1
|
Sahu SU, Castro M, Muldoon JJ, Asija K, Wyman SK, Krishnappa N, Eyquem J, Nguyen DN, Wilson RC. Peptide-enabled ribonucleoprotein delivery for CRISPR engineering (PERC) in primary human immune cells and hematopoietic stem cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.14.603391. [PMID: 39071446 PMCID: PMC11275745 DOI: 10.1101/2024.07.14.603391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Peptide-enabled ribonucleoprotein delivery for CRISPR engineering (PERC) is a new approach for ex vivo genome editing of primary human cells. PERC uses a single amphiphilic peptide reagent to mediate intracellular delivery of the same pre-formed CRISPR ribonucleoprotein enzymes that are broadly used in research and therapeutics, resulting in high-efficiency editing of stimulated immune cells and cultured hematopoietic stem and progenitor cells (HSPCs). PERC facilitates nuclease-mediated gene knockout, precise transgene knock-in, and base editing. PERC involves mixing the CRISPR ribonucleoprotein enzyme with peptide and then incubating the formulation with cultured cells. For efficient transgene knock-in, adeno-associated virus (AAV) bearing homology-directed repair template DNA may be included. In contrast to electroporation, PERC is appealing as it requires no dedicated hardware and has less impact on cell phenotype and viability. Due to the gentle nature of PERC, delivery can be performed multiple times without substantial impact to cell health or phenotype. Here we report methods for improved PERC-mediated editing of T cells as well as novel methods for PERC-mediated editing of HSPCs, including knockout and precise knock-in. Editing efficiencies can surpass 90% using either Cas9 or Cas12a in primary T cells or HSPCs. Because PERC calls for only three readily available reagents - protein, RNA, and peptide - and does not require dedicated hardware for any step, PERC demands no special expertise and is exceptionally straightforward to adopt. The inherent compatibility of PERC with established cell engineering pipelines makes this approach appealing for rapid deployment in research and clinical settings.
Collapse
|
2
|
Peng D, Vangipuram M, Wong J, Leonetti MD. protoSpaceJAM: an open-source, customizable and web-accessible design platform for CRISPR/Cas insertional knock-in. Nucleic Acids Res 2024:gkae553. [PMID: 38922690 DOI: 10.1093/nar/gkae553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 06/06/2024] [Accepted: 06/17/2024] [Indexed: 06/28/2024] Open
Abstract
CRISPR/Cas-mediated knock-in of DNA sequences enables precise genome engineering for research and therapeutic applications. However, designing effective guide RNAs (gRNAs) and homology-directed repair (HDR) donors remains a bottleneck. Here, we present protoSpaceJAM, an open-source algorithm to automate and optimize gRNA and HDR donor design for CRISPR/Cas insertional knock-in experiments, currently supporting SpCas9, SpCas9-VQR and enAsCas12a Cas enzymes. protoSpaceJAM utilizes biological rules to rank gRNAs based on specificity, distance to insertion site, and position relative to regulatory regions. protoSpaceJAM can introduce 'recoding' mutations (silent mutations and mutations in non-coding sequences) in HDR donors to prevent re-cutting and increase knock-in efficiency. Users can customize parameters and design double-stranded or single-stranded donors. We validated protoSpaceJAM's design rules by demonstrating increased knock-in efficiency with recoding mutations and optimal strand selection for single-stranded donors. An additional module enables the design of genotyping primers for deep sequencing of edited alleles. Overall, protoSpaceJAM streamlines and optimizes CRISPR knock-in experimental design in a flexible and modular manner to benefit diverse research and therapeutic applications. protoSpaceJAM is available open-source as an interactive web tool at protospacejam.czbiohub.org or as a standalone Python package at github.com/czbiohub-sf/protoSpaceJAM.
Collapse
Affiliation(s)
- Duo Peng
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | | | - Joan Wong
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | | |
Collapse
|
3
|
Singh PK, Devanna BN, Dubey H, Singh P, Joshi G, Kumar R. The potential of genome editing to create novel alleles of resistance genes in rice. Front Genome Ed 2024; 6:1415244. [PMID: 38933684 PMCID: PMC11201548 DOI: 10.3389/fgeed.2024.1415244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Accepted: 05/21/2024] [Indexed: 06/28/2024] Open
Abstract
Rice, a staple food for a significant portion of the global population, faces persistent threats from various pathogens and pests, necessitating the development of resilient crop varieties. Deployment of resistance genes in rice is the best practice to manage diseases and reduce environmental damage by reducing the application of agro-chemicals. Genome editing technologies, such as CRISPR-Cas, have revolutionized the field of molecular biology, offering precise and efficient tools for targeted modifications within the rice genome. This study delves into the application of these tools to engineer novel alleles of resistance genes in rice, aiming to enhance the plant's innate ability to combat evolving threats. By harnessing the power of genome editing, researchers can introduce tailored genetic modifications that bolster the plant's defense mechanisms without compromising its essential characteristics. In this study, we synthesize recent advancements in genome editing methodologies applicable to rice and discuss the ethical considerations and regulatory frameworks surrounding the creation of genetically modified crops. Additionally, it explores potential challenges and future prospects for deploying edited rice varieties in agricultural landscapes. In summary, this study highlights the promise of genome editing in reshaping the genetic landscape of rice to confront emerging challenges, contributing to global food security and sustainable agriculture practices.
Collapse
Affiliation(s)
- Pankaj Kumar Singh
- Department of Biotechnology, University Centre for Research & Development, Chandigarh University, Mohali, Punjab, India
| | | | - Himanshu Dubey
- Seri-Biotech Research Laboratory, Central Silk Board, Bangalore, India
| | - Prabhakar Singh
- Botany Department, Banaras Hindu University, Varanasi, India
| | - Gaurav Joshi
- Department of Pharmaceutical Sciences, Hemvati Nandan Bahuguna Garhwal (A Central University), Tehri Garhwal, Uttarakhand, India
| | - Roshan Kumar
- Department of Microbiology, Central University of Punjab, Bathinda, Punjab, India
| |
Collapse
|
4
|
Cloarec-Ung FM, Beaulieu J, Suthananthan A, Lehnertz B, Sauvageau G, Sheppard HM, Knapp DJHF. Near-perfect precise on-target editing of human hematopoietic stem and progenitor cells. eLife 2024; 12:RP91288. [PMID: 38829685 PMCID: PMC11147503 DOI: 10.7554/elife.91288] [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] [Indexed: 06/05/2024] Open
Abstract
Precision gene editing in primary hematopoietic stem and progenitor cells (HSPCs) would facilitate both curative treatments for monogenic disorders as well as disease modelling. Precise efficiencies even with the CRISPR/Cas system, however, remain limited. Through an optimization of guide RNA delivery, donor design, and additives, we have now obtained mean precise editing efficiencies >90% on primary cord blood HSCPs with minimal toxicity and without observed off-target editing. The main protocol modifications needed to achieve such high efficiencies were the addition of the DNA-PK inhibitor AZD7648, and the inclusion of spacer-breaking silent mutations in the donor in addition to mutations disrupting the PAM sequence. Critically, editing was even across the progenitor hierarchy, did not substantially distort the hierarchy or affect lineage outputs in colony-forming cell assays or the frequency of high self-renewal potential long-term culture initiating cells. As modelling of many diseases requires heterozygosity, we also demonstrated that the overall editing and zygosity can be tuned by adding in defined mixtures of mutant and wild-type donors. With these optimizations, editing at near-perfect efficiency can now be accomplished directly in human HSPCs. This will open new avenues in both therapeutic strategies and disease modelling.
Collapse
Affiliation(s)
- Fanny-Mei Cloarec-Ung
- Institut de Recherche en Immunologie et en Cancérologie, Université de MontréalMontéalCanada
| | - Jamie Beaulieu
- Institut de Recherche en Immunologie et en Cancérologie, Université de MontréalMontéalCanada
| | - Arunan Suthananthan
- Institut de Recherche en Immunologie et en Cancérologie, Université de MontréalMontéalCanada
| | - Bernhard Lehnertz
- Institut de Recherche en Immunologie et en Cancérologie, Université de MontréalMontéalCanada
| | - Guy Sauvageau
- Institut de Recherche en Immunologie et en Cancérologie, Université de MontréalMontéalCanada
| | - Hilary M Sheppard
- Institut de Recherche en Immunologie et en Cancérologie, Université de MontréalMontéalCanada
- School of Biological Sciences, Faculty of Science, University of AucklandAucklandNew Zealand
| | - David JHF Knapp
- Institut de Recherche en Immunologie et en Cancérologie, Université de MontréalMontéalCanada
- Département de Pathologie et Biologie Cellulaire, Université de MontréalMontréalCanada
| |
Collapse
|
5
|
Berthault C, Gaucher S, Gouin O, Schmitt A, Chen M, Woodley D, Titeux M, Hovnanian A, Izmiryan A. Highly Efficient Ex Vivo Correction of COL7A1 through Ribonucleoprotein-Based CRISPR/Cas9 and Homology-Directed Repair to Treat Recessive Dystrophic Epidermolysis Bullosa. J Invest Dermatol 2024; 144:1322-1333.e13. [PMID: 38043638 DOI: 10.1016/j.jid.2023.10.035] [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: 03/23/2023] [Revised: 10/19/2023] [Accepted: 10/30/2023] [Indexed: 12/05/2023]
Abstract
Recessive dystrophic epidermolysis bullosa (RDEB) is a rare and severe genetic skin disease responsible for blistering of the skin and mucosa after minor trauma. RDEB is caused by a wide variety of variants in COL7A1 encoding type VII Collagen, the major component of anchoring fibrils that form key attachment structures for dermal-epidermal adherence. In this study, we achieved highly efficient COL7A1 editing in primary RDEB keratinocytes and fibroblasts from 2 patients homozygous for the c.6508C>T (p.Gln2170∗) variant through CRISPR/Cas9-mediated homology-directed repair. Three guide RNAs targeting the c.6508C>T variant or harboring sequences were delivered together with high-fidelity Cas9 as a ribonucleoprotein complex. Among them, one achieved 73% cleavage activity in primary RDEB keratinocytes and RDEB fibroblasts. Then, we treated RDEB keratinocytes and RDEB fibroblasts with this specific ribonucleoprotein complex and the corresponding donor template delivered as single-stranded oligodeoxynucleotide and achieved up to 58% of genetic correction as well as type VII Collagen rescue. Finally, grafting of corrected 3-dimensional skin onto nude mice induced re-expression and normal localization of type VII Collagen as well as anchoring fibril formation at the dermal-epidermal junction 5 and 10 weeks after grafting. With this promising nonviral approach, we achieved therapeutically relevant specific gene editing that could be applicable to all variants in exon 80 of COL7A1 in primary RDEB cells.
Collapse
Affiliation(s)
- Camille Berthault
- INSERM UMR 1163, Laboratory of Genetic skin diseases, Imagine Institute, Paris, France; Paris Cité University, Paris, France
| | - Sonia Gaucher
- INSERM UMR 1163, Laboratory of Genetic skin diseases, Imagine Institute, Paris, France; Paris Cité University, Paris, France
| | - Olivier Gouin
- INSERM UMR 1163, Laboratory of Genetic skin diseases, Imagine Institute, Paris, France; Paris Cité University, Paris, France
| | - Alain Schmitt
- Electronic Microscopy Facility, INSERM UMR 1016, Cochin Institute, Paris, France
| | - Mei Chen
- Department of Dermatology, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - David Woodley
- Department of Dermatology, Keck School of Medicine, University of Southern California, Los Angeles, California, USA; Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Matthias Titeux
- INSERM UMR 1163, Laboratory of Genetic skin diseases, Imagine Institute, Paris, France; Paris Cité University, Paris, France
| | - Alain Hovnanian
- INSERM UMR 1163, Laboratory of Genetic skin diseases, Imagine Institute, Paris, France; Paris Cité University, Paris, France; Department of Genomic Medicine for Rare Diseases, Necker Hospital for Sick Children, Assistance Publique-Hôpitaux de Paris (APHP), Paris, France
| | - Araksya Izmiryan
- INSERM UMR 1163, Laboratory of Genetic skin diseases, Imagine Institute, Paris, France; Paris Cité University, Paris, France.
| |
Collapse
|
6
|
Haideri T, Lin J, Bao X, Lian XL. MAGIK: A rapid and efficient method to create lineage-specific reporters in human pluripotent stem cells. Stem Cell Reports 2024; 19:744-757. [PMID: 38579711 PMCID: PMC11103783 DOI: 10.1016/j.stemcr.2024.03.005] [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: 03/01/2024] [Revised: 03/08/2024] [Accepted: 03/08/2024] [Indexed: 04/07/2024] Open
Abstract
Precise insertion of fluorescent proteins into lineage-specific genes in human pluripotent stem cells (hPSCs) presents challenges due to low knockin efficiency and difficulties in isolating targeted cells. To overcome these hurdles, we present the modified mRNA (ModRNA)-based Activation for Gene Insertion and Knockin (MAGIK) method. MAGIK operates in two steps: first, it uses a Cas9-2A-p53DD modRNA with a mini-donor plasmid (without a drug selection cassette) to significantly enhance efficiency. Second, a deactivated Cas9 activator modRNA and a 'dead' guide RNA are used to temporarily activate the targeted gene, allowing for live cell sorting of targeted cells. Consequently, MAGIK eliminates the need for drug selection cassettes or labor-intensive single-cell colony screening, expediting precise gene editing. We showed MAGIK can be utilized to insert fluorescent proteins into various genes, including SOX17, NKX6.1, NKX2.5, and PDX1, across multiple hPSC lines. This underscores its robust performance and offers a promising solution for achieving knockin in hPSCs within a significantly shortened time frame.
Collapse
Affiliation(s)
- Tahir Haideri
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA 16802, USA
| | - Jirong Lin
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA 16802, USA
| | - Xiaoping Bao
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, IN 47907, USA.
| | - Xiaojun Lance Lian
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA 16802, USA; Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA; Department of Biology, Pennsylvania State University, University Park, PA 16802, USA.
| |
Collapse
|
7
|
Zhao Y, Li X, Liu C, Jiang C, Guo X, Xu Q, Yin Z, Liu Z, Mu Y. Improving the Efficiency of CRISPR Ribonucleoprotein-Mediated Precise Gene Editing by Small Molecules in Porcine Fibroblasts. Animals (Basel) 2024; 14:719. [PMID: 38473105 DOI: 10.3390/ani14050719] [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: 02/06/2024] [Revised: 02/21/2024] [Accepted: 02/23/2024] [Indexed: 03/14/2024] Open
Abstract
The aim of this study was to verify whether small molecules can improve the efficiency of precision gene editing using clustered regularly interspaced short palindromic repeats (CRISPR) ribonucleoprotein (RNP) in porcine cells. CRISPR associated 9 (Cas9) protein, small guide RNA (sgRNA), phosphorothioate-modified single-stranded oligonucleotides (ssODN), and different small molecules were used to generate precise nucleotide substitutions at the insulin (INS) gene by homology-directed repair (HDR) in porcine fetal fibroblasts (PFFs). These components were introduced into PFFs via electroporation, followed by polymerase chain reaction (PCR) for the target site. All samples were sequenced and analyzed, and the efficiencies of different small molecules at the target site were compared. The results showed that the optimal concentrations of the small molecules, including L-189, NU7441, SCR7, L755507, RS-1, and Brefeldin A, for in vitro-cultured PFFs' viability were determined. Compared with the control group, the single small molecules including L-189, NU7441, SCR7, L755507, RS-1, and Brefeldin A increased the efficiency of HDR-mediated precise gene editing from 1.71-fold to 2.28-fold, respectively. There are no benefits in using the combination of two small molecules, since none of the combinations improved the precise gene editing efficiency compared to single small molecules. In conclusion, these results suggested that a single small molecule can increase the efficiency of CRISPR RNP-mediated precise gene editing in porcine cells.
