1
|
Cazier A, Irvin OM, Chávez LS, Dalvi S, Abraham H, Wickramanayake N, Yellayi S, Blazeck J. A Rapid Antibody Enhancement Platform in Saccharomyces cerevisiae Using an Improved, Diversifying CRISPR Base Editor. ACS Synth Biol 2023; 12:3287-3300. [PMID: 37873982 PMCID: PMC10661033 DOI: 10.1021/acssynbio.3c00299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 10/02/2023] [Accepted: 10/03/2023] [Indexed: 10/25/2023]
Abstract
The yeast Saccharomyces cerevisiae is commonly used to interrogate and screen protein variants and to perform directed evolution studies to develop proteins with enhanced features. While several techniques have been described that help enable the use of yeast for directed evolution, there remains a need to increase their speed and ease of use. Here we present yDBE, a yeast diversifying base editor that functions in vivo and employs a CRISPR-dCas9-directed cytidine deaminase base editor to diversify DNA in a targeted, rapid, and high-breadth manner. To develop yDBE, we enhanced the mutation rate of an initial base editor by employing improved deaminase variants and characterizing several scaffolded guide constructs. We then demonstrate the ability of the yDBE platform to improve the affinity of a displayed antibody scFv, rapidly generating diversified libraries and isolating improved binders via cell sorting. By performing high-throughput sequencing analysis of the high-activity yDBE, we show that it enables a mutation rate of 2.13 × 10-4 substitutions/bp/generation over a window of 100 bp. As yDBE functions entirely in vivo and can be easily programmed to diversify nearly any such window of DNA, we posit that it can be a powerful tool for facilitating a variety of directed evolution experiments.
Collapse
Affiliation(s)
- Andrew
P. Cazier
- School
of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Olivia M. Irvin
- School
of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Lizmarie S. Chávez
- School
of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Saachi Dalvi
- School
of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Hannah Abraham
- School
of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Nevinka Wickramanayake
- School
of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Sreenivas Yellayi
- School
of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - John Blazeck
- School
of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| |
Collapse
|
2
|
Lue NZ, Liau BB. Base editor screens for in situ mutational scanning at scale. Mol Cell 2023; 83:2167-2187. [PMID: 37390819 PMCID: PMC10330937 DOI: 10.1016/j.molcel.2023.06.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 05/30/2023] [Accepted: 06/06/2023] [Indexed: 07/02/2023]
Abstract
A fundamental challenge in biology is understanding the molecular details of protein function. How mutations alter protein activity, regulation, and response to drugs is of critical importance to human health. Recent years have seen the emergence of pooled base editor screens for in situ mutational scanning: the interrogation of protein sequence-function relationships by directly perturbing endogenous proteins in live cells. These studies have revealed the effects of disease-associated mutations, discovered novel drug resistance mechanisms, and generated biochemical insights into protein function. Here, we discuss how this "base editor scanning" approach has been applied to diverse biological questions, compare it with alternative techniques, and describe the emerging challenges that must be addressed to maximize its utility. Given its broad applicability toward profiling mutations across the proteome, base editor scanning promises to revolutionize the investigation of proteins in their native contexts.
Collapse
Affiliation(s)
- Nicholas Z Lue
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Brian B Liau
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.
| |
Collapse
|
3
|
Nguyen NK, Devilder MC, Gautreau-Rolland L, Fourgeux C, Sinha D, Poschmann J, Hourmant M, Bressollette-Bodin C, Saulquin X, McIlroy D. A cluster of broadly neutralizing IgG against BK polyomavirus in a repertoire dominated by IgM. Life Sci Alliance 2023; 6:e202201567. [PMID: 36717250 PMCID: PMC9887757 DOI: 10.26508/lsa.202201567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 12/30/2022] [Accepted: 01/04/2023] [Indexed: 01/31/2023] Open
Abstract
The BK polyomavirus (BKPyV) is an opportunistic pathogen, which is only pathogenic in immunosuppressed individuals, such as kidney transplant recipients, in whom BKPyV can cause significant morbidity. To identify broadly neutralizing antibodies against this virus, we used fluorescence-labeled BKPyV virus-like particles to sort BKPyV-specific B cells from the PBMC of KTx recipients, then single-cell RNAseq to obtain paired heavy- and light-chain antibody sequences from 2,106 sorted B cells. The BKPyV-specific repertoire was highly diverse in terms of both V-gene usage and clonotype diversity and included most of the IgM B cells, including many with extensive somatic hypermutation. In two patients where sufficient data were available, IgM B cells in the BKPyV-specific dataset had significant differences in V-gene usage compared with IgG B cells from the same patient. CDR3 sequence-based clustering allowed us to identify and characterize three broadly neutralizing "41F17-like" clonotypes that were predominantly IgG, suggesting that some specific BKPyV capsid epitopes are preferentially targeted by IgG.
