6009, Australia
| | - K K Park
- Department of Neurological Surgery, Miami Project to Cure Paralysis, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - P Blancafort
- School of Human Sciences, Faculty of Science, The University of Western Australia, 35 Stirling Highway, Perth, WA, 6009, Australia.
- Cancer Epigenetics Laboratory, The Harry Perkins Institute of Medical Research, 6 Verdun Street, Nedlands, WA, 6009, Australia.
- Greehey Children's Cancer Research Institute, UT Health San Antonio, 8403 Floyd Curl Drive, San Antonio, TX, 78229, USA.
| | - A R Harvey
- School of Human Sciences, Faculty of Science, The University of Western Australia, 35 Stirling Highway, Perth, WA, 6009, Australia.
- Perron Institute for Neurological and Translational Science, 8 Verdun Street, Nedlands, WA, 6009, Australia.
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21
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Straume AH, Kjærner-Semb E, Ove Skaftnesmo K, Güralp H, Kleppe L, Wargelius A, Edvardsen RB. Indel locations are determined by template polarity in highly efficient in vivo CRISPR/Cas9-mediated HDR in Atlantic salmon. Sci Rep 2020; 10:409. [PMID: 31941961 PMCID: PMC6962318 DOI: 10.1038/s41598-019-57295-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Accepted: 12/19/2019] [Indexed: 01/20/2023] Open
Abstract
Precise gene editing such as CRISPR/Cas9-mediated homology directed repair (HDR) can increase our understanding of gene function and improve traits of importance for aquaculture. This fine-tuned technology has not been developed for farmed fish including Atlantic salmon. We performed knock-in (KI) of a FLAG element in the slc45a2 gene in salmon using sense (S), anti-sense (AS) and double-stranded (ds) oligodeoxynucleotide (ODN) templates with short (24/48/84 bp) homology arms. We show in vivo ODN integration in almost all the gene edited animals, and demonstrate perfect HDR rates up to 27% in individual F0 embryos, much higher than reported previously in any fish. HDR efficiency was dependent on template concentration, but not homology arm length. Analysis of imperfect HDR variants suggest that repair occurs by synthesis-dependent strand annealing (SDSA), as we show for the first time in any species that indel location is dependent on template polarity. Correct ODN polarity can be used to avoid 5'-indels interrupting the reading frame of an inserted sequence and be of importance for HDR template design in general.
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Affiliation(s)
- Anne Hege Straume
- Institute of Marine Research, P.O. Box 1870, Nordnes, NO-5817, Bergen, Norway
| | - Erik Kjærner-Semb
- Institute of Marine Research, P.O. Box 1870, Nordnes, NO-5817, Bergen, Norway
| | - Kai Ove Skaftnesmo
- Institute of Marine Research, P.O. Box 1870, Nordnes, NO-5817, Bergen, Norway
| | - Hilal Güralp
- Institute of Marine Research, P.O. Box 1870, Nordnes, NO-5817, Bergen, Norway
| | - Lene Kleppe
- Institute of Marine Research, P.O. Box 1870, Nordnes, NO-5817, Bergen, Norway
| | - Anna Wargelius
- Institute of Marine Research, P.O. Box 1870, Nordnes, NO-5817, Bergen, Norway
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