Collapse
Affiliation(s)
- Yunjing Zhao
- Key Laboratory of Animal Cellular and Genetic Engineering of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Xinyu Li
- Key Laboratory of Animal Cellular and Genetic Engineering of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Chang Liu
- Key Laboratory of Animal Cellular and Genetic Engineering of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China
| | - Chaoqian Jiang
- Key Laboratory of Animal Cellular and Genetic Engineering of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China
| | - Xiaochen Guo
- Key Laboratory of Animal Cellular and Genetic Engineering of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Qianqian Xu
- Key Laboratory of Animal Cellular and Genetic Engineering of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Zhi Yin
- Key Laboratory of Animal Cellular and Genetic Engineering of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Zhonghua Liu
- Key Laboratory of Animal Cellular and Genetic Engineering of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Yanshuang Mu
- Key Laboratory of Animal Cellular and Genetic Engineering of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| |
Collapse
|
8
|
Namipashaki A, Pugsley K, Liu X, Abrehart K, Lim SM, Sun G, Herold MJ, Polo JM, Bellgrove MA, Hawi Z. Integration of xeno-free single-cell cloning in CRISPR-mediated DNA editing of human iPSCs improves homogeneity and methodological efficiency of cellular disease modeling. Stem Cell Reports 2023; 18:2515-2527. [PMID: 37977144 PMCID: PMC10724053 DOI: 10.1016/j.stemcr.2023.10.013] [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: 12/13/2022] [Revised: 10/20/2023] [Accepted: 10/20/2023] [Indexed: 11/19/2023] Open
Abstract
The capability to generate induced pluripotent stem cell (iPSC) lines, in tandem with CRISPR-Cas9 DNA editing, offers great promise to understand the underlying genetic mechanisms of human disease. The low efficiency of available methods for homogeneous expansion of singularized CRISPR-transfected iPSCs necessitates the coculture of transfected cells in mixed populations and/or on feeder layers. Consequently, edited cells must be purified using labor-intensive screening and selection, culminating in inefficient editing. Here, we provide a xeno-free method for single-cell cloning of CRISPRed iPSCs achieving a clonal survival of up to 70% within 7-10 days. This is accomplished through improved viability of the transfected cells, paralleled with provision of an enriched environment for the robust establishment and proliferation of singularized iPSC clones. Enhanced cell survival was accompanied by a high transfection efficiency exceeding 97%, and editing efficiencies of 50%-65% for NHEJ and 10% for HDR, indicative of the method's utility in stem cell disease modeling.
Collapse
Affiliation(s)
- Atefeh Namipashaki
- Turner Institute for Brain and Mental Health, School of Psychological Sciences, Monash University, Melbourne, VIC, Australia
| | - Kealan Pugsley
- Turner Institute for Brain and Mental Health, School of Psychological Sciences, Monash University, Melbourne, VIC, Australia
| | - Xiaodong Liu
- Department of Anatomy & Developmental Biology, Monash University, Melbourne, VIC 3800, Australia; Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Melbourne, VIC 3800, Australia; Australian Regenerative Medicine Institute, Monash University, Melbourne, VIC 3800, Australia
| | - Kirra Abrehart
- Turner Institute for Brain and Mental Health, School of Psychological Sciences, Monash University, Melbourne, VIC, Australia
| | - Sue Mei Lim
- Department of Anatomy & Developmental Biology, Monash University, Melbourne, VIC 3800, Australia; Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Melbourne, VIC 3800, Australia; Australian Regenerative Medicine Institute, Monash University, Melbourne, VIC 3800, Australia
| | - Guizhi Sun
- Department of Anatomy & Developmental Biology, Monash University, Melbourne, VIC 3800, Australia; Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Melbourne, VIC 3800, Australia; Australian Regenerative Medicine Institute, Monash University, Melbourne, VIC 3800, Australia
| | - Marco J Herold
- Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia; Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Jose M Polo
- Department of Anatomy & Developmental Biology, Monash University, Melbourne, VIC 3800, Australia; Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Melbourne, VIC 3800, Australia; Australian Regenerative Medicine Institute, Monash University, Melbourne, VIC 3800, Australia; Adelaide Centre for Epigenetics and the South Australian Immunogenomics Cancer Institute, The University of Adelaide, Adelaide, SA, Australia
| | - Mark A Bellgrove
- Turner Institute for Brain and Mental Health, School of Psychological Sciences, Monash University, Melbourne, VIC, Australia
| | - Ziarih Hawi
- Turner Institute for Brain and Mental Health, School of Psychological Sciences, Monash University, Melbourne, VIC, Australia.
| |
Collapse
|
9
|
Stolzenburg LR, Esmaeeli S, Kulkarni AS, Murphy E, Kwon T, Preiss C, Bahnassawy L, Stender JD, Manos JD, Reinhardt P, Rahimov F, Waring JF, Ramathal CY. Functional characterization of a single nucleotide polymorphism associated with Alzheimer's disease in a hiPSC-based neuron model. PLoS One 2023; 18:e0291029. [PMID: 37751459 PMCID: PMC10521995 DOI: 10.1371/journal.pone.0291029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 08/20/2023] [Indexed: 09/28/2023] Open
Abstract
Neurodegenerative diseases encompass a group of debilitating conditions resulting from progressive nerve cell death. Of these, Alzheimer's disease (AD) occurs most frequently, but is currently incurable and has limited treatment success. Late onset AD, the most common form, is highly heritable but is caused by a combination of non-genetic risk factors and many low-effect genetic variants whose disease-causing mechanisms remain unclear. By mining the FinnGen study database of phenome-wide association studies, we identified a rare variant, rs148726219, enriched in the Finnish population that is associated with AD risk and dementia, and appears to have arisen on a common haplotype with older AD-associated variants such as rs429358. The rs148726219 variant lies in an overlapping intron of the FosB proto-oncogene (FOSB) and ERCC excision repair 1 (ERCC1) genes. To understand the impact of this SNP on disease phenotypes, we performed CRISPR/Cas9 editing in a human induced pluripotent stem cell (hiPSC) line to generate isogenic clones harboring heterozygous and homozygous alleles of rs148726219. hiPSC clones differentiated into induced excitatory neurons (iNs) did not exhibit detectable molecular or morphological variation in differentiation potential compared to isogenic controls. However, global transcriptome analysis showed differential regulation of nearby genes and upregulation of several biological pathways related to neuronal function, particularly synaptogenesis and calcium signaling, specifically in mature iNs harboring rs148726219 homozygous and heterozygous alleles. Functional differences in iN circuit maturation as measured by calcium imaging were observed across genotypes. Edited mature iNs also displayed downregulation of unfolded protein response and cell death pathways. This study implicates a phenotypic impact of rs148726219 in the context of mature neurons, consistent with its identification in late onset AD, and underscores a hiPSC-based experimental model to functionalize GWAS-identified variants.
Collapse
Affiliation(s)
| | - Sahar Esmaeeli
- AbbVie Inc., North Chicago, Illinois, United States of America
| | | | - Erin Murphy
- AbbVie Inc., North Chicago, Illinois, United States of America
| | - Taekyung Kwon
- AbbVie, Cambridge Research Center, Cambridge, Massachusetts, United States of America
| | - Christina Preiss
- AbbVie, Cambridge Research Center, Cambridge, Massachusetts, United States of America
| | - Lamiaa Bahnassawy
- AbbVie Deutschland GmbH & Co. KG, Neuroscience Discovery, Knollstrasse, Ludwigshafen, Germany
| | | | - Justine D. Manos
- AbbVie, Cambridge Research Center, Cambridge, Massachusetts, United States of America
| | - Peter Reinhardt
- AbbVie Deutschland GmbH & Co. KG, Neuroscience Discovery, Knollstrasse, Ludwigshafen, Germany
| | - Fedik Rahimov
- AbbVie Inc., North Chicago, Illinois, United States of America
| | | | | |
Collapse
|
10
|
Chadarevian JP, Davtyan H, Lombroso SI, Bennett FC, Blurton-Jones M. CRISPR generation of CSF1R-G795A human microglia for robust microglia replacement in a chimeric mouse model. STAR Protoc 2023; 4:102490. [PMID: 37516973 PMCID: PMC10407259 DOI: 10.1016/j.xpro.2023.102490] [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] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 06/07/2023] [Accepted: 07/13/2023] [Indexed: 08/01/2023] Open
Abstract
Chimeric mouse models have recently been developed to study human microglia in vivo. However, widespread engraftment of donor microglia within the adult brain has been challenging. Here, we present a protocol to introduce the G795A point mutation using CRISPR-Cas9 into the CSF1R locus of human pluripotent stem cells. We also describe an optimized microglial differentiation technique for transplantation into newborn or adult recipients. We then detail pharmacological paradigms to achieve widespread and near-complete engraftment of human microglia. For complete details on the use and execution of this protocol, please refer to Chadarevian et al. (2023).1.
Collapse
Affiliation(s)
- Jean Paul Chadarevian
- Department of Neurobiology & Behavior, University of California Irvine, Irvine, CA 92697, USA; Institute for Memory Impairments and Neurological Disorders, University of California Irvine, Irvine, CA 92697, USA; Sue and Bill Gross Stem Cell Research Center, University of California Irvine, Irvine, CA 92697, USA.
| | - Hayk Davtyan
- Institute for Memory Impairments and Neurological Disorders, University of California Irvine, Irvine, CA 92697, USA; Sue and Bill Gross Stem Cell Research Center, University of California Irvine, Irvine, CA 92697, USA
| | - Sonia I Lombroso
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA
| | - F Chris Bennett
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Mathew Blurton-Jones
- Department of Neurobiology & Behavior, University of California Irvine, Irvine, CA 92697, USA; Institute for Memory Impairments and Neurological Disorders, University of California Irvine, Irvine, CA 92697, USA; Sue and Bill Gross Stem Cell Research Center, University of California Irvine, Irvine, CA 92697, USA.
| |
Collapse
|
11
|
Balmas E, Sozza F, Bottini S, Ratto ML, Savorè G, Becca S, Snijders KE, Bertero A. Manipulating and studying gene function in human pluripotent stem cell models. FEBS Lett 2023; 597:2250-2287. [PMID: 37519013 DOI: 10.1002/1873-3468.14709] [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: 06/01/2023] [Revised: 07/04/2023] [Accepted: 07/05/2023] [Indexed: 08/01/2023]
Abstract
Human pluripotent stem cells (hPSCs) are uniquely suited to study human development and disease and promise to revolutionize regenerative medicine. These applications rely on robust methods to manipulate gene function in hPSC models. This comprehensive review aims to both empower scientists approaching the field and update experienced stem cell biologists. We begin by highlighting challenges with manipulating gene expression in hPSCs and their differentiated derivatives, and relevant solutions (transfection, transduction, transposition, and genomic safe harbor editing). We then outline how to perform robust constitutive or inducible loss-, gain-, and change-of-function experiments in hPSCs models, both using historical methods (RNA interference, transgenesis, and homologous recombination) and modern programmable nucleases (particularly CRISPR/Cas9 and its derivatives, i.e., CRISPR interference, activation, base editing, and prime editing). We further describe extension of these approaches for arrayed or pooled functional studies, including emerging single-cell genomic methods, and the related design and analytical bioinformatic tools. Finally, we suggest some directions for future advancements in all of these areas. Mastering the combination of these transformative technologies will empower unprecedented advances in human biology and medicine.
Collapse
Affiliation(s)
- Elisa Balmas
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy
| | - Federica Sozza
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy
| | - Sveva Bottini
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy
| | - Maria Luisa Ratto
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy
| | - Giulia Savorè
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy
| | - Silvia Becca
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy
| | - Kirsten Esmee Snijders
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy
| | - Alessandro Bertero
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy
| |
Collapse
|
12
|
Choi W, Wu H, Yserentant K, Huang B, Cheng Y. Efficient tagging of endogenous proteins in human cell lines for structural studies by single-particle cryo-EM. Proc Natl Acad Sci U S A 2023; 120:e2302471120. [PMID: 37487103 PMCID: PMC10401002 DOI: 10.1073/pnas.2302471120] [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: 02/12/2023] [Accepted: 06/21/2023] [Indexed: 07/26/2023] Open
Abstract
CRISPR/Cas9-based genome engineering has revolutionized our ability to manipulate biological systems, particularly in higher organisms. Here, we designed a set of homology-directed repair donor templates that enable efficient tagging of endogenous proteins with affinity tags by transient transfection and selection of genome-edited cells in various human cell lines. Combined with technological advancements in single-particle cryogenic electron microscopy, this strategy allows efficient structural studies of endogenous proteins captured in their native cellular environment and during different cellular processes. We demonstrated this strategy by tagging six different human proteins in both HEK293T and Jurkat cells. Moreover, analysis of endogenous glyceraldehyde 3-phosphate dehydrogenase (GAPDH) in HEK293T cells allowed us to follow its behavior spatially and temporally in response to prolonged oxidative stress, correlating the increased number of oxidation-induced inactive catalytic sites in GAPDH with its translocation from cytosol to nucleus.
Collapse
Affiliation(s)
- Wooyoung Choi
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA94143
| | - Hao Wu
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA94143
| | - Klaus Yserentant
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA94143
| | - Bo Huang
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA94143
- Chan Zuckerberg Biohub-San Francisco, San Francisco, CA94158
| | - Yifan Cheng
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA94143
- HHMI, University of California, San Francisco, CA94143
| |
Collapse
|
13
|
Chen H, Liu X, Li L, Tan Q, Li S, Li L, Li C, Fu J, Lu Y, Wang Y, Sun Y, Luo ZG, Lu Z, Sun Q, Liu Z. CATI: an efficient gene integration method for rodent and primate embryos by MMEJ suppression. Genome Biol 2023; 24:146. [PMID: 37353834 PMCID: PMC10288798 DOI: 10.1186/s13059-023-02987-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 06/13/2023] [Indexed: 06/25/2023] Open
Abstract
The efficiency of homology-directed repair (HDR) plays a crucial role in the development of animal models and gene therapy. We demonstrate that microhomology-mediated end-joining (MMEJ) constitutes a substantial proportion of DNA repair during CRISPR-mediated gene editing. Using CasRx to downregulate a key MMEJ factor, Polymerase Q (Polq), we improve the targeted integration efficiency of linearized DNA fragments and single-strand oligonucleotides (ssODN) in mouse embryos and offspring. CasRX-assisted targeted integration (CATI) also leads to substantial improvements in HDR efficiency during the CRISPR/Cas9 editing of monkey embryos. We present a promising tool for generating monkey models and developing gene therapies for clinical trials.