Collapse
Affiliation(s)
- Ngoc-Khanh Nguyen
- Nantes Universitéhttps://ror.org/05c1qsg97 , CHU Nantes, INSERM, Center for Research in Transplantation and Translational Immunology, UMR 1064, ITUN, Nantes, France
| | - Marie-Claire Devilder
- Nantes Université, Inserm UMR 1307, CNRS UMR 6075, Université d'Angers, CRCI2NA, Nantes, France
| | - Laetitia Gautreau-Rolland
- Nantes Université, Inserm UMR 1307, CNRS UMR 6075, Université d'Angers, CRCI2NA, Nantes, France
- UFR Sciences et Techniques, Nantes Université, Nantes, France
| | - Cynthia Fourgeux
- Nantes Universitéhttps://ror.org/05c1qsg97 , CHU Nantes, INSERM, Center for Research in Transplantation and Translational Immunology, UMR 1064, ITUN, Nantes, France
| | - Debajyoti Sinha
- Nantes Universitéhttps://ror.org/05c1qsg97 , CHU Nantes, INSERM, Center for Research in Transplantation and Translational Immunology, UMR 1064, ITUN, Nantes, France
| | - Jeremie Poschmann
- Nantes Universitéhttps://ror.org/05c1qsg97 , CHU Nantes, INSERM, Center for Research in Transplantation and Translational Immunology, UMR 1064, ITUN, Nantes, France
| | - Maryvonne Hourmant
- CHU Nanteshttps://ror.org/03gnr7b55 , Nantes Université, Service de Néphrologie-Immunologie clinique, Nantes, France
| | - Céline Bressollette-Bodin
- Nantes Universitéhttps://ror.org/05c1qsg97 , CHU Nantes, INSERM, Center for Research in Transplantation and Translational Immunology, UMR 1064, ITUN, Nantes, France
- CHU Nanteshttps://ror.org/03gnr7b55 , Nantes Université, Service de Virologie, Nantes, France
- UFR Médecine, Nantes Université, Nantes, France
| | - Xavier Saulquin
- Nantes Université, Inserm UMR 1307, CNRS UMR 6075, Université d'Angers, CRCI2NA, Nantes, France
- UFR Sciences et Techniques, Nantes Université, Nantes, France
| | - Dorian McIlroy
- Nantes Universitéhttps://ror.org/05c1qsg97 , CHU Nantes, INSERM, Center for Research in Transplantation and Translational Immunology, UMR 1064, ITUN, Nantes, France
- UFR Sciences et Techniques, Nantes Université, Nantes, France
| |
Collapse
|
4
|
de Brito PM, Saruga A, Cardoso M, Goncalves J. Methods and cell-based strategies to produce antibody libraries: current state. Appl Microbiol Biotechnol 2021; 105:7215-7224. [PMID: 34524471 DOI: 10.1007/s00253-021-11570-x] [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: 03/15/2021] [Revised: 09/01/2021] [Accepted: 09/02/2021] [Indexed: 11/24/2022]
Abstract
Antibodies are critical components of the adaptive immune system, whose therapeutic applications have been growing exponentially in the last years. Discovery and development of therapeutic antibodies encompasses in vivo immunization, synthetic libraries, and surface display methodologies. To overcome some of their limitations, several platforms in higher eukaryotic cells have been developed. Moreover, these platforms aim to replicate in the bench both primary and secondary antibody diversification mechanisms that occur in vivo. Here, we describe the latest strategies that have been used to mirror both naïve and affinity-maturated antibody repertoire. KEY POINTS: • Therapeutic antibodies are one of the most promising classes of drugs to fight diseases. • Antibodies discovered through hybridoma or display technologies require further engineering. • Innovative antibody discovery platforms in higher eukaryotic cells have been developed.
Collapse
Affiliation(s)
- Paula Matos de Brito
- Faculty of Pharmacy, iMed.ULisboa - Research Institute for Medicines, University of Lisbon, Av. Professor Gama Pinto, 1649-019, Lisbon, Portugal
| | - Andreia Saruga
- Faculty of Pharmacy, iMed.ULisboa - Research Institute for Medicines, University of Lisbon, Av. Professor Gama Pinto, 1649-019, Lisbon, Portugal.,INESC MN - Instituto de Engenharia de Sistemas e Computadores - Microsystems and Nanotecnologies, R. Alves Redol 9, 1000-029, Lisbon, Portugal
| | - Miguel Cardoso
- Faculty of Pharmacy, iMed.ULisboa - Research Institute for Medicines, University of Lisbon, Av. Professor Gama Pinto, 1649-019, Lisbon, Portugal
| | - Joao Goncalves
- Faculty of Pharmacy, iMed.ULisboa - Research Institute for Medicines, University of Lisbon, Av. Professor Gama Pinto, 1649-019, Lisbon, Portugal.
| |
Collapse
|
5
|
Denes CE, Cole AJ, Aksoy YA, Li G, Neely GG, Hesselson D. Approaches to Enhance Precise CRISPR/Cas9-Mediated Genome Editing. Int J Mol Sci 2021; 22:8571. [PMID: 34445274 PMCID: PMC8395304 DOI: 10.3390/ijms22168571] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 07/30/2021] [Accepted: 08/06/2021] [Indexed: 12/17/2022] Open
Abstract
Modification of the human genome has immense potential for preventing or treating disease. Modern genome editing techniques based on CRISPR/Cas9 show great promise for altering disease-relevant genes. The efficacy of precision editing at CRISPR/Cas9-induced double-strand breaks is dependent on the relative activities of nuclear DNA repair pathways, including the homology-directed repair and error-prone non-homologous end-joining pathways. The competition between multiple DNA repair pathways generates mosaic and/or therapeutically undesirable editing outcomes. Importantly, genetic models have validated key DNA repair pathways as druggable targets for increasing editing efficacy. In this review, we highlight approaches that can be used to achieve the desired genome modification, including the latest progress using small molecule modulators and engineered CRISPR/Cas proteins to enhance precision editing.
Collapse
Affiliation(s)
- Christopher E. Denes
- The Dr. John and Anne Chong Lab for Functional Genomics, Charles Perkins Centre and School of Life & Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia; (C.E.D.); (G.L.)
| | - Alexander J. Cole
- Centenary Institute, The University of Sydney, Sydney, NSW 2006, Australia;
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia
| | - Yagiz Alp Aksoy
- Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia;
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW 2113, Australia
| | - Geng Li
- The Dr. John and Anne Chong Lab for Functional Genomics, Charles Perkins Centre and School of Life & Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia; (C.E.D.); (G.L.)
| | - Graham Gregory Neely
- The Dr. John and Anne Chong Lab for Functional Genomics, Charles Perkins Centre and School of Life & Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia; (C.E.D.); (G.L.)