Collapse
Affiliation(s)
- Hongyu Chen
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science & Intelligence Technology, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai, 200031, China
| | - Xingchen Liu
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science & Intelligence Technology, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai, 200031, China
- University of Chinese Academy of Sciences, 19A Yu-Quan Road, Beijing, 100049, China
| | - Lanxin Li
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Qingtong Tan
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science & Intelligence Technology, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai, 200031, China
- University of Chinese Academy of Sciences, 19A Yu-Quan Road, Beijing, 100049, China
| | - Shiyan Li
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science & Intelligence Technology, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai, 200031, China
- University of Chinese Academy of Sciences, 19A Yu-Quan Road, Beijing, 100049, China
| | - Li Li
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science & Intelligence Technology, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai, 200031, China
| | - Chunyang Li
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science & Intelligence Technology, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai, 200031, China
| | - Jiqiang Fu
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science & Intelligence Technology, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai, 200031, China
| | - Yong Lu
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science & Intelligence Technology, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai, 200031, China
| | - Yan Wang
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science & Intelligence Technology, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai, 200031, China
| | - Yidi Sun
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science & Intelligence Technology, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai, 200031, China
- Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai, 201210, China
| | - Zhen-Ge Luo
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Zongyang Lu
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science & Intelligence Technology, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai, 200031, China.
- Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai, 201210, China.
| | - Qiang Sun
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science & Intelligence Technology, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai, 200031, China.
- Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai, 201210, China.
| | - Zhen Liu
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science & Intelligence Technology, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai, 200031, China.
- Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai, 201210, China.
| |
Collapse
|
14
|
Blin M, Dametto S, Agniwo P, Webster BL, Angora E, Dabo A, Boissier J. A duplex tetra-primer ARMS-PCR assay to discriminate three species of the Schistosoma haematobium group: Schistosoma curassoni, S. bovis, S. haematobium and their hybrids. Parasit Vectors 2023; 16:121. [PMID: 37029440 PMCID: PMC10082484 DOI: 10.1186/s13071-023-05754-9] [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: 01/24/2023] [Accepted: 03/22/2023] [Indexed: 04/09/2023] Open
Abstract
BACKGROUND The use of applications involving single nucleotide polymorphisms (SNPs) has greatly increased since the beginning of the 2000s, with the number of associated techniques expanding rapidly in the field of molecular research. Tetra-primer amplification refractory mutation system-PCR (T-ARMS-PCR) is one such technique involving SNP genotyping. It has the advantage of amplifying multiple alleles in a single reaction with the inclusion of an internal molecular control. We report here the development of a rapid, reliable and cost-effective duplex T-ARMS-PCR assay to distinguish between three Schistosoma species, namely Schistosoma haematobium (human parasite), Schistosoma bovis and Schistosoma curassoni (animal parasites), and their hybrids. This technique will facilitate studies of population genetics and the evolution of introgression events. METHODS During the development of the technique we focused on one of the five inter-species internal transcribed spacer (ITS) SNPs and one of the inter-species 18S SNPs which, when combined, discriminate between all three Schistosoma species and their hybrid forms. We designed T-ARMS-PCR primers to amplify amplicons of specific lengths for each species, which in turn can then be visualized on an electrophoresis gel. This was further tested using laboratory and field-collected adult worms and field-collected larval stages (miracidia) from Spain, Egypt, Mali, Senegal and Ivory Coast. The combined duplex T-ARMS-PCR and ITS + 18S primer set was then used to differentiate the three species in a single reaction. RESULTS The T-ARMS-PCR assay was able to detect DNA from both species being analysed at the maximum and minimum levels in the DNA ratios (95/5) tested. The duplex T-ARMS-PCR assay was also able to detect all hybrids tested and was validated by sequencing the ITS and the 18S amplicons of 148 of the field samples included in the study. CONCLUSIONS The duplex tetra-primer ARMS-PCR assay described here can be applied to differentiate between Schistosoma species and their hybrid forms that infect humans and animals, thereby providing a method to investigate the epidemiology of these species in endemic areas. The addition of several markers in a single reaction saves considerable time and is of long-standing interest for investigating genetic populations.
Collapse
Affiliation(s)
- Manon Blin
- Hosts Pathogens Environment Interactions, UMR 5244, CNRS, IFREMER, UM, University of Perpignan Via Domitia, Perpignan, 66860, France
- SAS ParaDev®, 66860, Perpignan, France
| | - Sarah Dametto
- Hosts Pathogens Environment Interactions, UMR 5244, CNRS, IFREMER, UM, University of Perpignan Via Domitia, Perpignan, 66860, France
| | - Privat Agniwo
- Hosts Pathogens Environment Interactions, UMR 5244, CNRS, IFREMER, UM, University of Perpignan Via Domitia, Perpignan, 66860, France
- Department of Epidemiology of Infectious Diseases, Faculty of Pharmacy, IRL 3189, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Bonnie L Webster
- Wolfson Wellcome Biomedical Laboratories, Department of Science, Natural History Museum, London, SW7 5BD, UK
- London Centre for Neglected Tropical Disease Research, Imperial College London School of Public Health, London, W2 1PG, UK
| | - Etienne Angora
- Swiss Tropical and Public Health Institute, P.O. Box, 4002, Basel, Switzerland
- University of Basel, Kreuzstrasse 2, 4123, Allschwil, Switzerland
- Unité de Formation et de Recherche Sciences Pharmaceutiques et Biologiques, Université Félix Houphouët-Boigny, BPV 34, Abidjan, Côte d'Ivoire
| | - Abdoulaye Dabo
- Department of Epidemiology of Infectious Diseases, Faculty of Pharmacy, IRL 3189, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Jérôme Boissier
- Hosts Pathogens Environment Interactions, UMR 5244, CNRS, IFREMER, UM, University of Perpignan Via Domitia, Perpignan, 66860, France.
| |
Collapse
|
15
|
Polikarpova AV, Egorova TV, Lunev EA, Tsitrina AA, Vassilieva SG, Savchenko IM, Silaeva YY, Deykin AV, Bardina MV. CRISPR/Cas9-generated mouse model with humanizing single-base substitution in the Gnao1 for safety studies of RNA therapeutics. Front Genome Ed 2023; 5:1034720. [PMID: 37077890 PMCID: PMC10106585 DOI: 10.3389/fgeed.2023.1034720] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 03/20/2023] [Indexed: 04/05/2023] Open
Abstract
The development of personalized medicine for genetic diseases requires preclinical testing in the appropriate animal models. GNAO1 encephalopathy is a severe neurodevelopmental disorder caused by heterozygous de novo mutations in the GNAO1 gene. GNAO1 c.607 G>A is one of the most common pathogenic variants, and the mutant protein Gαo-G203R likely adversely affects neuronal signaling. As an innovative approach, sequence-specific RNA-based therapeutics such as antisense oligonucleotides or effectors of RNA interference are potentially applicable for selective suppression of the mutant GNAO1 transcript. While in vitro validation can be performed in patient-derived cells, a humanized mouse model to rule out the safety of RNA therapeutics is currently lacking. In the present work, we employed CRISPR/Cas9 technology to introduce a single-base substitution into exon 6 of the Gnao1 to replace the murine Gly203-coding triplet (GGG) with the codon used in the human gene (GGA). We verified that genome-editing did not interfere with the Gnao1 mRNA or Gαo protein synthesis and did not alter localization of the protein in the brain structures. The analysis of blastocysts revealed the off-target activity of the CRISPR/Cas9 complexes; however, no modifications of the predicted off-target sites were detected in the founder mouse. Histological staining confirmed the absence of abnormal changes in the brain of genome-edited mice. The created mouse model with the “humanized” fragment of the endogenous Gnao1 is suitable to rule out unintended targeting of the wild-type allele by RNA therapeutics directed at lowering GNAO1 c.607 G>A transcripts.
Collapse
Affiliation(s)
- Anna V. Polikarpova
- Laboratory of Modeling and Gene Therapy of Hereditary Diseases, Institute of Gene Biology Russian Academy of Sciences, Moscow, Russia
- Marlin Biotech, Sochi, Russia
| | - Tatiana V. Egorova
- Laboratory of Modeling and Gene Therapy of Hereditary Diseases, Institute of Gene Biology Russian Academy of Sciences, Moscow, Russia
- Marlin Biotech, Sochi, Russia
| | - Evgenii A. Lunev
- Laboratory of Modeling and Gene Therapy of Hereditary Diseases, Institute of Gene Biology Russian Academy of Sciences, Moscow, Russia
- Marlin Biotech, Sochi, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Alexandra A. Tsitrina
- Koltzov Institute of Developmental Biology Russian Academy of Sciences, Moscow, Russia
| | - Svetlana G. Vassilieva
- Laboratory of Modeling and Gene Therapy of Hereditary Diseases, Institute of Gene Biology Russian Academy of Sciences, Moscow, Russia
- Marlin Biotech, Sochi, Russia
| | - Irina M. Savchenko
- Marlin Biotech, Sochi, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Yuliya Y. Silaeva
- Core Facility Center, Institute of Gene Biology Russian Academy of Sciences, Moscow, Russia
| | - Alexey V. Deykin
- Marlin Biotech, Sochi, Russia
- Core Facility Center, Institute of Gene Biology Russian Academy of Sciences, Moscow, Russia
- Laboratory of Genetic Technologies and Genome Editing for Biomedicine and Animal Health, Joint Center for Genetic Technologies, Belgorod National Research University, Belgorod, Russia
| | - Maryana V. Bardina
- Laboratory of Modeling and Gene Therapy of Hereditary Diseases, Institute of Gene Biology Russian Academy of Sciences, Moscow, Russia
- Marlin Biotech, Sochi, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
- *Correspondence: Maryana V. Bardina,
| |
Collapse
|
16
|
Anderson W, Barahmand-pour-Whitman F, Linsley PS, Cerosaletti K, Buckner JH, Rawlings DJ. PTPN22 R620W gene editing in T cells enhances low-avidity TCR responses. eLife 2023; 12:e81577. [PMID: 36961507 PMCID: PMC10065793 DOI: 10.7554/elife.81577] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 03/21/2023] [Indexed: 03/25/2023] Open
Abstract
A genetic variant in the gene PTPN22 (R620W, rs2476601) is strongly associated with increased risk for multiple autoimmune diseases and linked to altered TCR regulation and T cell activation. Here, we utilize Crispr/Cas9 gene editing with donor DNA repair templates in human cord blood-derived, naive T cells to generate PTPN22 risk edited (620W), non-risk edited (620R), or knockout T cells from the same donor. PTPN22 risk edited cells exhibited increased activation marker expression following non-specific TCR engagement, findings that mimicked PTPN22 KO cells. Next, using lentiviral delivery of T1D patient-derived TCRs against the pancreatic autoantigen, islet-specific glucose-6 phosphatase catalytic subunit-related protein (IGRP), we demonstrate that loss of PTPN22 function led to enhanced signaling in T cells expressing a lower avidity self-reactive TCR, but not a high-avidity TCR. In this setting, loss of PTPN22 mediated enhanced proliferation and Th1 skewing. Importantly, expression of the risk variant in association with a lower avidity TCR also increased proliferation relative to PTPN22 non-risk T cells. Together, these findings suggest that, in primary human T cells, PTPN22 rs2476601 contributes to autoimmunity risk by permitting increased TCR signaling and activation in mildly self-reactive T cells, thereby potentially expanding the self-reactive T cell pool and skewing this population toward an inflammatory phenotype.
Collapse
Affiliation(s)
- Warren Anderson
- Center for Immunity and Immunotherapies, Seattle Children's Research InstituteSeattleUnited States
| | | | - Peter S Linsley
- Benaroya Research Institute at Virginia MasonSeattleUnited States
| | | | - Jane H Buckner
- Benaroya Research Institute at Virginia MasonSeattleUnited States
| | - David J Rawlings
- Department of Pediatrics and Immunology, University of WashingtonSeattleUnited States
| |
Collapse
|
17
|
Ren X, Takagi MA, Shen Y. Efficient bi-allelic tagging in human induced pluripotent stem cells using CRISPR. STAR Protoc 2023; 4:102084. [PMID: 36853689 PMCID: PMC9918420 DOI: 10.1016/j.xpro.2023.102084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 12/16/2022] [Accepted: 01/17/2023] [Indexed: 02/04/2023] Open
Abstract
Allelic tagging of endogenous genes enables studying gene function and transcriptional control in the native genomic context. Here, we present an efficient protocol for bi-allelic tagging of protein-coding genes with fluorescent reporters in human iPSCs using the CRISPR-Cas9-mediated homology-directed repair. We detail steps for design, cloning, electroporation, and single-cell clone isolation and validation. The tagging strategy described in this protocol is readily applicable for knockin of other reporters in diverse cell types for biomedical research.
Collapse
Affiliation(s)
- Xingjie Ren
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA 94143, USA.
| | - Maya Asami Takagi
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Yin Shen
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Neurology, University of California, San Francisco, San Francisco, CA 94143, USA.
| |
Collapse
|
18
|
Mollashahi B, Latifi-Navid H, Owliaee I, Shamdani S, Uzan G, Jamehdor S, Naserian S. Research and Therapeutic Approaches in Stem Cell Genome Editing by CRISPR Toolkit. Molecules 2023; 28:molecules28041982. [PMID: 36838970 PMCID: PMC9961668 DOI: 10.3390/molecules28041982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 02/03/2023] [Accepted: 02/06/2023] [Indexed: 02/22/2023] Open
Abstract
The most widely used genome editing toolkit is CRISPR (clustered regularly interspaced short palindromic repeats). It provides the possibility of replacing and modifying DNA and RNA nucleotides. Furthermore, with advancements in biological technology, inhibition and activation of the transcription of specific gene(s) has become possible. Bioinformatics tools that target the evolution of CRISPR-associated protein 9 (Cas9) turn this protein into a vehicle that is specific for a DNA or RNA region with single guide RNA (sgRNA). This toolkit could be used by researchers to investigate the function of stem cell gene(s). Here, in this review article, we cover recent developments and applications of this technique in stem cells for research and clinical purposes and discuss different CRISPR/Cas technologies for knock-out, knock-in, activation, or inhibition of gene expression. Additionally, a comparison of several deliveries and off-target detecting strategies is discussed.