- Centenary Institute, The University of Sydney, Sydney, NSW 2006, Australia;
| | - Daniel Hesselson
- Centenary Institute, The University of Sydney, Sydney, NSW 2006, Australia;
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia
| |
Collapse
|
6
|
Cheng C, Zhou M, Su Q, Steigmeyer A, Niu J. Genome editor-directed in vivo library diversification. Cell Chem Biol 2021; 28:1109-1118. [PMID: 34107297 DOI: 10.1016/j.chembiol.2021.05.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 04/08/2021] [Accepted: 05/10/2021] [Indexed: 10/21/2022]
Abstract
The generation of a library of variant genes is a prerequisite of directed evolution, a powerful tool for biomolecular engineering. As the number of all possible sequences often far exceeds the diversity of a practical library, methods that allow efficient library diversification in living cells are essential for in vivo directed evolution technologies to effectively sample the sequence space and allow hits to emerge. While traditional whole-genome mutagenesis often results in toxicity and the emergence of "cheater" mutations, recent developments that exploit the targeting and editing abilities of genome editors to facilitate in vivo library diversification have allowed for precise mutagenesis focused on specific genes of interest, higher mutational density, and reduced the occurrence of cheater mutations. This minireview summarizes recent advances in genome editor-directed in vivo library diversification and provides an outlook on their future applications in chemical biology.
Collapse
Affiliation(s)
- Cristina Cheng
- Department of Chemistry, Boston College, Chestnut Hill, MA 02467, USA
| | - Mi Zhou
- Department of Chemistry, Boston College, Chestnut Hill, MA 02467, USA
| | - Qiwen Su
- Department of Chemistry, Boston College, Chestnut Hill, MA 02467, USA
| | | | - Jia Niu
- Department of Chemistry, Boston College, Chestnut Hill, MA 02467, USA.
| |
Collapse
|
7
|
Hendel SJ, Shoulders MD. Directed evolution in mammalian cells. Nat Methods 2021; 18:346-357. [PMID: 33828274 DOI: 10.1038/s41592-021-01090-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 02/01/2021] [Accepted: 02/09/2021] [Indexed: 02/06/2023]
Abstract
Directed evolution experiments are typically carried out using in vitro systems, bacteria, or yeast-even when the goal is to probe or modulate mammalian biology. Performing directed evolution in systems that do not match the intended mammalian environment severely constrains the scope and functionality of the targets that can be evolved. We review new platforms that are now making it possible to use the mammalian cell itself as the setting for directed evolution and present an overview of frontier challenges and high-impact targets for this approach.
Collapse
Affiliation(s)
- Samuel J Hendel
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Matthew D Shoulders
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA.
| |
Collapse
|
8
|
Iaffaldano B, Reiser J. Full-Spectrum Targeted Mutagenesis in Plant and Animal Cells. Int J Mol Sci 2021; 22:ijms22020857. [PMID: 33467049 PMCID: PMC7830027 DOI: 10.3390/ijms22020857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 12/31/2020] [Accepted: 01/13/2021] [Indexed: 11/26/2022] Open
Abstract
Directed evolution is a powerful approach for protein engineering and functional studies. However, directed evolution outputs from bacterial and yeast systems do not always translate to higher organisms. In situ directed evolution in plant and animal cells has previously been limited by an inability to introduce targeted DNA sequence diversity. New hypermutation tools have emerged that can generate targeted mutations in plant and animal cells, by recruiting mutagenic proteins to defined DNA loci. Progress in this field, such as the development of CRISPR-derived hypermutators, now allows for all DNA nucleotides within user-defined regions to be altered through the recruitment of error-prone DNA polymerases or highly active DNA deaminases. The further engineering of these mutagenesis systems will potentially allow for all transition and transversion substitutions to be generated within user-defined genomic windows. Such targeted full-spectrum mutagenesis tools would provide a powerful platform for evolving antibodies, enzymes, structural proteins and RNAs with specific desired properties in relevant cellular contexts. These tools are expected to benefit many aspects of biological research and, ultimately, clinical applications.