Collapse
Affiliation(s)
- Behrouz Mollashahi
- Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, 40126 Bologna, Italy
| | - Hamid Latifi-Navid
- Department of Molecular Medicine, National Institute of Genetic Engineering and Biotechnology, Tehran 14965/161, Iran
| | - Iman Owliaee
- Department of Virology, Faculty of Medicine, Hamadan University of Medical Sciences, Hamedan 6517838636, Iran
| | - Sara Shamdani
- INSERM UMR-S-MD 1197, Hôpital Paul Brousse, Paris-Saclay University, 94807 Villejuif, France
- CellMedEx, 94100 Saint Maur Des Fossés, France
| | - Georges Uzan
- INSERM UMR-S-MD 1197, Hôpital Paul Brousse, Paris-Saclay University, 94807 Villejuif, France
| | - Saleh Jamehdor
- Department of Virology, Faculty of Medicine, Hamadan University of Medical Sciences, Hamedan 6517838636, Iran
- Correspondence: (S.J.); (S.N.)
| | - Sina Naserian
- INSERM UMR-S-MD 1197, Hôpital Paul Brousse, Paris-Saclay University, 94807 Villejuif, France
- CellMedEx, 94100 Saint Maur Des Fossés, France
- Correspondence: (S.J.); (S.N.)
| |
Collapse
|
19
|
Kobayashi R, Horii T, Hatada I. Efficient Detection of Flox Mice Using In Vitro Cre Recombination. Methods Mol Biol 2023; 2637:149-159. [PMID: 36773145 DOI: 10.1007/978-1-0716-3016-7_12] [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] [Indexed: 02/12/2023]
Abstract
Advances in CRISPR/Cas9 genome editing technologies have allowed for the rapid generation of Cre-loxP conditional knockout mice. However, current strategies for genotyping flox mice, typically based on Sanger sequencing following cloning of target sequences from dozens of pups, are time-consuming. Here, we describe a rapid screening method for flox mice, using in vitro Cre recombination that can be performed using simple enzymatic reactions and enables detection of functional flox mouse within 1 day. In addition, we introduce an efficient strategy for subsequent sequence analysis by cloning of floxed regions using the In-Fusion system. Our genotyping pipeline reduces laborious tasks and thus contributes to the rapid selection of accurately edited flox mice.
Collapse
Affiliation(s)
- Ryosuke Kobayashi
- Laboratory of Genome Science, Biosignal Genome Resource Center, Institute for Molecular and Cellular Regulation, Gunma University, Maebashi, Gunma, Japan
| | - Takuro Horii
- Laboratory of Genome Science, Biosignal Genome Resource Center, Institute for Molecular and Cellular Regulation, Gunma University, Maebashi, Gunma, Japan
| | - Izuho Hatada
- Laboratory of Genome Science, Biosignal Genome Resource Center, Institute for Molecular and Cellular Regulation, Gunma University, Maebashi, Gunma, Japan.
| |
Collapse
|
20
|
Siles L, Gaudó P, Pomares E. High-Efficiency CRISPR/Cas9-Mediated Correction of a Homozygous Mutation in Achromatopsia-Patient-Derived iPSCs. Int J Mol Sci 2023; 24:ijms24043655. [PMID: 36835061 PMCID: PMC9964936 DOI: 10.3390/ijms24043655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 02/03/2023] [Accepted: 02/09/2023] [Indexed: 02/15/2023] Open
Abstract
Achromatopsia is an autosomal recessive disorder, in which cone photoreceptors undergo progressive degeneration, causing color blindness and poor visual acuity, among other significant eye affectations. It belongs to a group of inherited retinal dystrophies that currently have no treatment. Although functional improvements have been reported in several ongoing gene therapy studies, more efforts and research should be carried out to enhance their clinical application. In recent years, genome editing has arisen as one of the most promising tools for personalized medicine. In this study, we aimed to correct a homozygous PDE6C pathogenic variant in hiPSCs derived from a patient affected by achromatopsia through CRISPR/Cas9 and TALENs technologies. Here, we demonstrate high efficiency in gene editing by CRISPR/Cas9 but not with TALENs approximation. Despite a few of the edited clones displaying heterozygous on-target defects, the proportion of corrected clones with a potentially restored wild-type PDE6C protein was more than half of the total clones analyzed. In addition, none of them presented off-target aberrations. These results significantly contribute to advances in single-nucleotide gene editing and the development of future strategies for the treatment of achromatopsia.
Collapse
Affiliation(s)
- Laura Siles
- Fundació de Recerca de l’Institut de Microcirurgia Ocular, 08035 Barcelona, Spain
- Departament de Genètica, IMO Grupo Miranza, 08035 Barcelona, Spain
| | - Paula Gaudó
- Fundació de Recerca de l’Institut de Microcirurgia Ocular, 08035 Barcelona, Spain
- Departament de Genètica, IMO Grupo Miranza, 08035 Barcelona, Spain
| | - Esther Pomares
- Fundació de Recerca de l’Institut de Microcirurgia Ocular, 08035 Barcelona, Spain
- Departament de Genètica, IMO Grupo Miranza, 08035 Barcelona, Spain
- Correspondence:
| |
Collapse
|
21
|
Richardson C, Kelsh RN, J. Richardson R. New advances in CRISPR/Cas-mediated precise gene-editing techniques. Dis Model Mech 2023; 16:dmm049874. [PMID: 36847161 PMCID: PMC10003097 DOI: 10.1242/dmm.049874] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023] Open
Abstract
Over the past decade, CRISPR/Cas-based gene editing has become a powerful tool for generating mutations in a variety of model organisms, from Escherichia coli to zebrafish, rodents and large mammals. CRISPR/Cas-based gene editing effectively generates insertions or deletions (indels), which allow for rapid gene disruption. However, a large proportion of human genetic diseases are caused by single-base-pair substitutions, which result in more subtle alterations to protein function, and which require more complex and precise editing to recreate in model systems. Precise genome editing (PGE) methods, however, typically have efficiencies of less than a tenth of those that generate less-specific indels, and so there has been a great deal of effort to improve PGE efficiency. Such optimisations include optimal guide RNA and mutation-bearing donor DNA template design, modulation of DNA repair pathways that underpin how edits result from Cas-induced cuts, and the development of Cas9 fusion proteins that introduce edits via alternative mechanisms. In this Review, we provide an overview of the recent progress in optimising PGE methods and their potential for generating models of human genetic disease.
Collapse
Affiliation(s)
- Chris Richardson
- School of Physiology, Pharmacology and Neuroscience, Faculty of Biomedical Sciences, University of Bristol, Bristol BS8 1TD, UK
| | - Robert N. Kelsh
- Department of Life Sciences, University of Bath, Bath BA2 7AY, UK
| | - Rebecca J. Richardson
- School of Physiology, Pharmacology and Neuroscience, Faculty of Biomedical Sciences, University of Bristol, Bristol BS8 1TD, UK
| |
Collapse
|
22
|
Strategies for generation of mice via CRISPR/HDR-mediated knock-in. Mol Biol Rep 2023; 50:3189-3204. [PMID: 36701041 DOI: 10.1007/s11033-023-08278-8] [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: 05/24/2022] [Accepted: 01/12/2023] [Indexed: 01/27/2023]
Abstract
CRISPR/Cas9 framework is generally used to generate genetically modified mouse models. The clustered regularly interspaced short palindromic repeat gene editing technique, can efficiently generate knock-outs using the non-homologous end-joining repair pathway. Small knock-ins also work precisely using a repair template with help of homology-directed-repair (HDR) mechanism. However, when the fragment size is larger than 4-5 kb, the knock-in tends to be error prone and the efficiency decreases. Certain types of modifications, in particular insertions of very large DNA fragments (10-100 kb) or entire gene replacements, are still difficult. The HDR process needs further streamlining and improvement. Here in this review, we describe methods to enhance the efficiency of the knock-in through checking each step from the guide design to the microinjection and choice of the oocyte donors. This helps in understanding the parameters that can be modified to get improved knock-in efficiency via CRISPR targeting.
Collapse
|
23
|
Mohammadian Gol T, Ureña-Bailén G, Hou Y, Sinn R, Antony JS, Handgretinger R, Mezger M. CRISPR medicine for blood disorders: Progress and challenges in delivery. Front Genome Ed 2023; 4:1037290. [PMID: 36687779 PMCID: PMC9853164 DOI: 10.3389/fgeed.2022.1037290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 12/22/2022] [Indexed: 01/09/2023] Open
Abstract
Blood disorders are a group of diseases including hematological neoplasms, clotting disorders and orphan immune deficiency diseases that affects human health. Current improvements in genome editing based therapeutics demonstrated preclinical and clinical proof to treat different blood disorders. Genome editing components such as Cas nucleases, guide RNAs and base editors are supplied in the form of either a plasmid, an mRNA, or a ribonucleoprotein complex. The most common delivery vehicles for such components include viral vectors (e.g., AAVs and RV), non-viral vectors (e.g., LNPs and polymers) and physical delivery methods (e.g., electroporation and microinjection). Each of the delivery vehicles specified above has its own advantages and disadvantages and the development of a safe transferring method for ex vivo and in vivo application of genome editing components is still a big challenge. Moreover, the delivery of genome editing payload to the target blood cells possess key challenges to provide a possible cure for patients with inherited monogenic blood diseases and hematological neoplastic tumors. Here, we critically review and summarize the progress and challenges related to the delivery of genome editing elements to relevant blood cells in an ex vivo or in vivo setting. In addition, we have attempted to provide a future clinical perspective of genome editing to treat blood disorders with possible clinical grade improvements in delivery methods.
Collapse
Affiliation(s)
- Tahereh Mohammadian Gol
- Department of Hematology and Oncology, University Children’s Hospital, University of Tübingen, Tübingen, Germany
| | - Guillermo Ureña-Bailén
- Department of Hematology and Oncology, University Children’s Hospital, University of Tübingen, Tübingen, Germany
| | - Yujuan Hou
- Department of Hematology and Oncology, University Children’s Hospital, University of Tübingen, Tübingen, Germany
| | - Ralph Sinn
- Department of Hematology and Oncology, University Children’s Hospital, University of Tübingen, Tübingen, Germany
| | - Justin S. Antony
- Department of Hematology and Oncology, University Children’s Hospital, University of Tübingen, Tübingen, Germany
| | - Rupert Handgretinger
- Department of Hematology and Oncology, University Children’s Hospital, University of Tübingen, Tübingen, Germany,Abu Dhabi Stem Cells Center, Abu Dhabi, United Arab Emirates
| | - Markus Mezger
- Department of Hematology and Oncology, University Children’s Hospital, University of Tübingen, Tübingen, Germany,*Correspondence: Markus Mezger,
| |
Collapse
|
24
|
Shakirova A, Karpov T, Komarova Y, Lepik K. In search of an ideal template for therapeutic genome editing: A review of current developments for structure optimization. Front Genome Ed 2023; 5:1068637. [PMID: 36911237 PMCID: PMC9992834 DOI: 10.3389/fgeed.2023.1068637] [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: 10/13/2022] [Accepted: 02/08/2023] [Indexed: 02/24/2023] Open
Abstract
Gene therapy is a fast developing field of medicine with hundreds of ongoing early-stage clinical trials and numerous preclinical studies. Genome editing (GE) now is an increasingly important technology for achieving stable therapeutic effect in gene correction, with hematopoietic cells representing a key target cell population for developing novel treatments for a number of hereditary diseases, infections and cancer. By introducing a double strand break (DSB) in the defined locus of genomic DNA, GE tools allow to knockout the desired gene or to knock-in the therapeutic gene if provided with an appropriate repair template. Currently, the efficiency of methods for GE-mediated knock-in is limited. Significant efforts were focused on improving the parameters and interaction of GE nuclease proteins. However, emerging data suggests that optimal characteristics of repair templates may play an important role in the knock-in mechanisms. While viral vectors with notable example of AAVs as a donor template carrier remain the mainstay in many preclinical trials, non-viral templates, including plasmid and linear dsDNA, long ssDNA templates, single and double-stranded ODNs, represent a promising alternative. Furthermore, tuning of editing conditions for the chosen template as well as its structure, length, sequence optimization, homology arm (HA) modifications may have paramount importance for achieving highly efficient knock-in with favorable safety profile. This review outlines the current developments in optimization of templates for the GE mediated therapeutic gene correction.
Collapse
Affiliation(s)
- Alena Shakirova
- RM Gorbacheva Research Institute of Pediatric Oncology, Hematology and Transplantation, Pavlov University, Saint Petersburg, Russia
| | - Timofey Karpov
- RM Gorbacheva Research Institute of Pediatric Oncology, Hematology and Transplantation, Pavlov University, Saint Petersburg, Russia.,Peter the Great St. Petersburg Polytechnic University, Saint Petersburg, Russia
| | - Yaroslava Komarova
- RM Gorbacheva Research Institute of Pediatric Oncology, Hematology and Transplantation, Pavlov University, Saint Petersburg, Russia
| | - Kirill Lepik
- RM Gorbacheva Research Institute of Pediatric Oncology, Hematology and Transplantation, Pavlov University, Saint Petersburg, Russia
| |
Collapse
|
25
|
Liao J, Wu Y. Gene Editing in Hematopoietic Stem Cells. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1442:177-199. [PMID: 38228965 DOI: 10.1007/978-981-99-7471-9_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2024]
Abstract
Hematopoietic stem cells (HSCs) can be isolated and collected from the body, genetically modified, and expanded ex vivo. The invention of innovative and powerful gene editing tools has provided researchers with great convenience in genetically modifying a wide range of cells, including hematopoietic stem and progenitor cells (HSPCs). In addition to being used to modify genes to study the functional role that specific genes play in the hematopoietic system, the application of gene editing platforms in HSCs is largely focused on the development of cell-based gene editing therapies to treat diseases such as immune deficiency disorders and inherited blood disorders. Here, we review the application of gene editing tools in HSPCs. In particular, we provide a broad overview of the development of gene editing tools, multiple strategies for the application of gene editing tools in HSPCs, and exciting clinical advances in HSPC gene editing therapies. We also outline the various challenges integral to clinical translation of HSPC gene editing and provide the possible corresponding solutions.
Collapse
Affiliation(s)
- Jiaoyang Liao
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Yuxuan Wu
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China.
| |
Collapse
|
26
|
Challenges in Gene Therapy for Somatic Reverted Mosaicism in X-Linked Combined Immunodeficiency by CRISPR/Cas9 and Prime Editing. Genes (Basel) 2022; 13:genes13122348. [PMID: 36553615 PMCID: PMC9777626 DOI: 10.3390/genes13122348] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 12/02/2022] [Accepted: 12/10/2022] [Indexed: 12/15/2022] Open
Abstract
X-linked severe combined immunodeficiency (X-SCID) is a primary immunodeficiency that is caused by mutations in the interleukin-2 receptor gamma (IL2RG) gene. Some patients present atypical X-SCID with mild clinical symptoms due to somatic revertant mosaicism. CRISPR/Cas9 and prime editing are two advanced genome editing tools that paved the way for treating immune deficiency diseases. Prime editing overcomes the limitations of the CRISPR/Cas9 system, as it does not need to induce double-strand breaks (DSBs) or exogenous donor DNA templates to modify the genome. Here, we applied CRISPR/Cas9 with single-stranded oligodeoxynucleotides (ssODNs) and prime editing methods to generate an in vitro model of the disease in K-562 cells and healthy donors' T cells for the c. 458T>C point mutation in the IL2RG gene, which also resulted in a useful way to optimize the gene correction approach for subsequent experiments in patients' cells. Both methods proved to be successful and were able to induce the mutation of up to 31% of treated K-562 cells and 26% of treated T cells. We also applied similar strategies to correct the IL2RG c. 458T>C mutation in patient T cells that carry the mutation with revertant somatic mosaicism. However, both methods failed to increase the frequency of the wild-type sequence in the mosaic T cells of patients due to limited in vitro proliferation of mutant cells and the presence of somatic reversion. To the best of our knowledge, this is the first attempt to treat mosaic cells from atypical X-SCID patients employing CRISPR/Cas9 and prime editing. We showed that prime editing can be applied to the formation of specific-point IL2RG mutations without inducing nonspecific on-target modifications. We hypothesize that the feasibility of the nucleotide substitution of the IL2RG gene using gene therapy, especially prime editing, could provide an alternative strategy to treat X-SCID patients without revertant mutations, and further technological improvements need to be developed to correct somatic mosaicism mutations.
Collapse
|
27
|
Abstract
CRISPR-associated (Cas) enzymes have revolutionized biology by enabling RNA-guided genome editing. Homology-directed repair (HDR) in the presence of donor templates is currently the most versatile method to introduce precise edits following CRISPR-Cas-induced double-stranded DNA cuts, but HDR efficiency is generally low relative to end-joining pathways that lead to insertions and deletions (indels). We tested the hypothesis that HDR could be increased using a Cas9 construct fused to PRDM9, a chromatin remodeling factor that deposits histone methylations H3K36me3 and H3K4me3 to mediate homologous recombination in human cells. Our results show that the fusion protein contacts chromatin specifically at the Cas9 cut site in the genome to increase the observed HDR efficiency by threefold and HDR:indel ratio by fivefold compared with that induced by unmodified Cas9. HDR enhancement occurred in multiple cell lines with no increase in off-target genome editing. These findings underscore the importance of chromatin features for the balance between DNA repair mechanisms during CRISPR-Cas genome editing and provide a strategy to increase HDR efficiency.
Collapse
|
28
|
Umbach A, Maule G, Kheir E, Cutarelli A, Foglia M, Guarrera L, Fava LL, Conti L, Garattini E, Terao M, Cereseto A. Generation of corrected hiPSC clones from a Cornelia de Lange Syndrome (CdLS) patient through CRISPR-Cas-based technology. Stem Cell Res Ther 2022; 13:440. [PMID: 36056433 PMCID: PMC9438151 DOI: 10.1186/s13287-022-03135-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 08/12/2022] [Indexed: 11/20/2022] Open
Abstract
Background Cornelia de Lange syndrome (CdLS) is a rare multisystem genetic disorder which is caused by genetic defects involving the Nipped-B-like protein (NIPBL) gene in the majority of clinical cases (60–70%). Currently, there are no specific cures available for CdLS and clinical management is needed for life. Disease models are highly needed to find a cure. Among therapeutic possibilities are genome editing strategies based on CRISPR-Cas technology. Methods A comparative analysis was performed to test the most recent CRISPR-Cas technologies comprising base- and prime-editors which introduce modifications without DNA cleavages and compared with sequence substitution approaches through homology directed repair (HDR) induced by Cas9 nuclease activity. The HDR method that was found more efficient was applied to repair a CdLS-causing mutation in the NIPBL gene. Human-induced pluripotent stem cells (hiPSCs) derived from a CdLS patient carrying the c.5483G > A mutation in the NIPBL were modified through HDR to generate isogenic corrected clones. Results This study reports an efficient method to repair the NIPBL gene through HDR mediated by CRISPR-Cas and induced with a compound (NU7441) inhibiting non-homologous end joining (NHEJ) repair. This sequence repair method allowed the generation of isogenic wild-type hiPSCs clones with regular karyotype and preserved pluripotency. Conclusions CdLS cellular models were generated which will facilitate the investigation of the disease molecular determinants and the identification of therapeutic targets. In particular, the hiPSC-based cellular models offer the paramount advantage to study the tissue differentiation stages which are altered in the CdLS clinical development. Importantly, the hiPSCs that were generated are isogenic thus providing the most controlled experimental set up between wild-type and mutated conditions. Supplementary Information The online version contains supplementary material available at 10.1186/s13287-022-03135-0.
Collapse
Affiliation(s)
- Alessandro Umbach
- Department CIBIO, University of Trento, Via Sommarive 9, 38123, Povo, Italy
| | - Giulia Maule
- Department CIBIO, University of Trento, Via Sommarive 9, 38123, Povo, Italy
| | - Eyemen Kheir
- Department CIBIO, University of Trento, Via Sommarive 9, 38123, Povo, Italy
| | | | - Marika Foglia
- Laboratory of Molecular Biology, Istituto Di Ricerche Farmacologiche Mario Negri IRCCS, Via Mario Negri 2, 20156, Milan, Italy
| | - Luca Guarrera
- Laboratory of Molecular Biology, Istituto Di Ricerche Farmacologiche Mario Negri IRCCS, Via Mario Negri 2, 20156, Milan, Italy
| | - Luca L Fava
- Department CIBIO, University of Trento, Via Sommarive 9, 38123, Povo, Italy
| | - Luciano Conti
- Department CIBIO, University of Trento, Via Sommarive 9, 38123, Povo, Italy
| | - Enrico Garattini
- Laboratory of Molecular Biology, Istituto Di Ricerche Farmacologiche Mario Negri IRCCS, Via Mario Negri 2, 20156, Milan, Italy
| | - Mineko Terao
- Laboratory of Molecular Biology, Istituto Di Ricerche Farmacologiche Mario Negri IRCCS, Via Mario Negri 2, 20156, Milan, Italy
| | - Anna Cereseto
- Department CIBIO, University of Trento, Via Sommarive 9, 38123, Povo, Italy.
| |
Collapse
|
29
|
Usher I, Ligammari L, Ahrabi S, Hepburn E, Connolly C, Bond GL, Flanagan AM, Cottone L. Optimizing CRISPR/Cas9 Editing of Repetitive Single Nucleotide Variants. Front Genome Ed 2022; 4:932434. [PMID: 35865001 PMCID: PMC9294353 DOI: 10.3389/fgeed.2022.932434] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 05/31/2022] [Indexed: 11/13/2022] Open
Abstract
CRISPR/Cas9, base editors and prime editors comprise the contemporary genome editing toolbox. Many studies have optimized the use of CRISPR/Cas9, as the original CRISPR genome editing system, in substituting single nucleotides by homology directed repair (HDR), although this remains challenging. Studies describing modifications that improve editing efficiency fall short of isolating clonal cell lines or have not been validated for challenging loci or cell models. We present data from 95 transfections using a colony forming and an immortalized cell line comparing the effect on editing efficiency of donor template modifications, concentration of components, HDR enhancing agents and cold shock. We found that in silico predictions of guide RNA efficiency correlated poorly withactivity in cells. Using NGS and ddPCR we detected editing efficiencies of 5–12% in the transfected populations which fell to 1% on clonal cell line isolation. Our data demonstrate the variability of CRISPR efficiency by cell model, target locus and other factors. Successful genome editing requires a comparison of systems and modifications to develop the optimal protocol for the cell model and locus. We describe the steps in this process in a flowchart for those embarking on genome editing using any system and incorporate validated HDR-boosting modifications for those using CRISPR/Cas9.
Collapse
Affiliation(s)
- Inga Usher
- Department of Pathology (Research), UCL Cancer Institute, University College London, London, United Kingdom
| | - Lorena Ligammari
- Department of Pathology (Research), UCL Cancer Institute, University College London, London, United Kingdom
| | - Sara Ahrabi
- Department of Haematology, UCL Cancer Institute, University College London, London, United Kingdom
| | - Emily Hepburn
- UCL Medical School, University College London, London, United Kingdom
| | - Calum Connolly
- UCL Medical School, University College London, London, United Kingdom
| | - Gareth L. Bond
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Adrienne M. Flanagan
- Department of Pathology (Research), UCL Cancer Institute, University College London, London, United Kingdom
- Department of Histopathology, Royal National Orthopaedic Hospital, London, United Kingdom
| | - Lucia Cottone
- Department of Pathology (Research), UCL Cancer Institute, University College London, London, United Kingdom
- *Correspondence: Lucia Cottone,
| |
Collapse
|
30
|
Hancock-Cerutti W, Wu Z, Xu P, Yadavalli N, Leonzino M, Tharkeshwar AK, Ferguson SM, Shadel GS, De Camilli P. ER-lysosome lipid transfer protein VPS13C/PARK23 prevents aberrant mtDNA-dependent STING signaling. J Cell Biol 2022; 221:e202106046. [PMID: 35657605 PMCID: PMC9170524 DOI: 10.1083/jcb.202106046] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 05/03/2022] [Indexed: 02/03/2023] Open
Abstract
Mutations in VPS13C cause early-onset, autosomal recessive Parkinson's disease (PD). We have established that VPS13C encodes a lipid transfer protein localized to contact sites between the ER and late endosomes/lysosomes. In the current study, we demonstrate that depleting VPS13C in HeLa cells causes an accumulation of lysosomes with an altered lipid profile, including an accumulation of di-22:6-BMP, a biomarker of the PD-associated leucine-rich repeat kinase 2 (LRRK2) G2019S mutation. In addition, the DNA-sensing cGAS-STING pathway, which was recently implicated in PD pathogenesis, is activated in these cells. This activation results from a combination of elevated mitochondrial DNA in the cytosol and a defect in the degradation of activated STING, a lysosome-dependent process. These results suggest a link between ER-lysosome lipid transfer and innate immune activation in a model human cell line and place VPS13C in pathways relevant to PD pathogenesis.
Collapse
Affiliation(s)
- William Hancock-Cerutti
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT
- Interdepartmental Neuroscience Program, Yale School of Medicine, New Haven, CT
- MD/PhD Program, Yale School of Medicine, New Haven, CT
- Howard Hughes Medical Institute, Chevy Chase, MD
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, CT
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD
| | - Zheng Wu
- Department of Genetics, Yale School of Medicine, New Haven, CT
- Salk Institute for Biological Studies, La Jolla, CA
| | - Peng Xu
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT
- Howard Hughes Medical Institute, Chevy Chase, MD
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, CT
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD
| | - Narayana Yadavalli
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD
| | - Marianna Leonzino
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT
- Howard Hughes Medical Institute, Chevy Chase, MD
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, CT
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD
| | | | - Shawn M. Ferguson
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, CT
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD
| | | | - Pietro De Camilli
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT
- Howard Hughes Medical Institute, Chevy Chase, MD
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, CT
- Kavli Institute for Neuroscience, Yale University School of Medicine, New Haven, CT
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD
| |
Collapse
|
31
|
Vuong JK, Ergin V, Chen L, Zheng S. Multilayered regulations of alternative splicing, NMD, and protein stability control temporal induction and tissue-specific expression of TRIM46 during axon formation. Nat Commun 2022; 13:2081. [PMID: 35440129 PMCID: PMC9019110 DOI: 10.1038/s41467-022-29786-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 03/16/2022] [Indexed: 12/15/2022] Open
Abstract
The gene regulation underlying axon formation and its exclusiveness to neurons remains elusive. TRIM46 is postulated to determine axonal fate. We show Trim46 mRNA is expressed before axonogenesis, but TRIM46 protein level is inhibited by alternative splicing of two cassette exons coupled separately to stability controls of Trim46 mRNA and proteins, effectively inducing functional knockout of TRIM46 proteins. Exon 8 inclusion causes nonsense-mediated mRNA decay of Trim46 transcripts. PTBP2-mediated exon 10 skipping produces transcripts encoding unstable TRIM46 proteins. During axonogenesis, transcriptional activation, decreased exon 8 inclusion, and enhanced exon 10 inclusion converge to increase TRIM46 proteins, leading to its neural-specific expression. Genetic deletion of these exons alters TRIM46 protein levels and shows TRIM46 is instructive though not always required for AnkG localization nor a determinant of AnkG density. Therefore, two concurrently but independently regulated alternative exons orchestrate the temporal induction and tissue-specific expression of TRIM46 proteins to mediate axon formation.
Collapse
Affiliation(s)
- John K Vuong
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, Riverside, CA, 92521, USA
| | - Volkan Ergin
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, Riverside, CA, 92521, USA
| | - Liang Chen
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, 90089, USA
| | - Sika Zheng
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, Riverside, CA, 92521, USA.
- Center for RNA Biology and Medicine, University of California Riverside, Riverside, CA, 91521, USA.
| |
Collapse
|
32
|
Simkin D, Papakis V, Bustos BI, Ambrosi CM, Ryan SJ, Baru V, Williams LA, Dempsey GT, McManus OB, Landers JE, Lubbe SJ, George AL, Kiskinis E. Homozygous might be hemizygous: CRISPR/Cas9 editing in iPSCs results in detrimental on-target defects that escape standard quality controls. Stem Cell Reports 2022; 17:993-1008. [PMID: 35276091 PMCID: PMC9023783 DOI: 10.1016/j.stemcr.2022.02.008] [Citation(s) in RCA: 26] [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: 06/04/2021] [Revised: 02/03/2022] [Accepted: 02/08/2022] [Indexed: 12/20/2022] Open
Abstract
The ability to precisely edit the genome of human induced pluripotent stem cell (iPSC) lines using CRISPR/Cas9 has enabled the development of cellular models that can address genotype to phenotype relationships. While genome editing is becoming an essential tool in iPSC-based disease modeling studies, there is no established quality control workflow for edited cells. Moreover, large on-target deletions and insertions that occur through DNA repair mechanisms have recently been uncovered in CRISPR/Cas9-edited loci. Yet the frequency of these events in human iPSCs remains unclear, as they can be difficult to detect. We examined 27 iPSC clones generated after targeting 9 loci and found that 33% had acquired large, on-target genomic defects, including insertions and loss of heterozygosity. Critically, all defects had escaped standard PCR and Sanger sequencing analysis. We describe a cost-efficient quality control strategy that successfully identified all edited clones with detrimental on-target events and could facilitate the integrity of iPSC-based studies.