Collapse
|
9
|
Oh EJ, Liu R, Liang L, Freed EF, Eckert CA, Gill RT. Multiplex Evolution of Antibody Fragments Utilizing a Yeast Surface Display Platform. ACS Synth Biol 2020; 9:2197-2202. [PMID: 32551581 DOI: 10.1021/acssynbio.0c00159] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Advances in high-throughput synthetic biology technologies based on the CRISPR/Cas9 system have enabled a comprehensive assessment of mutations conferring desired phenotypes, as well as a better understanding of genotype-phenotype correlations in protein engineering. Engineering antibodies to enhance properties such as binding affinity and stability plays an essential role in therapeutic applications. Here we report a method, multiplex navigation of antibody structure (MINAS), that combines a CRISPR/Cas9-based trackable editing method and fluorescent-activated cell sorting (FACS) of yeast-displayed libraries. We designed mutations in all of the complementarity-determining and framework regions of a well-characterized scFv antibody and mapped the contribution of these regions to enhanced properties. We identified specific mutants that showed higher binding affinities up to 100-fold compared to the wild-type. This study expands the applicability of CRISPR/Cas9-based trackable protein engineering by combining it with a surface display platform.
Collapse
Affiliation(s)
- Eun Joong Oh
- Renewable and Sustainable Energy Institute (RASEI), University of Colorado Boulder, Boulder, Colorado 80303, United States
| | - Rongming Liu
- Renewable and Sustainable Energy Institute (RASEI), University of Colorado Boulder, Boulder, Colorado 80303, United States
| | - Liya Liang
- Renewable and Sustainable Energy Institute (RASEI), University of Colorado Boulder, Boulder, Colorado 80303, United States
| | - Emily F. Freed
- Renewable and Sustainable Energy Institute (RASEI), University of Colorado Boulder, Boulder, Colorado 80303, United States
| | - Carrie A. Eckert
- Renewable and Sustainable Energy Institute (RASEI), University of Colorado Boulder, Boulder, Colorado 80303, United States
- National Renewable Energy Laboratory (NREL), Bioscience Center, Golden, Colorado 80401, United States
| | - Ryan T. Gill
- Renewable and Sustainable Energy Institute (RASEI), University of Colorado Boulder, Boulder, Colorado 80303, United States
- Novo Nordisk Foundation Center for Biosustainability, Danish Technical University, Lyngby, Denmark
| |
Collapse
|
10
|
Luo R, Zhao Y, Fan Y, An L, Jiang T, Ma S, Hang H. High efficiency CHO cell display-based antibody maturation. Sci Rep 2020; 10:8102. [PMID: 32415149 PMCID: PMC7229201 DOI: 10.1038/s41598-020-65044-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 04/21/2020] [Indexed: 11/09/2022] Open
Abstract
Previously, we developed a CHO cell display-based antibody maturation procedure in which an antibody (or other protein) gene of interest was induced to mutate by activation-induced cytidine deaminase (AID) and then form a library by simply proliferating the CHO cells in culture. In this study, we further improved the efficiency of this maturation system by reengineering AID, and optimizing the nucleic acid sequence of the target antibody gene and AID gene as well as the protocol for AID gene transfection. These changes have increased both the mutation rate and the number of mutation type of antibody genes by more than 10 fold, and greatly improved the maturation efficiency of antibody/other proteins.
Collapse
Affiliation(s)
- Ruiqi Luo
- Key Laboratory for Protein and Peptide Pharmaceuticals, National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Yun Zhao
- Key Laboratory for Protein and Peptide Pharmaceuticals, National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yingjun Fan
- Key Laboratory for Protein and Peptide Pharmaceuticals, National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Lili An
- Key Laboratory for Protein and Peptide Pharmaceuticals, National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Tao Jiang
- University of Chinese Academy of Sciences, Beijing, 100039, China.,National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Shaohua Ma
- Department of Thoracic Surgery, Peking University Third Hospital, Beijing, 100191, China.