Collapse
Affiliation(s)
- Dina Simkin
- The Ken & Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Vasileios Papakis
- The Ken & Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Bernabe I Bustos
- The Ken & Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Simpson Querrey Center of Neurogenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | | | | | | | | | | | | | - John E Landers
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Steven J Lubbe
- The Ken & Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Simpson Querrey Center of Neurogenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Alfred L George
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Evangelos Kiskinis
- The Ken & Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Simpson Querrey Institute, Northwestern University, Chicago, IL 60611, USA; Department of Neuroscience, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.
| |
Collapse
|
33
|
Stankevičius V, Gibas P, Masiulionytė B, Gasiulė L, Masevičius V, Klimašauskas S, Vilkaitis G. Selective chemical tracking of Dnmt1 catalytic activity in live cells. Mol Cell 2022; 82:1053-1065.e8. [PMID: 35245449 PMCID: PMC8901439 DOI: 10.1016/j.molcel.2022.02.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 12/04/2021] [Accepted: 02/01/2022] [Indexed: 12/24/2022]
Abstract
Enzymatic methylation of cytosine to 5-methylcytosine in DNA is a fundamental epigenetic mechanism involved in mammalian development and disease. DNA methylation is brought about by collective action of three AdoMet-dependent DNA methyltransferases, whose catalytic interactions and temporal interplay are poorly understood. We used structure-guided engineering of the Dnmt1 methyltransferase to enable catalytic transfer of azide tags onto DNA from a synthetic cofactor analog, Ado-6-azide, in vitro. We then CRISPR-edited the Dnmt1 locus in mouse embryonic stem cells to install the engineered codon, which, following pulse internalization of the Ado-6-azide cofactor by electroporation, permitted selective azide tagging of Dnmt1-specific genomic targets in cellulo. The deposited covalent tags were exploited as “click” handles for reading adjoining sequences and precise genomic mapping of the methylation sites. The proposed approach, Dnmt-TOP-seq, enables high-resolution temporal tracking of the Dnmt1 catalysis in mammalian cells, paving the way to selective studies of other methylation pathways in eukaryotic systems. A single alanine substitution in Dnmt1 confers catalytic transfer of extended groups Electroporation permits facile delivery of AdoMet analogs into live mammalian cells Engineered Dnmt1 adds trackable azide tags at its native target sites in cellulo Dnmt-TOP-seq enables genome-wide tracking of Dnmt1 activity in live mammalian cells
Collapse
Affiliation(s)
- Vaidotas Stankevičius
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius 10257, Lithuania
| | - Povilas Gibas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius 10257, Lithuania
| | - Bernadeta Masiulionytė
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius 10257, Lithuania
| | - Liepa Gasiulė
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius 10257, Lithuania
| | - Viktoras Masevičius
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius 10257, Lithuania; Institute of Chemistry, Faculty of Chemistry and Geosciences, Vilnius University, Vilnius 03225, Lithuania
| | - Saulius Klimašauskas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius 10257, Lithuania.
| | - Giedrius Vilkaitis
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius 10257, Lithuania.
| |
Collapse
|
34
|
Liu J, Li Y, Lyu L, Xiao L, Memon AA, Yu X, Halim A, Patel S, Osman A, Yin W, Jiang J, Naini S, Lim K, Zhang A, Williams JD, Koester R, Qi KZ, Fucci QA, Ding L, Chang S, Patel A, Mori Y, Chaudhari A, Bao A, Liu J, Lu TS, Siedlecki A. Integrin α5 Is Regulated by miR-218-5p in Endothelial Progenitor Cells. J Am Soc Nephrol 2022; 33:565-582. [PMID: 35091451 PMCID: PMC8975065 DOI: 10.1681/asn.2021020140] [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] [Received: 02/01/2021] [Accepted: 12/27/2021] [Indexed: 11/03/2022] Open
Abstract
BACKGROUND Endothelial cell injury is a common nidus of renal injury in patients and consistent with the high prevalence of AKI reported during the coronavirus disease 2019 pandemic. This cell type expresses integrin α5 (ITGA5), which is essential to the Tie2 signaling pathway. The microRNA miR-218-5p is upregulated in endothelial progenitor cells (EPCs) after hypoxia, but microRNA regulation of Tie2 in the EPC lineage is unclear. METHODS We isolated human kidney-derived EPCs (hkEPCs) and surveyed microRNA target transcripts. A preclinical model of ischemic kidney injury was used to evaluate the effect of hkEPCs on capillary repair. We used a genetic knockout model to evaluate the effect of deleting endogenous expression of miR-218 specifically in angioblasts. RESULTS After ischemic in vitro preconditioning, miR-218-5p was elevated in hkEPCs. We found miR-218-5p bound to ITGA5 mRNA transcript and decreased ITGA5 protein expression. Phosphorylation of 42/44 MAPK decreased by 73.6% in hkEPCs treated with miR-218-5p. Cells supplemented with miR-218-5p downregulated ITGA5 synthesis and decreased 42/44 MAPK phosphorylation. In a CD309-Cre/miR-218-2-LoxP mammalian model (a conditional knockout mouse model designed to delete pre-miR-218-2 exclusively in CD309+ cells), homozygotes at e18.5 contained avascular glomeruli, whereas heterozygote adults showed susceptibility to kidney injury. Isolated EPCs from the mouse kidney contained high amounts of ITGA5 and showed decreased migratory capacity in three-dimensional cell culture. CONCLUSIONS These results demonstrate the critical regulatory role of miR-218-5p in kidney EPC migration, a finding that may inform efforts to treat microvascular kidney injury via therapeutic cell delivery.
Collapse
Affiliation(s)
- Jialing Liu
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts,Nephrology, Department of Medicine, Guangzhou University of Chinese Medicine, The Second Affiliated Hospital of Chinese Medicine, Guangzhou, China
| | - Yi Li
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts
| | - Lingna Lyu
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts,Department of Molecular Biology, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Liang Xiao
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts,Department of Surgery and Oncology, Shenzhen Second People’s Hospital/the First Affiliated Hospital of Shenzhen University Health Science Center, Shenzhen, China
| | - Aliza A. Memon
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts
| | - Xin Yu
- Blood Transfusion Research Institute, Wuxi Red Cross Blood Center, Wuxi, Jiangsu, China
| | - Arvin Halim
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts
| | - Shivani Patel
- Division of Nephrology, Department of Medicine, Boston Medical Center, Boston University School of Medicine, Boston, Massachusetts
| | | | - Wenqing Yin
- Division of Nephrology, Department of Medicine, Boston Medical Center, Boston University School of Medicine, Boston, Massachusetts
| | - Jie Jiang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts
| | - Said Naini
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts
| | - Kenneth Lim
- Division of Nephrology, Indiana University School of Medicine, Indianapolis, Indiana
| | - Aifeng Zhang
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts
| | - Jonathan D. Williams
- DNA Identification Testing Division, Laboratory Corporation of America Holdings, Burlington, North Carolina
| | - Ruth Koester
- DNA Identification Testing Division, Laboratory Corporation of America Holdings, Burlington, North Carolina
| | | | - Quynh-Anh Fucci
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts
| | - Lai Ding
- Program for Interdisciplinary Neuroscience, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts
| | - Steven Chang
- Department of Surgery, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts
| | - Ankit Patel
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts
| | - Yutaro Mori
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts
| | - Advika Chaudhari
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts
| | - Aaron Bao
- Washington University in St. Louis, St. Louis, Missouri
| | - Jia Liu
- Shenzhen Jiake Biotechnology, Shenzhen, China
| | - Tzong-Shi Lu
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts
| | - Andrew Siedlecki
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| |
Collapse
|
35
|
Zhao Z, Shang P, Sage F, Geijsen N. Ligation-assisted homologous recombination enables precise genome editing by deploying both MMEJ and HDR. Nucleic Acids Res 2022; 50:e62. [PMID: 35212386 PMCID: PMC9226534 DOI: 10.1093/nar/gkac118] [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] [Received: 10/07/2020] [Revised: 02/02/2022] [Accepted: 02/21/2022] [Indexed: 11/20/2022] Open
Abstract
CRISPR/Cas12a is a single effector nuclease that, like CRISPR/Cas9, has been harnessed for genome editing based on its ability to generate targeted DNA double strand breaks (DSBs). Unlike the blunt-ended DSB generated by Cas9, Cas12a generates sticky-ended DSB that could potentially aid precise genome editing, but this unique feature has thus far been underutilized. In the current study, we found that a short double-stranded DNA (dsDNA) repair template containing a sticky end that matched one of the Cas12a-generated DSB ends and a homologous arm sharing homology with the genomic region adjacent to the other end of the DSB enabled precise repair of the DSB and introduced a desired nucleotide substitution. We termed this strategy ‘Ligation-Assisted Homologous Recombination’ (LAHR). Compared to the single-stranded oligo deoxyribonucleotide (ssODN)-mediated homology directed repair (HDR), LAHR yields relatively high editing efficiency as demonstrated for both a reporter gene and endogenous genes. We found that both HDR and microhomology-mediated end joining (MMEJ) mechanisms are involved in the LAHR process. Our LAHR genome editing strategy, extends the repertoire of genome editing technologies and provides a broader understanding of the type and role of DNA repair mechanisms involved in genome editing.
Collapse
Affiliation(s)
- Zhihan Zhao
- Dept. of Anatomy & Embryology, Leiden University Medical Center, Einthovenweg 20, 2300 RC Leiden, The Netherlands
| | - Peng Shang
- Dept. of Anatomy & Embryology, Leiden University Medical Center, Einthovenweg 20, 2300 RC Leiden, The Netherlands
| | - Fanny Sage
- Dept. of Anatomy & Embryology, Leiden University Medical Center, Einthovenweg 20, 2300 RC Leiden, The Netherlands
| | - Niels Geijsen
- Dept. of Anatomy & Embryology, Leiden University Medical Center, Einthovenweg 20, 2300 RC Leiden, The Netherlands
| |
Collapse
|
36
|
Rezazade Bazaz M, Dehghani H. From DNA break repair pathways to CRISPR/Cas-mediated gene knock-in methods. Life Sci 2022; 295:120409. [PMID: 35182556 DOI: 10.1016/j.lfs.2022.120409] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 02/11/2022] [Accepted: 02/14/2022] [Indexed: 12/11/2022]
Abstract
Various DNA breaks created via programmable CRISPR/Cas9 nuclease activity results in different intracellular DNA break repair pathways. Based on the cellular repair pathways, CRISPR-based gene knock-in methods can be categorized into two major strategies: 1) Homology-independent strategies which are targeted insertion events based on non-homologous end joining, and 2) Homology-dependent strategies which are targeted insertion events based on the homology-directed repair. This review elaborates on various gene knock-in methods in mammalian cells using the CRISPR/Cas9 system and in sync with DNA-break repair pathways. Gene knock-in methods are applied in functional genomics and gene therapy. To compensate or correct genetic defects, different CRISPR-based gene knock-in strategies can be used. Thus, researchers need to make a conscious decision about the most suitable knock-in method. For a successful gene-targeted insertion, some determinant factors should be considered like cell cycle, dominant DNA repair pathway, size of insertions, and donor properties. In this review, different aspects of each gene knock-in strategy are discussed to provide a framework for choosing the most appropriate gene knock-in method in different applications.
Collapse
Affiliation(s)
- Mahere Rezazade Bazaz
- Division of Biotechnology, Faculty of Veterinary Medicine, Ferdowsi University of Mashhad, Mashhad, Iran; Stem Cell Biology and Regenerative Medicine Research Group, Research Institute of Biotechnology, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Hesam Dehghani
- Division of Biotechnology, Faculty of Veterinary Medicine, Ferdowsi University of Mashhad, Mashhad, Iran; Stem Cell Biology and Regenerative Medicine Research Group, Research Institute of Biotechnology, Ferdowsi University of Mashhad, Mashhad, Iran; Department of Basic Sciences, Faculty of Veterinary Medicine, Ferdowsi University of Mashhad, Mashhad, Iran.
| |
Collapse
|
37
|
Nakano Y, Susa K, Yanagi T, Hiraoka Y, Suzuki T, Mori T, Ando F, Mandai S, Fujiki T, Rai T, Uchida S, Sohara E. Generation of NPHP1 knockout human pluripotent stem cells by a practical biallelic gene deletion strategy using CRISPR/Cas9 and ssODN. In Vitro Cell Dev Biol Anim 2022; 58:85-95. [PMID: 35165826 DOI: 10.1007/s11626-022-00655-0] [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: 12/03/2021] [Accepted: 02/01/2022] [Indexed: 11/25/2022]
Abstract
CRISPR/Cas9 genome editing underwent remarkable progress and significantly contributed to the development of life sciences. Induced pluripotent stem cells (iPSCs) have also made a relevant contribution to regenerative medicine, pharmacological research, and genetic disease analysis. However, knockout iPSC generation with CRISPR/Cas9 in general has been difficult to achieve using approaches such as frameshift mutations to reproduce genetic diseases with full-length or nearly full-length gene deletions. Moreover, splicing and illegitimate translation could make complete knockouts difficult. Full-length gene deletion methods in iPSCs might solve these problems, although no such approach has been reported yet. In this study, we present a practical two-step gene-editing strategy leading to the precise, biallelic, and complete deletion of the full-length NPHP1 gene in iPSCs, which is the first report of biallelic (compound heterozygous) full-gene deletion in iPSCs using CRISPR/Cas9 and single-stranded oligodeoxynucleotides mainly via single-strand template repair (SSTR). Our strategy requires no selection or substances to enhance SSTR and can be used for the analysis of genetic disorders that are difficult to reproduce by conventional knockout methods.
Collapse
Affiliation(s)
- Yuta Nakano
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8519, Japan
| | - Koichiro Susa
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8519, Japan.
| | - Tomoki Yanagi
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8519, Japan
| | - Yuichi Hiraoka
- Laboratory of Molecular Neuroscience, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
- Laboratory of Genome Editing for Biomedical Research, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
| | - Takefumi Suzuki
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8519, Japan
| | - Takayasu Mori
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8519, Japan
| | - Fumiaki Ando
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8519, Japan
| | - Shintaro Mandai
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8519, Japan
| | - Tamami Fujiki
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8519, Japan
| | - Tatemitsu Rai
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8519, Japan
| | - Shinichi Uchida
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8519, Japan
| | - Eisei Sohara
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8519, Japan
| |
Collapse
|
38
|
Heryanto C, Hanly JJ, Mazo-Vargas A, Tendolkar A, Martin A. Mapping and CRISPR homology-directed repair of a recessive white eye mutation in Plodia moths. iScience 2022; 25:103885. [PMID: 35243245 PMCID: PMC8861637 DOI: 10.1016/j.isci.2022.103885] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 12/23/2021] [Accepted: 01/11/2022] [Indexed: 11/29/2022] Open
Abstract
The pantry moth Plodia interpunctella is a worldwide pest of stored food products and a promising laboratory model system for lepidopteran functional genomics. Here we describe efficient methods for precise genome editing in this insect. A spontaneous recessive white-eyed phenotype maps to a frameshift deletion (c.737delC) in the white gene. CRISPR NHEJ mutagenesis of white replicates this phenotype with high rates of somatic biallelic knockout. G0 individuals with mutant clones on both eyes produced 100% mutant progeny, making white an ideal marker for co-conversion when targeting other genes. CRISPR HDR experiments corrected c.737delC and reverted white eyes to a pigmented state in 37% of G0 mosaic adults. These repaired alleles showed practical rates of germline transmission in backcrosses, demonstrating the potential of the technique for precise genome editing. Plodia offers a promising avenue for research in this taxon because of its lab-ready features, egg injectability, and editability. Plodia pantry moths are an emerging model organism for functional genomics in Lepidoptera Spontaneous and CRISPR-induced white mutations yield recessive-white eye phenotypes CRISPR HDR repair with ssODN donor result in practical rates of base editing We provide optimized protocols for Plodia handling and genome editing
Collapse
|
39
|
Rezalotfi A, Fritz L, Förster R, Bošnjak B. Challenges of CRISPR-Based Gene Editing in Primary T Cells. Int J Mol Sci 2022; 23:ijms23031689. [PMID: 35163611 PMCID: PMC8835901 DOI: 10.3390/ijms23031689] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 01/29/2022] [Indexed: 12/30/2022] Open
Abstract
Adaptive T-cell immunotherapy holds great promise for the successful treatment of leukemia, as well as other types of cancers. More recently, it was also shown to be an effective treatment option for chronic virus infections in immunosuppressed patients. Autologous or allogeneic T cells used for immunotherapy are usually genetically modified to express novel T-cell or chimeric antigen receptors. The production of such cells was significantly simplified with the CRISPR/Cas system, allowing for the deletion or insertion of novel genes at specific locations within the genome. In this review, we describe recent methodological breakthroughs that were important for the conduction of these genetic modifications, summarize crucial points to be considered when conducting such experiments, and highlight the potential pitfalls of these approaches.