| | - Haiying Hang
- Key Laboratory for Protein and Peptide Pharmaceuticals, National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
| |
Collapse
|
11
|
Burke MJ, Stockley PG, Boyes J. Broadly Neutralizing Bovine Antibodies: Highly Effective New Tools against Evasive Pathogens? Viruses 2020; 12:v12040473. [PMID: 32331321 PMCID: PMC7232318 DOI: 10.3390/v12040473] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Revised: 04/16/2020] [Accepted: 04/21/2020] [Indexed: 02/07/2023] Open
Abstract
Potent antibody-mediated neutralization is critical for an organism to combat the vast array of pathogens it will face during its lifetime. Due to the potential genetic diversity of some viruses, such as HIV-1 and influenza, standard neutralizing antibodies are often ineffective or easily evaded as their targets are masked or rapidly mutated. This has thwarted efforts to both prevent and treat HIV-1 infections and means that entirely new formulations are required to vaccinate against influenza each year. However, some rare antibodies isolated from infected individuals confer broad and potent neutralization. A subset of these broadly neutralizing antibodies possesses a long complementarity-determining 3 region of the immunoglobulin heavy chain (CDR H3). This feature generates unique antigen binding site configurations that can engage conserved but otherwise inaccessible epitope targets thus neutralizing many viral variants. Remarkably, ultralong CDR H3s are a common feature of the cow antibody repertoire and are encoded by a single variable, diversity, joining (VDJ) recombination that is extensively diversified prior to antigen exposure. Recently, it was shown that cows rapidly generate a broadly neutralizing response upon exposure to HIV-1 and this is primarily mediated by these novel ultralong antibody types. This review summarises the current knowledge of these unusual CDR H3 structures and discusses their known and potential future uses.
Collapse
Affiliation(s)
- Matthew J. Burke
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK; (M.J.B.); (P.G.S.)
| | - Peter G. Stockley
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK; (M.J.B.); (P.G.S.)
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Joan Boyes
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK; (M.J.B.); (P.G.S.)
- Correspondence:
| |
Collapse
|
12
|
Wang J, Zhang C, Feng B. The rapidly advancing Class 2 CRISPR-Cas technologies: A customizable toolbox for molecular manipulations. J Cell Mol Med 2020; 24:3256-3270. [PMID: 32037739 PMCID: PMC7131926 DOI: 10.1111/jcmm.15039] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 01/09/2020] [Accepted: 01/14/2020] [Indexed: 12/11/2022] Open
Abstract
The CRISPR-Cas technologies derived from bacterial and archaeal adaptive immune systems have emerged as a series of groundbreaking nucleic acid-guided gene editing tools, ultimately standing out among several engineered nucleases because of their high efficiency, sequence-specific targeting, ease of programming and versatility. Facilitated by the advancement across multiple disciplines such as bioinformatics, structural biology and high-throughput sequencing, the discoveries and engineering of various innovative CRISPR-Cas systems are rapidly expanding the CRISPR toolbox. This is revolutionizing not only genome editing but also various other types of nucleic acid-guided manipulations such as transcriptional control and genomic imaging. Meanwhile, the adaptation of various CRISPR strategies in multiple settings has realized numerous previously non-existing applications, ranging from the introduction of sophisticated approaches in basic research to impactful agricultural and therapeutic applications. Here, we summarize the recent advances of CRISPR technologies and strategies, as well as their impactful applications.