Collapse
Affiliation(s)
- Alaleh Rezalotfi
- Institute of Immunology, Hannover Medical School, 30625 Hannover, Germany; (A.R.); (L.F.); (R.F.)
| | - Lea Fritz
- Institute of Immunology, Hannover Medical School, 30625 Hannover, Germany; (A.R.); (L.F.); (R.F.)
| | - Reinhold Förster
- Institute of Immunology, Hannover Medical School, 30625 Hannover, Germany; (A.R.); (L.F.); (R.F.)
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, 30625 Hannover, Germany
- German Centre for Infection Research (DZIF), Partner Site Hannover, 30625 Hannover, Germany
| | - Berislav Bošnjak
- Institute of Immunology, Hannover Medical School, 30625 Hannover, Germany; (A.R.); (L.F.); (R.F.)
- Correspondence: ; Tel.: +49-511-532-9731
| |
Collapse
|
40
|
Simone BW, Lee HB, Daby CL, Ata H, Restrepo-Castillo S, Martínez-Gálvez G, Kar B, Gendron WA, Clark KJ, Ekker SC. Chimeric RNA: DNA TracrRNA Improves Homology-Directed Repair In Vitro and In Vivo. CRISPR J 2022; 5:40-52. [PMID: 34935462 PMCID: PMC8892967 DOI: 10.1089/crispr.2021.0087] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Nearly 90% of human pathogenic mutations are caused by small genetic variations, and methods to correct these errors efficiently are critically important. One way to make small DNA changes is providing a single-stranded oligo deoxynucleotide (ssODN) containing an alteration coupled with a targeted double-strand break (DSB) at the target locus in the genome. Coupling an ssODN donor with a CRISPR-Cas9-mediated DSB is one of the most streamlined approaches to introduce small changes. However, in many systems, this approach is inefficient and introduces imprecise repair at the genetic junctions. We herein report a technology that uses spatiotemporal localization of an ssODN with CRISPR-Cas9 to improve gene alteration. We show that by fusing an ssODN template to the trans-activating RNA (tracrRNA), we recover precise genetic alterations, with increased integration and precision in vitro and in vivo. Finally, we show that this technology can be used to enhance gene conversion with other gene editing tools such as transcription activator like effector nucleases.
Collapse
Affiliation(s)
- Brandon W. Simone
- Department of Biochemistry and Molecular Biology, Biomedical Engineering and Physiology Track, Mayo Clinic, Rochester, Minnesota, USA
| | - Han B. Lee
- Department of Biochemistry and Molecular Biology, Biomedical Engineering and Physiology Track, Mayo Clinic, Rochester, Minnesota, USA
| | - Camden L. Daby
- Department of Biochemistry and Molecular Biology, Biomedical Engineering and Physiology Track, Mayo Clinic, Rochester, Minnesota, USA
| | - Hirotaka Ata
- Department of Clinical and Translational Sciences, Biomedical Engineering and Physiology Track, Mayo Clinic, Rochester, Minnesota, USA
| | - Santiago Restrepo-Castillo
- Mayo Clinic Graduate School of Biomedical Sciences, Virology and Gene Therapy Track, Biomedical Engineering and Physiology Track, Mayo Clinic, Rochester, Minnesota, USA
| | - Gabriel Martínez-Gálvez
- Mayo Clinic Graduate School of Biomedical Sciences, Biomedical Engineering and Physiology Track, Mayo Clinic, Rochester, Minnesota, USA
| | - Bibekananda Kar
- Department of Biochemistry and Molecular Biology, Biomedical Engineering and Physiology Track, Mayo Clinic, Rochester, Minnesota, USA
| | - William A.C. Gendron
- Mayo Clinic Graduate School of Biomedical Sciences, Virology and Gene Therapy Track, Biomedical Engineering and Physiology Track, Mayo Clinic, Rochester, Minnesota, USA
| | - Karl J. Clark
- Department of Biochemistry and Molecular Biology, Biomedical Engineering and Physiology Track, Mayo Clinic, Rochester, Minnesota, USA
| | - Stephen C. Ekker
- Department of Biochemistry and Molecular Biology, Biomedical Engineering and Physiology Track, Mayo Clinic, Rochester, Minnesota, USA
- Address correspondence to: Stephen C. Ekker, PhD, Department of Biochemistry and Molecular Biology, Mayo Clinic, 200 1st Street SW, Rochester, MN 55905, USA,
| |
Collapse
|
41
|
Papasavva PL, Patsali P, Loucari CC, Kurita R, Nakamura Y, Kleanthous M, Lederer CW. CRISPR Editing Enables Consequential Tag-Activated MicroRNA-Mediated Endogene Deactivation. Int J Mol Sci 2022; 23:1082. [PMID: 35163006 PMCID: PMC8834719 DOI: 10.3390/ijms23031082] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 01/09/2022] [Accepted: 01/12/2022] [Indexed: 02/01/2023] Open
Abstract
Molecular therapies and functional studies greatly benefit from spatial and temporal precision of genetic intervention. We therefore conceived and explored tag-activated microRNA (miRNA)-mediated endogene deactivation (TAMED) as a research tool and potential lineage-specific therapy. For proof of principle, we aimed to deactivate γ-globin repressor BCL11A in erythroid cells by tagging the 3' untranslated region (UTR) of BCL11A with miRNA recognition sites (MRSs) for the abundant erythromiR miR-451a. To this end, we employed nucleofection of CRISPR/Cas9 ribonucleoprotein (RNP) particles alongside double- or single-stranded oligodeoxynucleotides for, respectively, non-homologous-end-joining (NHEJ)- or homology-directed-repair (HDR)-mediated MRS insertion. NHEJ-based tagging was imprecise and inefficient (≤6%) and uniformly produced knock-in- and indel-containing MRS tags, whereas HDR-based tagging was more efficient (≤18%), but toxic for longer donors encoding concatenated and thus potentially more efficient MRS tags. Isolation of clones for robust HEK293T cells tagged with a homozygous quadruple MRS resulted in 25% spontaneous reduction in BCL11A and up to 36% reduction after transfection with an miR-451a mimic. Isolation of clones for human umbilical cord blood-derived erythroid progenitor-2 (HUDEP-2) cells tagged with single or double MRS allowed detection of albeit weak γ-globin induction. Our study demonstrates suitability of TAMED for physiologically relevant modulation of gene expression and its unsuitability for therapeutic application in its current form.
Collapse
Affiliation(s)
- Panayiota L. Papasavva
- Department of Molecular Genetics Thalassemia, The Cyprus Institute of Neurology and Genetics, Nicosia 2371, Cyprus; (P.L.P.); (P.P.); (C.C.L.); (M.K.)
- Cyprus School of Molecular Medicine, Nicosia 2371, Cyprus
| | - Petros Patsali
- Department of Molecular Genetics Thalassemia, The Cyprus Institute of Neurology and Genetics, Nicosia 2371, Cyprus; (P.L.P.); (P.P.); (C.C.L.); (M.K.)
- Cyprus School of Molecular Medicine, Nicosia 2371, Cyprus
| | - Constantinos C. Loucari
- Department of Molecular Genetics Thalassemia, The Cyprus Institute of Neurology and Genetics, Nicosia 2371, Cyprus; (P.L.P.); (P.P.); (C.C.L.); (M.K.)
- Cyprus School of Molecular Medicine, Nicosia 2371, Cyprus
| | - Ryo Kurita
- Research and Development Department, Central Blood Institute, Blood Service Headquarters, Japanese Red Cross Society, Koto-ku, Tokyo 135-8521, Japan;
| | - Yukio Nakamura
- Cell Engineering Division, RIKEN BioResource Research Center, Tsukuba 305-0074, Japan;
| | - Marina Kleanthous
- Department of Molecular Genetics Thalassemia, The Cyprus Institute of Neurology and Genetics, Nicosia 2371, Cyprus; (P.L.P.); (P.P.); (C.C.L.); (M.K.)
- Cyprus School of Molecular Medicine, Nicosia 2371, Cyprus
| | - Carsten W. Lederer
- Department of Molecular Genetics Thalassemia, The Cyprus Institute of Neurology and Genetics, Nicosia 2371, Cyprus; (P.L.P.); (P.P.); (C.C.L.); (M.K.)
- Cyprus School of Molecular Medicine, Nicosia 2371, Cyprus
| |
Collapse
|
42
|
Huang MY, Joshi MB, Boucher MJ, Lee S, Loza LC, Gaylord EA, Doering TL, Madhani HD. Short homology-directed repair using optimized Cas9 in the pathogen Cryptococcus neoformans enables rapid gene deletion and tagging. Genetics 2022; 220:iyab180. [PMID: 34791226 PMCID: PMC8733451 DOI: 10.1093/genetics/iyab180] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 10/08/2021] [Indexed: 01/07/2023] Open
Abstract
Cryptococcus neoformans, the most common cause of fungal meningitis, is a basidiomycete haploid budding yeast with a complete sexual cycle. Genome modification by homologous recombination is feasible using biolistic transformation and long homology arms, but the method is arduous and unreliable. Recently, multiple groups have reported the use of CRISPR-Cas9 as an alternative to biolistics, but long homology arms are still necessary, limiting the utility of this method. Since the S. pyogenes Cas9 derivatives used in prior studies were not optimized for expression in C. neoformans, we designed, synthesized, and tested a fully C. neoformans-optimized (Cno) Cas9. We found that a Cas9 harboring only common C. neoformans codons and a consensus C. neoformans intron together with a TEF1 promoter and terminator and a nuclear localization signal (Cno CAS9 or "CnoCAS9") reliably enabled genome editing in the widely used KN99α C. neoformans strain. Furthermore, editing was accomplished using donors harboring short (50 bp) homology arms attached to marker DNAs produced with synthetic oligonucleotides and PCR amplification. We also demonstrated that prior stable integration of CnoCAS9 further enhances both transformation and homologous recombination efficiency; importantly, this manipulation does not impact virulence in animals. We also implemented a universal tagging module harboring a codon-optimized fluorescent protein (mNeonGreen) and a tandem Calmodulin Binding Peptide-2X FLAG Tag that allows for both localization and purification studies of proteins for which the corresponding genes are modified by short homology-directed recombination. These tools enable short-homology genome engineering in C. neoformans.
Collapse
Affiliation(s)
- Manning Y Huang
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94158, USA
| | - Meenakshi B Joshi
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94158, USA
| | - Michael J Boucher
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94158, USA
| | - Sujin Lee
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94158, USA
| | - Liza C Loza
- Department of Molecular Microbiology, Washington University School of Medicine, Washington University, St. Louis, MO 63110, USA
| | - Elizabeth A Gaylord
- Department of Molecular Microbiology, Washington University School of Medicine, Washington University, St. Louis, MO 63110, USA
| | - Tamara L Doering
- Department of Molecular Microbiology, Washington University School of Medicine, Washington University, St. Louis, MO 63110, USA
| | - Hiten D Madhani
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94158, USA
- Chan-Zuckerberg Biohub, San Francisco, CA 94158, USA
| |
Collapse
|
43
|
Medley JC, Hebbar S, Sydzyik JT, Zinovyeva AY. Single nucleotide substitutions effectively block Cas9 and allow for scarless genome editing in Caenorhabditis elegans. Genetics 2022; 220:iyab199. [PMID: 34791245 PMCID: PMC8733430 DOI: 10.1093/genetics/iyab199] [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: 09/13/2021] [Accepted: 10/28/2021] [Indexed: 11/17/2022] Open
Abstract
In Caenorhabditis elegans, germline injection of Cas9 complexes is reliably used to achieve genome editing through homology-directed repair of Cas9-generated DNA breaks. To prevent Cas9 from targeting repaired DNA, additional blocking mutations are often incorporated into homologous repair templates. Cas9 can be blocked either by mutating the PAM sequence that is essential for Cas9 activity or by mutating the guide sequence that targets Cas9 to a specific genomic location. However, it is unclear how many nucleotides within the guide sequence should be mutated, since Cas9 can recognize "off-target" sequences that are imperfectly paired to its guide. In this study, we examined whether single-nucleotide substitutions within the guide sequence are sufficient to block Cas9 and allow for efficient genome editing. We show that a single mismatch within the guide sequence effectively blocks Cas9 and allows for recovery of edited animals. Surprisingly, we found that a low rate of edited animals can be recovered without introducing any blocking mutations, suggesting a temporal block to Cas9 activity in C. elegans. Furthermore, we show that the maternal genome of hermaphrodite animals is preferentially edited over the paternal genome. We demonstrate that maternally provided haplotypes can be selected using balancer chromosomes and propose a method of mutant isolation that greatly reduces screening efforts postinjection. Collectively, our findings expand the repertoire of genome editing strategies in C. elegans and demonstrate that extraneous blocking mutations are not required to recover edited animals when the desired mutation is located within the guide sequence.