Collapse
Affiliation(s)
- Jingyi Wang
- Key Laboratory for Regenerative Medicine, Ministry of EducationSchool of Biomedical Sciences, Faculty of MedicineCUHK-GIBH Joint Research Laboratory on Stem Cells and Regenerative MedicineThe Chinese University of Hong KongHong Kong SARChina
| | - Chenzi Zhang
- Key Laboratory for Regenerative Medicine, Ministry of EducationSchool of Biomedical Sciences, Faculty of MedicineCUHK-GIBH Joint Research Laboratory on Stem Cells and Regenerative MedicineThe Chinese University of Hong KongHong Kong SARChina
- Institute for Tissue Engineering and Regenerative Medicine (iTERM)The Chinese University of Hong KongHong Kong SARChina
| | - Bo Feng
- Key Laboratory for Regenerative Medicine, Ministry of EducationSchool of Biomedical Sciences, Faculty of MedicineCUHK-GIBH Joint Research Laboratory on Stem Cells and Regenerative MedicineThe Chinese University of Hong KongHong Kong SARChina
- Institute for Tissue Engineering and Regenerative Medicine (iTERM)The Chinese University of Hong KongHong Kong SARChina
- Guangzhou Institute of Biomedicine and Health, Chinese Academy of SciencesGuangzhou Regenerative Medicine and Health Guangdong LaboratoryGuangzhouChina
| |
Collapse
|
13
|
Ministro JH, Oliveira SS, Oliveira JG, Cardoso M, Aires-da-Silva F, Corte-Real S, Goncalves J. Synthetic antibody discovery against native antigens by CRISPR/Cas9-library generation and endoplasmic reticulum screening. Appl Microbiol Biotechnol 2020; 104:2501-2512. [PMID: 32020276 DOI: 10.1007/s00253-020-10423-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Revised: 01/18/2020] [Accepted: 01/26/2020] [Indexed: 01/03/2023]
Abstract
Despite the significant advances of antibodies as therapeutic agents, there is still much room for improvement concerning the discovery of these macromolecules. Here, we present a new synthetic cell-based strategy that takes advantage of eukaryotic cell biology to produce highly diverse antibody libraries and, simultaneously, link them to a high-throughput selection mechanism, replicating B cell diversification mechanisms. The interference of site-specific recognition by CRISPR/Cas9 with error-prone DNA repair mechanisms was explored for the generation of diversity, in a cell population containing a gene for a light chain antibody fragment. We achieved up to 93% of cells containing a mutated antibody gene after diversification mechanisms, specifically inside one of the antigen-binding sites. This targeted variability strategy was then integrated into an intracellular selection mechanism. By fusing the antibody with a KDEL retention signal, the interaction of antibodies and native membrane antigens occurs inside the endoplasmic reticulum during the process of protein secretion, enabling the detection of high-quality leads for expression and affinity by flow cytometry. We successfully obtained antibody lead candidates against CD3 as proof of concept. In summary, we developed a novel antibody discovery platform against native antigens by endoplasmic synthetic library generation using CRISPR/Cas9, which will contribute to a faster discovery of new biotherapeutic molecules, reducing the time-to-market.
Collapse
Affiliation(s)
- Joana H Ministro
- iMed.ULisboa - Research Institute for Medicines, Faculty of Pharmacy, University of Lisbon, Av. Professor Gama Pinto, 1649-019, Lisbon, Portugal.,Technophage SA, Av. Prof. Egas Moniz, Edifício Egas Moniz, 1649-028, Lisbon, Portugal
| | - Soraia S Oliveira
- iMed.ULisboa - Research Institute for Medicines, Faculty of Pharmacy, University of Lisbon, Av. Professor Gama Pinto, 1649-019, Lisbon, Portugal.,Technophage SA, Av. Prof. Egas Moniz, Edifício Egas Moniz, 1649-028, Lisbon, Portugal
| | - Joana G Oliveira
- iMed.ULisboa - Research Institute for Medicines, Faculty of Pharmacy, University of Lisbon, Av. Professor Gama Pinto, 1649-019, Lisbon, Portugal.,Technophage SA, Av. Prof. Egas Moniz, Edifício Egas Moniz, 1649-028, Lisbon, Portugal
| | - Miguel Cardoso
- iMed.ULisboa - Research Institute for Medicines, Faculty of Pharmacy, University of Lisbon, Av. Professor Gama Pinto, 1649-019, Lisbon, Portugal
| | - Frederico Aires-da-Silva
- CIISA - Faculdade de Medicina Veterinária, Universidade de Lisboa, Av. da Universidade Técnica, 1300-477, Lisbon, Portugal
| | - Sofia Corte-Real
- iMed.ULisboa - Research Institute for Medicines, Faculty of Pharmacy, University of Lisbon, Av. Professor Gama Pinto, 1649-019, Lisbon, Portugal.,Technophage SA, Av. Prof. Egas Moniz, Edifício Egas Moniz, 1649-028, Lisbon, Portugal
| | - Joao Goncalves
- iMed.ULisboa - Research Institute for Medicines, Faculty of Pharmacy, University of Lisbon, Av. Professor Gama Pinto, 1649-019, Lisbon, Portugal.
| |
Collapse
|