Collapse
Affiliation(s)
- Jeffrey C Medley
- Division of Biology, Kansas State University, Manhattan, KS 66502, USA
| | - Shilpa Hebbar
- Division of Biology, Kansas State University, Manhattan, KS 66502, USA
| | - Joel T Sydzyik
- Division of Biology, Kansas State University, Manhattan, KS 66502, USA
| | - Anna Y Zinovyeva
- Division of Biology, Kansas State University, Manhattan, KS 66502, USA
| |
Collapse
|
44
|
Benetó N, Grinberg D, Vilageliu L, Canals I. Genome Editing Using Cas9-gRNA Ribonucleoprotein in Human Pluripotent Stem Cells for Disease Modeling. Methods Mol Biol 2022; 2549:409-425. [PMID: 33755903 DOI: 10.1007/7651_2021_374] [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] [Indexed: 06/12/2023]
Abstract
The discovery that the CRISPR/Cas9 system could be used for genome editing purposes represented a major breakthrough in the field. This advancement has notably facilitated the introduction or correction of disease-specific mutations in healthy or disease stem cell lines respectively; therefore, easing disease modeling studies in combination with differentiation protocols. For many years, variability in the genetic background of different stem cell lines has been a major burden to specifically identify phenotypes arising uniquely from the presence of the mutation and not from differences in other genomic regions.Here, we provide a complete protocol to introduce random indels in human wild type pluripotent stem cells using CRISPR/Cas9 in order to generate clonal lines with potential pathogenic alterations in any gene of interest. In this protocol, we use transfection of a ribonucleoprotein complex to diminish the risk of off-target effects, and select clonal lines with promising indels to obtain disease induced pluripotent stem cell lines.
Collapse
Affiliation(s)
- Noelia Benetó
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, CIBERER, IBUB, IRSJD, Barcelona, Spain
| | - Daniel Grinberg
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, CIBERER, IBUB, IRSJD, Barcelona, Spain
| | - Lluïsa Vilageliu
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, CIBERER, IBUB, IRSJD, Barcelona, Spain
| | - Isaac Canals
- Division of Neurology, Department of Clinical Sciences, Faculty of Medicine, Lund Stem Cell Center, Lund University, Lund, Sweden.
| |
Collapse
|
45
|
Schubert MS, Thommandru B, Woodley J, Turk R, Yan S, Kurgan G, McNeill MS, Rettig GR. Optimized design parameters for CRISPR Cas9 and Cas12a homology-directed repair. Sci Rep 2021; 11:19482. [PMID: 34593942 PMCID: PMC8484621 DOI: 10.1038/s41598-021-98965-y] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 09/13/2021] [Indexed: 12/26/2022] Open
Abstract
CRISPR-Cas proteins are RNA-guided nucleases used to introduce double-stranded breaks (DSBs) at targeted genomic loci. DSBs are repaired by endogenous cellular pathways such as non-homologous end joining (NHEJ) and homology-directed repair (HDR). Providing an exogenous DNA template during repair allows for the intentional, precise incorporation of a desired mutation via the HDR pathway. However, rates of repair by HDR are often slow compared to the more rapid but less accurate NHEJ-mediated repair. Here, we describe comprehensive design considerations and optimized methods for highly efficient HDR using single-stranded oligodeoxynucleotide (ssODN) donor templates for several CRISPR-Cas systems including S.p. Cas9, S.p. Cas9 D10A nickase, and A.s. Cas12a delivered as ribonucleoprotein (RNP) complexes. Features relating to guide RNA selection, donor strand preference, and incorporation of blocking mutations in the donor template to prevent re-cleavage were investigated and were implemented in a novel online tool for HDR donor template design. These findings allow for high frequencies of precise repair utilizing HDR in multiple mammalian cell lines. Tool availability: https://www.idtdna.com/HDR.
Collapse
Affiliation(s)
- Mollie S Schubert
- Integrated DNA Technologies, Inc., 1710 Commercial Park, Coralville, IA, 52241, USA
| | - Bernice Thommandru
- Integrated DNA Technologies, Inc., 1710 Commercial Park, Coralville, IA, 52241, USA
| | - Jessica Woodley
- Integrated DNA Technologies, Inc., 1710 Commercial Park, Coralville, IA, 52241, USA
| | - Rolf Turk
- Integrated DNA Technologies, Inc., 1710 Commercial Park, Coralville, IA, 52241, USA
| | - Shuqi Yan
- Integrated DNA Technologies, Inc., 1710 Commercial Park, Coralville, IA, 52241, USA
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Gavin Kurgan
- Integrated DNA Technologies, Inc., 1710 Commercial Park, Coralville, IA, 52241, USA
| | - Matthew S McNeill
- Integrated DNA Technologies, Inc., 1710 Commercial Park, Coralville, IA, 52241, USA
| | - Garrett R Rettig
- Integrated DNA Technologies, Inc., 1710 Commercial Park, Coralville, IA, 52241, USA.
| |
Collapse
|
46
|
Manipulation of the Tyrosinase gene permits improved CRISPR/Cas editing and neural imaging in cichlid fish. Sci Rep 2021; 11:15138. [PMID: 34302019 PMCID: PMC8302579 DOI: 10.1038/s41598-021-94577-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 07/13/2021] [Indexed: 12/12/2022] Open
Abstract
Direct tests of gene function have historically been performed in a limited number of model organisms. The CRISPR/Cas system is species-agnostic, offering the ability to manipulate genes in a range of models, enabling insights into evolution, development, and physiology. Astatotilapia burtoni, a cichlid fish from the rivers and shoreline around Lake Tanganyika, has been extensively studied in the laboratory to understand evolution and the neural control of behavior. Here we develop protocols for the creation of CRISPR-edited cichlids and create a broadly useful mutant line. By manipulating the Tyrosinase gene, which is necessary for eumelanin pigment production, we describe a fast and reliable approach to quantify and optimize gene editing efficiency. Tyrosinase mutants also remove a major obstruction to imaging, enabling visualization of subdermal structures and fluorophores in situ. These protocols will facilitate broad application of CRISPR/Cas9 to studies of cichlids as well as other non-traditional model aquatic species.
Collapse
|
47
|
Sledzinski P, Dabrowska M, Nowaczyk M, Olejniczak M. Paving the way towards precise and safe CRISPR genome editing. Biotechnol Adv 2021; 49:107737. [PMID: 33785374 DOI: 10.1016/j.biotechadv.2021.107737] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 03/11/2021] [Accepted: 03/19/2021] [Indexed: 12/13/2022]
Abstract
As the possibilities of CRISPR-Cas9 technology have been revealed, we have entered a new era of research aimed at increasing its specificity and safety. This stage of technology development is necessary not only for its wider application in the clinic but also in basic research to better control the process of genome editing. Research during the past eight years has identified some factors influencing editing outcomes and led to the development of highly specific endonucleases, modified guide RNAs and computational tools supporting experiments. More recently, large-scale experiments revealed a previously overlooked feature: Cas9 can generate reproducible mutation patterns. As a result, it has become apparent that Cas9-induced double-strand break (DSB) repair is nonrandom and can be predicted to some extent. Here, we review the present state of knowledge regarding the specificity and safety of CRISPR-Cas9 technology to define gRNA, protein and target-related problems and solutions. These issues include sequence-specific off-target effects, immune responses, genetic variation and chromatin accessibility. We present new insights into the role of DNA repair in genome editing and define factors influencing editing outcomes. In addition, we propose practical guidelines for increasing the specificity of editing and discuss novel perspectives in improvement of this technology.
Collapse
Affiliation(s)
- Pawel Sledzinski
- Department of Genome Engineering, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Noskowskiego 12/14, 61-704, Poland
| | - Magdalena Dabrowska
- Department of Genome Engineering, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Noskowskiego 12/14, 61-704, Poland
| | - Mateusz Nowaczyk
- Department of Genome Engineering, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Noskowskiego 12/14, 61-704, Poland
| | - Marta Olejniczak
- Department of Genome Engineering, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Noskowskiego 12/14, 61-704, Poland.
| |
Collapse
|
48
|
Abstract
Polymerase Chain Reaction (PCR) is a powerful tool to detect natural variation or experimentally introduced variation in research and clinical settings and a widely-used method for genotyping. Single nucleotide polymorphisms (SNP) detection is challenging by PCR as the variant and wild type alleles differ by only one nucleotide. Traditional methods to detect SNPs, including Sanger sequencing and commercial kits, are usually time-consuming. Here we describe a simple primer design strategy that enables specific variant detection through regular one-step PCR. The strategy employs the differential efficiency of genomic PCR using a primer that has a single mismatch with the chromosome that contains the SNP to be detected (typically the variant allele) versus two mismatches with the corresponding alternative allele (typically the wild type allele). To date, we have successfully employed this approach to detect more than 20 SNPs. The simplicity and robustness of the approach allows rapid application to legacy mutations as well as newly discovered or generated SNPs.
Collapse
Affiliation(s)
- Jian Chen
- Department of Genetics, School of Medicine, Washington University in St. Louis, Missouri 63110
| | - Tim Schedl
- Department of Genetics, School of Medicine, Washington University in St. Louis, Missouri 63110
| |
Collapse
|
49
|
Schep R, Brinkman EK, Leemans C, Vergara X, van der Weide RH, Morris B, van Schaik T, Manzo SG, Peric-Hupkes D, van den Berg J, Beijersbergen RL, Medema RH, van Steensel B. Impact of chromatin context on Cas9-induced DNA double-strand break repair pathway balance. Mol Cell 2021; 81:2216-2230.e10. [PMID: 33848455 PMCID: PMC8153251 DOI: 10.1016/j.molcel.2021.03.032] [Citation(s) in RCA: 97] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 12/23/2020] [Accepted: 03/19/2021] [Indexed: 01/01/2023]
Abstract
DNA double-strand break (DSB) repair is mediated by multiple pathways. It is thought that the local chromatin context affects the pathway choice, but the underlying principles are poorly understood. Using a multiplexed reporter assay in combination with Cas9 cutting, we systematically measure the relative activities of three DSB repair pathways as a function of chromatin context in >1,000 genomic locations. This reveals that non-homologous end-joining (NHEJ) is broadly biased toward euchromatin, while the contribution of microhomology-mediated end-joining (MMEJ) is higher in specific heterochromatin contexts. In H3K27me3-marked heterochromatin, inhibition of the H3K27 methyltransferase EZH2 reverts the balance toward NHEJ. Single-stranded template repair (SSTR), often used for precise CRISPR editing, competes with MMEJ and is moderately linked to chromatin context. These results provide insight into the impact of chromatin on DSB repair pathway balance and guidance for the design of Cas9-mediated genome editing experiments.
Collapse
Affiliation(s)
- Ruben Schep
- Oncode Institute, Netherlands Cancer Institute, 1066 CX, Amsterdam, the Netherlands; Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX, Amsterdam, the Netherlands
| | - Eva K Brinkman
- Oncode Institute, Netherlands Cancer Institute, 1066 CX, Amsterdam, the Netherlands; Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX, Amsterdam, the Netherlands
| | - Christ Leemans
- Oncode Institute, Netherlands Cancer Institute, 1066 CX, Amsterdam, the Netherlands; Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX, Amsterdam, the Netherlands
| | - Xabier Vergara
- Oncode Institute, Netherlands Cancer Institute, 1066 CX, Amsterdam, the Netherlands; Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX, Amsterdam, the Netherlands; Division of Cell Biology, Netherlands Cancer Institute, 1066 CX, Amsterdam, the Netherlands
| | - Robin H van der Weide
- Oncode Institute, Netherlands Cancer Institute, 1066 CX, Amsterdam, the Netherlands; Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX, Amsterdam, the Netherlands
| | - Ben Morris
- Division of Molecular Carcinogenesis, Netherlands Cancer Institute, 1066 CX, Amsterdam, the Netherlands; Robotics Screening Center, Netherlands Cancer Institute, 1066 CX, Amsterdam, the Netherlands
| | - Tom van Schaik
- Oncode Institute, Netherlands Cancer Institute, 1066 CX, Amsterdam, the Netherlands; Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX, Amsterdam, the Netherlands
| | - Stefano G Manzo
- Oncode Institute, Netherlands Cancer Institute, 1066 CX, Amsterdam, the Netherlands; Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX, Amsterdam, the Netherlands
| | - Daniel Peric-Hupkes
- Oncode Institute, Netherlands Cancer Institute, 1066 CX, Amsterdam, the Netherlands; Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX, Amsterdam, the Netherlands
| | - Jeroen van den Berg
- Oncode Institute, Netherlands Cancer Institute, 1066 CX, Amsterdam, the Netherlands; Division of Cell Biology, Netherlands Cancer Institute, 1066 CX, Amsterdam, the Netherlands
| | - Roderick L Beijersbergen
- Division of Molecular Carcinogenesis, Netherlands Cancer Institute, 1066 CX, Amsterdam, the Netherlands; Robotics Screening Center, Netherlands Cancer Institute, 1066 CX, Amsterdam, the Netherlands
| | - René H Medema
- Oncode Institute, Netherlands Cancer Institute, 1066 CX, Amsterdam, the Netherlands; Division of Cell Biology, Netherlands Cancer Institute, 1066 CX, Amsterdam, the Netherlands
| | - Bas van Steensel
- Oncode Institute, Netherlands Cancer Institute, 1066 CX, Amsterdam, the Netherlands; Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX, Amsterdam, the Netherlands; Department of Cell Biology, Erasmus University Medical Centre, 3015 CN, Rotterdam, the Netherlands.
| |
Collapse
|
50
|
Li PP, Margolis RL. Use of single guided Cas9 nickase to facilitate precise and efficient genome editing in human iPSCs. Sci Rep 2021; 11:9865. [PMID: 33972655 PMCID: PMC8110799 DOI: 10.1038/s41598-021-89312-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Accepted: 04/21/2021] [Indexed: 11/09/2022] Open
Abstract
Cas9 nucleases permit rapid and efficient generation of gene-edited cell lines. However, in typical protocols, mutations are intentionally introduced into the donor template to avoid the cleavage of donor template or re-cleavage of the successfully edited allele, compromising the fidelity of the isogenic lines generated. In addition, the double-stranded breaks (DSBs) used for editing can introduce undesirable "on-target" indels within the second allele of successfully modified cells via non-homologous end joining (NHEJ). To address these problems, we present an optimized protocol for precise genome editing in human iPSCs that employs (1) single guided Cas9 nickase to generate single-stranded breaks (SSBs), (2) transient overexpression of BCL-XL to enhance survival post electroporation, and (3) the PiggyBac transposon system for seamless removal of dual selection markers. We have used this method to modify the length of the CAG repeat contained in exon 7 of PPP2R2B. When longer than 43 triplets, this repeat causes the neurodegenerative disorder spinocerebellar ataxia type 12 (SCA12); our goal was to seamlessly introduce the SCA12 mutation into a human control iPSC line. With our protocol, ~ 15% of iPSC clones selected had the desired gene editing without "on target" indels or off-target changes, and without the deliberate introduction of mutations via the donor template. This method will allow for the precise and efficient editing of human iPSCs for disease modeling and other purposes.
Collapse
Affiliation(s)
- Pan P Li
- Department of Psychiatry and Behavioral Sciences, Division of Neurobiology, Johns Hopkins University School of Medicine, CMSC 8-121, 600 N. Wolfe St, Baltimore, MD, 21287, USA.
| | - Russell L Margolis
- Department of Psychiatry and Behavioral Sciences, Division of Neurobiology, Johns Hopkins University School of Medicine, CMSC 8-121, 600 N. Wolfe St, Baltimore, MD, 21287, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| |
Collapse
|